MiMeDB: Showing metabocard for c-di-UMP (MMDBc0055786)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-06-17 20:06:23 UTC

Update Date

2022-08-12 20:09:27 UTC

Metabolite ID

MMDBc0055786

Metabolite Identification

Common Name

c-di-UMP

Description

c-di-UMP 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. Based on a literature review very few articles have been published on c-di-UMP.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652306172222062D          

 48 52  0  0  1  0            999 V2000
    9.5718    2.9519    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1712    1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.7468    2.9519    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
    5.8273    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5733    3.3644    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2398    1.8249    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.1608    2.6499    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    9.9843    2.2374    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5837    2.2374    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0244    2.9049    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.3762    1.5700    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.2398    2.6499    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.1608    1.8249    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    7.5093    2.2374    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.8913    2.2374    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    8.7468    1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6538    2.9519    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.5718    1.5229    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1712    2.9519    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    8.3343    2.2374    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.0663    2.2374    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   10.8093    2.2374    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -1.4087    2.2374    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    7.2793    3.6895    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1213    0.7854    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.3343    0.8085    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0663    3.6664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.8306    4.5521    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7448    4.3072    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5700   -0.0773    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6558    0.1676    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1128    0.6979    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2878    3.7769    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.0244    1.5700    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3762    2.9049    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.8273    3.3644    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5733    1.1104    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1128    3.7769    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    4.2878    0.6979    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    5.4429    2.0384    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9577    2.4364    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4410    3.4882    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9596    0.9866    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4429    2.4364    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9577    2.0384    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.8839    2.9725    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5168    1.5023    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  2  0  0  0  0
  4  2  2  0  0  0  0
  7  5  1  0  0  0  0
  8  6  1  0  0  0  0
  9  1  1  0  0  0  0
 10  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 11  1  0  0  0  0
 16 12  1  0  0  0  0
 19  9  2  0  0  0  0
 19 17  1  0  0  0  0
 20 10  2  0  0  0  0
 20 18  1  0  0  0  0
 21  3  1  0  0  0  0
 15 21  1  6  0  0  0
 21 17  1  0  0  0  0
 22  4  1  0  0  0  0
 16 22  1  6  0  0  0
 22 18  1  0  0  0  0
 23  9  1  0  0  0  0
 24 10  1  0  0  0  0
 11 25  1  1  0  0  0
 12 26  1  1  0  0  0
 27 17  2  0  0  0  0
 28 18  2  0  0  0  0
 33  5  1  0  0  0  0
 34  6  1  0  0  0  0
 35  7  1  0  0  0  0
 35 15  1  0  0  0  0
 36  8  1  0  0  0  0
 36 16  1  0  0  0  0
 37 13  1  0  0  0  0
 38 14  1  0  0  0  0
 39 29  1  0  0  0  0
 39 30  2  0  0  0  0
 39 34  1  0  0  0  0
 39 37  1  0  0  0  0
 40 31  1  0  0  0  0
 40 32  2  0  0  0  0
 40 33  1  0  0  0  0
 40 38  1  0  0  0  0
  7 41  1  1  0  0  0
  8 42  1  1  0  0  0
 11 43  1  6  0  0  0
 12 44  1  6  0  0  0
 13 45  1  6  0  0  0
 14 46  1  6  0  0  0
 15 47  1  1  0  0  0
 16 48  1  1  0  0  0
M  CHG  2  23  -1  24  -1
M  END


