MiMeDB: Showing metabocard for 3',3'-c-di-AMP (MMDBc0055440)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2022-06-17 19:52:05 UTC

Update Date

2025-10-07 16:09:07 UTC

Metabolite ID

MMDBc0055440

Metabolite Identification

Common Name

3',3'-c-di-AMP

Description

3',3'-c-di-AMP is a cyclic dinucleotide belonging to the class of second messengers. There is limited literature available on this metabolite, indicating that further research is needed to fully understand its biological roles and implications.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652306172221522D          

 52 58  0  0  1  0            999 V2000
    0.9475   -0.6797    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7876    0.7674    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9690   -3.6673    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7041    3.7549    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7295   -4.0798    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0056    4.1674    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4995   -1.2928    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.2356    1.3805    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.4599   -4.4923    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2751    4.5799    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2841   -2.3728    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.4509    2.4604    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.2841   -1.5478    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.4509    1.6354    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.2545   -4.9048    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9896    4.9924    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4599   -3.6673    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2751    3.7549    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4995   -2.6277    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.2356    2.7154    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.2545   -5.7298    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.9896    5.8174    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9690   -4.4923    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.7041    4.5799    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2545   -3.2548    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.9896    3.3424    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2446   -4.7472    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.4905    4.8349    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2446   -3.4123    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.4905    3.5000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.9516   -2.8577    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7835    2.9453    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2064    0.8831    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.7218    1.6768    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5287   -0.7954    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    4.0132   -1.5891    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7759    0.1272    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9591   -0.0396    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0146   -1.9603    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7205    2.0479    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0911   -1.3762    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6440    1.4639    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0309    0.9119    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    3.7042   -0.8242    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    1.9488   -0.6009    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7862    0.6886    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0192   -1.9982    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7159    2.0859    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3273   -0.7239    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4078    0.8115    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0829   -3.2111    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6522    3.2987    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  7  1  1  0  0  0  0
  8  2  1  0  0  0  0
 13  7  1  0  0  0  0
 13 11  1  0  0  0  0
 14  8  1  0  0  0  0
 14 12  1  0  0  0  0
 15  9  2  0  0  0  0
 16 10  2  0  0  0  0
 17  9  1  0  0  0  0
 18 10  1  0  0  0  0
 19 11  1  0  0  0  0
 20 12  1  0  0  0  0
 21 15  1  0  0  0  0
 22 16  1  0  0  0  0
 23  3  2  0  0  0  0
 23 15  1  0  0  0  0
 24  4  2  0  0  0  0
 24 16  1  0  0  0  0
 25  3  1  0  0  0  0
 25 17  2  0  0  0  0
 26  4  1  0  0  0  0
 26 18  2  0  0  0  0
 27  5  2  0  0  0  0
 27  9  1  0  0  0  0
 28  6  2  0  0  0  0
 28 10  1  0  0  0  0
 29  5  1  0  0  0  0
 29 17  1  0  0  0  0
 19 29  1  6  0  0  0
 30  6  1  0  0  0  0
 30 18  1  0  0  0  0
 20 30  1  6  0  0  0
 11 31  1  1  0  0  0
 12 32  1  1  0  0  0
 37  1  1  0  0  0  0
 38  2  1  0  0  0  0
 39  7  1  0  0  0  0
 39 19  1  0  0  0  0
 40  8  1  0  0  0  0
 40 20  1  0  0  0  0
 41 13  1  0  0  0  0
 42 14  1  0  0  0  0
 43 33  1  0  0  0  0
 43 34  2  0  0  0  0
 43 37  1  0  0  0  0
 43 42  1  0  0  0  0
 44 35  1  0  0  0  0
 44 36  2  0  0  0  0
 44 38  1  0  0  0  0
 44 41  1  0  0  0  0
  7 45  1  1  0  0  0
  8 46  1  1  0  0  0
 11 47  1  6  0  0  0
 12 48  1  6  0  0  0
 13 49  1  6  0  0  0
 14 50  1  6  0  0  0
 19 51  1  1  0  0  0
 20 52  1  1  0  0  0
M  CHG  2  33  -1  35  -1
M  END


