MiMeDB: Showing metabocard for 2'-Deoxyadenosine 5'-diphosphate (MMDBc0057193)

Microbial

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2022-11-09 20:24:39 UTC

Update Date

2025-10-07 16:09:55 UTC

Metabolite ID

MMDBc0057193

Metabolite Identification

Common Name

2'-Deoxyadenosine 5'-diphosphate

Description

2'-Deoxyadenosine 5'-diphosphate is a nucleotide, specifically a deoxynucleotide, which plays a role in various biochemical processes, including DNA synthesis and repair. There is limited literature available on this metabolite, indicating a need for further research to fully understand its biological significance and functions.

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI


  Mrv1652309182017582D          

 26 28  0  0  0  0            999 V2000
10001.0181 9999.9193    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.5107 9998.0589    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10001.7317 9999.5058    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10002.4453 9999.9193    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
10003.1672 9999.5202    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10002.034910000.6342    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10002.859910000.6342    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10003.8829 9999.9315    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
10003.468310000.6465    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10004.5944 9999.5202    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10004.293310000.6465    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9999.632310000.0002    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9999.2198 9998.7306    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.0448 9998.7306    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
10000.2997 9999.5152    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9996.138710000.0297    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9995.8838 9999.2451    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 9996.4359 9998.6319    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9997.2429 9998.8034    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 9997.4978 9999.5880    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9996.945710000.2012    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.2515 9999.9235    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 9998.165310000.7440    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9997.358410000.9156    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 9995.586710000.6427    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 9998.9659 9999.5109    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
  1  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  4  6  2  0  0  0  0
  4  7  1  0  0  0  0
  5  8  1  0  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
  8 11  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 12 15  1  0  0  0  0
 15  1  1  6  0  0  0
 14  2  1  1  0  0  0
 20 21  2  0  0  0  0
 21 16  1  0  0  0  0
 16 17  2  0  0  0  0
 17 18  1  0  0  0  0
 18 19  2  0  0  0  0
 19 20  1  0  0  0  0
 23 24  2  0  0  0  0
 21 24  1  0  0  0  0
 22 23  1  0  0  0  0
 20 22  1  0  0  0  0
 16 25  1  0  0  0  0
 26 22  1  6  0  0  0
 26 13  1  0  0  0  0
 12 26  1  0  0  0  0
M  END

HMDB0001508
     RDKit          3D
dADP
 41 43  0  0  0  0  0  0  0  0999 V2000
   -6.8556    1.1110   -0.1848 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5892    0.4437   -0.3737 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5629   -0.8846   -0.3317 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3546   -1.5527   -0.3503 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2462   -0.8203   -0.4040 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2081    0.5043   -0.4518 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4451    1.1689   -0.4386 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0956    2.4799   -0.4996 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7626    2.6167   -0.5327 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2067    1.4363   -0.4956 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8118    1.0625   -0.1551 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.0808    0.4708    1.3139 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4829   -0.9130    1.1823 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0814   -1.3178    2.4081 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5177   -0.5911    0.1221 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.5614   -1.5659   -0.1765 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5273   -0.7602   -0.8874 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9642   -0.8980    0.0115 P   0  0  0  0  0  5  0  0  0  0  0  0
    3.9529    0.4696    0.8779 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9229   -2.1180    1.1393 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3290   -0.7332   -0.8977 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.4641    0.2823   -0.0831 P   0  0  0  0  0  5  0  0  0  0  0  0
    7.8467   -0.1989   -0.4004 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.1460    0.2208    1.6029 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.3135    1.8858   -0.5833 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2156    0.0639   -0.8239 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.7466    0.6366   -0.2878 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8351    2.1367    0.1186 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3865   -2.6265   -0.3348 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1983    3.5619   -0.6019 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2344    1.9529    0.0413 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5996    1.0790    2.0501 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2164    0.4047    1.4124 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1470   -1.6864    0.7906 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2533   -2.2382    2.5526 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1311    0.2952    0.6915 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0396   -2.0392    0.6371 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1510   -2.3471   -0.8879 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3843   -2.9234    0.8583 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.6165   -0.5446    1.9751 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.5850    2.4756    0.1937 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 13 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  1  0
 18 19  2  0
 18 20  1  0
 18 21  1  0
 21 22  1  0
 22 23  2  0
 22 24  1  0
 22 25  1  0
 15 26  1  0
  7  2  1  0
 26 11  1  0
 10  6  1  0
  1 27  1  0
  1 28  1  0
  4 29  1  0
  9 30  1  0
 11 31  1  1
 12 32  1  0
 12 33  1  0
 13 34  1  6
 14 35  1  0
 15 36  1  1
 16 37  1  0
 16 38  1  0
 20 39  1  0
 24 40  1  0
 25 41  1  0
M  END


