MiMeDB: Showing metabocard for adenosylcob(III)inamide-GDP (MMDBc0055685)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-06-17 20:02:10 UTC

Update Date

2022-08-12 20:09:27 UTC

Metabolite ID

MMDBc0055685

Metabolite Identification

Common Name

adenosylcob(III)inamide-GDP

Description

adenosylcobinamide guanosyl diphosphate(1-), also known as adenosine-GDP-cobinamide(1-) or adenosylcob(iii)inamide-GDP, belongs to the class of organic compounds known as purine ribonucleoside diphosphates. These are purine ribobucleotides with diphosphate group linked to the ribose moiety. Based on a literature review very few articles have been published on adenosylcobinamide guanosyl diphosphate(1-).

Structure

MOL SDF PDB SMILES InChI


  Mrv1652306172222022D          

127135  0  0  1  0            999 V2000
    3.4024    2.8754    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0121    0.9654    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9107   -3.0083    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3914   -0.5764    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4552    0.1323    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2886   -0.9460    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5567   -1.4040    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5759   -3.3658    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6518   -2.8255    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4479   -0.1756    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6227   -0.5077    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5496   -4.1539    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1890   -0.5381    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2362   -1.2366    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    4.6203    0.1615    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    3.0942    2.1101    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.4039    0.4080    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    0.9360   -3.4250    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.3529   -1.5322    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.9885   -0.3531    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    0.1611    1.0483    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    2.5115   -4.5202    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    1.4928    0.9567    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5735   -2.6839    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6901    1.8486    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2729    4.1883    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.0140    3.8258    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.7664   -0.3331    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9404   -1.6871    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5361   -1.6479    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.3037    2.5775    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5146    1.8189    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    3.4953   -0.7195    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
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    4.9535   -1.1311    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7932   -3.3689    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.2106   -4.0822    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0041    3.9460    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.4197    1.5763    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1164    1.2558    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4798   -1.0026    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.8602    1.4863    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1736   -0.9068    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7417    3.2766    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9526    2.5180    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.1663   -2.1101    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4910    2.4352    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
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   -0.3736    3.0618    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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    1.7687    2.6438    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    8.1024   -1.8273    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.0230    0.7771    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.3245    1.1896    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.7698   -1.3424    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   10.5940    1.6021    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   10.0394   -0.9299    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   11.3085    2.0146    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    9.5545   -0.2624    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
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   11.3085    0.3646    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    9.8094    1.8570    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
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   -5.3556   -0.8026    0.0000 Co  0  2  0  0  0  0  0  0  0  0  0  0
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   -1.6638    0.1828    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -3.6893    3.3518    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7149   -1.5689    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6561    2.2203    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.8989   -2.1572    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.3693   -1.7264    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.4139   -0.1948    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.9711    0.3209    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
 13 10  1  0  0  0  0
 14 11  1  0  0  0  0
 15 12  1  0  0  0  0
 17 16  1  0  0  0  0
 25  1  1  6  0  0  0
 25 22  1  0  0  0  0
 26  2  1  4  0  0  0
 27  3  1  4  0  0  0
 28 10  1  6  0  0  0
 29 11  1  1  0  0  0
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 31 18  1  1  0  0  0
 32 19  2  0  0  0  0
 32 28  1  0  0  0  0
 33 23  1  1  0  0  0
 19 34  1  4  0  0  0
 35 13  1  0  0  0  0
 36 14  1  0  0  0  0
 37 15  1  0  0  0  0
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 55  6  1  1  0  0  0
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 56  7  1  6  0  0  0
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 66 22  1  4  0  0  0
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 73 43  1  0  0  0  0
 73 58  1  0  0  0  0
 74 24  2  0  0  0  0
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 89 23  1  0  0  0  0
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101100  1  0  0  0  0
102 99  2  0  0  0  0
103 99  1  0  0  0  0
104101  1  0  0  0  0
105102  1  0  0  0  0
106 96  2  0  0  0  0
106102  1  0  0  0  0
107 96  1  0  0  0  0
107103  2  0  0  0  0
108 97  2  0  0  0  0
108 99  1  0  0  0  0
109 97  1  0  0  0  0
109103  1  0  0  0  0
104109  1  1  0  0  0
100110  1  6  0  0  0
101111  1  6  0  0  0
112 98  1  0  0  0  0
112104  1  0  0  0  0
 25114  1  1  0  0  0
 28115  1  1  0  0  0
 29116  1  6  0  0  0
 30117  1  1  0  0  0
 31118  1  6  0  0  0
 33119  1  6  0  0  0
 45120  1  1  0  0  0
 46121  1  1  0  0  0
 49122  1  1  0  0  0
 52123  1  6  0  0  0
 98124  1  6  0  0  0
100125  1  1  0  0  0
101126  1  1  0  0  0
104127  1  6  0  0  0
M  CHG  6  74   1  75  -1  76  -1  77  -1  78  -1 113   2
M  RAD  1  95   2
M  END