  Mrv1652306172221522D          

 52 58  0  0  1  0            999 V2000
    0.9475   -0.6797    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7876    0.7674    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9690   -3.6673    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7041    3.7549    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7295   -4.0798    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0056    4.1674    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4995   -1.2928    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.2356    1.3805    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.4599   -4.4923    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2751    4.5799    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2841   -2.3728    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.4509    2.4604    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.2841   -1.5478    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.4509    1.6354    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.2545   -4.9048    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9896    4.9924    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4599   -3.6673    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2751    3.7549    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4995   -2.6277    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.2356    2.7154    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.2545   -5.7298    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.9896    5.8174    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9690   -4.4923    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.7041    4.5799    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2545   -3.2548    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.9896    3.3424    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2446   -4.7472    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.4905    4.8349    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.2446   -3.4123    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.4905    3.5000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.9516   -2.8577    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7835    2.9453    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2064    0.8831    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.7218    1.6768    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5287   -0.7954    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    4.0132   -1.5891    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7759    0.1272    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9591   -0.0396    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0146   -1.9603    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7205    2.0479    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0911   -1.3762    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6440    1.4639    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0309    0.9119    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    3.7042   -0.8242    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    1.9488   -0.6009    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7862    0.6886    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0192   -1.9982    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7159    2.0859    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3273   -0.7239    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4078    0.8115    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0829   -3.2111    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6522    3.2987    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  7  1  1  0  0  0  0
  8  2  1  0  0  0  0
 13  7  1  0  0  0  0
 13 11  1  0  0  0  0
 14  8  1  0  0  0  0
 14 12  1  0  0  0  0
 15  9  2  0  0  0  0
 16 10  2  0  0  0  0
 17  9  1  0  0  0  0
 18 10  1  0  0  0  0
 19 11  1  0  0  0  0
 20 12  1  0  0  0  0
 21 15  1  0  0  0  0
 22 16  1  0  0  0  0
 23  3  2  0  0  0  0
 23 15  1  0  0  0  0
 24  4  2  0  0  0  0
 24 16  1  0  0  0  0
 25  3  1  0  0  0  0
 25 17  2  0  0  0  0
 26  4  1  0  0  0  0
 26 18  2  0  0  0  0
 27  5  2  0  0  0  0
 27  9  1  0  0  0  0
 28  6  2  0  0  0  0
 28 10  1  0  0  0  0
 29  5  1  0  0  0  0
 29 17  1  0  0  0  0
 19 29  1  6  0  0  0
 30  6  1  0  0  0  0
 30 18  1  0  0  0  0
 20 30  1  6  0  0  0
 11 31  1  1  0  0  0
 12 32  1  1  0  0  0
 37  1  1  0  0  0  0
 38  2  1  0  0  0  0
 39  7  1  0  0  0  0
 39 19  1  0  0  0  0
 40  8  1  0  0  0  0
 40 20  1  0  0  0  0
 41 13  1  0  0  0  0
 42 14  1  0  0  0  0
 43 33  1  0  0  0  0
 43 34  2  0  0  0  0
 43 37  1  0  0  0  0
 43 42  1  0  0  0  0
 44 35  1  0  0  0  0
 44 36  2  0  0  0  0
 44 38  1  0  0  0  0
 44 41  1  0  0  0  0
  7 45  1  1  0  0  0
  8 46  1  1  0  0  0
 11 47  1  6  0  0  0
 12 48  1  6  0  0  0
 13 49  1  6  0  0  0
 14 50  1  6  0  0  0
 19 51  1  1  0  0  0
 20 52  1  1  0  0  0
M  CHG  2  33  -1  35  -1
M  END
> <DATABASE_ID>
MMDBc0055440

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@@]12COP([O-])(=O)O[C@]3([H])[C@@]([H])(COP([O-])(=O)O[C@@]1([H])[C@@]([H])(O)[C@@]([H])(O2)N1C=NC2=C(N)N=CN=C12)O[C@@]([H])(N1C=NC2=C(N)N=CN=C12)[C@]3([H])O