  Mrv1652309182017582D          

 26 28  0  0  0  0            999 V2000
10001.0181 9999.9193    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.5107 9998.0589    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10001.7317 9999.5058    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10002.4453 9999.9193    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
10003.1672 9999.5202    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10002.034910000.6342    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10002.859910000.6342    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10003.8829 9999.9315    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
10003.468310000.6465    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10004.5944 9999.5202    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10004.293310000.6465    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9999.632310000.0002    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9999.2198 9998.7306    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.0448 9998.7306    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
10000.2997 9999.5152    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
 9996.138710000.0297    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9995.8838 9999.2451    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 9996.4359 9998.6319    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9997.2429 9998.8034    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 9997.4978 9999.5880    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9996.945710000.2012    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.2515 9999.9235    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 9998.165310000.7440    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9997.358410000.9156    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 9995.586710000.6427    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
 9998.9659 9999.5109    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
  1  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  4  6  2  0  0  0  0
  4  7  1  0  0  0  0
  5  8  1  0  0  0  0
  8  9  2  0  0  0  0
  8 10  1  0  0  0  0
  8 11  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 12 15  1  0  0  0  0
 15  1  1  6  0  0  0
 14  2  1  1  0  0  0
 20 21  2  0  0  0  0
 21 16  1  0  0  0  0
 16 17  2  0  0  0  0
 17 18  1  0  0  0  0
 18 19  2  0  0  0  0
 19 20  1  0  0  0  0
 23 24  2  0  0  0  0
 21 24  1  0  0  0  0
 22 23  1  0  0  0  0
 20 22  1  0  0  0  0
 16 25  1  0  0  0  0
 26 22  1  6  0  0  0
 26 13  1  0  0  0  0
 12 26  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0057193

> <DATABASE_NAME>
MIME

> <SMILES>
NC1=NC=NC2=C1N=CN2[C@H]1C[C@H](O)[C@@H](COP(O)(=O)OP(O)(O)=O)O1

> <INCHI_IDENTIFIER>
InChI=1S/C10H15N5O9P2/c11-9-8-10(13-3-12-9)15(4-14-8)7-1-5(16)6(23-7)2-22-26(20,21)24-25(17,18)19/h3-7,16H,1-2H2,(H,20,21)(H2,11,12,13)(H2,17,18,19)/t5-,6+,7+/m0/s1

> <INCHI_KEY>
DAEAPNUQQAICNR-RRKCRQDMSA-N

> <FORMULA>
C10H15N5O9P2

> <MOLECULAR_WEIGHT>
411.2017

> <EXACT_MASS>
411.034500127

> <JCHEM_ACCEPTOR_COUNT>
11

> <JCHEM_ATOM_COUNT>
41

> <JCHEM_AVERAGE_POLARIZABILITY>
33.60408616221964

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[({[(2R,3S,5R)-5-(6-amino-9H-purin-9-yl)-3-hydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]phosphonic acid

> <ALOGPS_LOGP>
-1.57

> <JCHEM_LOGP>
-3.8208162402226273

> <ALOGPS_LOGS>
-2.17

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.1392558743057477

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.7688842589671903

> <JCHEM_PKA_STRONGEST_BASIC>
4.014841097084696

> <JCHEM_POLAR_SURFACE_AREA>
212.36999999999998

> <JCHEM_REFRACTIVITY>
83.43069999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.80e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
dADP

