Showing metabocard for Molybdopterin cytosine dinucleotide (MMDBc0031667)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2021-11-18 01:43:35 UTC
Update Date2022-08-31 18:22:56 UTC
Metabolite IDMMDBc0031667
Metabolite Identification
Common NameMolybdopterin cytosine dinucleotide
DescriptionMolybdopterin cytosine dinucleotide is a member of the chemical class known as Pyrimidine Ribonucleoside Diphosphates. These are pyrimidine ribobucleotides with diphosphate group linked to the ribose moiety. MocA is a specific cytidylyltransferase involved in molybdopterin cytosine dinucleotide biosynthesis in Escherichia coli. (PMID 19542235 ) Qox is the first MCD-containing enzyme to be synthesized in a catalytically fully competent form by a heterologous host, P. (PMID 12730200 )
Structure
MOLSDFPDBSMILESInChI

MOL for #<Metabolite:0x00007f46e04d6060>

49792073
  Mrv0541 07101213572D          

 67 71  0  0  1  0            999 V2000
    6.6218   -4.9084    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    8.0917   -5.7420    0.0000 S   0  5  0  0  0  0  0  0  0  0  0  0
    5.2024   -0.7380    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    5.9121   -1.9783    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    3.8303    1.8147    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.9488    1.5516    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.4008    3.2607    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.0822   -3.2099    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.2056    0.0870    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.6250   -2.3936    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.1992   -1.5630    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.7652    4.1031    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3775   -0.7348    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    6.0274   -0.7413    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.9766   -5.7420    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.3273   -1.2654    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
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    3.6059    3.2677    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    9.5341   -4.8885    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    9.5341   -3.2385    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   10.9861   -3.2099    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.4620    4.6893    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   11.7336   -4.4931    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1589    5.2755    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   12.4465   -3.2186    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
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   10.9861   -4.9171    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   11.7336   -3.6338    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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  1 35  1  0  0  0  0
  1 63  1  0  0  0  0
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  5 29  1  0  0  0  0
 26  6  1  6  0  0  0
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 30 50  1  0  0  0  0
 31 32  1  0  0  0  0
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 31 51  1  6  0  0  0
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 39 58  1  0  0  0  0
 39 59  1  0  0  0  0
 42 43  1  0  0  0  0
 42 62  1  0  0  0  0
M  CHG  3   2  -1  13  -1  16  -1
M  END
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3D MOL for #<Metabolite:0x00007f46e04d6060>

Download
3D SDF for #<Metabolite:0x00007f46e04d6060>
49792073
  Mrv0541 07101213572D          

 67 71  0  0  1  0            999 V2000
    6.6218   -4.9084    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    8.0917   -5.7420    0.0000 S   0  5  0  0  0  0  0  0  0  0  0  0
    5.2024   -0.7380    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    5.9121   -1.9783    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    3.8303    1.8147    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.9488    1.5516    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.4008    3.2607    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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    8.8197   -4.4760    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    8.8197   -3.6510    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
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    8.0822   -4.9171    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   11.7336   -3.6338    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    3.9893    0.5929    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
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    8.8251   -5.1772    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
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   10.9802   -2.6984    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
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   12.4445   -2.7071    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1 35  1  0  0  0  0
  1 63  1  0  0  0  0
  2 34  1  0  0  0  0
  3  9  1  0  0  0  0
  3 11  1  0  0  0  0
  3 13  1  0  0  0  0
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 39 58  1  0  0  0  0
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 42 43  1  0  0  0  0
 42 62  1  0  0  0  0
M  CHG  3   2  -1  13  -1  16  -1
M  END
> <DATABASE_ID>
MMDBc0031667

> <DATABASE_NAME>
MIME

> <SMILES>
[H]O[C@@]1([H])[C@@]([H])(O[C@]([H])(C([H])([H])OP([O-])(=O)OP([O-])(=O)OC([H])([H])[C@@]2([H])O[C@@]3([H])N([H])C4=C(N([H])[C@@]3([H])C([S-])=C2S[H])C(=O)N=C(N([H])[H])N4[H])[C@@]1([H])O[H])N1C([H])=C([H])C(=NC1=O)N([H])[H]