> <INCHI_IDENTIFIER>
InChI=1S/C20H24N10O12P2/c21-15-9-17(25-3-23-15)29(5-27-9)19-11(31)13-7(39-19)1-37-43(33,34)42-14-8(2-38-44(35,36)41-13)40-20(12(14)32)30-6-28-10-16(22)24-4-26-18(10)30/h3-8,11-14,19-20,31-32H,1-2H2,(H,33,34)(H,35,36)(H2,21,23,25)(H2,22,24,26)/p-2/t7-,8-,11-,12-,13-,14-,19-,20-/m1/s1

> <INCHI_KEY>
PDXMFTWFFKBFIN-XPWFQUROSA-L

> <FORMULA>
C20H22N10O12P2

> <MOLECULAR_WEIGHT>
656.403

> <EXACT_MASS>
656.090487344

> <JCHEM_ACCEPTOR_COUNT>
16

> <JCHEM_ATOM_COUNT>
66

> <JCHEM_AVERAGE_POLARIZABILITY>
56.622178702688736

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
-2

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1S,6R,8R,9R,10S,15R,17R,18R)-8,17-bis(6-amino-9H-purin-9-yl)-9,18-dihydroxy-3,12-dioxo-2,4,7,11,13,16-hexaoxa-3lambda5,12lambda5-diphosphatricyclo[13.3.0.0^{6,10}]octadecane-3,12-bis(olate)

> <JCHEM_LOGP>
-6.741391304500086

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
7

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
2.12336552629309

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.5283246287947159

> <JCHEM_PKA_STRONGEST_BASIC>
4.22583501928646

> <JCHEM_POLAR_SURFACE_AREA>
315.34

> <JCHEM_REFRACTIVITY>
138.33559999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(1S,6R,8R,9R,10S,15R,17R,18R)-8,17-bis(6-aminopurin-9-yl)-9,18-dihydroxy-3,12-dioxo-2,4,7,11,13,16-hexaoxa-3lambda5,12lambda5-diphosphatricyclo[13.3.0.0^{6,10}]octadecane-3,12-bis(olate)