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0001508
     RDKit          3D
dADP
 41 43  0  0  0  0  0  0  0  0999 V2000
   -6.8556    1.1110   -0.1848 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5892    0.4437   -0.3737 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5629   -0.8846   -0.3317 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3546   -1.5527   -0.3503 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2462   -0.8203   -0.4040 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2081    0.5043   -0.4518 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4451    1.1689   -0.4386 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0956    2.4799   -0.4996 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7626    2.6167   -0.5327 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2067    1.4363   -0.4956 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8118    1.0625   -0.1551 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.0808    0.4708    1.3139 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4829   -0.9130    1.1823 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0814   -1.3178    2.4081 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5177   -0.5911    0.1221 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.5614   -1.5659   -0.1765 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5273   -0.7602   -0.8874 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9642   -0.8980    0.0115 P   0  0  0  0  0  5  0  0  0  0  0  0
    3.9529    0.4696    0.8779 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9229   -2.1180    1.1393 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3290   -0.7332   -0.8977 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.4641    0.2823   -0.0831 P   0  0  0  0  0  5  0  0  0  0  0  0
    7.8467   -0.1989   -0.4004 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.1460    0.2208    1.6029 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.3135    1.8858   -0.5833 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2156    0.0639   -0.8239 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.7466    0.6366   -0.2878 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8351    2.1367    0.1186 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3865   -2.6265   -0.3348 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1983    3.5619   -0.6019 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2344    1.9529    0.0413 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5996    1.0790    2.0501 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2164    0.4047    1.4124 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1470   -1.6864    0.7906 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2533   -2.2382    2.5526 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1311    0.2952    0.6915 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0396   -2.0392    0.6371 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1510   -2.3471   -0.8879 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3843   -2.9234    0.8583 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.6165   -0.5446    1.9751 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.5850    2.4756    0.1937 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 13 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  1  0
 18 19  2  0
 18 20  1  0
 18 21  1  0
 21 22  1  0
 22 23  2  0
 22 24  1  0
 22 25  1  0
 15 26  1  0
  7  2  1  0
 26 11  1  0
 10  6  1  0
  1 27  1  0
  1 28  1  0
  4 29  1  0
  9 30  1  0
 11 31  1  1
 12 32  1  0
 12 33  1  0
 13 34  1  6
 14 35  1  0
 15 36  1  1
 16 37  1  0
 16 38  1  0
 20 39  1  0
 24 40  1  0
 25 41  1  0
M  END

HEADER    PROTEIN                                 18-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   18-SEP-20         0                                  
HETATM    1  C   UNK     0    8668.5678666.516   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0    8667.6208663.043   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0    8669.8998665.744   0.000  0.00  0.00           O+0
HETATM    4  P   UNK     0    8671.2318666.516   0.000  0.00  0.00           P+0
HETATM    5  O   UNK     0    8672.5798665.771   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0    8670.4658667.851   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0    8672.0058667.851   0.000  0.00  0.00           O+0
HETATM    8  P   UNK     0    8673.9158666.539   0.000  0.00  0.00           P+0
HETATM    9  O   UNK     0    8673.1418667.873   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0    8675.2438665.771   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0    8674.6818667.873   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0    8665.9808666.667   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0    8665.2108664.297   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0    8666.7508664.297   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0    8667.2268665.762   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0    8659.4598666.722   0.000  0.00  0.00           C+0
HETATM   17  N   UNK     0    8658.9838665.258   0.000  0.00  0.00           N+0
HETATM   18  C   UNK     0    8660.0148664.113   0.000  0.00  0.00           C+0
HETATM   19  N   UNK     0    8661.5208664.433   0.000  0.00  0.00           N+0
HETATM   20  C   UNK     0    8661.9968665.898   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0    8660.9658667.042   0.000  0.00  0.00           C+0
HETATM   22  N   UNK     0    8663.4038666.524   0.000  0.00  0.00           N+0
HETATM   23  C   UNK     0    8663.2428668.055   0.000  0.00  0.00           C+0
HETATM   24  N   UNK     0    8661.7368668.376   0.000  0.00  0.00           N+0
HETATM   25  N   UNK     0    8658.4298667.866   0.000  0.00  0.00           N+0
HETATM   26  C   UNK     0    8664.7368665.754   0.000  0.00  0.00           C+0
CONECT    1    3   15                                                       
CONECT    2   14                                                            
CONECT    3    1    4                                                       
CONECT    4    3    5    6    7                                             
CONECT    5    4    8                                                       
CONECT    6    4                                                            
CONECT    7    4                                                            
CONECT    8    5    9   10   11                                             
CONECT    9    8                                                            
CONECT   10    8                                                            
CONECT   11    8                                                            
CONECT   12   15   26                                                       
CONECT   13   14   26                                                       
CONECT   14   13   15    2                                                  
CONECT   15   14   12    1                                                  
CONECT   16   21   17   25                                                  
CONECT   17   16   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   21   19   22                                                  
CONECT   21   20   16   24                                                  
CONECT   22   23   20   26                                                  
CONECT   23   24   22                                                       
CONECT   24   23   21                                                       
CONECT   25   16                                                            
CONECT   26   22   13   12                                                  
MASTER        0    0    0    0    0    0    0    0   26    0   56    0
END