  Mrv1652306172222022D          

127135  0  0  1  0            999 V2000
    3.4024    2.8754    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0121    0.9654    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9107   -3.0083    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3914   -0.5764    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4552    0.1323    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2886   -0.9460    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5567   -1.4040    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5759   -3.3658    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6518   -2.8255    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4479   -0.1756    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6227   -0.5077    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5496   -4.1539    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  CHG  6  74   1  75  -1  76  -1  77  -1  78  -1 113   2
M  RAD  1  95   2
M  END
> <DATABASE_ID>
MMDBc0055685

> <DATABASE_NAME>
MIME

> <SMILES>
[Co++].[H][C@]1([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=N[C@]([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)OP(O)(=O)OC[C@@]1([H])O[C@@]([H])([N+]2=CNC3=C2NC(=N)N=C3O)[C@]([H])(O)[C@]1([H])O

> <INCHI_IDENTIFIER>
InChI=1S/C58H86N16O18P2.C10H12N5O3.Co/c1-25(91-94(87,88)92-93(85,86)89-23-33-45(82)46(83)52(90-33)74-24-67-44-50(74)71-53(65)72-51(44)84)22-66-41(81)16-17-55(6)31(18-38(62)78)49-58(9)57(8,21-40(64)80)30(12-15-37(61)77)43(73-58)27(3)48-56(7,20-39(63)79)28(10-13-35(59)75)32(68-48)19-34-54(4,5)29(11-14-36(60)76)42(69-34)26(2)47(55)70-49;1-4-6(16)7(17)10(18-4)15-3-14-5-8(11)12-2-13-9(5)15;/h19,24-25,28-31,33,45-46,49,52,82-83H,10-18,20-23H2,1-9H3,(H19,59,60,61,62,63,64,65,66,68,69,70,71,72,73,75,76,77,78,79,80,81,84,85,86,87,88);2-4,6-7,10,16-17H,1H2,(H2,11,12,13);/q;;+2/p-3/t25-,28-,29-,30-,31+,33-,45-,46-,49-,52-,55-,56+,57+,58+;4-,6-,7-,10-;/m11./s1

> <INCHI_KEY>
IQTYKHRKNGVJEO-RRMAJTJESA-K

> <FORMULA>
C68H95CoN21O21P2

> <MOLECULAR_WEIGHT>
1663.515

> <EXACT_MASS>
1662.582406

> <JCHEM_ACCEPTOR_COUNT>
29

> <JCHEM_ATOM_COUNT>
208

> <JCHEM_AVERAGE_POLARIZABILITY>
132.63457839818426

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
18

> <JCHEM_FORMAL_CHARGE>
-1

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
lambda2-cobalt(2+) ion 9-[(2R,3R,4S,5R)-3,4-dihydroxy-5-({[hydroxy({[hydroxy({[(2R)-1-({1-hydroxy-3-[(1R,2R,3R,4R,8S,13S,14S,18S,19S)-8,13,18-tris[2-(C-hydroxycarbonimidoyl)ethyl]-3,14,19-tris[(C-hydroxycarbonimidoyl)methyl]-1,4,6,9,9,14,16,19-octamethyl-20,21,22,23-tetraazapentacyclo[15.2.1.1^{2,5}.1^{7,10}.1^{12,15}]tricosa-5(23),6,10(22),11,15(21),16-hexaen-4-yl]propylidene}amino)propan-2-yl]oxy})phosphoryl]oxy})phosphoryl]oxy}methyl)oxolan-2-yl]-6-hydroxy-2-imino-3,7-dihydro-2H-9lambda5-purin-9-ylium [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl

