MiMeDB: Showing metabocard for Cyclic di-3',5'-guanylate (MMDBc0031787)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-18 01:49:18 UTC

Update Date

2022-08-31 18:24:44 UTC

Metabolite ID

MMDBc0031787

Metabolite Identification

Common Name

Cyclic di-3',5'-guanylate

Description

Cyclic di-3',5'-guanylate or Cyclic-di-GMP is a second messenger which controls cell surface-associated traits in bacteria. It is a substrate for the enzyme Cyclic di-GMP phosphodiesterase which catalyzes the reaction Cyclic di-3',5'-guanylate + H2O = 5'-phosphoguanylyl(3'->5')guanosine.

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 10101211202D          

 54 60  0  0  0  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
    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
    0.4599   -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
   -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
    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
   -0.9690   -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
   -1.6835   -3.2548    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.4185    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
   -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
   -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
    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
   -0.2545   -5.7298    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9896    5.8174    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2064    0.8831    0.0000 O   0  0  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  0  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
    0.6756   -1.3360    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0594    1.4237    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0880   -2.5584    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6471    2.6460    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1090   -1.5334    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6261    1.6210    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
  5  1  1  0  0  0  0
  6  2  1  0  0  0  0
 11  5  1  0  0  0  0
 11  9  1  0  0  0  0
 12  6  1  0  0  0  0
 12 10  1  0  0  0  0
 13  7  2  0  0  0  0
 14  8  2  0  0  0  0
 15  7  1  0  0  0  0
 16  8  1  0  0  0  0
 17  9  1  0  0  0  0
 18 10  1  0  0  0  0
 21 19  2  0  0  0  0
 22 20  2  0  0  0  0
 23  3  2  0  0  0  0
 23  7  1  0  0  0  0
 24  4  2  0  0  0  0
 24  8  1  0  0  0  0
 25 13  1  0  0  0  0
 25 19  1  0  0  0  0
 26 14  1  0  0  0  0
 26 20  1  0  0  0  0
 27 15  2  0  0  0  0
 27 19  1  0  0  0  0
 28 16  2  0  0  0  0
 28 20  1  0  0  0  0
 29  3  1  0  0  0  0
 29 13  1  0  0  0  0
 17 29  1  6  0  0  0
 30  4  1  0  0  0  0
 30 14  1  0  0  0  0
 18 30  1  6  0  0  0
  9 31  1  1  0  0  0
 10 32  1  1  0  0  0
 33 15  1  0  0  0  0
 34 16  1  0  0  0  0
 39  1  1  0  0  0  0
 40  2  1  0  0  0  0
 41  5  1  0  0  0  0
 41 17  1  0  0  0  0
 42  6  1  0  0  0  0
 42 18  1  0  0  0  0
 43 11  1  0  0  0  0
 44 12  1  0  0  0  0
 45 35  1  0  0  0  0
 45 36  2  0  0  0  0
 45 39  1  0  0  0  0
 45 44  1  0  0  0  0
 46 37  1  0  0  0  0
 46 38  2  0  0  0  0
 46 40  1  0  0  0  0
 46 43  1  0  0  0  0
  5 47  1  1  0  0  0
  6 48  1  1  0  0  0
  9 49  1  6  0  0  0
 10 50  1  6  0  0  0
 11 51  1  6  0  0  0
 12 52  1  6  0  0  0
 17 53  1  1  0  0  0
 18 54  1  1  0  0  0
M  END


