MiMeDB: Showing metabocard for adenosine 3'-diphosphate,5'-diphosphate (MMDBc0055679)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2022-06-17 20:01:59 UTC

Update Date

2025-10-07 16:09:16 UTC

Metabolite ID

MMDBc0055679

Metabolite Identification

Common Name

adenosine 3'-diphosphate,5'-diphosphate

Description

adenosine 3'-diphosphate,5'-diphosphate is a nucleotide derivative belonging to the class of dinucleotides. There is limited literature available on this metabolite, indicating that it may not be extensively studied in the context of biochemical pathways or physiological functions.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652306172222012D          

 39 41  0  0  1  0            999 V2000
   -0.5683   -1.4940    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6538    1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0992   -1.0091    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.9233    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3687   -0.5966    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.8838   -1.2640    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.6378    2.3479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8838    0.0709    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.6378    3.1729    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523    1.9354    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    0.6979    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    2.1904    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    0.8555    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1937   -0.5966    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6444   -4.9253    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -2.5512   -4.1910    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -0.9102   -4.0186    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2049   -3.5370    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    1.2445   -4.0667    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.7346   -2.4974    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6344   -2.1319    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -0.6646   -3.4668    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7527   -2.3917    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1172   -1.4132    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4820   -2.3145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0992   -0.1841    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387   -2.0486    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8169   -3.2843    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7742   -3.0271    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7307   -4.1048    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    0.9895   -3.2821    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1495   -2.7994    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    1.9457   -2.2201    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    0.2282   -1.8239    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7432   -1.3316    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6288   -0.4794    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6986    0.1999    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  4  1  1  1  0  0  0
  7  4  1  0  0  0  0
  7  6  1  0  0  0  0
  8  5  2  0  0  0  0
  9  5  1  0  0  0  0
 10  6  1  0  0  0  0
 11  8  1  0  0  0  0
 12  2  2  0  0  0  0
 12  8  1  0  0  0  0
 13  2  1  0  0  0  0
 13  9  2  0  0  0  0
 14  3  2  0  0  0  0
 14  5  1  0  0  0  0
 15  3  1  0  0  0  0
 15  9  1  0  0  0  0
 10 15  1  1  0  0  0
  6 16  1  6  0  0  0
 27  1  1  0  0  0  0
 28  4  1  0  0  0  0
 28 10  1  0  0  0  0
  7 29  1  1  0  0  0
 32 17  1  0  0  0  0
 32 18  1  0  0  0  0
 32 19  2  0  0  0  0
 32 30  1  0  0  0  0
 33 20  1  0  0  0  0
 33 21  1  0  0  0  0
 33 22  2  0  0  0  0
 33 31  1  0  0  0  0
 34 23  1  0  0  0  0
 34 24  2  0  0  0  0
 34 27  1  0  0  0  0
 34 30  1  0  0  0  0
 35 25  1  0  0  0  0
 35 26  2  0  0  0  0
 35 29  1  0  0  0  0
 35 31  1  0  0  0  0
  4 36  1  6  0  0  0
  6 37  1  1  0  0  0
  7 38  1  1  0  0  0
 10 39  1  6  0  0  0
M  CHG  5  17  -1  18  -1  20  -1  21  -1  23  -1
M  END