> <JCHEM_LOGP>
-2.1588042574717425

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
11

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
3.2114750577382445

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.8469365658866117

> <JCHEM_POLAR_SURFACE_AREA>
597.6200000000002

> <JCHEM_REFRACTIVITY>
455.81579999999957

> <JCHEM_ROTATABLE_BOND_COUNT>
29

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
lambda2-cobalt(2+) ion 9-[(2R,3R,4S,5R)-3,4-dihydroxy-5-({[hydroxy([hydroxy([(2R)-1-({1-hydroxy-3-[(1R,2R,3R,4R,8S,13S,14S,18S,19S)-8,13,18-tris[2-(C-hydroxycarbonimidoyl)ethyl]-3,14,19-tris(C-hydroxycarbonimidoylmethyl)-1,4,6,9,9,14,16,19-octamethyl-20,21,22,23-tetraazapentacyclo[15.2.1.1^{2,5}.1^{7,10}.1^{12,15}]tricosa-5(23),6,10(22),11,15(21),16-hexaen-4-yl]propylidene}amino)propan-2-yl]oxy)phosphoryl]oxy)phosphoryl]oxy}methyl)oxolan-2-yl]-6-hydroxy-2-imino-3,7-dihydro-9lambda5-purin-9-ylium [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl

> <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       6.351   5.367   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       5.623   1.802   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -1.700  -5.615   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.731  -1.076   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.850   0.247   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       8.005  -1.766   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -4.773  -2.621   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.808  -6.283   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       4.950  -5.274   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -4.569  -0.328   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       3.029  -0.948   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       1.026  -7.754   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -5.953  -1.005   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       2.308  -2.308   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       1.843  -9.059   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       8.624   0.302   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       7.100   0.085   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       7.330  -3.967   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      -1.004   1.139   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -3.502  -4.243   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       3.328  -7.716   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       6.725   2.726   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      -1.647   6.928   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -6.301   3.021   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       5.776   3.939   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       4.487   0.762   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      -0.806  -4.362   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      -3.292  -1.187   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       2.211   0.357   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       1.747  -6.393   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       6.259  -2.860   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      -1.845  -0.659   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      -3.172   6.712   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       0.301   1.957   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      -7.230  -0.145   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0       0.769  -2.364   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0       1.122 -10.420   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0       8.824  -3.592   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0      -4.948  -4.772   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0       4.688  -8.438   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0       9.200   1.730   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0       2.787   1.786   0.000  0.00  0.00           C+0
HETATM   43  C   UNK     0       1.071  -5.010   0.000  0.00  0.00           C+0
HETATM   44  C   UNK     0      -8.755   3.451   0.000  0.00  0.00           C+0
HETATM   45  C   UNK     0      -4.243   7.818   0.000  0.00  0.00           C+0
HETATM   46  C   UNK     0      -5.626   7.142   0.000  0.00  0.00           C+0
HETATM   47  C   UNK     0       5.164  -0.622   0.000  0.00  0.00           C+0
HETATM   48  C   UNK     0      -1.755  -3.149   0.000  0.00  0.00           C+0
HETATM   49  C   UNK     0       4.734  -3.076   0.000  0.00  0.00           C+0
HETATM   50  C   UNK     0      -8.034   4.811   0.000  0.00  0.00           C+0
HETATM   51  C   UNK     0     -10.294   3.395   0.000  0.00  0.00           C+0
HETATM   52  C   UNK     0      -5.410   5.617   0.000  0.00  0.00           C+0
HETATM   53  C   UNK     0     -10.390   6.061   0.000  0.00  0.00           C+0
HETATM   54  C   UNK     0       0.675   0.463   0.000  0.00  0.00           C+0
HETATM   55  C   UNK     0       6.524  -1.343   0.000  0.00  0.00           C+0
