MiMeDB: Showing metabocard for coenzyme M-coenzyme B heterodisulfide (MMDBc0055827)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-06-17 20:07:58 UTC

Update Date

2022-08-12 20:09:28 UTC

MiMeDB ID

MMDBc0055827

Metabolite Identification

Common Name

coenzyme M-coenzyme B heterodisulfide

Description

CoM-S-S-CoB(4-), also known as cob-S-S-com, belongs to the class of organic compounds known as n-acyl-l-alpha-amino acids. These are n-acylated alpha amino acids which have the L-configuration of the alpha-carbon atom. Based on a literature review a significant number of articles have been published on CoM-S-S-CoB(4-).

Structure

MOL SDF PDB SMILES InChI


  Mrv1652306172222072D          

 30 29  0  0  1  0            999 V2000
    7.9697   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6829   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9684    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3974    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2539    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1118    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5395    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6039    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3184    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.9697    0.0000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.8263    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2552    0.4125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    7.2552    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5408    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.8263    1.2375    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    6.5408    1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.9697    1.6500    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   10.1131   -0.4125    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    9.8112    0.7145    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    8.9862   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7474   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4454    0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6204   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.6842    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.3987    0.0000    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.1105    0.4125    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0329    0.0000    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    7.2552   -0.4125    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.9697    0.8250    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  1  0  0  0  0
  6  4  1  0  0  0  0
  7  5  1  0  0  0  0
  9  8  1  0  0  0  0
 10  1  1  6  0  0  0
 11  6  1  0  0  0  0
 12 10  1  0  0  0  0
 13 12  1  0  0  0  0
 14 11  2  0  0  0  0
 12 14  1  1  0  0  0
 11 15  1  4  0  0  0
 16 13  2  0  0  0  0
 17 13  1  0  0  0  0
 24 10  1  0  0  0  0
 25 18  1  0  0  0  0
 25 19  1  0  0  0  0
 25 20  2  0  0  0  0
 25 24  1  0  0  0  0
 26  7  1  0  0  0  0
 27  8  1  0  0  0  0
 27 26  1  0  0  0  0
 28  9  1  0  0  0  0
 28 21  1  0  0  0  0
 28 22  2  0  0  0  0
 28 23  2  0  0  0  0
 10 29  1  1  0  0  0
 12 30  1  1  0  0  0
M  CHG  4  15  -1  17  -1  18  -1  19  -1
M  END


  Mrv1652306172222072D          

 30 29  0  0  1  0            999 V2000
    7.9697   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6829   -0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9684    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3974    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2539    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1118    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5395    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6039    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3184    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.9697    0.0000    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.8263    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2552    0.4125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    7.2552    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5408    0.0000    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.8263    1.2375    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    6.5408    1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.9697    1.6500    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   10.1131   -0.4125    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    9.8112    0.7145    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    8.9862   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7474   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4454    0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6204   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.6842    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.3987    0.0000    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    0.1105    0.4125    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0329    0.0000    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    7.2552   -0.4125    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.9697    0.8250    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  1  0  0  0  0
  6  4  1  0  0  0  0
  7  5  1  0  0  0  0
  9  8  1  0  0  0  0
 10  1  1  6  0  0  0
 11  6  1  0  0  0  0
 12 10  1  0  0  0  0
 13 12  1  0  0  0  0
 14 11  2  0  0  0  0
 12 14  1  1  0  0  0
 11 15  1  4  0  0  0
 16 13  2  0  0  0  0
 17 13  1  0  0  0  0
 24 10  1  0  0  0  0
 25 18  1  0  0  0  0
 25 19  1  0  0  0  0
 25 20  2  0  0  0  0
 25 24  1  0  0  0  0
 26  7  1  0  0  0  0
 27  8  1  0  0  0  0
 27 26  1  0  0  0  0
 28  9  1  0  0  0  0
 28 21  1  0  0  0  0
 28 22  2  0  0  0  0
 28 23  2  0  0  0  0
 10 29  1  1  0  0  0
 12 30  1  1  0  0  0
M  CHG  4  15  -1  17  -1  18  -1  19  -1
M  END
> <DATABASE_ID>
MMDBc0055827

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@](C)(OP([O-])([O-])=O)[C@]([H])(N=C([O-])CCCCCCSSCCS(O)(=O)=O)C([O-])=O