COMPND    HMDB0001508
HETATM    1  N1  UNL     1      -6.856   1.111  -0.185  1.00  0.00           N  
HETATM    2  C1  UNL     1      -5.589   0.444  -0.374  1.00  0.00           C  
HETATM    3  N2  UNL     1      -5.563  -0.885  -0.332  1.00  0.00           N  
HETATM    4  C2  UNL     1      -4.355  -1.553  -0.350  1.00  0.00           C  
HETATM    5  N3  UNL     1      -3.246  -0.820  -0.404  1.00  0.00           N  
HETATM    6  C3  UNL     1      -3.208   0.504  -0.452  1.00  0.00           C  
HETATM    7  C4  UNL     1      -4.445   1.169  -0.439  1.00  0.00           C  
HETATM    8  N4  UNL     1      -4.096   2.480  -0.500  1.00  0.00           N  
HETATM    9  C5  UNL     1      -2.763   2.617  -0.533  1.00  0.00           C  
HETATM   10  N5  UNL     1      -2.207   1.436  -0.496  1.00  0.00           N  
HETATM   11  C6  UNL     1      -0.812   1.062  -0.155  1.00  0.00           C  
HETATM   12  C7  UNL     1      -1.081   0.471   1.314  1.00  0.00           C  
HETATM   13  C8  UNL     1      -0.483  -0.913   1.182  1.00  0.00           C  
HETATM   14  O1  UNL     1       0.081  -1.318   2.408  1.00  0.00           O  
HETATM   15  C9  UNL     1       0.518  -0.591   0.122  1.00  0.00           C  
HETATM   16  C10 UNL     1       1.561  -1.566  -0.176  1.00  0.00           C  
HETATM   17  O2  UNL     1       2.527  -0.760  -0.887  1.00  0.00           O  
HETATM   18  P1  UNL     1       3.964  -0.898   0.012  1.00  0.00           P  
HETATM   19  O3  UNL     1       3.953   0.470   0.878  1.00  0.00           O  
HETATM   20  O4  UNL     1       3.923  -2.118   1.139  1.00  0.00           O  
HETATM   21  O5  UNL     1       5.329  -0.733  -0.898  1.00  0.00           O  
HETATM   22  P2  UNL     1       6.464   0.282  -0.083  1.00  0.00           P  
HETATM   23  O6  UNL     1       7.847  -0.199  -0.400  1.00  0.00           O  
HETATM   24  O7  UNL     1       6.146   0.221   1.603  1.00  0.00           O  
HETATM   25  O8  UNL     1       6.314   1.886  -0.583  1.00  0.00           O  
HETATM   26  O9  UNL     1      -0.216   0.064  -0.824  1.00  0.00           O  
HETATM   27  H1  UNL     1      -7.747   0.637  -0.288  1.00  0.00           H  
HETATM   28  H2  UNL     1      -6.835   2.137   0.119  1.00  0.00           H  
HETATM   29  H3  UNL     1      -4.387  -2.627  -0.335  1.00  0.00           H  
HETATM   30  H4  UNL     1      -2.198   3.562  -0.602  1.00  0.00           H  
HETATM   31  H5  UNL     1      -0.234   1.953   0.041  1.00  0.00           H  
HETATM   32  H6  UNL     1      -0.600   1.079   2.050  1.00  0.00           H  
HETATM   33  H7  UNL     1      -2.216   0.405   1.412  1.00  0.00           H  
HETATM   34  H8  UNL     1      -1.147  -1.686   0.791  1.00  0.00           H  
HETATM   35  H9  UNL     1      -0.253  -2.238   2.553  1.00  0.00           H  
HETATM   36  H10 UNL     1       1.131   0.295   0.692  1.00  0.00           H  
HETATM   37  H11 UNL     1       2.040  -2.039   0.637  1.00  0.00           H  
HETATM   38  H12 UNL     1       1.151  -2.347  -0.888  1.00  0.00           H  
HETATM   39  H13 UNL     1       4.384  -2.923   0.858  1.00  0.00           H  
HETATM   40  H14 UNL     1       6.617  -0.545   1.975  1.00  0.00           H  
HETATM   41  H15 UNL     1       6.585   2.476   0.194  1.00  0.00           H  
CONECT    1    2   27   28
CONECT    2    3    3    7
CONECT    3    4
CONECT    4    5    5   29
CONECT    5    6
CONECT    6    7    7   10
CONECT    7    8
CONECT    8    9    9
CONECT    9   10   30
CONECT   10   11
CONECT   11   12   26   31
CONECT   12   13   32   33
CONECT   13   14   15   34
CONECT   14   35
CONECT   15   16   26   36
CONECT   16   17   37   38
CONECT   17   18
CONECT   18   19   19   20   21
CONECT   20   39
CONECT   21   22
CONECT   22   23   23   24   25
CONECT   24   40
CONECT   25   41
END