> <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       1.769  -1.269   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       7.070   1.432   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.809  -6.846   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      10.648   7.009   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       3.228  -7.616   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       5.610   7.779   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.799  -2.413   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       6.040   2.577   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.859  -8.386   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       7.980   8.549   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.264  -4.429   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.575   4.593   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       4.264  -2.889   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       4.575   3.053   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -0.475  -9.156   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       9.314   9.319   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       0.859  -6.846   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       7.980   7.009   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       2.799  -4.905   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       6.040   5.069   0.000  0.00  0.00           C+0
HETATM   21  N   UNK     0      -0.475 -10.696   0.000  0.00  0.00           N+0
HETATM   22  N   UNK     0       9.314  10.859   0.000  0.00  0.00           N+0
HETATM   23  N   UNK     0      -1.809  -8.386   0.000  0.00  0.00           N+0
HETATM   24  N   UNK     0      10.648   8.549   0.000  0.00  0.00           N+0
HETATM   25  N   UNK     0      -0.475  -6.076   0.000  0.00  0.00           N+0
HETATM   26  N   UNK     0       9.314   6.239   0.000  0.00  0.00           N+0
HETATM   27  N   UNK     0       2.323  -8.861   0.000  0.00  0.00           N+0
HETATM   28  N   UNK     0       6.516   9.025   0.000  0.00  0.00           N+0
HETATM   29  N   UNK     0       2.323  -6.370   0.000  0.00  0.00           N+0
HETATM   30  N   UNK     0       6.516   6.533   0.000  0.00  0.00           N+0
HETATM   31  O   UNK     0       5.510  -5.334   0.000  0.00  0.00           O+0
HETATM   32  O   UNK     0       3.329   5.498   0.000  0.00  0.00           O+0
HETATM   33  O   UNK     0       0.385   1.648   0.000  0.00  0.00           O-1
HETATM   34  O   UNK     0       1.347   3.130   0.000  0.00  0.00           O+0
HETATM   35  O   UNK     0       8.454  -1.485   0.000  0.00  0.00           O-1
HETATM   36  O   UNK     0       7.491  -2.966   0.000  0.00  0.00           O+0
HETATM   37  O   UNK     0       1.448   0.238   0.000  0.00  0.00           O+0
HETATM   38  O   UNK     0       7.390  -0.074   0.000  0.00  0.00           O+0
HETATM   39  O   UNK     0       1.894  -3.659   0.000  0.00  0.00           O+0
HETATM   40  O   UNK     0       6.945   3.823   0.000  0.00  0.00           O+0
HETATM   41  O   UNK     0       5.770  -2.569   0.000  0.00  0.00           O+0
HETATM   42  O   UNK     0       3.069   2.733   0.000  0.00  0.00           O+0
HETATM   43  P   UNK     0       1.924   1.702   0.000  0.00  0.00           P+0
HETATM   44  P   UNK     0       6.914  -1.539   0.000  0.00  0.00           P+0
HETATM   45  H   UNK     0       3.638  -1.122   0.000  0.00  0.00           H+0
HETATM   46  H   UNK     0       5.201   1.285   0.000  0.00  0.00           H+0
HETATM   47  H   UNK     0       5.636  -3.730   0.000  0.00  0.00           H+0
HETATM   48  H   UNK     0       3.203   3.894   0.000  0.00  0.00           H+0
HETATM   49  H   UNK     0       4.344  -1.351   0.000  0.00  0.00           H+0
HETATM   50  H   UNK     0       4.495   1.515   0.000  0.00  0.00           H+0
HETATM   51  H   UNK     0       3.888  -5.994   0.000  0.00  0.00           H+0
HETATM   52  H   UNK     0       4.951   6.158   0.000  0.00  0.00           H+0
CONECT    1    7   37                                                       
CONECT    2    8   38                                                       
CONECT    3   23   25                                                       
CONECT    4   24   26                                                       
CONECT    5   27   29                                                       
CONECT    6   28   30                                                       
CONECT    7    1   13   39   45                                             
CONECT    8    2   14   40   46                                             
CONECT    9   15   17   27                                                  
CONECT   10   16   18   28                                                  
CONECT   11   13   19   31   47                                             
CONECT   12   14   20   32   48                                             
CONECT   13    7   11   41   49                                             
CONECT   14    8   12   42   50                                             
CONECT   15    9   21   23                                                  
CONECT   16   10   22   24                                                  
CONECT   17    9   25   29                                                  
CONECT   18   10   26   30                                                  
CONECT   19   11   29   39   51                                             
CONECT   20   12   30   40   52                                             
CONECT   21   15                                                            
CONECT   22   16                                                            
CONECT   23    3   15                                                       
CONECT   24    4   16                                                       
CONECT   25    3   17                                                       
CONECT   26    4   18                                                       
CONECT   27    5    9                                                       
CONECT   28    6   10                                                       
CONECT   29    5   17   19                                                  
CONECT   30    6   18   20                                                  
CONECT   31   11                                                            
CONECT   32   12                                                            
CONECT   33   43                                                            
CONECT   34   43                                                            
CONECT   35   44                                                            
CONECT   36   44                                                            
CONECT   37    1   43                                                       
CONECT   38    2   44                                                       
CONECT   39    7   19                                                       
CONECT   40    8   20                                                       
CONECT   41   13   44                                                       
CONECT   42   14   43                                                       
CONECT   43   33   34   37   42                                             
CONECT   44   35   36   38   41                                             
CONECT   45    7                                                            
CONECT   46    8                                                            
CONECT   47   11                                                            
CONECT   48   12                                                            
CONECT   49   13                                                            
CONECT   50   14                                                            
CONECT   51   19                                                            
CONECT   52   20                                                            
MASTER        0    0    0    0    0    0    0    0   52    0  116    0
END

Synonyms

Value	Source
3',3'-c-Di-AMP	ChEBI
3',5'-Cyclic di-AMP(2-)	ChEBI
Cyclic di-3',5'-guanylate(2-)	ChEBI
Cyclic di-3',5'-guanylic acid(2-)	Generator

Molecular Formula

C₂₀H₂₂N₁₀O₁₂P₂

Average Mass

656.403

Monoisotopic Mass

656.090487344

IUPAC Name

(1S,6R,8R,9R,10S,15R,17R,18R)-8,17-bis(6-amino-9H-purin-9-yl)-9,18-dihydroxy-3,12-dioxo-2,4,7,11,13,16-hexaoxa-3lambda5,12lambda5-diphosphatricyclo[13.3.0.0^{6,10}]octadecane-3,12-bis(olate)