HETATM   56  C   UNK     0      -3.236  -2.726   0.000  0.00  0.00           C+0
HETATM   57  C   UNK     0       3.272  -6.177   0.000  0.00  0.00           C+0
HETATM   58  C   UNK     0       3.538  -4.660   0.000  0.00  0.00           C+0
HETATM   59  N   UNK     0      -7.125   1.392   0.000  0.00  0.00           N+0
HETATM   60  N   UNK     0      -0.049  -1.059   0.000  0.00  0.00           N+0
HETATM   61  N   UNK     0      -0.417 -10.475   0.000  0.00  0.00           N+0
HETATM   62  N   UNK     0       9.246  -2.111   0.000  0.00  0.00           N+0
HETATM   63  N   UNK     0      -5.214  -6.289   0.000  0.00  0.00           N+0
HETATM   64  N   UNK     0       5.993  -7.620   0.000  0.00  0.00           N+0
HETATM   65  N   UNK     0     -11.208   7.366   0.000  0.00  0.00           N+0
HETATM   66  N   UNK     0       8.250   2.942   0.000  0.00  0.00           N+0
HETATM   67  N   UNK     0      -7.684   2.344   0.000  0.00  0.00           N+0
HETATM   68  N   UNK     0      -0.896  -1.872   0.000  0.00  0.00           N+0
HETATM   69  N   UNK     0       1.606   2.774   0.000  0.00  0.00           N+0
HETATM   70  N   UNK     0       4.057  -1.693   0.000  0.00  0.00           N+0
HETATM   71  N   UNK     0      -8.851   6.116   0.000  0.00  0.00           N+0
HETATM   72  N   UNK     0     -11.112   4.700   0.000  0.00  0.00           N+0
HETATM   73  N   UNK     0       2.177  -3.939   0.000  0.00  0.00           N+0
HETATM   74  N   UNK     0      -6.517   4.546   0.000  0.00  0.00           N+1
HETATM   75  O   UNK     0      -8.614  -0.822   0.000  0.00  0.00           O-1
HETATM   76  O   UNK     0       0.047  -3.724   0.000  0.00  0.00           O-1
HETATM   77  O   UNK     0       1.940 -11.725   0.000  0.00  0.00           O-1
HETATM   78  O   UNK     0       9.895  -4.699   0.000  0.00  0.00           O-1
HETATM   79  O   UNK     0      -6.129  -3.783   0.000  0.00  0.00           O+0
HETATM   80  O   UNK     0       4.744  -9.977   0.000  0.00  0.00           O+0
HETATM   81  O   UNK     0      10.724   1.946   0.000  0.00  0.00           O+0
HETATM   82  O   UNK     0      -3.977   9.335   0.000  0.00  0.00           O+0
HETATM   83  O   UNK     0      -6.987   7.863   0.000  0.00  0.00           O+0
HETATM   84  O   UNK     0     -11.015   2.035   0.000  0.00  0.00           O+0
HETATM   85  O   UNK     0       1.043   4.407   0.000  0.00  0.00           O+0
HETATM   86  O   UNK     0       0.611   7.456   0.000  0.00  0.00           O+0
HETATM   87  O   UNK     0       2.089   3.986   0.000  0.00  0.00           O+0
HETATM   88  O   UNK     0       4.514   5.885   0.000  0.00  0.00           O+0
HETATM   89  O   UNK     0      -0.697   5.715   0.000  0.00  0.00           O+0
HETATM   90  O   UNK     0      -3.893   5.351   0.000  0.00  0.00           O+0
HETATM   91  O   UNK     0       4.251   3.723   0.000  0.00  0.00           O+0
HETATM   92  O   UNK     0       2.352   6.148   0.000  0.00  0.00           O+0
HETATM   93  P   UNK     0       0.827   5.931   0.000  0.00  0.00           P+0
HETATM   94  P   UNK     0       3.302   4.935   0.000  0.00  0.00           P+0
HETATM   95  C   UNK     0      15.124  -3.411   0.000  0.00  0.00           C+0
HETATM   96  C   UNK     0      22.443   1.451   0.000  0.00  0.00           C+0
HETATM   97  C   UNK     0      17.406   2.221   0.000  0.00  0.00           C+0
HETATM   98  C   UNK     0      16.370  -2.506   0.000  0.00  0.00           C+0
HETATM   99  C   UNK     0      19.775   2.991   0.000  0.00  0.00           C+0
HETATM  100  C   UNK     0      17.835  -2.982   0.000  0.00  0.00           C+0
HETATM  101  C   UNK     0      18.740  -1.736   0.000  0.00  0.00           C+0
HETATM  102  C   UNK     0      21.109   3.761   0.000  0.00  0.00           C+0
HETATM  103  C   UNK     0      19.775   1.451   0.000  0.00  0.00           C+0
HETATM  104  C   UNK     0      17.835  -0.490   0.000  0.00  0.00           C+0
HETATM  105  N   UNK     0      21.109   5.301   0.000  0.00  0.00           N+0
HETATM  106  N   UNK     0      22.443   2.991   0.000  0.00  0.00           N+0
HETATM  107  N   UNK     0      21.109   0.681   0.000  0.00  0.00           N+0
HETATM  108  N   UNK     0      18.311   3.466   0.000  0.00  0.00           N+0
HETATM  109  N   UNK     0      18.311   0.975   0.000  0.00  0.00           N+0
HETATM  110  O   UNK     0      18.311  -4.446   0.000  0.00  0.00           O+0
HETATM  111  O   UNK     0      20.280  -1.736   0.000  0.00  0.00           O+0
HETATM  112  O   UNK     0      16.370  -0.966   0.000  0.00  0.00           O+0
HETATM  113 Co   UNK     0      -9.997  -1.498   0.000  0.00  0.00          Co+2
HETATM  114  H   UNK     0       7.301   4.155   0.000  0.00  0.00           H+0
HETATM  115  H   UNK     0      -3.106   0.341   0.000  0.00  0.00           H+0
HETATM  116  H   UNK     0       3.745   0.493   0.000  0.00  0.00           H+0
HETATM  117  H   UNK     0       0.207  -6.368   0.000  0.00  0.00           H+0
HETATM  118  H   UNK     0       5.759  -4.317   0.000  0.00  0.00           H+0
HETATM  119  H   UNK     0      -2.672   8.168   0.000  0.00  0.00           H+0