HMDB0001508
     RDKit          3D
dADP
 41 43  0  0  0  0  0  0  0  0999 V2000
   -6.8556    1.1110   -0.1848 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5892    0.4437   -0.3737 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5629   -0.8846   -0.3317 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3546   -1.5527   -0.3503 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2462   -0.8203   -0.4040 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2081    0.5043   -0.4518 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4451    1.1689   -0.4386 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0956    2.4799   -0.4996 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7626    2.6167   -0.5327 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2067    1.4363   -0.4956 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8118    1.0625   -0.1551 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.0808    0.4708    1.3139 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4829   -0.9130    1.1823 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.0814   -1.3178    2.4081 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5177   -0.5911    0.1221 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.5614   -1.5659   -0.1765 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5273   -0.7602   -0.8874 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9642   -0.8980    0.0115 P   0  0  0  0  0  5  0  0  0  0  0  0
    3.9529    0.4696    0.8779 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9229   -2.1180    1.1393 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3290   -0.7332   -0.8977 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.4641    0.2823   -0.0831 P   0  0  0  0  0  5  0  0  0  0  0  0
    7.8467   -0.1989   -0.4004 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.1460    0.2208    1.6029 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.3135    1.8858   -0.5833 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2156    0.0639   -0.8239 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.7466    0.6366   -0.2878 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8351    2.1367    0.1186 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3865   -2.6265   -0.3348 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1983    3.5619   -0.6019 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2344    1.9529    0.0413 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5996    1.0790    2.0501 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2164    0.4047    1.4124 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1470   -1.6864    0.7906 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2533   -2.2382    2.5526 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1311    0.2952    0.6915 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0396   -2.0392    0.6371 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1510   -2.3471   -0.8879 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3843   -2.9234    0.8583 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.6165   -0.5446    1.9751 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.5850    2.4756    0.1937 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 13 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  1  0
 18 19  2  0
 18 20  1  0
 18 21  1  0
 21 22  1  0
 22 23  2  0
 22 24  1  0
 22 25  1  0
 15 26  1  0
  7  2  1  0
 26 11  1  0
 10  6  1  0
  1 27  1  0
  1 28  1  0
  4 29  1  0
  9 30  1  0
 11 31  1  1
 12 32  1  0
 12 33  1  0
 13 34  1  6
 14 35  1  0
 15 36  1  1
 16 37  1  0
 16 38  1  0
 20 39  1  0
 24 40  1  0
 25 41  1  0
M  END