Traditional Name

(1S,6R,8R,9R,10S,15R,17R,18R)-8,17-bis(6-aminopurin-9-yl)-9,18-dihydroxy-3,12-dioxo-2,4,7,11,13,16-hexaoxa-3lambda5,12lambda5-diphosphatricyclo[13.3.0.0^{6,10}]octadecane-3,12-bis(olate)

CAS Registry Number

Not Available

SMILES

[H][C@@]12COP([O-])(=O)O[C@]3([H])[C@@]([H])(COP([O-])(=O)O[C@@]1([H])[C@@]([H])(O)[C@@]([H])(O2)N1C=NC2=C(N)N=CN=C12)O[C@@]([H])(N1C=NC2=C(N)N=CN=C12)[C@]3([H])O

InChI Identifier

InChI=1S/C20H24N10O12P2/c21-15-9-17(25-3-23-15)29(5-27-9)19-11(31)13-7(39-19)1-37-43(33,34)42-14-8(2-38-44(35,36)41-13)40-20(12(14)32)30-6-28-10-16(22)24-4-26-18(10)30/h3-8,11-14,19-20,31-32H,1-2H2,(H,33,34)(H,35,36)(H2,21,23,25)(H2,22,24,26)/p-2/t7-,8-,11-,12-,13-,14-,19-,20-/m1/s1

InChI Key

PDXMFTWFFKBFIN-XPWFQUROSA-L

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as (3'->5')-cyclic dinucleotides and analogues. These are cyclic compounds consisting of two ribose moieties connected by two 5',3'-phosphodiester bonds to form a cycle. Each ribose unit is N-linked to a nucleic base or an analogue thereof. Some natural (3'->5')-cyclic dinucleotides include c-di-AMP. Synthetic derivatives are generally more elaborated molecules in which one or the two nucleobase moieties, and/or sugar residues, and/or phosphodiester linkers have been modified.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

(3'->5')-dinucleotides and analogues

Sub Class

(3'->5')-cyclic dinucleotides and analogues

Direct Parent

(3'->5')-cyclic dinucleotides and analogues

Alternative Parents

Substituents

(3'->5')-cyclic dinucleotide or analogue
Purine ribonucleoside 3',5'-bisphosphate
Purine ribonucleoside bisphosphate
Pentose phosphate
Pentose-5-phosphate
Glycosyl compound
N-glycosyl compound
6-aminopurine
Monosaccharide phosphate
Imidazopyrimidine
Purine
Aminopyrimidine
Monosaccharide
N-substituted imidazole
Organic phosphoric acid derivative
Imidolactam
Pyrimidine
Tetrahydrofuran
Azole
Imidazole
Heteroaromatic compound
Secondary alcohol
Oxacycle
Azacycle
Organoheterocyclic compound
Organooxygen compound
Organonitrogen compound
Amine
Alcohol
Organic nitrogen compound
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Organic oxygen compound
Primary amine
Organic anion
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

organophosphate oxoanion (CHEBI:71500 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
logP	-6.7	ChemAxon
pKa (Strongest Acidic)	1.53	ChemAxon
pKa (Strongest Basic)	4.23	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	16	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	315.34 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	138.34 m³·mol⁻¹	ChemAxon
Polarizability	56.62 Å³	ChemAxon
Number of Rings	7	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Spectrum Type	Description	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)	2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)	2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)	2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)	2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)	2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)	2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)	2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)	2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	2022-08-17	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)	2022-08-17	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	2022-08-17	View Spectrum