> <INCHI_IDENTIFIER>
InChI=1S/C19H26N8O13P2S2/c20-7-1-2-27(19(31)22-7)17-11(29)10(28)5(39-17)3-36-41(32,33)40-42(34,35)37-4-6-12(43)13(44)8-16(38-6)24-14-9(23-8)15(30)26-18(21)25-14/h1-2,5-6,8,10-11,16-17,23,28-29,43-44H,3-4H2,(H,32,33)(H,34,35)(H2,20,22,31)(H4,21,24,25,26,30)/p-3/t5-,6-,8+,10-,11-,16-,17-/m1/s1

> <INCHI_KEY>
WKSPNQYEWZEMMI-FEFZDOOUSA-K

> <FORMULA>
C19H23N8O13P2S2

> <MOLECULAR_WEIGHT>
697.509

> <EXACT_MASS>
697.030122266

> <JCHEM_ACCEPTOR_COUNT>
17

> <JCHEM_AVERAGE_POLARIZABILITY>
58.449615878284334

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
-3

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[(5aR,8R,9aR)-2-amino-8-({[({[(2R,3S,4R,5R)-5-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methyl phosphonato}oxy)phosphinato]oxy}methyl)-4-oxo-7-sulfanyl-1H,4H,5H,5aH,8H,9aH,10H-pyrano[3,2-g]pteridin-6-yl]sulfanide

> <ALOGPS_LOGP>
-0.59

> <JCHEM_LOGP>
-5.666506977154942

> <ALOGPS_LOGS>
-2.01

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-3

> <JCHEM_PKA>
3.246575208225005

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.8179591344030643

> <JCHEM_PKA_STRONGEST_BASIC>
3.132676788375102

> <JCHEM_POLAR_SURFACE_AREA>
317.09999999999997

> <JCHEM_REFRACTIVITY>
158.902

> <JCHEM_ROTATABLE_BOND_COUNT>
9

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
7.39e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[(5aR,8R,9aR)-2-amino-8-{[({[(2R,3S,4R,5R)-5-(4-amino-2-oxopyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methyl phosphonato}oxyphosphinato)oxy]methyl}-4-oxo-7-sulfanyl-1H,5H,5aH,8H,9aH,10H-pyrano[3,2-g]pteridin-6-yl]sulfanide