Synonyms

Value	Source
2'-Deoxyadenosine 5'-diphosphate	ChEBI
2'-Deoxyadenosine-5'-diphosphate	ChEBI
Deoxyadenosine diphosphate	ChEBI
2'-Deoxyadenosine 5'-diphosphoric acid	Generator
2'-Deoxyadenosine-5'-diphosphoric acid	Generator
Deoxyadenosine diphosphoric acid	Generator
2'-Deoxyadenosine 5'-(trihydrogen diphosphate)	HMDB
2'-Deoxyadenosine 5'-pyrophosphate	HMDB
2'-Deoxyadenosine diphosphate	HMDB
2'-dADP	HMDB
2’-Deoxyadenosine 5’-(trihydrogen diphosphate)	HMDB
2’-Deoxyadenosine 5’-diphosphate	HMDB
2’-Deoxyadenosine 5’-pyrophosphate	HMDB
2’-Deoxyadenosine diphosphate	HMDB
2’-dADP	HMDB
Deoxyadenosine 5'-diphosphate	HMDB
Deoxyadenosine 5’-diphosphate	HMDB
dADP	HMDB
2’-Deoxyadenosine-5’-diphosphate	HMDB
2’-Deoxyadenosine-5’-diphosphoric acid	HMDB

Molecular Formula

C₁₀H₁₅N₅O₉P₂

Average Mass

411.2017

Monoisotopic Mass

411.034500127

IUPAC Name

[({[(2R,3S,5R)-5-(6-amino-9H-purin-9-yl)-3-hydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]phosphonic acid

Traditional Name

dADP

CAS Registry Number

Not Available

SMILES

NC1=NC=NC2=C1N=CN2[C@H]1C[C@H](O)[C@@H](COP(O)(=O)OP(O)(O)=O)O1

InChI Identifier

InChI=1S/C10H15N5O9P2/c11-9-8-10(13-3-12-9)15(4-14-8)7-1-5(16)6(23-7)2-22-26(20,21)24-25(17,18)19/h3-7,16H,1-2H2,(H,20,21)(H2,11,12,13)(H2,17,18,19)/t5-,6+,7+/m0/s1

InChI Key

DAEAPNUQQAICNR-RRKCRQDMSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as purine 2'-deoxyribonucleoside diphosphates. These are purine nucleotides with diphosphate group linked to the ribose moiety lacking a hydroxyl group at position 2.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Purine nucleotides

Sub Class

Purine deoxyribonucleotides

Direct Parent

Purine 2'-deoxyribonucleoside diphosphates

Alternative Parents

Substituents

Purine 2'-deoxyribonucleoside diphosphate
6-aminopurine
Organic pyrophosphate
Imidazopyrimidine
Purine
Aminopyrimidine
Monoalkyl phosphate
N-substituted imidazole
Organic phosphoric acid derivative
Phosphoric acid ester
Pyrimidine
Alkyl phosphate
Imidolactam
Heteroaromatic compound
Azole
Tetrahydrofuran
Imidazole
Secondary alcohol
Azacycle
Organoheterocyclic compound
Oxacycle
Organic oxygen compound
Organic oxide
Alcohol
Organic nitrogen compound
Organopnictogen compound
Organonitrogen compound
Organooxygen compound
Amine
Primary amine
Hydrocarbon derivative
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

2'-deoxyadenosine 5'-phosphate (CHEBI:16174 )
purine 2'-deoxyribonucleoside 5'-diphosphate (CHEBI:16174 )
Deoxyribonucleotides (C00206 )

Functional Ontology

Not Available

Physical Properties

State

Not Available

Predicted Properties

Property	Value	Source
Water Solubility	2.8 g/L	ALOGPS
logP	-1.6	ALOGPS
logP	-3.8	ChemAxon
logS	-2.2	ALOGPS
pKa (Strongest Acidic)	1.77	ChemAxon
pKa (Strongest Basic)	4.01	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	11	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	212.37 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	83.43 m³·mol⁻¹	ChemAxon
Polarizability	33.6 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 35V, Negative	splash10-056r-9511000000-f0d93c0208f02b92105f	2021-09-20	View Spectrum
LC-MS/MS	LC-MS/MS Spectrum - 35V, Positive	splash10-000i-1900000000-eb4d2ec7ae606992b749	2021-09-20	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-000i-0901000000-81bcc9c0732abcab5587	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-000i-0900000000-07e1d9f74d49eff2efac	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-000i-0900000000-fbafa2b04b5f162aeacc	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-03di-0602900000-f99abf5b772cd38d9906	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0059-6900000000-e7f368f6a5bcd9cdbdb9	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9100000000-9e49ebc21922de6f1976	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-01p9-0920500000-9ae69b0964fe5f4fdb3e	2021-09-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-000i-0900000000-b89f2f69db7f6bbbb0a2	2021-09-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-000i-0900000000-c4ddc055f77bb57a0a5a	2021-09-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-03di-0100900000-6bf3b2c8bee61774a4da	2021-09-25	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-03fr-7312900000-d577c42071baae3515b1	2021-09-25	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-a5e502a2627af2048a1f	2021-09-25	View Spectrum