  Mrv1652306172222012D          

 39 41  0  0  1  0            999 V2000
   -0.5683   -1.4940    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6538    1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0992   -1.0091    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.9233    1.9354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3687   -0.5966    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.8838   -1.2640    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.6378    2.3479    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9233    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8838    0.0709    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.6378    3.1729    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.3523    1.9354    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.6378    0.6979    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    2.1904    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387    0.8555    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1937   -0.5966    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6444   -4.9253    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -2.5512   -4.1910    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -0.9102   -4.0186    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2049   -3.5370    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    1.2445   -4.0667    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.7346   -2.4974    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6344   -2.1319    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -0.6646   -3.4668    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7527   -2.3917    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1172   -1.4132    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4820   -2.3145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0992   -0.1841    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1387   -2.0486    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8169   -3.2843    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7742   -3.0271    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7307   -4.1048    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    0.9895   -3.2821    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1495   -2.7994    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    1.9457   -2.2201    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    0.2282   -1.8239    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7432   -1.3316    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6288   -0.4794    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6986    0.1999    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  4  1  1  1  0  0  0
  7  4  1  0  0  0  0
  7  6  1  0  0  0  0
  8  5  2  0  0  0  0
  9  5  1  0  0  0  0
 10  6  1  0  0  0  0
 11  8  1  0  0  0  0
 12  2  2  0  0  0  0
 12  8  1  0  0  0  0
 13  2  1  0  0  0  0
 13  9  2  0  0  0  0
 14  3  2  0  0  0  0
 14  5  1  0  0  0  0
 15  3  1  0  0  0  0
 15  9  1  0  0  0  0
 10 15  1  1  0  0  0
  6 16  1  6  0  0  0
 27  1  1  0  0  0  0
 28  4  1  0  0  0  0
 28 10  1  0  0  0  0
  7 29  1  1  0  0  0
 32 17  1  0  0  0  0
 32 18  1  0  0  0  0
 32 19  2  0  0  0  0
 32 30  1  0  0  0  0
 33 20  1  0  0  0  0
 33 21  1  0  0  0  0
 33 22  2  0  0  0  0
 33 31  1  0  0  0  0
 34 23  1  0  0  0  0
 34 24  2  0  0  0  0
 34 27  1  0  0  0  0
 34 30  1  0  0  0  0
 35 25  1  0  0  0  0
 35 26  2  0  0  0  0
 35 29  1  0  0  0  0
 35 31  1  0  0  0  0
  4 36  1  6  0  0  0
  6 37  1  1  0  0  0
  7 38  1  1  0  0  0
 10 39  1  6  0  0  0
M  CHG  5  17  -1  18  -1  20  -1  21  -1  23  -1
M  END
> <DATABASE_ID>
MMDBc0055679

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@]1(COP([O-])(=O)OP([O-])([O-])=O)O[C@@]([H])(N2C=NC3=C(N)N=CN=C23)[C@]([H])(O)[C@]1([H])OP(O)(=O)OP([O-])([O-])=O

> <INCHI_IDENTIFIER>
InChI=1S/C10H17N5O16P4/c11-8-5-9(13-2-12-8)15(3-14-5)10-6(16)7(29-35(25,26)31-33(20,21)22)4(28-10)1-27-34(23,24)30-32(17,18)19/h2-4,6-7,10,16H,1H2,(H,23,24)(H,25,26)(H2,11,12,13)(H2,17,18,19)(H2,20,21,22)/p-5/t4-,6-,7-,10-/m1/s1

> <INCHI_KEY>
DWZMGWMGGHNJLF-KQYNXXCUSA-I

> <FORMULA>
C10H12N5O16P4

> <MOLECULAR_WEIGHT>
582.123

> <EXACT_MASS>
581.925695218

> <JCHEM_ACCEPTOR_COUNT>
16

> <JCHEM_ATOM_COUNT>
47

> <JCHEM_AVERAGE_POLARIZABILITY>
42.11824930527509

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
-5

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
({[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-{[hydroxy(phosphonooxy)phosphoryl]oxy}oxolan-2-yl]methyl phosphono}oxy)phosphonate

> <JCHEM_LOGP>
-5.693407579375792

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-5

> <JCHEM_PKA>
2.0289003614260017

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.4600768178328325

> <JCHEM_PKA_STRONGEST_BASIC>
4.058991123680744

> <JCHEM_POLAR_SURFACE_AREA>
339.8100000000001

> <JCHEM_REFRACTIVITY>
101.07869999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
10