HETATM  120  H   UNK     0      -5.474   8.744   0.000  0.00  0.00           H+0
HETATM  121  H   UNK     0      -6.887   6.257   0.000  0.00  0.00           H+0
HETATM  122  H   UNK     0       3.201  -2.929   0.000  0.00  0.00           H+0
HETATM  123  H   UNK     0      -4.958   4.145   0.000  0.00  0.00           H+0
HETATM  124  H   UNK     0      16.611  -4.027   0.000  0.00  0.00           H+0
HETATM  125  H   UNK     0      19.356  -3.223   0.000  0.00  0.00           H+0
HETATM  126  H   UNK     0      19.439  -0.364   0.000  0.00  0.00           H+0
HETATM  127  H   UNK     0      16.746   0.599   0.000  0.00  0.00           H+0
CONECT    1   25                                                            
CONECT    2   26                                                            
CONECT    3   27                                                            
CONECT    4   54                                                            
CONECT    5   54                                                            
CONECT    6   55                                                            
CONECT    7   56                                                            
CONECT    8   57                                                            
CONECT    9   58                                                            
CONECT   10   13   28                                                       
CONECT   11   14   29                                                       
CONECT   12   15   30                                                       
CONECT   13   10   35                                                       
CONECT   14   11   36                                                       
CONECT   15   12   37                                                       
CONECT   16   17   41                                                       
CONECT   17   16   55                                                       
CONECT   18   31   38                                                       
CONECT   19   32   34                                                       
CONECT   20   39   56                                                       
CONECT   21   40   57                                                       
CONECT   22   25   66                                                       
CONECT   23   33   89                                                       
CONECT   24   67   74                                                       
CONECT   25    1   22   91  114                                             
CONECT   26    2   42   47                                                  
CONECT   27    3   43   48                                                  
CONECT   28   10   32   56  115                                             
CONECT   29   11   42   54  116                                             
CONECT   30   12   43   57  117                                             
CONECT   31   18   49   55  118                                             
CONECT   32   19   28   68                                                  
CONECT   33   23   45   90  119                                             
CONECT   34   19   54   69                                                  
CONECT   35   13   59   75                                                  
CONECT   36   14   60   76                                                  
CONECT   37   15   61   77                                                  
CONECT   38   18   62   78                                                  
CONECT   39   20   63   79                                                  
CONECT   40   21   64   80                                                  
CONECT   41   16   66   81                                                  
CONECT   42   26   29   69                                                  
CONECT   43   27   30   73                                                  
CONECT   44   50   51   67                                                  
CONECT   45   33   46   82  120                                             
CONECT   46   45   52   83  121                                             
CONECT   47   26   55   70                                                  
CONECT   48   27   56   68                                                  
CONECT   49   31   58   70  122                                             
CONECT   50   44   71   74                                                  
CONECT   51   44   72   84                                                  
CONECT   52   46   74   90  123                                             
CONECT   53   65   71   72                                                  
CONECT   54    4    5   29   34                                             
CONECT   55    6   17   31   47                                             
CONECT   56    7   20   28   48                                             
CONECT   57    8   21   30   58                                             
CONECT   58    9   49   57   73                                             
CONECT   59   35                                                            
