MiMeDB: Showing metabocard for coenzyme B12 (MMDBc0052969)

Microbial

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-05-16 21:10:32 UTC

Update Date

2025-10-07 16:08:17 UTC

Metabolite ID

MMDBc0052969

Metabolite Identification

Common Name

coenzyme B12

Description

Coenzyme B12 is a cobalt-containing organometallic compound classified as a coenzyme and is part of the vitamin B12 family. Its chemical structure features a corrin ring with a central cobalt ion, which can exist in different oxidation states, allowing it to participate in various enzymatic reactions. Coenzyme B12 plays a crucial role in several biochemical pathways, particularly in the metabolism of certain amino acids and fatty acids. One notable pathway involves its function as a cofactor for mutases, where it facilitates the rearrangement of carbon skeletons. For instance, the Lcm module relies on the new-to-nature activity of a coenzyme B12-dependent mutase for the conversion of 3-hydroxypropionyl-CoA into lactyl-CoA, showcasing its importance in metabolic processes (PMID:39592584 ). Through these enzymatic actions, coenzyme B12 is integral to the synthesis and transformation of various biomolecules, highlighting its significance in both chemistry and biology.

Structure

MOL SDF PDB SMILES InChI


  Mrv1572010151518142D          

123131  0  0  1  0            999 V2000
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  2  3  1  0  0  0  0
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105106  1  0  0  0  0
103107  1  0  0  0  0
107108  1  0  0  0  0
108109  1  1  0  0  0
108110  1  6  0  0  0
110111  2  0  0  0  0
111112  1  0  0  0  0
112113  1  0  0  0  0
113114  2  0  0  0  0
110114  1  0  0  0  0
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108121  1  0  0  0  0
101121  1  0  0  0  0
121122  1  0  0  0  0
121123  1  0  0  0  0
M  CHG  6   1   3   4  -1  65  -1  75  -1  88  -1 110   1
M  END


  Mrv1572010151518142D          

123131  0  0  1  0            999 V2000
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   10.7345    0.7617    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.3873    0.1848    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.7112   -0.6502    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.3064   -1.3899    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   12.5671   -0.8415    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   10.8228    2.2207    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.5618    2.7025    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.6035    1.8113    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.9872    5.4282    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   10.0981    6.2457    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.8406    5.6656    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.7301    5.5572    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.5963    5.7729    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.2945    5.2888    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   12.9155    6.5851    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    9.2800    5.8529    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    8.6435    6.4649    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.4574    6.7571    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    8.5370    8.1221    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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112113  1  0  0  0  0
113114  2  0  0  0  0
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116117  1  0  0  0  0
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121122  1  0  0  0  0
121123  1  0  0  0  0
M  CHG  6   1   3   4  -1  65  -1  75  -1  88  -1 110   1
M  END
> <DATABASE_ID>
MMDBc0052969

> <DATABASE_NAME>
MIME

> <SMILES>
[Co+3].[H]C1([CH2-])O[C@]([H])(N2C=NC3=C(N)N=CN=C23)[C@@]([H])(O)[C@@]1([H])O.[H]C(C)(CN=C(O)CC[C@@]1(C)C2=NC([H])([C@]1([H])CC(O)=N)[C@]1(C)NC(=C(C)C3=NC(=CC4=NC(=C2C)[C@@]([H])(CCC([O-])=N)C4(C)C)[C@@]([H])(CCC([O-])=N)[C@]3(C)CC(O)=N)[C@@]([H])(CCC([O-])=N)[C@]1(C)CC(O)=N)OP(O)(=O)OC1([H])[C@@]([H])(CO)O[C@]([H])([N+]2=CNC3=C2C=C(C)C(C)=C3)C1([H])O