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
{[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-3-{[hydroxy(phosphonooxy)phosphoryl]oxy}oxolan-2-yl]methyl phosphono}oxyphosphonate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 17-JUN-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-JUN-22         0                                  
HETATM    1  C   UNK     0      -1.061  -2.789   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       6.258   2.073   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.220   2.843   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.185  -1.884   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       3.590   3.613   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.555  -1.114   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.650  -2.359   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.924   4.383   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       3.590   2.073   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.650   0.132   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0       4.924   5.923   0.000  0.00  0.00           N+0
HETATM   12  N   UNK     0       6.258   3.613   0.000  0.00  0.00           N+0
HETATM   13  N   UNK     0       4.924   1.303   0.000  0.00  0.00           N+0
HETATM   14  N   UNK     0       2.126   4.089   0.000  0.00  0.00           N+0
HETATM   15  N   UNK     0       2.126   1.597   0.000  0.00  0.00           N+0
HETATM   16  O   UNK     0       4.095  -1.114   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0      -3.070  -9.194   0.000  0.00  0.00           O-1
HETATM   18  O   UNK     0      -4.762  -7.823   0.000  0.00  0.00           O-1
HETATM   19  O   UNK     0      -1.699  -7.501   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0       0.383  -6.602   0.000  0.00  0.00           O-1
HETATM   21  O   UNK     0       2.323  -7.591   0.000  0.00  0.00           O-1
HETATM   22  O   UNK     0       1.371  -4.662   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0      -3.051  -3.980   0.000  0.00  0.00           O-1
HETATM   24  O   UNK     0      -1.241  -6.471   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0       5.138  -4.464   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0       3.952  -2.638   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0      -0.900  -4.320   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0       0.185  -0.344   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0       2.126  -3.824   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0      -3.392  -6.131   0.000  0.00  0.00           O+0
HETATM   31  O   UNK     0       3.312  -5.651   0.000  0.00  0.00           O+0
HETATM   32  P   UNK     0      -3.231  -7.662   0.000  0.00  0.00           P+0
HETATM   33  P   UNK     0       1.847  -6.127   0.000  0.00  0.00           P+0
HETATM   34  P   UNK     0      -2.146  -5.226   0.000  0.00  0.00           P+0
HETATM   35  P   UNK     0       3.632  -4.144   0.000  0.00  0.00           P+0
HETATM   36  H   UNK     0       0.426  -3.405   0.000  0.00  0.00           H+0
HETATM   37  H   UNK     0       3.254  -2.486   0.000  0.00  0.00           H+0
HETATM   38  H   UNK     0       1.174  -0.895   0.000  0.00  0.00           H+0
HETATM   39  H   UNK     0       3.171   0.373   0.000  0.00  0.00           H+0
CONECT    1    4   27                                                       
CONECT    2   12   13                                                       
CONECT    3   14   15                                                       
CONECT    4    1    7   28   36                                             
CONECT    5    8    9   14                                                  
CONECT    6    7   10   16   37                                             
CONECT    7    4    6   29   38                                             
CONECT    8    5   11   12                                                  
CONECT    9    5   13   15                                                  
CONECT   10    6   15   28   39                                             
CONECT   11    8                                                            
CONECT   12    2    8                                                       
CONECT   13    2    9                                                       
CONECT   14    3    5                                                       
CONECT   15    3    9   10                                                  
CONECT   16    6                                                            
CONECT   17   32                                                            
CONECT   18   32                                                            
CONECT   19   32                                                            
CONECT   20   33                                                            
CONECT   21   33                                                            
CONECT   22   33                                                            
CONECT   23   34                                                            
CONECT   24   34                                                            
CONECT   25   35                                                            
CONECT   26   35                                                            
CONECT   27    1   34                                                       
CONECT   28    4   10                                                       
CONECT   29    7   35                                                       
CONECT   30   32   34                                                       
CONECT   31   33   35                                                       
CONECT   32   17   18   19   30                                             
CONECT   33   20   21   22   31                                             
CONECT   34   23   24   27   30                                             
CONECT   35   25   26   29   31                                             
CONECT   36    4                                                            
CONECT   37    6                                                            
CONECT   38    7                                                            
CONECT   39   10                                                            
MASTER        0    0    0    0    0    0    0    0   39    0   82    0
END

Synonyms

Value	Source
Adenosine 3'-diphosphate 5'-diphosphate	MeSH
Adenosine-5'-3'(2')-bis(diphosphate)	MeSH

Molecular Formula

C₁₀H₁₂N₅O₁₆P₄

Average Mass

582.123

Monoisotopic Mass

581.925695218

IUPAC Name

({[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-{[hydroxy(phosphonooxy)phosphoryl]oxy}oxolan-2-yl]methyl phosphono}oxy)phosphonate

Traditional Name

{[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-3-{[hydroxy(phosphonooxy)phosphoryl]oxy}oxolan-2-yl]methyl phosphono}oxyphosphonate

CAS Registry Number

Not Available

SMILES

[H][C@]1(COP([O-])(=O)OP([O-])([O-])=O)O[C@@]([H])(N2C=NC3=C(N)N=CN=C23)[C@]([H])(O)[C@]1([H])OP(O)(=O)OP([O-])([O-])=O

InChI Identifier

InChI=1S/C10H17N5O16P4/c11-8-5-9(13-2-12-8)15(3-14-5)10-6(16)7(29-35(25,26)31-33(20,21)22)4(28-10)1-27-34(23,24)30-32(17,18)19/h2-4,6-7,10,16H,1H2,(H,23,24)(H,25,26)(H2,11,12,13)(H2,17,18,19)(H2,20,21,22)/p-5/t4-,6-,7-,10-/m1/s1