CONECT   60   36                                                            
CONECT   61   37                                                            
CONECT   62   38                                                            
CONECT   63   39                                                            
CONECT   64   40                                                            
CONECT   65   53                                                            
CONECT   66   22   41                                                       
CONECT   67   24   44                                                       
CONECT   68   32   48                                                       
CONECT   69   34   42                                                       
CONECT   70   47   49                                                       
CONECT   71   50   53                                                       
CONECT   72   51   53                                                       
CONECT   73   43   58                                                       
CONECT   74   24   50   52                                                  
CONECT   75   35                                                            
CONECT   76   36                                                            
CONECT   77   37                                                            
CONECT   78   38                                                            
CONECT   79   39                                                            
CONECT   80   40                                                            
CONECT   81   41                                                            
CONECT   82   45                                                            
CONECT   83   46                                                            
CONECT   84   51                                                            
CONECT   85   93                                                            
CONECT   86   93                                                            
CONECT   87   94                                                            
CONECT   88   94                                                            
CONECT   89   23   93                                                       
CONECT   90   33   52                                                       
CONECT   91   25   94                                                       
CONECT   92   93   94                                                       
CONECT   93   85   86   89   92                                             
CONECT   94   87   88   91   92                                             
CONECT   95   98                                                            
CONECT   96  106  107                                                       
CONECT   97  108  109                                                       
CONECT   98   95  100  112  124                                             
CONECT   99  102  103  108                                                  
CONECT  100   98  101  110  125                                             
CONECT  101  100  104  111  126                                             
CONECT  102   99  105  106                                                  
CONECT  103   99  107  109                                                  
CONECT  104  101  109  112  127                                             
CONECT  105  102                                                            
CONECT  106   96  102                                                       
CONECT  107   96  103                                                       
CONECT  108   97   99                                                       
CONECT  109   97  103  104                                                  
CONECT  110  100                                                            
CONECT  111  101                                                            
CONECT  112   98  104                                                       
CONECT  114   25                                                            
CONECT  115   28                                                            
CONECT  116   29                                                            
CONECT  117   30                                                            
CONECT  118   31                                                            
CONECT  119   33                                                            
CONECT  120   45                                                            
CONECT  121   46                                                            
CONECT  122   49                                                            
CONECT  123   52                                                            
CONECT  124   98                                                            
CONECT  125  100                                                            
CONECT  126  101                                                            
CONECT  127  104                                                            
MASTER        0    0    0    0    0    0    0    0  127    0  270    0
END