  Mrv1652306172222062D          

 48 52  0  0  1  0            999 V2000
    9.5718    2.9519    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1712    1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.7468    2.9519    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
    5.8273    1.1104    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5733    3.3644    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2398    1.8249    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.1608    2.6499    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    9.9843    2.2374    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5837    2.2374    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0244    2.9049    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.3762    1.5700    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.2398    2.6499    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.1608    1.8249    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    7.5093    2.2374    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.8913    2.2374    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    8.7468    1.5229    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6538    2.9519    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.5718    1.5229    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1712    2.9519    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    8.3343    2.2374    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.0663    2.2374    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   10.8093    2.2374    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -1.4087    2.2374    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    7.2793    3.6895    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1213    0.7854    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.3343    0.8085    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0663    3.6664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.8306    4.5521    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7448    4.3072    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5700   -0.0773    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6558    0.1676    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1128    0.6979    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2878    3.7769    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.0244    1.5700    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3762    2.9049    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.8273    3.3644    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5733    1.1104    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1128    3.7769    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    4.2878    0.6979    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    5.4429    2.0384    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9577    2.4364    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4410    3.4882    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9596    0.9866    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4429    2.4364    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9577    2.0384    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.8839    2.9725    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5168    1.5023    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  2  0  0  0  0
  4  2  2  0  0  0  0
  7  5  1  0  0  0  0
  8  6  1  0  0  0  0
  9  1  1  0  0  0  0
 10  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 11  1  0  0  0  0
 16 12  1  0  0  0  0
 19  9  2  0  0  0  0
 19 17  1  0  0  0  0
 20 10  2  0  0  0  0
 20 18  1  0  0  0  0
 21  3  1  0  0  0  0
 15 21  1  6  0  0  0
 21 17  1  0  0  0  0
 22  4  1  0  0  0  0
 16 22  1  6  0  0  0
 22 18  1  0  0  0  0
 23  9  1  0  0  0  0
 24 10  1  0  0  0  0
 11 25  1  1  0  0  0
 12 26  1  1  0  0  0
 27 17  2  0  0  0  0
 28 18  2  0  0  0  0
 33  5  1  0  0  0  0
 34  6  1  0  0  0  0
 35  7  1  0  0  0  0
 35 15  1  0  0  0  0
 36  8  1  0  0  0  0
 36 16  1  0  0  0  0
 37 13  1  0  0  0  0
 38 14  1  0  0  0  0
 39 29  1  0  0  0  0
 39 30  2  0  0  0  0
 39 34  1  0  0  0  0
 39 37  1  0  0  0  0
 40 31  1  0  0  0  0
 40 32  2  0  0  0  0
 40 33  1  0  0  0  0
 40 38  1  0  0  0  0
  7 41  1  1  0  0  0
  8 42  1  1  0  0  0
 11 43  1  6  0  0  0
 12 44  1  6  0  0  0
 13 45  1  6  0  0  0
 14 46  1  6  0  0  0
 15 47  1  1  0  0  0
 16 48  1  1  0  0  0
M  CHG  2  23  -1  24  -1
M  END
> <DATABASE_ID>
MMDBc0055786

> <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=CC([O-])=NC1=O)O[C@@]([H])(N1C=CC([O-])=NC1=O)[C@]3([H])O

> <INCHI_IDENTIFIER>
InChI=1S/C18H22N4O16P2/c23-9-1-3-21(17(27)19-9)15-11(25)13-7(35-15)5-33-40(31,32)38-14-8(6-34-39(29,30)37-13)36-16(12(14)26)22-4-2-10(24)20-18(22)28/h1-4,7-8,11-16,25-26H,5-6H2,(H,29,30)(H,31,32)(H,19,23,27)(H,20,24,28)/p-2/t7-,8-,11-,12-,13-,14-,15-,16-/m1/s1

> <INCHI_KEY>
ADHSUZMEJHOWOL-NCOIDOBVSA-L

> <FORMULA>
C18H20N4O16P2

> <MOLECULAR_WEIGHT>
610.319

> <EXACT_MASS>
610.036051736

> <JCHEM_ACCEPTOR_COUNT>
14

> <JCHEM_ATOM_COUNT>
60

> <JCHEM_AVERAGE_POLARIZABILITY>
50.20527549794339

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
-2

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-oxo-1-[(1S,6R,8R,9R,10S,15R,17R,18R)-3,9,12,18-tetrahydroxy-17-(4-oxido-2-oxo-1,2-dihydropyrimidin-1-yl)-3,12-dioxo-2,4,7,11,13,16-hexaoxa-3lambda5,12lambda5-diphosphatricyclo[13.3.0.0^{6,10}]octadecan-8-yl]-1,2-dihydropyrimidin-4-olate