> <JCHEM_VEBER_RULE>
0

$$$$

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3D-SDF for #<Metabolite:0x00007f46e04d6060>
Download
PDB for #<Metabolite:0x00007f46e04d6060>
HEADER    PROTEIN                                 10-JUL-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 49792073                                          
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   10-JUL-12         0                                  
HETATM    1  S   UNK     0      12.361  -9.162   0.000  0.00  0.00           S+0
HETATM    2  S   UNK     0      15.104 -10.718   0.000  0.00  0.00           S-1
HETATM    3  P   UNK     0       9.711  -1.378   0.000  0.00  0.00           P+0
HETATM    4  P   UNK     0      11.036  -3.693   0.000  0.00  0.00           P+0
HETATM    5  O   UNK     0       7.150   3.387   0.000  0.00  0.00           O+0
HETATM    6  O   UNK     0      11.104   2.896   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0      10.081   6.087   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      15.087  -5.992   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       9.717   0.162   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0      12.367  -4.468   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       9.705  -2.918   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       8.895   7.659   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       8.171  -1.372   0.000  0.00  0.00           O-1
HETATM   14  O   UNK     0      11.251  -1.384   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0      20.490 -10.718   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0      11.811  -2.362   0.000  0.00  0.00           O-1
HETATM   17  O   UNK     0      10.261  -5.023   0.000  0.00  0.00           O+0
HETATM   18  N   UNK     0       6.731   6.100   0.000  0.00  0.00           N+0
HETATM   19  N   UNK     0      17.797  -9.125   0.000  0.00  0.00           N+0
HETATM   20  N   UNK     0      17.797  -6.045   0.000  0.00  0.00           N+0
HETATM   21  N   UNK     0      20.507  -5.992   0.000  0.00  0.00           N+0
HETATM   22  N   UNK     0       6.462   8.753   0.000  0.00  0.00           N+0
HETATM   23  N   UNK     0      21.903  -8.387   0.000  0.00  0.00           N+0
HETATM   24  N   UNK     0       4.030   9.848   0.000  0.00  0.00           N+0
HETATM   25  N   UNK     0      23.234  -6.008   0.000  0.00  0.00           N+0
HETATM   26  C   UNK     0       9.642   3.378   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       9.171   4.844   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       8.392   2.477   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       7.631   4.850   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       8.386   0.937   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      16.463  -8.355   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      16.463  -6.815   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      13.691  -6.783   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      15.087  -9.179   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      13.691  -8.387   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      19.131  -6.815   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0      19.131  -8.355   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0       5.199   5.945   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0      12.361  -6.008   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0       7.363   7.504   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0      20.507  -9.179   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0       4.299   7.194   0.000  0.00  0.00           C+0
HETATM   43  C   UNK     0       4.930   8.598   0.000  0.00  0.00           C+0
HETATM   44  C   UNK     0      21.903  -6.783   0.000  0.00  0.00           C+0
HETATM   45  H   UNK     0      10.319   4.050   0.000  0.00  0.00           H+0
HETATM   46  H   UNK     0      10.114   4.691   0.000  0.00  0.00           H+0
HETATM   47  H   UNK     0       7.540   2.047   0.000  0.00  0.00           H+0
HETATM   48  H   UNK     0       6.688   4.704   0.000  0.00  0.00           H+0
HETATM   49  H   UNK     0       7.447   1.107   0.000  0.00  0.00           H+0
HETATM   50  H   UNK     0       8.056   0.041   0.000  0.00  0.00           H+0
HETATM   51  H   UNK     0      16.474  -9.664   0.000  0.00  0.00           H+0
HETATM   52  H   UNK     0      16.474  -5.506   0.000  0.00  0.00           H+0
HETATM   53  H   UNK     0      13.697  -5.828   0.000  0.00  0.00           H+0
HETATM   54  H   UNK     0      17.797 -10.080   0.000  0.00  0.00           H+0
HETATM   55  H   UNK     0      17.797  -5.090   0.000  0.00  0.00           H+0
HETATM   56  H   UNK     0      11.816   3.532   0.000  0.00  0.00           H+0
HETATM   57  H   UNK     0      11.031   5.983   0.000  0.00  0.00           H+0
HETATM   58  H   UNK     0      11.421  -5.838   0.000  0.00  0.00           H+0
HETATM   59  H   UNK     0      12.031  -6.904   0.000  0.00  0.00           H+0
HETATM   60  H   UNK     0       4.807   5.074   0.000  0.00  0.00           H+0
HETATM   61  H   UNK     0      20.496  -5.037   0.000  0.00  0.00           H+0
HETATM   62  H   UNK     0       3.349   7.098   0.000  0.00  0.00           H+0
HETATM   63  H   UNK     0      11.532  -8.688   0.000  0.00  0.00           H+0
HETATM   64  H   UNK     0       3.080   9.752   0.000  0.00  0.00           H+0
HETATM   65  H   UNK     0       4.422  10.718   0.000  0.00  0.00           H+0
HETATM   66  H   UNK     0      24.062  -6.482   0.000  0.00  0.00           H+0
HETATM   67  H   UNK     0      23.230  -5.053   0.000  0.00  0.00           H+0
CONECT    1   35   63                                                       
CONECT    2   34                                                            
CONECT    3    9   11   13   14                                             
CONECT    4   10   11   16   17                                             
CONECT    5   28   29                                                       
CONECT    6   26   56                                                       
CONECT    7   27   57                                                       
CONECT    8   32   33                                                       
CONECT    9    3   30                                                       
CONECT   10    4   39                                                       
CONECT   11    3    4                                                       
CONECT   12   40                                                            
CONECT   13    3                                                            
CONECT   14    3                                                            
CONECT   15   41                                                            
CONECT   16    4                                                            
CONECT   17    4                                                            
CONECT   18   29   38   40                                                  
CONECT   19   31   37   54                                                  
CONECT   20   32   36   55                                                  
CONECT   21   36   44   61                                                  
CONECT   22   40   43                                                       
CONECT   23   41   44                                                       
CONECT   24   43   64   65                                                  
CONECT   25   44   66   67                                                  
CONECT   26    6   27   28   45                                             
CONECT   27    7   26   29   46                                             
CONECT   28    5   26   30   47                                             
CONECT   29    5   18   27   48                                             
CONECT   30    9   28   49   50                                             
CONECT   31   19   32   34   51                                             
CONECT   32    8   20   31   52                                             
CONECT   33    8   35   39   53                                             
CONECT   34    2   31   35                                                  
CONECT   35    1   33   34                                                  
CONECT   36   20   21   37                                                  
CONECT   37   19   36   41                                                  
CONECT   38   18   42   60                                                  
CONECT   39   10   33   58   59                                             
CONECT   40   12   18   22                                                  
CONECT   41   15   23   37                                                  
CONECT   42   38   43   62                                                  
CONECT   43   22   24   42                                                  
CONECT   44   21   23   25                                                  
CONECT   45   26                                                            
CONECT   46   27                                                            
CONECT   47   28                                                            
CONECT   48   29                                                            
CONECT   49   30                                                            
CONECT   50   30                                                            
CONECT   51   31                                                            
CONECT   52   32                                                            
CONECT   53   33                                                            
CONECT   54   19                                                            
CONECT   55   20                                                            
CONECT   56    6                                                            
CONECT   57    7                                                            
CONECT   58   39                                                            
CONECT   59   39                                                            
CONECT   60   38                                                            
CONECT   61   21                                                            
CONECT   62   42                                                            
CONECT   63    1                                                            
CONECT   64   24                                                            
CONECT   65   24                                                            
CONECT   66   25                                                            
CONECT   67   25                                                            
MASTER        0    0    0    0    0    0    0    0   67    0  142    0
END