> <INCHI_IDENTIFIER>
InChI=1S/C62H90N13O14P.C10H12N5O3.Co/c1-29-20-39-40(21-30(29)2)75(28-70-39)57-52(84)53(41(27-76)87-57)89-90(85,86)88-31(3)26-69-49(83)18-19-59(8)37(22-46(66)80)56-62(11)61(10,25-48(68)82)36(14-17-45(65)79)51(74-62)33(5)55-60(9,24-47(67)81)34(12-15-43(63)77)38(71-55)23-42-58(6,7)35(13-16-44(64)78)50(72-42)32(4)54(59)73-56;1-4-6(16)7(17)10(18-4)15-3-14-5-8(11)12-2-13-9(5)15;/h20-21,23,28,31,34-37,41,52-53,56-57,76,84H,12-19,22,24-27H2,1-11H3,(H15,63,64,65,66,67,68,69,71,72,73,74,77,78,79,80,81,82,83,85,86);2-4,6-7,10,16-17H,1H2,(H2,11,12,13);/q;-1;+3/p-2/t31?,34-,35-,36-,37+,41-,52?,53?,56?,57+,59-,60+,61+,62+;4?,6-,7-,10-;/m10./s1

> <INCHI_KEY>
OAJLVMGLJZXSGX-VCABRDNDSA-L

> <FORMULA>
C72H100CoN18O17P

> <MOLECULAR_WEIGHT>
1579.608

> <EXACT_MASS>
1578.65834

> <JCHEM_ACCEPTOR_COUNT>
23

> <JCHEM_ATOM_COUNT>
209

> <JCHEM_AVERAGE_POLARIZABILITY>
133.75091189719382

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
15

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
cobalt(3+) ion 1-[(2S,5R)-3-hydroxy-4-{[hydroxy({[1-({1-hydroxy-3-[(1R,3R,4R,8S,13S,14S,18S,19S)-8,13,18-tris(2-carboximidatoethyl)-3,14,19-tris[(C-hydroxycarbonimidoyl)methyl]-1,4,6,9,9,14,16,19-octamethyl-20,21,22,23-tetraazapentacyclo[15.2.1.1²,⁵.1⁷,¹⁰.1¹²,¹⁵]tricosa-5(23),6,10(22),11,15(21),16-hexaen-4-yl]propylidene}amino)propan-2-yl]oxy})phosphoryl]oxy}-5-(hydroxymethyl)oxolan-2-yl]-5,6-dimethyl-3H-1λ⁵,3-benzodiazol-1-ylium [(3R,4S,5S)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methanide

> <ALOGPS_LOGP>
2.23

> <JCHEM_LOGP>
1.1086597925282549

> <ALOGPS_LOGS>
-4.36

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
11

> <JCHEM_PHYSIOLOGICAL_CHARGE>
2

> <JCHEM_PKA>
4.944610527293002

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.8091777127095998

> <JCHEM_POLAR_SURFACE_AREA>
479.7900000000002

> <JCHEM_REFRACTIVITY>
430.8375999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
27

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
7.10e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
cobalt(3+) ion 1-[(2S,5R)-3-hydroxy-4-{[hydroxy([1-({1-hydroxy-3-[(1R,3R,4R,8S,13S,14S,18S,19S)-8,13,18-tris(2-carboximidatoethyl)-3,14,19-tris(C-hydroxycarbonimidoylmethyl)-1,4,6,9,9,14,16,19-octamethyl-20,21,22,23-tetraazapentacyclo[15.2.1.1²,⁵.1⁷,¹⁰.1¹²,¹⁵]tricosa-5(23),6,10(22),11,15(21),16-hexaen-4-yl]propylidene}amino)propan-2-yl]oxy)phosphoryl]oxy}-5-(hydroxymethyl)oxolan-2-yl]-5,6-dimethyl-3H-1λ⁵,3-benzodiazol-1-ylium [(3R,4S,5S)-5-(6-aminopurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methanide