InChI Key

DWZMGWMGGHNJLF-KQYNXXCUSA-I

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as purine ribonucleoside diphosphates. These are purine ribobucleotides with diphosphate group linked to the ribose moiety.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Purine nucleotides

Sub Class

Purine ribonucleotides

Direct Parent

Purine ribonucleoside diphosphates

Alternative Parents

Substituents

Purine ribonucleoside diphosphate
Purine ribonucleoside bisphosphate
Purine ribonucleoside 3',5'-bisphosphate
Ribonucleoside 3'-phosphate
Pentose-5-phosphate
Pentose phosphate
N-glycosyl compound
Glycosyl compound
Organic pyrophosphate
Monosaccharide phosphate
6-aminopurine
Purine
Imidazopyrimidine
Monoalkyl phosphate
Aminopyrimidine
Imidolactam
Alkyl phosphate
Pyrimidine
Phosphoric acid ester
Organic phosphoric acid derivative
N-substituted imidazole
Monosaccharide
Heteroaromatic compound
Tetrahydrofuran
Imidazole
Azole
Secondary alcohol
Oxacycle
Azacycle
Organoheterocyclic compound
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Primary amine
Organooxygen compound
Organonitrogen compound
Amine
Alcohol
Organic anion
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
logP	-5.7	ChemAxon
pKa (Strongest Acidic)	1.46	ChemAxon
pKa (Strongest Basic)	4.06	ChemAxon
Physiological Charge	-5	ChemAxon
Hydrogen Acceptor Count	16	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	339.81 Å²	ChemAxon
Rotatable Bond Count	10	ChemAxon
Refractivity	101.08 m³·mol⁻¹	ChemAxon
Polarizability	42.12 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

Not Available

Chromatographic Retention Times and Retention Indices

Retention Times

Chromatography Type	Technique	Column	Deposition Date	Retention Time (s)
Liquid Chromatography	HILIC	Waters Acquity UPLC-BEH Amide column (eluted)	2025-10-24	416.6
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (eluted)	2025-10-24	174.5
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (void)	2025-10-24	369.0
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-24	565.9
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (eluted)	2025-10-24	453.9
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (eluted)	2025-10-24	203.0
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	1946.8
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-24	158.2
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (eluted)	2025-10-24	896.4
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	165.2
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-24	227.0
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	143.2
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	83.6
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	345.2
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	365.8
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (void)	2025-10-24	78.1
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	195.3
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-24	1077.6
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-24	719.0