Synonyms

Value	Source
Adenosine-GDP-cobinamide(1-)	ChEBI
Adenosylcob(III)inamide-GDP	ChEBI
Adenosylcobinamide-GDP(1-)	ChEBI
Adenosylcobinamide guanosyl diphosphoric acid(1-)	Generator

Molecular Formula

C₆₈H₉₅CoN₂₁O₂₁P₂

Average Mass

1663.515

Monoisotopic Mass

1662.582406

IUPAC Name

lambda2-cobalt(2+) ion 9-[(2R,3R,4S,5R)-3,4-dihydroxy-5-({[hydroxy({[hydroxy({[(2R)-1-({1-hydroxy-3-[(1R,2R,3R,4R,8S,13S,14S,18S,19S)-8,13,18-tris[2-(C-hydroxycarbonimidoyl)ethyl]-3,14,19-tris[(C-hydroxycarbonimidoyl)methyl]-1,4,6,9,9,14,16,19-octamethyl-20,21,22,23-tetraazapentacyclo[15.2.1.1^{2,5}.1^{7,10}.1^{12,15}]tricosa-5(23),6,10(22),11,15(21),16-hexaen-4-yl]propylidene}amino)propan-2-yl]oxy})phosphoryl]oxy})phosphoryl]oxy}methyl)oxolan-2-yl]-6-hydroxy-2-imino-3,7-dihydro-2H-9lambda5-purin-9-ylium [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl

Traditional Name

lambda2-cobalt(2+) ion 9-[(2R,3R,4S,5R)-3,4-dihydroxy-5-({[hydroxy([hydroxy([(2R)-1-({1-hydroxy-3-[(1R,2R,3R,4R,8S,13S,14S,18S,19S)-8,13,18-tris[2-(C-hydroxycarbonimidoyl)ethyl]-3,14,19-tris(C-hydroxycarbonimidoylmethyl)-1,4,6,9,9,14,16,19-octamethyl-20,21,22,23-tetraazapentacyclo[15.2.1.1^{2,5}.1^{7,10}.1^{12,15}]tricosa-5(23),6,10(22),11,15(21),16-hexaen-4-yl]propylidene}amino)propan-2-yl]oxy)phosphoryl]oxy)phosphoryl]oxy}methyl)oxolan-2-yl]-6-hydroxy-2-imino-3,7-dihydro-9lambda5-purin-9-ylium [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl

CAS Registry Number

Not Available

SMILES

[Co++].[H][C@]1([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=N[C@]([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)OP(O)(=O)OC[C@@]1([H])O[C@@]([H])([N+]2=CNC3=C2NC(=N)N=C3O)[C@]([H])(O)[C@]1([H])O

InChI Identifier

InChI=1S/C58H86N16O18P2.C10H12N5O3.Co/c1-25(91-94(87,88)92-93(85,86)89-23-33-45(82)46(83)52(90-33)74-24-67-44-50(74)71-53(65)72-51(44)84)22-66-41(81)16-17-55(6)31(18-38(62)78)49-58(9)57(8,21-40(64)80)30(12-15-37(61)77)43(73-58)27(3)48-56(7,20-39(63)79)28(10-13-35(59)75)32(68-48)19-34-54(4,5)29(11-14-36(60)76)42(69-34)26(2)47(55)70-49;1-4-6(16)7(17)10(18-4)15-3-14-5-8(11)12-2-13-9(5)15;/h19,24-25,28-31,33,45-46,49,52,82-83H,10-18,20-23H2,1-9H3,(H19,59,60,61,62,63,64,65,66,68,69,70,71,72,73,75,76,77,78,79,80,81,84,85,86,87,88);2-4,6-7,10,16-17H,1H2,(H2,11,12,13);/q;;+2/p-3/t25-,28-,29-,30-,31+,33-,45-,46-,49-,52-,55-,56+,57+,58+;4-,6-,7-,10-;/m11./s1

InChI Key

IQTYKHRKNGVJEO-RRMAJTJESA-K

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as purine ribonucleoside diphosphates. These are purine ribobucleotides with diphosphate group linked to the ribose moiety.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Purine nucleotides