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 15-OCT-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   15-OCT-15         0                                  
HETATM    1 Co   UNK     0      -4.787  -4.046   0.000  0.00  0.00          Co+3
HETATM    2  H   UNK     0      -2.054  -3.757   0.000  0.00  0.00           H+0
HETATM    3  C   UNK     0      -2.295  -2.236   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -3.541  -3.141   0.000  0.00  0.00           C-1
HETATM    5  O   UNK     0      -2.295  -0.696   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      -0.830  -0.220   0.000  0.00  0.00           C+0
HETATM    7  H   UNK     0       0.691   0.021   0.000  0.00  0.00           H+0
HETATM    8  N   UNK     0      -0.354   1.244   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0      -1.260   2.490   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0      -0.354   3.736   0.000  0.00  0.00           N+0
HETATM   11  C   UNK     0       1.110   3.260   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       2.444   4.030   0.000  0.00  0.00           C+0
HETATM   13  N   UNK     0       2.444   5.570   0.000  0.00  0.00           N+0
HETATM   14  N   UNK     0       3.778   3.260   0.000  0.00  0.00           N+0
HETATM   15  C   UNK     0       3.778   1.720   0.000  0.00  0.00           C+0
HETATM   16  N   UNK     0       2.444   0.950   0.000  0.00  0.00           N+0
HETATM   17  C   UNK     0       1.110   1.720   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       0.075  -1.466   0.000  0.00  0.00           C+0
HETATM   19  H   UNK     0       0.774  -2.838   0.000  0.00  0.00           H+0
HETATM   20  O   UNK     0       1.615  -1.466   0.000  0.00  0.00           O+0
HETATM   21  C   UNK     0      -0.830  -2.712   0.000  0.00  0.00           C+0
HETATM   22  H   UNK     0      -1.306  -1.247   0.000  0.00  0.00           H+0
HETATM   23  O   UNK     0      -0.354  -4.177   0.000  0.00  0.00           O+0
HETATM   24  H   UNK     0      10.465  -5.304   0.000  0.00  0.00           H+0
HETATM   25  C   UNK     0      11.711  -6.209   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      10.304  -6.835   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      11.872  -4.677   0.000  0.00  0.00           C+0
HETATM   28  N   UNK     0      10.626  -3.772   0.000  0.00  0.00           N+0
HETATM   29  C   UNK     0      10.790  -2.211   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0       9.178  -2.058   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0      12.134  -1.226   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      12.518   0.405   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      13.159   1.990   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      13.711   0.430   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      14.505   2.737   0.000  0.00  0.00           C+0
HETATM   36  N   UNK     0      14.211   4.249   0.000  0.00  0.00           N+0
HETATM   37  C   UNK     0      12.682   4.436   0.000  0.00  0.00           C+0
HETATM   38  H   UNK     0      11.152   4.267   0.000  0.00  0.00           H+0
HETATM   39  C   UNK     0      12.032   3.040   0.000  0.00  0.00           C+0
HETATM   40  H   UNK     0      11.496   1.596   0.000  0.00  0.00           H+0
HETATM   41  C   UNK     0      10.341   2.973   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0       8.873   3.695   0.000  0.00  0.00           C+0
HETATM   43  O   UNK     0       7.298   3.589   0.000  0.00  0.00           O+0
HETATM   44  N   UNK     0       8.030   5.079   0.000  0.00  0.00           N+0
HETATM   45  C   UNK     0      12.007   6.303   0.000  0.00  0.00           C+0
HETATM   46  C   UNK     0      10.418   6.676   0.000  0.00  0.00           C+0
HETATM   47  N   UNK     0      11.713   7.814   0.000  0.00  0.00           N+0
HETATM   48  C   UNK     0      13.060   8.561   0.000  0.00  0.00           C+0
HETATM   49  C   UNK     0      14.627   9.780   0.000  0.00  0.00           C+0
HETATM   50  C   UNK     0      13.193  10.681   0.000  0.00  0.00           C+0
HETATM   51  C   UNK     0      16.161   9.915   0.000  0.00  0.00           C+0
HETATM   52  N   UNK     0      16.763   8.497   0.000  0.00  0.00           N+0
HETATM   53  C   UNK     0      18.297   8.632   0.000  0.00  0.00           C+0
HETATM   54  C   UNK     0      19.345   6.946   0.000  0.00  0.00           C+0
HETATM   55  C   UNK     0      19.319   5.407   0.000  0.00  0.00           C+0
HETATM   56  N   UNK     0      18.061   4.918   0.000  0.00  0.00           N+0
HETATM   57  C   UNK     0      17.820   3.416   0.000  0.00  0.00           C+0
HETATM   58  C   UNK     0      16.034   2.550   0.000  0.00  0.00           C+0
HETATM   59  C   UNK     0      16.291   0.902   0.000  0.00  0.00           C+0
HETATM   60  C   UNK     0      19.276   2.915   0.000  0.00  0.00           C+0
HETATM   61  H   UNK     0      18.266   1.753   0.000  0.00  0.00           H+0
HETATM   62  C   UNK     0      20.038   1.422   0.000  0.00  0.00           C+0
HETATM   63  C   UNK     0      21.256   0.345   0.000  0.00  0.00           C+0
HETATM   64  C   UNK     0      21.861  -1.214   0.000  0.00  0.00           C+0
HETATM   65  O   UNK     0      21.105  -2.595   0.000  0.00  0.00           O-1
HETATM   66  N   UNK     0      23.459  -1.571   0.000  0.00  0.00           N+0
HETATM   67  C   UNK     0      20.203   4.145   0.000  0.00  0.00           C+0
HETATM   68  C   UNK     0      21.582   5.045   0.000  0.00  0.00           C+0
HETATM   69  C   UNK     0      21.660   3.381   0.000  0.00  0.00           C+0
HETATM   70  C   UNK     0      18.643  10.133   0.000  0.00  0.00           C+0
HETATM   71  H   UNK     0      18.850  11.659   0.000  0.00  0.00           H+0
HETATM   72  C   UNK     0      20.236  10.576   0.000  0.00  0.00           C+0
HETATM   73  C   UNK     0      21.896  10.374   0.000  0.00  0.00           C+0
HETATM   74  C   UNK     0      23.513  10.776   0.000  0.00  0.00           C+0
HETATM   75  O   UNK     0      24.816   9.872   0.000  0.00  0.00           O-1
HETATM   76  N   UNK     0      24.109  12.292   0.000  0.00  0.00           N+0
HETATM   77  C   UNK     0      17.323  10.926   0.000  0.00  0.00           C+0