> <JCHEM_LOGP>
-2.5495391546666664

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
2.1338696588534414

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.5317976697816231

> <JCHEM_PKA_STRONGEST_BASIC>
-3.808820701973006

> <JCHEM_POLAR_SURFACE_AREA>
281.9

> <JCHEM_REFRACTIVITY>
141.063

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
2-oxo-1-[(1S,6R,8R,9R,10S,15R,17R,18R)-3,9,12,18-tetrahydroxy-17-(4-oxido-2-oxopyrimidin-1-yl)-3,12-dioxo-2,4,7,11,13,16-hexaoxa-3lambda5,12lambda5-diphosphatricyclo[13.3.0.0^{6,10}]octadecan-8-yl]pyrimidin-4-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      17.867   5.510   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -0.320   2.843   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      16.327   5.510   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.220   2.843   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      10.878   2.073   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.670   6.280   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      11.648   3.407   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       5.900   4.947   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      18.637   4.177   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -1.090   4.177   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      13.112   5.422   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.436   2.931   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      11.648   4.947   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       5.900   3.407   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      14.017   4.177   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       3.530   4.177   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      16.327   2.843   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       1.220   5.510   0.000  0.00  0.00           C+0
HETATM   19  N   UNK     0      17.867   2.843   0.000  0.00  0.00           N+0
HETATM   20  N   UNK     0      -0.320   5.510   0.000  0.00  0.00           N+0
HETATM   21  N   UNK     0      15.557   4.177   0.000  0.00  0.00           N+0
HETATM   22  N   UNK     0       1.990   4.177   0.000  0.00  0.00           N+0
HETATM   23  O   UNK     0      20.177   4.177   0.000  0.00  0.00           O-1
HETATM   24  O   UNK     0      -2.630   4.177   0.000  0.00  0.00           O-1
HETATM   25  O   UNK     0      13.588   6.887   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0       3.960   1.466   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0      15.557   1.509   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0       1.990   6.844   0.000  0.00  0.00           O+0
HETATM   29  O   UNK     0       9.017   8.497   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0      10.724   8.040   0.000  0.00  0.00           O+0
HETATM   31  O   UNK     0       8.531  -0.144   0.000  0.00  0.00           O+0
HETATM   32  O   UNK     0       6.824   0.313   0.000  0.00  0.00           O+0
HETATM   33  O   UNK     0       9.544   1.303   0.000  0.00  0.00           O+0
HETATM   34  O   UNK     0       8.004   7.050   0.000  0.00  0.00           O+0
HETATM   35  O   UNK     0      13.112   2.931   0.000  0.00  0.00           O+0
HETATM   36  O   UNK     0       4.436   5.422   0.000  0.00  0.00           O+0
HETATM   37  O   UNK     0      10.878   6.280   0.000  0.00  0.00           O+0
HETATM   38  O   UNK     0       6.670   2.073   0.000  0.00  0.00           O+0
HETATM   39  P   UNK     0       9.544   7.050   0.000  0.00  0.00           P+0
HETATM   40  P   UNK     0       8.004   1.303   0.000  0.00  0.00           P+0
HETATM   41  H   UNK     0      10.160   3.805   0.000  0.00  0.00           H+0
HETATM   42  H   UNK     0       7.388   4.548   0.000  0.00  0.00           H+0
HETATM   43  H   UNK     0      12.023   6.511   0.000  0.00  0.00           H+0
HETATM   44  H   UNK     0       5.525   1.842   0.000  0.00  0.00           H+0
HETATM   45  H   UNK     0      10.160   4.548   0.000  0.00  0.00           H+0
HETATM   46  H   UNK     0       7.388   3.805   0.000  0.00  0.00           H+0
HETATM   47  H   UNK     0      14.717   5.549   0.000  0.00  0.00           H+0
HETATM   48  H   UNK     0       2.831   2.804   0.000  0.00  0.00           H+0
CONECT    1    3    9                                                       
CONECT    2    4   10                                                       
CONECT    3    1   21                                                       
CONECT    4    2   22                                                       
CONECT    5    7   33                                                       
CONECT    6    8   34                                                       
CONECT    7    5   13   35   41                                             
CONECT    8    6   14   36   42                                             
CONECT    9    1   19   23                                                  
CONECT   10    2   20   24                                                  
CONECT   11   13   15   25   43                                             
CONECT   12   14   16   26   44                                             
CONECT   13    7   11   37   45                                             
CONECT   14    8   12   38   46                                             
CONECT   15   11   21   35   47                                             
CONECT   16   12   22   36   48                                             
CONECT   17   19   21   27                                                  
CONECT   18   20   22   28                                                  
CONECT   19    9   17                                                       
CONECT   20   10   18                                                       
CONECT   21    3   15   17                                                  
CONECT   22    4   16   18                                                  
CONECT   23    9                                                            
CONECT   24   10                                                            
CONECT   25   11                                                            
CONECT   26   12                                                            
CONECT   27   17                                                            
CONECT   28   18                                                            
CONECT   29   39                                                            
CONECT   30   39                                                            
CONECT   31   40                                                            
CONECT   32   40                                                            
CONECT   33    5   40                                                       
CONECT   34    6   39                                                       
CONECT   35    7   15                                                       
CONECT   36    8   16                                                       
CONECT   37   13   39                                                       
CONECT   38   14   40                                                       
CONECT   39   29   30   34   37                                             
CONECT   40   31   32   33   38                                             
CONECT   41    7                                                            
CONECT   42    8                                                            
CONECT   43   11                                                            
CONECT   44   12                                                            
CONECT   45   13                                                            
CONECT   46   14                                                            
CONECT   47   15                                                            
CONECT   48   16                                                            
MASTER        0    0    0    0    0    0    0    0   48    0  104    0
END