Sub Class

Purine ribonucleotides

Direct Parent

Purine ribonucleoside diphosphates

Alternative Parents

Substituents

Purine ribonucleoside diphosphate
Metallotetrapyrrole skeleton
Purine ribonucleoside monophosphate
Tetrapyrrole skeleton
Pentose phosphate
Pentose-5-phosphate
5'-deoxyribonucleoside
N-glycosyl compound
Glycosyl compound
Organic pyrophosphate
6-oxopurine
Hypoxanthine
6-aminopurine
Monosaccharide phosphate
Purine
Imidazopyrimidine
Phosphoethanolamine
Monoalkyl phosphate
Aminopyrimidine
Hydroxypyrimidine
Pyrimidone
Phosphoric acid ester
Fatty amide
Fatty acyl
Imidolactam
Pyrimidine
Alkyl phosphate
Monosaccharide
Organic phosphoric acid derivative
N-substituted imidazole
Pyrrolidine
Pyrroline
Vinylogous amide
Azole
Heteroaromatic compound
Tetrahydrofuran
Imidazole
Primary carboxylic acid amide
Secondary alcohol
Amino acid or derivatives
Secondary carboxylic acid amide
Ketimine
Carboxamide group
Carboximidic acid
Carboximidic acid derivative
Oxacycle
Carboxylic acid derivative
Secondary aliphatic amine
Enamine
Azacycle
Organic transition metal salt
Organoheterocyclic compound
Carbene-type 1,3-dipolar compound
Secondary amine
Organic oxide
Organopnictogen compound
Amine
Alcohol
Hydrocarbon derivative
Organic cobalt salt
Carbonyl group
Organic salt
Organic nitrogen compound
Imine
Organic oxygen compound
Primary amine
Organooxygen compound
Organonitrogen compound
Organic anion
Aromatic heteropolycyclic compound

Molecular Framework

Not Available

External Descriptors

organophosphate oxoanion (CHEBI:60487 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
logP	-2.2	ChemAxon
pKa (Strongest Acidic)	1.85	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	29	ChemAxon
Hydrogen Donor Count	18	ChemAxon
Polar Surface Area	597.62 Å²	ChemAxon
Rotatable Bond Count	29	ChemAxon
Refractivity	455.82 m³·mol⁻¹	ChemAxon
Polarizability	132.63 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

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_3_2) - 70eV, Positive	Not Available	2022-08-08	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-18	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
MMDBr0013489	adenosylcob(III)inamide-GDP	coenzyme B12	Adenosylcobinamide-GDP ribazoletransferase	Transfer of ribazole	RHEA	34755880
MMDBr0014239	adenosylcob(III)inamide phosphate	adenosylcob(III)inamide-GDP	Bifunctional adenosylcobalamin biosynthesis protein CobP	Synthesis	RHEA	34755880
MMDBr0014353	adenosylcob(III)inamide-GDP	adenosylcob(III)alamin 5'-phosphate	Adenosylcobinamide-GDP ribazoletransferase	Transfer of ribazole	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	Firmicutes	40	Human feces; Human ; Catfish
Bacteria	Proteobacteria	120	Human ; Human feces; Sheep ; Pig
Bacteria	Chlorobi	7
Bacteria	Actinobacteria	22	Human ; Cattle
Bacteria	Deinococcus-thermus	1
Bacteria	Thermotogae	4
Bacteria	Fusobacteria	1	Human ; Human feces
Archaea/Archaea	Euryarchaeota	21
Bacteria	Chloroflexi	2
Bacteria	Spirochaetes	5	Human
Bacteria	Cyanobacteria	8
Archaea/Archaea	Crenarchaeota	11
Archaea	Crenarchaeota	1
Bacteria	nah	1
Bacteria	Nitrospirae	1
Bacteria/NULL	Proteobacteria	1	Human ; Human feces; Sheep ; Pig

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

29367942

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

60487

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 adenosylcob(III)inamide-GDP (MMDBc0055685)

MOL for #<Metabolite:0x000055c79c2c8378>

3D MOL for #<Metabolite:0x000055c79c2c8378>

3D SDF for #<Metabolite:0x000055c79c2c8378>

3D-SDF for #<Metabolite:0x000055c79c2c8378>

PDB for #<Metabolite:0x000055c79c2c8378>

3D PDB for #<Metabolite:0x000055c79c2c8378>

SMILES for #<Metabolite:0x000055c79c2c8378>

INCHI for #<Metabolite:0x000055c79c2c8378>

Structure for #<Metabolite:0x000055c79c2c8378>

3D Structure for #<Metabolite:0x000055c79c2c8378>