Chromatographic Retention Times and Retention Indices

Retention Times

Not Available

Retention Indices

Not Available

Biological Properties

Cellular Locations

Mitochondria
Nucleus

Biospecimen Locations

Cartilage
Epidermis
Fibroblasts
Neuron
Platelet
Skeletal Muscle
Spleen

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Microbial Pathways

Pathways

Not Available

Metabolic Reactions

Reactions

This table shows at most 20 reactions. For the full list of associated reactions:

See All Associated Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0026018	Deoxyadenosine monophosphate	2'-Deoxyadenosine 5'-diphosphate	Deoxynucleotide monophosphate kinase	Phosphorylation	RHEA	34755880
MMDBr0026059	2'-Deoxyadenosine 5'-diphosphate	L-Cysteine	Vitamin B12-dependent ribonucleoside-diphosphate reductase	Reduction	RHEA	34755880
MMDBr0026087	2'-Deoxyadenosine 5'-diphosphate	Deoxyadenosine triphosphate	Nucleoside diphosphate kinase	Phosphorylation	RHEA	34755880

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links

Exposure Sources

Other Exposures

Source Type	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Age	Sex	Health Condition	Data Source	Reference
Human Cartilage	Detected but not Quantified	Not Specified	Not Specified	Normal	HMDB	34986597
Human Epidermis	Detected but not Quantified	Not Specified	Not Specified	Normal	HMDB	34986597
Human Fibroblasts	Detected but not Quantified	Not Specified	Not Specified	Normal	HMDB	34986597
Human Neuron	Detected but not Quantified	Not Specified	Not Specified	Normal	HMDB	34986597
Human Platelet	Detected but not Quantified	Not Specified	Not Specified	Normal	HMDB	34986597
Human Skeletal muscle	Detected but not Quantified	Not Specified	Not Specified	Normal	HMDB	34986597
Human Spleen	Detected but not Quantified	Not Specified	Not Specified	Normal	HMDB	34986597

External Links

HMDB ID

HMDB0001508

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB022662

KNApSAcK ID

Not Available

Chemspider ID

164196

KEGG Compound ID

C00206

BioCyc ID

CPD-11700

BiGG ID

Not Available

Wikipedia Link

Deoxyadenosine_diphosphate

METLIN ID

Not Available

PubChem Compound

188966

PDB ID

Not Available

ChEBI ID

16174

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

General References

Bansal P, Morgat A, Axelsen KB, Muthukrishnan V, Coudert E, Aimo L, Hyka-Nouspikel N, Gasteiger E, Kerhornou A, Neto TB, Pozzato M, Blatter MC, Ignatchenko A, Redaschi N, Bridge A: Rhea, the reaction knowledgebase in 2022. Nucleic Acids Res. 2022 Jan 7;50(D1):D693-D700. doi: 10.1093/nar/gkab1016. [PubMed:34755880 ]

Showing metabocard for 2'-Deoxyadenosine 5'-diphosphate (MMDBc0057193)

MOL for #<Metabolite:0x0000561537481640>

3D MOL for #<Metabolite:0x0000561537481640>

3D SDF for #<Metabolite:0x0000561537481640>

3D-SDF for #<Metabolite:0x0000561537481640>

PDB for #<Metabolite:0x0000561537481640>

3D PDB for #<Metabolite:0x0000561537481640>

SMILES for #<Metabolite:0x0000561537481640>

INCHI for #<Metabolite:0x0000561537481640>

Structure for #<Metabolite:0x0000561537481640>

3D Structure for #<Metabolite:0x0000561537481640>