HETATM   78  C   UNK     0      16.135  12.068   0.000  0.00  0.00           C+0
HETATM   79  C   UNK     0      17.654  12.613   0.000  0.00  0.00           C+0
HETATM   80  C   UNK     0      17.279  14.286   0.000  0.00  0.00           C+0
HETATM   81  O   UNK     0      15.936  15.161   0.000  0.00  0.00           O+0
HETATM   82  N   UNK     0      18.030  15.699   0.000  0.00  0.00           N+0
HETATM   83  C   UNK     0      14.186   7.511   0.000  0.00  0.00           C+0
HETATM   84  H   UNK     0      12.675   7.217   0.000  0.00  0.00           H+0
HETATM   85  C   UNK     0      15.220   8.871   0.000  0.00  0.00           C+0
HETATM   86  C   UNK     0      16.308   7.425   0.000  0.00  0.00           C+0
HETATM   87  C   UNK     0      16.539   6.146   0.000  0.00  0.00           C+0
HETATM   88  O   UNK     0      15.696   4.204   0.000  0.00  0.00           O-1
HETATM   89  N   UNK     0      16.488   3.754   0.000  0.00  0.00           N+0
HETATM   90  C   UNK     0      13.536   6.115   0.000  0.00  0.00           C+0
HETATM   91  C   UNK     0      12.102   5.190   0.000  0.00  0.00           C+0
HETATM   92  C   UNK     0      14.867   5.069   0.000  0.00  0.00           C+0
HETATM   93  C   UNK     0      16.447   5.454   0.000  0.00  0.00           C+0
HETATM   94  O   UNK     0      15.556   6.581   0.000  0.00  0.00           O+0
HETATM   95  N   UNK     0      17.397   4.291   0.000  0.00  0.00           N+0
HETATM   96  O   UNK     0      12.957  -7.114   0.000  0.00  0.00           O+0
HETATM   97  P   UNK     0      12.796  -8.646   0.000  0.00  0.00           P+0
HETATM   98  O   UNK     0      11.264  -8.485   0.000  0.00  0.00           O+0
HETATM   99  O   UNK     0      14.327  -8.807   0.000  0.00  0.00           O+0
HETATM  100  O   UNK     0      12.635 -10.177   0.000  0.00  0.00           O+0
HETATM  101  C   UNK     0      13.881 -11.082   0.000  0.00  0.00           C+0
HETATM  102  H   UNK     0      12.509 -11.781   0.000  0.00  0.00           H+0
HETATM  103  C   UNK     0      15.345 -10.606   0.000  0.00  0.00           C+0
HETATM  104  H   UNK     0      14.256  -9.517   0.000  0.00  0.00           H+0
HETATM  105  C   UNK     0      15.821  -9.142   0.000  0.00  0.00           C+0
HETATM  106  O   UNK     0      17.328  -8.822   0.000  0.00  0.00           O+0
HETATM  107  O   UNK     0      16.251 -11.852   0.000  0.00  0.00           O+0
HETATM  108  C   UNK     0      15.345 -13.098   0.000  0.00  0.00           C+0
HETATM  109  H   UNK     0      14.256 -14.187   0.000  0.00  0.00           H+0
HETATM  110  N   UNK     0      15.821 -14.563   0.000  0.00  0.00           N+1
HETATM  111  C   UNK     0      14.916 -15.809   0.000  0.00  0.00           C+0
HETATM  112  N   UNK     0      15.821 -17.055   0.000  0.00  0.00           N+0
HETATM  113  C   UNK     0      17.286 -16.579   0.000  0.00  0.00           C+0
HETATM  114  C   UNK     0      17.286 -15.039   0.000  0.00  0.00           C+0
HETATM  115  C   UNK     0      18.620 -14.269   0.000  0.00  0.00           C+0
HETATM  116  C   UNK     0      19.953 -15.039   0.000  0.00  0.00           C+0
HETATM  117  C   UNK     0      21.287 -14.269   0.000  0.00  0.00           C+0
HETATM  118  C   UNK     0      19.953 -16.579   0.000  0.00  0.00           C+0
HETATM  119  C   UNK     0      21.287 -17.349   0.000  0.00  0.00           C+0
HETATM  120  C   UNK     0      18.620 -17.349   0.000  0.00  0.00           C+0
HETATM  121  C   UNK     0      13.881 -12.622   0.000  0.00  0.00           C+0
HETATM  122  H   UNK     0      15.127 -11.717   0.000  0.00  0.00           H+0
HETATM  123  O   UNK     0      12.635 -13.528   0.000  0.00  0.00           O+0
CONECT    2    3                                                            
CONECT    3    2    4    5   21                                             
CONECT    4    3                                                            
CONECT    5    3    6                                                       
CONECT    6    5    7    8   18                                             
CONECT    7    6                                                            
CONECT    8    6    9   17                                                  
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   17                                                  
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16    8   11                                                  
CONECT   18    6   19   20   21                                             
CONECT   19   18                                                            
CONECT   20   18                                                            
CONECT   21   18    3   22   23                                             
CONECT   22   21                                                            
CONECT   23   21                                                            
CONECT   24   25                                                            
CONECT   25   24   26   27   96                                             
CONECT   26   25                                                            
CONECT   27   25   28                                                       
CONECT   28   27   29                                                       
CONECT   29   28   30   31                                                  
CONECT   30   29                                                            
CONECT   31   29   32                                                       
CONECT   32   31   33                                                       
CONECT   33   32   34   35   39                                             
CONECT   34   33                                                            
CONECT   35   33   36   58                                                  
CONECT   36   35   37                                                       
CONECT   37   36   38   39   45                                             
CONECT   38   37                                                            
CONECT   39   37   33   40   41                                             
CONECT   40   39                                                            
CONECT   41   39   42                                                       