Chromatographic Retention Times and Retention Indices

Retention Times

Not Available

Retention Indices

Chromatography Type	Peak Label	SMILES	Stationary Phase	Deposition Date	Retention Index
Gas Chromatography	3',3'-c-di-AMP_TMS_1	C[Si](C)(C)O[C@@H]1[C@@H]2OP(=O)([O-])OC[C@H]3O[C@@H](N4C=NC5=C(N)N=CN=C54)[C@H](O)[C@@H]3OP(=O)([O-])OC[C@H]2O[C@H]1N1C=NC2=C(N)N=CN=C21	standard non polar	2025-10-24	971.687
Gas Chromatography	3',3'-c-di-AMP_TMS_2	C[Si](C)(C)NC1=NC=NC2=C1N=CN2[C@@H]1O[C@@H]2COP(=O)([O-])O[C@@H]3[C@@H](COP(=O)([O-])O[C@H]2[C@H]1O)O[C@@H](N1C=NC2=C(N)N=CN=C21)[C@@H]3O	standard non polar	2025-10-24	1109.29
Gas Chromatography	3',3'-c-di-AMP_TMS_3	C[Si](C)(C)O[C@@H]1[C@@H]2OP(=O)([O-])OC[C@H]3O[C@@H](N4C=NC5=C(N)N=CN=C54)[C@H](O[Si](C)(C)C)[C@@H]3OP(=O)([O-])OC[C@H]2O[C@H]1N1C=NC2=C(N)N=CN=C21	standard non polar	2025-10-24	3715.24
Gas Chromatography	3',3'-c-di-AMP_TMS_4	C[Si](C)(C)NC1=NC=NC2=C1N=CN2[C@@H]1O[C@@H]2COP(=O)([O-])O[C@@H]3[C@@H](COP(=O)([O-])O[C@H]2[C@H]1O)O[C@@H](N1C=NC2=C(N)N=CN=C21)[C@@H]3O[Si](C)(C)C	standard non polar	2025-10-24	1650.08
Gas Chromatography	3',3'-c-di-AMP_TMS_5	C[Si](C)(C)NC1=NC=NC2=C1N=CN2[C@@H]1O[C@@H]2COP(=O)([O-])O[C@@H]3[C@@H](COP(=O)([O-])O[C@H]2[C@H]1O[Si](C)(C)C)O[C@@H](N1C=NC2=C(N)N=CN=C21)[C@@H]3O	standard non polar	2025-10-24	2173.26
Gas Chromatography	3',3'-c-di-AMP_TMS_6	C[Si](C)(C)NC1=NC=NC2=C1N=CN2[C@@H]1O[C@@H]2COP(=O)([O-])O[C@@H]3[C@@H](COP(=O)([O-])O[C@H]2[C@H]1O)O[C@@H](N1C=NC2=C(N[Si](C)(C)C)N=CN=C21)[C@@H]3O	standard non polar	2025-10-24	3841.86
Gas Chromatography	3',3'-c-di-AMP_TMS_7	C[Si](C)(C)N(C1=NC=NC2=C1N=CN2[C@@H]1O[C@@H]2COP(=O)([O-])O[C@@H]3[C@@H](COP(=O)([O-])O[C@H]2[C@H]1O)O[C@@H](N1C=NC2=C(N)N=CN=C21)[C@@H]3O)[Si](C)(C)C	standard non polar	2025-10-24	2531.94
Gas Chromatography	3',3'-c-di-AMP_TMS_8	C[Si](C)(C)NC1=NC=NC2=C1N=CN2[C@@H]1O[C@@H]2COP(=O)([O-])O[C@@H]3[C@@H](COP(=O)([O-])O[C@H]2[C@H]1O[Si](C)(C)C)O[C@@H](N1C=NC2=C(N)N=CN=C21)[C@@H]3O[Si](C)(C)C	standard non polar	2025-10-24	1991.22
Gas Chromatography	3',3'-c-di-AMP_TMS_9	C[Si](C)(C)NC1=NC=NC2=C1N=CN2[C@@H]1O[C@@H]2COP(=O)([O-])O[C@@H]3[C@@H](COP(=O)([O-])O[C@H]2[C@H]1O)O[C@@H](N1C=NC2=C(N[Si](C)(C)C)N=CN=C21)[C@@H]3O[Si](C)(C)C	standard non polar	2025-10-24	3846.67
Gas Chromatography	3',3'-c-di-AMP_TMS_10	C[Si](C)(C)O[C@@H]1[C@@H]2OP(=O)([O-])OC[C@H]3O[C@@H](N4C=NC5=C(N([Si](C)(C)C)[Si](C)(C)C)N=CN=C54)[C@H](O)[C@@H]3OP(=O)([O-])OC[C@H]2O[C@H]1N1C=NC2=C(N)N=CN=C21	standard non polar	2025-10-24	1072.9
Gas Chromatography	3',3'-c-di-AMP_TMS_11	C[Si](C)(C)O[C@@H]1[C@@H]2OP(=O)([O-])OC[C@H]3O[C@@H](N4C=NC5=C(N)N=CN=C54)[C@H](O)[C@@H]3OP(=O)([O-])OC[C@H]2O[C@H]1N1C=NC2=C(N([Si](C)(C)C)[Si](C)(C)C)N=CN=C21	standard non polar	2025-10-24	912.745