Retention Indices

Chromatography Type	Peak Label	SMILES	Stationary Phase	Deposition Date	Retention Index
Gas Chromatography	adenosine 3'-diphosphate,5'-diphosphate_TMS_1	C[Si](C)(C)O[C@@H]1[C@H](OP(=O)(O)OP(=O)([O-])[O-])[C@@H](COP(=O)([O-])OP(=O)([O-])[O-])O[C@H]1N1C=NC2=C(N)N=CN=C21	standard non polar	2025-10-24	1813.47
Gas Chromatography	adenosine 3'-diphosphate,5'-diphosphate_TMS_2	C[Si](C)(C)OP(=O)(O[C@@H]1[C@@H](COP(=O)([O-])OP(=O)([O-])[O-])O[C@@H](N2C=NC3=C(N)N=CN=C32)[C@@H]1O)OP(=O)([O-])[O-]	standard non polar	2025-10-24	1849.8
Gas Chromatography	adenosine 3'-diphosphate,5'-diphosphate_TMS_3	C[Si](C)(C)NC1=NC=NC2=C1N=CN2[C@@H]1O[C@H](COP(=O)([O-])OP(=O)([O-])[O-])[C@@H](OP(=O)(O)OP(=O)([O-])[O-])[C@H]1O	standard non polar	2025-10-24	2162.85
Gas Chromatography	adenosine 3'-diphosphate,5'-diphosphate_TMS_4	C[Si](C)(C)O[C@@H]1[C@H](OP(=O)(O[Si](C)(C)C)OP(=O)([O-])[O-])[C@@H](COP(=O)([O-])OP(=O)([O-])[O-])O[C@H]1N1C=NC2=C(N)N=CN=C21	standard non polar	2025-10-24	2035.96
Gas Chromatography	adenosine 3'-diphosphate,5'-diphosphate_TMS_5	C[Si](C)(C)NC1=NC=NC2=C1N=CN2[C@@H]1O[C@H](COP(=O)([O-])OP(=O)([O-])[O-])[C@@H](OP(=O)(O)OP(=O)([O-])[O-])[C@H]1O[Si](C)(C)C	standard non polar	2025-10-24	1696.55
Gas Chromatography	adenosine 3'-diphosphate,5'-diphosphate_TMS_6	C[Si](C)(C)NC1=NC=NC2=C1N=CN2[C@@H]1O[C@H](COP(=O)([O-])OP(=O)([O-])[O-])[C@@H](OP(=O)(O[Si](C)(C)C)OP(=O)([O-])[O-])[C@H]1O	standard non polar	2025-10-24	2815.57
Gas Chromatography	adenosine 3'-diphosphate,5'-diphosphate_TMS_7	C[Si](C)(C)N(C1=NC=NC2=C1N=CN2[C@@H]1O[C@H](COP(=O)([O-])OP(=O)([O-])[O-])[C@@H](OP(=O)(O)OP(=O)([O-])[O-])[C@H]1O)[Si](C)(C)C	standard non polar	2025-10-24	2101.42
Gas Chromatography	adenosine 3'-diphosphate,5'-diphosphate_TMS_8	C[Si](C)(C)NC1=NC=NC2=C1N=CN2[C@@H]1O[C@H](COP(=O)([O-])OP(=O)([O-])[O-])[C@@H](OP(=O)(O[Si](C)(C)C)OP(=O)([O-])[O-])[C@H]1O[Si](C)(C)C	standard non polar	2025-10-24	2400.94
Gas Chromatography	adenosine 3'-diphosphate,5'-diphosphate_TMS_9	C[Si](C)(C)O[C@@H]1[C@H](OP(=O)(O)OP(=O)([O-])[O-])[C@@H](COP(=O)([O-])OP(=O)([O-])[O-])O[C@H]1N1C=NC2=C(N([Si](C)(C)C)[Si](C)(C)C)N=CN=C21	standard non polar	2025-10-24	2161.16
Gas Chromatography	adenosine 3'-diphosphate,5'-diphosphate_TMS_10	C[Si](C)(C)OP(=O)(O[C@@H]1[C@@H](COP(=O)([O-])OP(=O)([O-])[O-])O[C@@H](N2C=NC3=C(N([Si](C)(C)C)[Si](C)(C)C)N=CN=C32)[C@@H]1O)OP(=O)([O-])[O-]	standard non polar	2025-10-24	2054.1
Gas Chromatography	adenosine 3'-diphosphate,5'-diphosphate_TMS_11	C[Si](C)(C)O[C@@H]1[C@H](OP(=O)(O[Si](C)(C)C)OP(=O)([O-])[O-])[C@@H](COP(=O)([O-])OP(=O)([O-])[O-])O[C@H]1N1C=NC2=C(N([Si](C)(C)C)[Si](C)(C)C)N=CN=C21	standard non polar	2025-10-24	1639.79
Gas Chromatography	adenosine 3'-diphosphate,5'-diphosphate_TMS_1	C[Si](C)(C)O[C@@H]1[C@H](OP(=O)(O)OP(=O)([O-])[O-])[C@@H](COP(=O)([O-])OP(=O)([O-])[O-])O[C@H]1N1C=NC2=C(N)N=CN=C21	standard polar	2025-10-24	1948.38
Gas Chromatography	adenosine 3'-diphosphate,5'-diphosphate_TMS_2	C[Si](C)(C)OP(=O)(O[C@@H]1[C@@H](COP(=O)([O-])OP(=O)([O-])[O-])O[C@@H](N2C=NC3=C(N)N=CN=C32)[C@@H]1O)OP(=O)([O-])[O-]	standard polar	2025-10-24	1897.78