CONECT   42   41   43   44                                                  
CONECT   43   42                                                            
CONECT   44   42                                                            
CONECT   45   37   46   47   90                                             
CONECT   46   45                                                            
CONECT   47   45   48                                                       
CONECT   48   47   49   83                                                  
CONECT   49   48   50   51                                                  
CONECT   50   49                                                            
CONECT   51   49   52   77                                                  
CONECT   52   51   53                                                       
CONECT   53   52   54   70                                                  
CONECT   54   53   55                                                       
CONECT   55   54   56   67                                                  
CONECT   56   55   57                                                       
CONECT   57   56   58   60                                                  
CONECT   58   57   35   59                                                  
CONECT   59   58                                                            
CONECT   60   57   61   62   67                                             
CONECT   61   60                                                            
CONECT   62   60   63                                                       
CONECT   63   62   64                                                       
CONECT   64   63   65   66                                                  
CONECT   65   64                                                            
CONECT   66   64                                                            
CONECT   67   60   55   68   69                                             
CONECT   68   67                                                            
CONECT   69   67                                                            
CONECT   70   53   71   72   77                                             
CONECT   71   70                                                            
CONECT   72   70   73                                                       
CONECT   73   72   74                                                       
CONECT   74   73   75   76                                                  
CONECT   75   74                                                            
CONECT   76   74                                                            
CONECT   77   70   51   78   79                                             
CONECT   78   77                                                            
CONECT   79   77   80                                                       
CONECT   80   79   81   82                                                  
CONECT   81   80                                                            
CONECT   82   80                                                            
CONECT   83   48   84   85   90                                             
CONECT   84   83                                                            
CONECT   85   83   86                                                       
CONECT   86   85   87                                                       
CONECT   87   86   88   89                                                  
CONECT   88   87                                                            
CONECT   89   87                                                            
CONECT   90   83   45   91   92                                             
CONECT   91   90                                                            
CONECT   92   90   93                                                       
CONECT   93   92   94   95                                                  
CONECT   94   93                                                            
CONECT   95   93                                                            
CONECT   96   25   97                                                       
CONECT   97   96   98   99  100                                             
CONECT   98   97                                                            
CONECT   99   97                                                            
CONECT  100   97  101                                                       
CONECT  101  100  102  103  121                                             
CONECT  102  101                                                            
CONECT  103  101  104  105  107                                             
CONECT  104  103                                                            
CONECT  105  103  106                                                       
CONECT  106  105                                                            
CONECT  107  103  108                                                       
CONECT  108  107  109  110  121                                             
CONECT  109  108                                                            
CONECT  110  108  111  114                                                  
CONECT  111  110  112                                                       
CONECT  112  111  113                                                       
CONECT  113  112  114  120                                                  
CONECT  114  113  110  115                                                  
CONECT  115  114  116                                                       
CONECT  116  115  117  118                                                  
CONECT  117  116                                                            
CONECT  118  116  119  120                                                  
CONECT  119  118                                                            
CONECT  120  118  113                                                       
CONECT  121  108  101  122  123                                             
CONECT  122  121                                                            
CONECT  123  121                                                            
MASTER        0    0    0    0    0    0    0    0  123    0  262    0
END