  Mrv0541 10101211202D          

 54 60  0  0  0  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
    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
    0.4599   -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
   -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
    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
   -0.9690   -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
   -1.6835   -3.2548    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    6.4185    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
   -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
   -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
    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
   -0.2545   -5.7298    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9896    5.8174    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2064    0.8831    0.0000 O   0  0  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  0  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
    0.6756   -1.3360    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0594    1.4237    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0880   -2.5584    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6471    2.6460    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1090   -1.5334    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6261    1.6210    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
  5  1  1  0  0  0  0
  6  2  1  0  0  0  0
 11  5  1  0  0  0  0
 11  9  1  0  0  0  0
 12  6  1  0  0  0  0
 12 10  1  0  0  0  0
 13  7  2  0  0  0  0
 14  8  2  0  0  0  0
 15  7  1  0  0  0  0
 16  8  1  0  0  0  0
 17  9  1  0  0  0  0
 18 10  1  0  0  0  0
 21 19  2  0  0  0  0
 22 20  2  0  0  0  0
 23  3  2  0  0  0  0
 23  7  1  0  0  0  0
 24  4  2  0  0  0  0
 24  8  1  0  0  0  0
 25 13  1  0  0  0  0
 25 19  1  0  0  0  0
 26 14  1  0  0  0  0
 26 20  1  0  0  0  0
 27 15  2  0  0  0  0
 27 19  1  0  0  0  0
 28 16  2  0  0  0  0
 28 20  1  0  0  0  0
 29  3  1  0  0  0  0
 29 13  1  0  0  0  0
 17 29  1  6  0  0  0
 30  4  1  0  0  0  0
 30 14  1  0  0  0  0
 18 30  1  6  0  0  0
  9 31  1  1  0  0  0
 10 32  1  1  0  0  0
 33 15  1  0  0  0  0
 34 16  1  0  0  0  0
 39  1  1  0  0  0  0
 40  2  1  0  0  0  0
 41  5  1  0  0  0  0
 41 17  1  0  0  0  0
 42  6  1  0  0  0  0
 42 18  1  0  0  0  0
 43 11  1  0  0  0  0
 44 12  1  0  0  0  0
 45 35  1  0  0  0  0
 45 36  2  0  0  0  0
 45 39  1  0  0  0  0
 45 44  1  0  0  0  0
 46 37  1  0  0  0  0
 46 38  2  0  0  0  0
 46 40  1  0  0  0  0
 46 43  1  0  0  0  0
  5 47  1  1  0  0  0
  6 48  1  1  0  0  0
  9 49  1  6  0  0  0
 10 50  1  6  0  0  0
 11 51  1  6  0  0  0
 12 52  1  6  0  0  0
 17 53  1  1  0  0  0
 18 54  1  1  0  0  0
M  END
> <DATABASE_ID>
MMDBc0031787

> <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=C1NC(=N)N=C2O)O[C@@]([H])(N1C=NC2=C1NC(=N)N=C2O)[C@]3([H])O

> <INCHI_IDENTIFIER>
InChI=1S/C20H24N10O14P2/c21-19-25-13-7(15(33)27-19)23-3-29(13)17-9(31)11-5(41-17)1-39-45(35,36)44-12-6(2-40-46(37,38)43-11)42-18(10(12)32)30-4-24-8-14(30)26-20(22)28-16(8)34/h3-6,9-12,17-18,31-32H,1-2H2,(H,35,36)(H,37,38)(H3,21,25,27,33)(H3,22,26,28,34)/t5-,6-,9-,10-,11-,12-,17-,18-/m1/s1

> <INCHI_KEY>
PKFDLKSEZWEFGL-MHARETSRSA-N

> <FORMULA>
C20H24N10O14P2

> <MOLECULAR_WEIGHT>
690.4107

> <EXACT_MASS>
690.09486855

> <JCHEM_ACCEPTOR_COUNT>
18

> <JCHEM_AVERAGE_POLARIZABILITY>
60.01158460939246

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
10

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(1S,6R,8R,9R,10S,15R,17R,18R)-3,9,12,18-tetrahydroxy-8,17-bis(6-hydroxy-2-imino-3,9-dihydro-2H-purin-9-yl)-2,4,7,11,13,16-hexaoxa-3λ⁵,12λ⁵-diphosphatricyclo[13.3.0.0⁶,¹⁰]octadecane-3,12-dione

> <ALOGPS_LOGP>
-1.04

> <JCHEM_LOGP>
-3.4712854512254188

> <ALOGPS_LOGS>
-2.26

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
7

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
2.1058773401843034

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.5313246301930614

> <JCHEM_PKA_STRONGEST_BASIC>
5.183061397160955

> <JCHEM_POLAR_SURFACE_AREA>
343.02000000000004

> <JCHEM_REFRACTIVITY>
164.59220000000008

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
3.77e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
cyclic di-GMP