Synonyms

Not Available

Molecular Formula

C₁₈H₂₀N₄O₁₆P₂

Average Mass

610.319

Monoisotopic Mass

610.036051736

IUPAC Name

2-oxo-1-[(1S,6R,8R,9R,10S,15R,17R,18R)-3,9,12,18-tetrahydroxy-17-(4-oxido-2-oxo-1,2-dihydropyrimidin-1-yl)-3,12-dioxo-2,4,7,11,13,16-hexaoxa-3lambda5,12lambda5-diphosphatricyclo[13.3.0.0^{6,10}]octadecan-8-yl]-1,2-dihydropyrimidin-4-olate

Traditional Name

2-oxo-1-[(1S,6R,8R,9R,10S,15R,17R,18R)-3,9,12,18-tetrahydroxy-17-(4-oxido-2-oxopyrimidin-1-yl)-3,12-dioxo-2,4,7,11,13,16-hexaoxa-3lambda5,12lambda5-diphosphatricyclo[13.3.0.0^{6,10}]octadecan-8-yl]pyrimidin-4-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=CC([O-])=NC1=O)O[C@@]([H])(N1C=CC([O-])=NC1=O)[C@]3([H])O

InChI Identifier

InChI=1S/C18H22N4O16P2/c23-9-1-3-21(17(27)19-9)15-11(25)13-7(35-15)5-33-40(31,32)38-14-8(6-34-39(29,30)37-13)36-16(12(14)26)22-4-2-10(24)20-18(22)28/h1-4,7-8,11-16,25-26H,5-6H2,(H,29,30)(H,31,32)(H,19,23,27)(H,20,24,28)/p-2/t7-,8-,11-,12-,13-,14-,15-,16-/m1/s1

InChI Key

ADHSUZMEJHOWOL-NCOIDOBVSA-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
Pentose-5-phosphate
Pentose phosphate
N-glycosyl compound
Glycosyl compound
Monosaccharide phosphate
Pyrimidone
Pyrimidine
Organic phosphoric acid derivative
Monosaccharide
Hydropyrimidine
Heteroaromatic compound
Tetrahydrofuran
Secondary alcohol
Oxacycle
Azacycle
Organoheterocyclic compound
Polyol
Organic nitrogen compound
Organic oxygen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Organonitrogen compound
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	-2.5	ChemAxon
pKa (Strongest Acidic)	1.53	ChemAxon
pKa (Strongest Basic)	-3.8	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	14	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	281.9 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	141.06 m³·mol⁻¹	ChemAxon
Polarizability	50.21 Å³	ChemAxon
Number of Rings	5	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Not Available

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
MMDBr0017083	Uridine triphosphate	c-di-UMP	Cyclic dipyrimidine nucleotide synthase	Synthesis	RHEA	34755880
MMDBr0017084	Uridine triphosphate	c-di-UMP	Cyclic dipyrimidine nucleotide synthase	Synthesis	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	1	Human

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

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

138388138

PDB ID

Not Available

ChEBI ID

Not Available

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 c-di-UMP (MMDBc0055786)

MOL for #<Metabolite:0x00007fa4a21977f8>

3D MOL for #<Metabolite:0x00007fa4a21977f8>

3D SDF for #<Metabolite:0x00007fa4a21977f8>

3D-SDF for #<Metabolite:0x00007fa4a21977f8>

PDB for #<Metabolite:0x00007fa4a21977f8>

3D PDB for #<Metabolite:0x00007fa4a21977f8>

SMILES for #<Metabolite:0x00007fa4a21977f8>

INCHI for #<Metabolite:0x00007fa4a21977f8>

Structure for #<Metabolite:0x00007fa4a21977f8>

3D Structure for #<Metabolite:0x00007fa4a21977f8>