Synonyms

Value	Source
Indusil T	MeSH
Cobamamide	MeSH
Desoxyadenosylcobalamine	MeSH
Adenosylcobalamin	MeSH
Dibencozide	MeSH
Vitamin b12 coenzyme	MeSH
AdoCbl	MeSH
3',4'-Anhydroadenosylcobalamin	MeSH
5'-Deoxyadenosylcobalamin	MeSH
Coenzyme b12	MeSH

Molecular Formula

C₇₂H₁₀₀CoN₁₈O₁₇P

Average Mass

1579.608

Monoisotopic Mass

1578.65834

IUPAC Name

cobalt(3+) ion 1-[(2S,5R)-3-hydroxy-4-{[hydroxy({[1-({1-hydroxy-3-[(1R,3R,4R,8S,13S,14S,18S,19S)-8,13,18-tris(2-carboximidatoethyl)-3,14,19-tris[(C-hydroxycarbonimidoyl)methyl]-1,4,6,9,9,14,16,19-octamethyl-20,21,22,23-tetraazapentacyclo[15.2.1.1²,⁵.1⁷,¹⁰.1¹²,¹⁵]tricosa-5(23),6,10(22),11,15(21),16-hexaen-4-yl]propylidene}amino)propan-2-yl]oxy})phosphoryl]oxy}-5-(hydroxymethyl)oxolan-2-yl]-5,6-dimethyl-3H-1λ⁵,3-benzodiazol-1-ylium [(3R,4S,5S)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methanide