Gas Chromatography	3',3'-c-di-AMP_TMS_12	C[Si](C)(C)NC1=NC=NC2=C1N=CN2[C@@H]1O[C@@H]2COP(=O)([O-])O[C@@H]3[C@@H](COP(=O)([O-])O[C@H]2[C@H]1O)O[C@@H](N1C=NC2=C(N([Si](C)(C)C)[Si](C)(C)C)N=CN=C21)[C@@H]3O	standard non polar	2025-10-24	1746.44
Gas Chromatography	3',3'-c-di-AMP_TMS_1	C[Si](C)(C)O[C@@H]1[C@@H]2OP(=O)([O-])OC[C@H]3O[C@@H](N4C=NC5=C(N)N=CN=C54)[C@H](O)[C@@H]3OP(=O)([O-])OC[C@H]2O[C@H]1N1C=NC2=C(N)N=CN=C21	standard polar	2025-10-24	1544.16
Gas Chromatography	3',3'-c-di-AMP_TMS_2	C[Si](C)(C)NC1=NC=NC2=C1N=CN2[C@@H]1O[C@@H]2COP(=O)([O-])O[C@@H]3[C@@H](COP(=O)([O-])O[C@H]2[C@H]1O)O[C@@H](N1C=NC2=C(N)N=CN=C21)[C@@H]3O	standard polar	2025-10-24	2974.5
Gas Chromatography	3',3'-c-di-AMP_TMS_3	C[Si](C)(C)O[C@@H]1[C@@H]2OP(=O)([O-])OC[C@H]3O[C@@H](N4C=NC5=C(N)N=CN=C54)[C@H](O[Si](C)(C)C)[C@@H]3OP(=O)([O-])OC[C@H]2O[C@H]1N1C=NC2=C(N)N=CN=C21	standard polar	2025-10-24	1081.57
Gas Chromatography	3',3'-c-di-AMP_TMS_4	C[Si](C)(C)NC1=NC=NC2=C1N=CN2[C@@H]1O[C@@H]2COP(=O)([O-])O[C@@H]3[C@@H](COP(=O)([O-])O[C@H]2[C@H]1O)O[C@@H](N1C=NC2=C(N)N=CN=C21)[C@@H]3O[Si](C)(C)C	standard polar	2025-10-24	1590.46
Gas Chromatography	3',3'-c-di-AMP_TMS_5	C[Si](C)(C)NC1=NC=NC2=C1N=CN2[C@@H]1O[C@@H]2COP(=O)([O-])O[C@@H]3[C@@H](COP(=O)([O-])O[C@H]2[C@H]1O[Si](C)(C)C)O[C@@H](N1C=NC2=C(N)N=CN=C21)[C@@H]3O	standard polar	2025-10-24	1283.29
Gas Chromatography	3',3'-c-di-AMP_TMS_6	C[Si](C)(C)NC1=NC=NC2=C1N=CN2[C@@H]1O[C@@H]2COP(=O)([O-])O[C@@H]3[C@@H](COP(=O)([O-])O[C@H]2[C@H]1O)O[C@@H](N1C=NC2=C(N[Si](C)(C)C)N=CN=C21)[C@@H]3O	standard polar	2025-10-24	2833.36
Gas Chromatography	3',3'-c-di-AMP_TMS_7	C[Si](C)(C)N(C1=NC=NC2=C1N=CN2[C@@H]1O[C@@H]2COP(=O)([O-])O[C@@H]3[C@@H](COP(=O)([O-])O[C@H]2[C@H]1O)O[C@@H](N1C=NC2=C(N)N=CN=C21)[C@@H]3O)[Si](C)(C)C	standard polar	2025-10-24	1577.2
Gas Chromatography	3',3'-c-di-AMP_TMS_8	C[Si](C)(C)NC1=NC=NC2=C1N=CN2[C@@H]1O[C@@H]2COP(=O)([O-])O[C@@H]3[C@@H](COP(=O)([O-])O[C@H]2[C@H]1O[Si](C)(C)C)O[C@@H](N1C=NC2=C(N)N=CN=C21)[C@@H]3O[Si](C)(C)C	standard polar	2025-10-24	868.057
Gas Chromatography	3',3'-c-di-AMP_TMS_9	C[Si](C)(C)NC1=NC=NC2=C1N=CN2[C@@H]1O[C@@H]2COP(=O)([O-])O[C@@H]3[C@@H](COP(=O)([O-])O[C@H]2[C@H]1O)O[C@@H](N1C=NC2=C(N[Si](C)(C)C)N=CN=C21)[C@@H]3O[Si](C)(C)C	standard polar	2025-10-24	1936.37
Gas Chromatography	3',3'-c-di-AMP_TMS_10	C[Si](C)(C)O[C@@H]1[C@@H]2OP(=O)([O-])OC[C@H]3O[C@@H](N4C=NC5=C(N([Si](C)(C)C)[Si](C)(C)C)N=CN=C54)[C@H](O)[C@@H]3OP(=O)([O-])OC[C@H]2O[C@H]1N1C=NC2=C(N)N=CN=C21	standard polar	2025-10-24	2211.39
Gas Chromatography	3',3'-c-di-AMP_TMS_11	C[Si](C)(C)O[C@@H]1[C@@H]2OP(=O)([O-])OC[C@H]3O[C@@H](N4C=NC5=C(N)N=CN=C54)[C@H](O)[C@@H]3OP(=O)([O-])OC[C@H]2O[C@H]1N1C=NC2=C(N([Si](C)(C)C)[Si](C)(C)C)N=CN=C21	standard polar	2025-10-24	3006.55
Gas Chromatography	3',3'-c-di-AMP_TMS_12	C[Si](C)(C)NC1=NC=NC2=C1N=CN2[C@@H]1O[C@@H]2COP(=O)([O-])O[C@@H]3[C@@H](COP(=O)([O-])O[C@H]2[C@H]1O)O[C@@H](N1C=NC2=C(N([Si](C)(C)C)[Si](C)(C)C)N=CN=C21)[C@@H]3O	standard polar	2025-10-24	2364.29