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3D PDB for #<Metabolite:0x00007f46e04d6060>
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SMILES for #<Metabolite:0x00007f46e04d6060>
[H]O[C@@]1([H])[C@@]([H])(O[C@]([H])(C([H])([H])OP([O-])(=O)OP([O-])(=O)OC([H])([H])[C@@]2([H])O[C@@]3([H])N([H])C4=C(N([H])[C@@]3([H])C([S-])=C2S[H])C(=O)N=C(N([H])[H])N4[H])[C@@]1([H])O[H])N1C([H])=C([H])C(=NC1=O)N([H])[H]
Download
INCHI for #<Metabolite:0x00007f46e04d6060>
InChI=1S/C19H26N8O13P2S2/c20-7-1-2-27(19(31)22-7)17-11(29)10(28)5(39-17)3-36-41(32,33)40-42(34,35)37-4-6-12(43)13(44)8-16(38-6)24-14-9(23-8)15(30)26-18(21)25-14/h1-2,5-6,8,10-11,16-17,23,28-29,43-44H,3-4H2,(H,32,33)(H,34,35)(H2,20,22,31)(H4,21,24,25,26,30)/p-3/t5-,6-,8+,10-,11-,16-,17-/m1/s1
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Synonyms
ValueSource
BactopterinMeSH
Molecular FormulaC19H23N8O13P2S2
Average Mass697.509
Monoisotopic Mass697.030122266
IUPAC Name[(5aR,8R,9aR)-2-amino-8-({[({[(2R,3S,4R,5R)-5-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methyl phosphonato}oxy)phosphinato]oxy}methyl)-4-oxo-7-sulfanyl-1H,4H,5H,5aH,8H,9aH,10H-pyrano[3,2-g]pteridin-6-yl]sulfanide
Traditional Name[(5aR,8R,9aR)-2-amino-8-{[({[(2R,3S,4R,5R)-5-(4-amino-2-oxopyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methyl phosphonato}oxyphosphinato)oxy]methyl}-4-oxo-7-sulfanyl-1H,5H,5aH,8H,9aH,10H-pyrano[3,2-g]pteridin-6-yl]sulfanide
CAS Registry NumberNot Available
SMILES
[H]O[C@@]1([H])[C@@]([H])(O[C@]([H])(C([H])([H])OP([O-])(=O)OP([O-])(=O)OC([H])([H])[C@@]2([H])O[C@@]3([H])N([H])C4=C(N([H])[C@@]3([H])C([S-])=C2S[H])C(=O)N=C(N([H])[H])N4[H])[C@@]1([H])O[H])N1C([H])=C([H])C(=NC1=O)N([H])[H]
InChI Identifier
InChI=1S/C19H26N8O13P2S2/c20-7-1-2-27(19(31)22-7)17-11(29)10(28)5(39-17)3-36-41(32,33)40-42(34,35)37-4-6-12(43)13(44)8-16(38-6)24-14-9(23-8)15(30)26-18(21)25-14/h1-2,5-6,8,10-11,16-17,23,28-29,43-44H,3-4H2,(H,32,33)(H,34,35)(H2,20,22,31)(H4,21,24,25,26,30)/p-3/t5-,6-,8+,10-,11-,16-,17-/m1/s1
InChI KeyWKSPNQYEWZEMMI-FEFZDOOUSA-K