Traditional Name

cobalt(3+) ion 1-[(2S,5R)-3-hydroxy-4-{[hydroxy([1-({1-hydroxy-3-[(1R,3R,4R,8S,13S,14S,18S,19S)-8,13,18-tris(2-carboximidatoethyl)-3,14,19-tris(C-hydroxycarbonimidoylmethyl)-1,4,6,9,9,14,16,19-octamethyl-20,21,22,23-tetraazapentacyclo[15.2.1.1²,⁵.1⁷,¹⁰.1¹²,¹⁵]tricosa-5(23),6,10(22),11,15(21),16-hexaen-4-yl]propylidene}amino)propan-2-yl]oxy)phosphoryl]oxy}-5-(hydroxymethyl)oxolan-2-yl]-5,6-dimethyl-3H-1λ⁵,3-benzodiazol-1-ylium [(3R,4S,5S)-5-(6-aminopurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methanide

CAS Registry Number

Not Available

SMILES

[Co+3].[H]C1([CH2-])O[C@]([H])(N2C=NC3=C(N)N=CN=C23)[C@@]([H])(O)[C@@]1([H])O.[H]C(C)(CN=C(O)CC[C@@]1(C)C2=NC([H])([C@]1([H])CC(O)=N)[C@]1(C)NC(=C(C)C3=NC(=CC4=NC(=C2C)[C@@]([H])(CCC([O-])=N)C4(C)C)[C@@]([H])(CCC([O-])=N)[C@]3(C)CC(O)=N)[C@@]([H])(CCC([O-])=N)[C@]1(C)CC(O)=N)OP(O)(=O)OC1([H])[C@@]([H])(CO)O[C@]([H])([N+]2=CNC3=C2C=C(C)C(C)=C3)C1([H])O

InChI Identifier

InChI=1S/C62H90N13O14P.C10H12N5O3.Co/c1-29-20-39-40(21-30(29)2)75(28-70-39)57-52(84)53(41(27-76)87-57)89-90(85,86)88-31(3)26-69-49(83)18-19-59(8)37(22-46(66)80)56-62(11)61(10,25-48(68)82)36(14-17-45(65)79)51(74-62)33(5)55-60(9,24-47(67)81)34(12-15-43(63)77)38(71-55)23-42-58(6,7)35(13-16-44(64)78)50(72-42)32(4)54(59)73-56;1-4-6(16)7(17)10(18-4)15-3-14-5-8(11)12-2-13-9(5)15;/h20-21,23,28,31,34-37,41,52-53,56-57,76,84H,12-19,22,24-27H2,1-11H3,(H15,63,64,65,66,67,68,69,71,72,73,74,77,78,79,80,81,82,83,85,86);2-4,6-7,10,16-17H,1H2,(H2,11,12,13);/q;-1;+3/p-2/t31?,34-,35-,36-,37+,41-,52?,53?,56?,57+,59-,60+,61+,62+;4?,6-,7-,10-;/m10./s1

InChI Key

OAJLVMGLJZXSGX-VCABRDNDSA-L

Chemical Taxonomy

Description

This compound belongs to the class of organic compounds known as hydrocarbon derivatives. These are derivatives of hydrocarbons obtained by substituting one or more carbon atoms by an heteroatom. They contain at least one carbon atom and heteroatom.