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
Bacteria/Eubacteria	Firmicutes	43	Human feces; Human
Bacteria	Proteobacteria	1	Human ; Human sputum; Human subgingival plaque; Human feces
Bacteria/Eubacteria	Proteobacteria	1	Human ; Human sputum; Human subgingival plaque; Human feces
Bacteria/Eubacteria	Bacteroidetes	1	Human
Bacteria/Eubacteria	Tenericutes	2	Human
Archaea/Archaea	Euryarchaeota	2
Bacteria/Eubacteria	Actinobacteria	22	Human ; Human feces; Cattle
Bacteria/Eubacteria	Fusobacteria	1	Human ; Human feces
Bacteria/Eubacteria	Thermotogae	3

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

28533624

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

70698365

PDB ID

Not Available

ChEBI ID

71500

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 3',3'-c-di-AMP (MMDBc0055440)

MOL for #<Metabolite:0x00007fae027a47b8>

3D MOL for #<Metabolite:0x00007fae027a47b8>

3D SDF for #<Metabolite:0x00007fae027a47b8>

3D-SDF for #<Metabolite:0x00007fae027a47b8>

PDB for #<Metabolite:0x00007fae027a47b8>

3D PDB for #<Metabolite:0x00007fae027a47b8>

SMILES for #<Metabolite:0x00007fae027a47b8>

INCHI for #<Metabolite:0x00007fae027a47b8>

Structure for #<Metabolite:0x00007fae027a47b8>

3D Structure for #<Metabolite:0x00007fae027a47b8>