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 10-OCT-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   10-OCT-12         0                                  
HETATM    1  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   21  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   22  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   23  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   24  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   25  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   26  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   27  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   28  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   29  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   30  N   UNK     0       0.000   0.000   0.000  0.00  0.00           N+0
HETATM   31  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   32  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   33  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   34  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   35  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   36  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   37  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   38  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   39  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   40  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   41  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   42  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   43  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   44  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   45  P   UNK     0       0.000   0.000   0.000  0.00  0.00           P+0
HETATM   46  P   UNK     0       0.000   0.000   0.000  0.00  0.00           P+0
HETATM   47  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   48  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   49  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   50  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   51  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   52  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   53  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   54  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
CONECT    1    5   39                                                       
CONECT    2    6   40                                                       
CONECT    3   23   29                                                       
CONECT    4   24   30                                                       
CONECT    5    1   11   41   47                                             
CONECT    6    2   12   42   48                                             
CONECT    7   13   15   23                                                  
CONECT    8   14   16   24                                                  
CONECT    9   11   17   31   49                                             
CONECT   10   12   18   32   50                                             
CONECT   11    5    9   43   51                                             
CONECT   12    6   10   44   52                                             
CONECT   13    7   25   29                                                  
CONECT   14    8   26   30                                                  
CONECT   15    7   27   33                                                  
CONECT   16    8   28   34                                                  
CONECT   17    9   29   41   53                                             
CONECT   18   10   30   42   54                                             
CONECT   19   21   25   27                                                  
CONECT   20   22   26   28                                                  
CONECT   21   19                                                            
CONECT   22   20                                                            
CONECT   23    3    7                                                       
CONECT   24    4    8                                                       
CONECT   25   13   19                                                       
CONECT   26   14   20                                                       
CONECT   27   15   19                                                       
CONECT   28   16   20                                                       
CONECT   29    3   13   17                                                  
CONECT   30    4   14   18                                                  
CONECT   31    9                                                            
CONECT   32   10                                                            
CONECT   33   15                                                            
CONECT   34   16                                                            
CONECT   35   45                                                            
CONECT   36   45                                                            
CONECT   37   46                                                            
CONECT   38   46                                                            
CONECT   39    1   45                                                       
CONECT   40    2   46                                                       
CONECT   41    5   17                                                       
CONECT   42    6   18                                                       
CONECT   43   11   46                                                       
CONECT   44   12   45                                                       
CONECT   45   35   36   39   44                                             
CONECT   46   37   38   40   43                                             
CONECT   47    5                                                            
CONECT   48    6                                                            
CONECT   49    9                                                            
CONECT   50   10                                                            
CONECT   51   11                                                            
CONECT   52   12                                                            
CONECT   53   17                                                            
CONECT   54   18                                                            
MASTER        0    0    0    0    0    0    0    0   54    0  120    0
END

Synonyms

Value	Source
3',5'-Cyclic di-GMP	ChEBI
3',5'-Cyclic diguanylic acid	ChEBI
Bis(3',5')-cyclic diguanylic acid	ChEBI
Bis-(3',5')-cyclic digmp	ChEBI
Bis-(3'-5')-cyclic dimeric guanosine monophosphate	ChEBI
c-(GPGP)	ChEBI
CdiGMP	ChEBI
CGPGP	ChEBI
Cyclic di-3',5'-guanylic acid	ChEBI
Cyclic di-GMP	ChEBI
Cyclic diguanylic acid	ChEBI
Cyclic dinucleotide di-GMP	ChEBI
Cyclic-bis(3',5')diguanylic acid	ChEBI
Cyclic-bis(3'->5') dimeric GMP	ChEBI
Guanylyl-(3'->5')-3'-guanylic acid, cyclic 3'->5'''-nucleotide	ChEBI
3',5'-Cyclic diguanylate	Generator
Bis(3',5')-cyclic diguanylate	Generator
Bis-(3'-5')-cyclic dimeric guanosine monophosphoric acid	Generator
Cyclic diguanylate	Generator
Cyclic-bis(3',5')diguanylate	Generator
Guanylyl-(3'->5')-3'-guanylate, cyclic 3'->5'''-nucleotide	Generator
Bis-(3'-5')-cyclic-GMP	MeSH
Bis-(3',5')-cyclic-di-guanosine monophosphate	MeSH
Cyclic-di-GMP	MeSH
Bis-(3'-5')-cyclic dimeric GMP	MeSH

Molecular Formula

C₂₀H₂₄N₁₀O₁₄P₂

Average Mass

690.4107

Monoisotopic Mass

690.09486855

IUPAC Name

(1S,6R,8R,9R,10S,15R,17R,18R)-3,9,12,18-tetrahydroxy-8,17-bis(6-hydroxy-2-imino-3,9-dihydro-2H-purin-9-yl)-2,4,7,11,13,16-hexaoxa-3λ⁵,12λ⁵-diphosphatricyclo[13.3.0.0⁶,¹⁰]octadecane-3,12-dione

Traditional Name

cyclic di-GMP

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=C1NC(=N)N=C2O)O[C@@]([H])(N1C=NC2=C1NC(=N)N=C2O)[C@]3([H])O