Gas Chromatography	adenosine 3'-diphosphate,5'-diphosphate_TMS_3	C[Si](C)(C)NC1=NC=NC2=C1N=CN2[C@@H]1O[C@H](COP(=O)([O-])OP(=O)([O-])[O-])[C@@H](OP(=O)(O)OP(=O)([O-])[O-])[C@H]1O	standard polar	2025-10-24	1369.72
Gas Chromatography	adenosine 3'-diphosphate,5'-diphosphate_TMS_4	C[Si](C)(C)O[C@@H]1[C@H](OP(=O)(O[Si](C)(C)C)OP(=O)([O-])[O-])[C@@H](COP(=O)([O-])OP(=O)([O-])[O-])O[C@H]1N1C=NC2=C(N)N=CN=C21	standard polar	2025-10-24	404.317
Gas Chromatography	adenosine 3'-diphosphate,5'-diphosphate_TMS_5	C[Si](C)(C)NC1=NC=NC2=C1N=CN2[C@@H]1O[C@H](COP(=O)([O-])OP(=O)([O-])[O-])[C@@H](OP(=O)(O)OP(=O)([O-])[O-])[C@H]1O[Si](C)(C)C	standard polar	2025-10-24	2692.54
Gas Chromatography	adenosine 3'-diphosphate,5'-diphosphate_TMS_6	C[Si](C)(C)NC1=NC=NC2=C1N=CN2[C@@H]1O[C@H](COP(=O)([O-])OP(=O)([O-])[O-])[C@@H](OP(=O)(O[Si](C)(C)C)OP(=O)([O-])[O-])[C@H]1O	standard polar	2025-10-24	1785.8
Gas Chromatography	adenosine 3'-diphosphate,5'-diphosphate_TMS_7	C[Si](C)(C)N(C1=NC=NC2=C1N=CN2[C@@H]1O[C@H](COP(=O)([O-])OP(=O)([O-])[O-])[C@@H](OP(=O)(O)OP(=O)([O-])[O-])[C@H]1O)[Si](C)(C)C	standard polar	2025-10-24	1994.72
Gas Chromatography	adenosine 3'-diphosphate,5'-diphosphate_TMS_8	C[Si](C)(C)NC1=NC=NC2=C1N=CN2[C@@H]1O[C@H](COP(=O)([O-])OP(=O)([O-])[O-])[C@@H](OP(=O)(O[Si](C)(C)C)OP(=O)([O-])[O-])[C@H]1O[Si](C)(C)C	standard polar	2025-10-24	2852.28
Gas Chromatography	adenosine 3'-diphosphate,5'-diphosphate_TMS_9	C[Si](C)(C)O[C@@H]1[C@H](OP(=O)(O)OP(=O)([O-])[O-])[C@@H](COP(=O)([O-])OP(=O)([O-])[O-])O[C@H]1N1C=NC2=C(N([Si](C)(C)C)[Si](C)(C)C)N=CN=C21	standard polar	2025-10-24	2973.55
Gas Chromatography	adenosine 3'-diphosphate,5'-diphosphate_TMS_10	C[Si](C)(C)OP(=O)(O[C@@H]1[C@@H](COP(=O)([O-])OP(=O)([O-])[O-])O[C@@H](N2C=NC3=C(N([Si](C)(C)C)[Si](C)(C)C)N=CN=C32)[C@@H]1O)OP(=O)([O-])[O-]	standard polar	2025-10-24	1971.57
Gas Chromatography	adenosine 3'-diphosphate,5'-diphosphate_TMS_11	C[Si](C)(C)O[C@@H]1[C@H](OP(=O)(O[Si](C)(C)C)OP(=O)([O-])[O-])[C@@H](COP(=O)([O-])OP(=O)([O-])[O-])O[C@H]1N1C=NC2=C(N([Si](C)(C)C)[Si](C)(C)C)N=CN=C21	standard polar	2025-10-24	2459.22

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

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

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
Bacteria/Eubacteria	Proteobacteria	1	Human

Exposure Sources

Other Exposures

Source Type	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

145712531

PDB ID

Not Available

ChEBI ID

Not Available

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 adenosine 3'-diphosphate,5'-diphosphate (MMDBc0055679)

MOL for #<Metabolite:0x00007fae00515e90>

3D MOL for #<Metabolite:0x00007fae00515e90>

3D SDF for #<Metabolite:0x00007fae00515e90>

3D-SDF for #<Metabolite:0x00007fae00515e90>

PDB for #<Metabolite:0x00007fae00515e90>

3D PDB for #<Metabolite:0x00007fae00515e90>

SMILES for #<Metabolite:0x00007fae00515e90>

INCHI for #<Metabolite:0x00007fae00515e90>

Structure for #<Metabolite:0x00007fae00515e90>

3D Structure for #<Metabolite:0x00007fae00515e90>