Kingdom

Organic compounds

Super Class

Hydrocarbon derivatives

Class

Not Available

Sub Class

Not Available

Direct Parent

Hydrocarbon derivatives

Alternative Parents

Organic zwitterions

Substituents

Hydrocarbon derivative
Organic zwitterion
Aromatic heteropolycyclic compound

Molecular Framework

Not Available

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.071 g/L	ALOGPS
logP	2.23	ALOGPS
logP	1.11	ChemAxon
logS	-4.4	ALOGPS
pKa (Strongest Acidic)	1.81	ChemAxon
Physiological Charge	2	ChemAxon
Hydrogen Acceptor Count	23	ChemAxon
Hydrogen Donor Count	15	ChemAxon
Polar Surface Area	479.79 Å²	ChemAxon
Rotatable Bond Count	27	ChemAxon
Refractivity	430.84 m³·mol⁻¹	ChemAxon
Polarizability	133.75 Å³	ChemAxon
Number of Rings	11	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Spectra

Not Available

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

This table shows at most 5 pathways. For the full list of associated pathways:

See All Associated Bacterial Pathways

Name	SMPDB/PathBank
Adenosylcobalamin Salvage from Cobinamide

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
MMDBr0018830	Adenosylcobalamin 5'-phosphate	coenzyme B12	Adenosylcobalamin/alpha-ribazole phosphatase	Dephosphorylation	PathBank	31602464
MMDBr0018831	vitamin B12	Polyphosphate	Corrinoid adenosyltransferase	Transfers of an adenosyl group	PathBank	31602464
MMDBr0025439	Cob(II)alamin	Triphosphate	Cobalamin adenosyltransferase	Transfers of an adenosyl group	RHEA	34755880
MMDBr0025623	Adenosine triphosphate	Triphosphate	Corrinoid adenosyltransferase PduO	Transfers of an adenosyl group	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
Bacteria/Eubacteria	Firmicutes	41	Human feces; Human ; Catfish
Bacteria/Eubacteria	Proteobacteria	119	Human ; Human feces; Sheep ; Pig
Bacteria/Eubacteria	Chlorobi	7
Bacteria/Eubacteria	Actinobacteria	23	Human ; Cattle
Bacteria/Eubacteria	Deinococcus-thermus	1
Bacteria	Proteobacteria	3	Human ; Human feces; Sheep ; Pig
Bacteria/Eubacteria	Thermotogae	4
Bacteria/Eubacteria	Fusobacteria	1	Human ; Human feces
Archaea/Archaea	Euryarchaeota	21
Bacteria/Eubacteria	Chloroflexi	2
Bacteria/Eubacteria	Spirochaetes	5	Human
Bacteria/Eubacteria	Cyanobacteria	8
Archaea/Archaea	Crenarchaeota	11
Archaea	Crenarchaeota	1
Bacteria	nah	1
Bacteria/Eubacteria	Nitrospirae	1

Exposure Sources

Other Exposures

Source Type	Data Source	Reference

Host Biospecimen and Location

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

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

6436143

PDB ID

Not Available

ChEBI ID

Not Available

CMMC Knowledgebase

Not Available

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Wishart DS, Li C, Marcu A, Badran H, Pon A, Budinski Z, Patron J, Lipton D, Cao X, Oler E, Li K, Paccoud M, Hong C, Guo AC, Chan C, Wei W, Ramirez-Gaona M: PathBank: a comprehensive pathway database for model organisms. Nucleic Acids Res. 2020 Jan 8;48(D1):D470-D478. doi: 10.1093/nar/gkz861. [PubMed:31602464 ]
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 coenzyme B12 (MMDBc0052969)

MOL for #<Metabolite:0x00007fd44b7b6548>

3D MOL for #<Metabolite:0x00007fd44b7b6548>

3D SDF for #<Metabolite:0x00007fd44b7b6548>

3D-SDF for #<Metabolite:0x00007fd44b7b6548>

PDB for #<Metabolite:0x00007fd44b7b6548>

3D PDB for #<Metabolite:0x00007fd44b7b6548>

SMILES for #<Metabolite:0x00007fd44b7b6548>

INCHI for #<Metabolite:0x00007fd44b7b6548>

Structure for #<Metabolite:0x00007fd44b7b6548>

3D Structure for #<Metabolite:0x00007fd44b7b6548>