InChI Identifier

InChI=1S/C20H24N10O14P2/c21-19-25-13-7(15(33)27-19)23-3-29(13)17-9(31)11-5(41-17)1-39-45(35,36)44-12-6(2-40-46(37,38)43-11)42-18(10(12)32)30-4-24-8-14(30)26-20(22)28-16(8)34/h3-6,9-12,17-18,31-32H,1-2H2,(H,35,36)(H,37,38)(H3,21,25,27,33)(H3,22,26,28,34)/t5-,6-,9-,10-,11-,12-,17-,18-/m1/s1

InChI Key

PKFDLKSEZWEFGL-MHARETSRSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as d-alpha-amino acids. These are alpha amino acids which have the D-configuration of the alpha-carbon atom.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

D-alpha-amino acids

Alternative Parents

Substituents

D-alpha-amino acid
Carboxylic acid salt
Amino acid
Carboxylic acid
Monocarboxylic acid or derivatives
Organic oxygen compound
Hydrocarbon derivative
Organic nitrogen compound
Organic salt
Organic zwitterion
Primary amine
Organooxygen compound
Organonitrogen compound
Organochloride
Organohalogen compound
Alkyl chloride
Primary aliphatic amine
Organic oxide
Carbonyl group
Amine
Alkyl halide
Organopnictogen compound
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

chloroalanine (CHEBI:17092 )
D-alanine derivative (CHEBI:17092 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	3.77 g/L	ALOGPS
logP	-1	ALOGPS
logP	-3.5	ChemAxon
logS	-2.3	ALOGPS
pKa (Strongest Acidic)	1.53	ChemAxon
pKa (Strongest Basic)	5.18	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	18	ChemAxon
Hydrogen Donor Count	10	ChemAxon
Polar Surface Area	343.02 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	164.59 m³·mol⁻¹	ChemAxon
Polarizability	60.01 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	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_22) - 70eV, Positive	Not Available	2022-08-08	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0udi-0902003000-e714278e50df8020df9d	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0udi-0900000000-805d685a4a60cc6521c8	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0udi-0901000000-f966dd9a12345ea25d0c	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0f79-1700109000-5c992a7b596f80ec0b1d	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0udi-1900000000-a366df89a35ae5755147	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0ufr-6900000000-e76693b19ac5868f3b31	2015-09-15	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-20	View Spectrum

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

Metabolic Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0014499	Guanosine triphosphate	Cyclic di-3',5'-guanylate	Probable diguanylate cyclase CdgI	Cycle formation; Synthesis	RHEA	34755880
MMDBr0014500	Guanosine triphosphate	Cyclic di-3',5'-guanylate	Cyclic dipurine nucleotide synthase	Synthesis	RHEA	34755880
MMDBr0014501	Cyclic di-3',5'-guanylate	Linear dimeric GMP	Cyclic di-GMP phosphodiesterase CdgJ	Formation of 2'-nucleotide products from 2',3'-cyclic substrates	RHEA	34755880
MMDBr0016642	Cyclic di-3',5'-guanylate	GMP	Cyclic di-GMP phosphodiesterase TM_0186	Formation of 2'-nucleotide products from 2',3'-cyclic substrates	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
Bacteria	Proteobacteria	21	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool	Unknown
Bacteria	Bacteroidetes	3	Human feces; Human
Bacteria	nah	2
Bacteria	Spirochaetes	2	Human
Bacteria	Thermotogae	1

Exposure Sources

Source Type	Source Sub-type	Species	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

C16463

BioCyc ID

C-DI-GMP

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

5287531

PDB ID

Not Available

ChEBI ID

49537

Food Biomarker Ontology

Not Available

References

Synthesis Reference

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 Cyclic di-3',5'-guanylate (MMDBc0031787)

MOL for #<Metabolite:0x00007f5a5ede1b28>

3D MOL for #<Metabolite:0x00007f5a5ede1b28>

3D SDF for #<Metabolite:0x00007f5a5ede1b28>

3D-SDF for #<Metabolite:0x00007f5a5ede1b28>

PDB for #<Metabolite:0x00007f5a5ede1b28>

3D PDB for #<Metabolite:0x00007f5a5ede1b28>

SMILES for #<Metabolite:0x00007f5a5ede1b28>

INCHI for #<Metabolite:0x00007f5a5ede1b28>

Structure for #<Metabolite:0x00007f5a5ede1b28>

3D Structure for #<Metabolite:0x00007f5a5ede1b28>