> <INCHI_IDENTIFIER>
InChI=1S/C13H26NO10PS3/c1-10(24-25(18,19)20)12(13(16)17)14-11(15)6-4-2-3-5-7-26-27-8-9-28(21,22)23/h10,12H,2-9H2,1H3,(H,14,15)(H,16,17)(H2,18,19,20)(H,21,22,23)/p-4/t10-,12+/m1/s1

> <INCHI_KEY>
OBGQLHXSMIBYLN-PWSUYJOCSA-J

> <FORMULA>
C13H22NO10PS3

> <MOLECULAR_WEIGHT>
479.47

> <EXACT_MASS>
479.016540752

> <JCHEM_ACCEPTOR_COUNT>
10

> <JCHEM_ATOM_COUNT>
50

> <JCHEM_AVERAGE_POLARIZABILITY>
43.37863323092198

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
-4

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(2S,3R)-2-({1-oxido-7-[(2-sulfoethyl)disulfanyl]heptylidene}amino)-3-(phosphonooxy)butanoate

> <JCHEM_LOGP>
-0.2751840357585991

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-4

> <JCHEM_PKA>
1.2527164757408635

> <JCHEM_PKA_STRONGEST_ACIDIC>
-0.9200841750608761

> <JCHEM_PKA_STRONGEST_BASIC>
0.24301447686298538

> <JCHEM_POLAR_SURFACE_AREA>
202.33999999999997

> <JCHEM_REFRACTIVITY>
125.02879999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
16

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(2S,3R)-2-({1-oxido-7-[(2-sulfoethyl)disulfanyl]heptylidene}amino)-3-(phosphonooxy)butanoate

> <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      14.877  -1.540   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       6.875  -0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.541   0.770   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       8.208   0.770   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.207   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       9.542   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.874   0.770   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -1.127   0.000   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -2.461   0.770   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      14.877   0.000   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      10.876   0.770   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      13.543   0.770   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      13.543   2.310   0.000  0.00  0.00           C+0
HETATM   14  N   UNK     0      12.209   0.000   0.000  0.00  0.00           N+0
HETATM   15  O   UNK     0      10.876   2.310   0.000  0.00  0.00           O-1
HETATM   16  O   UNK     0      12.209   3.080   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0      14.877   3.080   0.000  0.00  0.00           O-1
HETATM   18  O   UNK     0      18.878  -0.770   0.000  0.00  0.00           O-1
HETATM   19  O   UNK     0      18.314   1.334   0.000  0.00  0.00           O-1
HETATM   20  O   UNK     0      16.774  -1.334   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0      -5.128  -0.770   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0      -4.565   1.334   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0      -3.025  -1.334   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0      16.210   0.770   0.000  0.00  0.00           O+0
HETATM   25  P   UNK     0      17.544   0.000   0.000  0.00  0.00           P+0
HETATM   26  S   UNK     0       1.540   0.000   0.000  0.00  0.00           S+0
HETATM   27  S   UNK     0       0.206   0.770   0.000  0.00  0.00           S+0
HETATM   28  S   UNK     0      -3.795   0.000   0.000  0.00  0.00           S+0
HETATM   29  H   UNK     0      13.543  -0.770   0.000  0.00  0.00           H+0
HETATM   30  H   UNK     0      14.877   1.540   0.000  0.00  0.00           H+0
CONECT    1   10                                                            
CONECT    2    3    4                                                       
CONECT    3    2    5                                                       
CONECT    4    2    6                                                       
CONECT    5    3    7                                                       
CONECT    6    4   11                                                       
CONECT    7    5   26                                                       
CONECT    8    9   27                                                       
CONECT    9    8   28                                                       
CONECT   10    1   12   24   29                                             
CONECT   11    6   14   15                                                  
CONECT   12   10   13   14   30                                             
CONECT   13   12   16   17                                                  
CONECT   14   11   12                                                       
CONECT   15   11                                                            
CONECT   16   13                                                            
CONECT   17   13                                                            
CONECT   18   25                                                            
CONECT   19   25                                                            
CONECT   20   25                                                            
CONECT   21   28                                                            
CONECT   22   28                                                            
CONECT   23   28                                                            
CONECT   24   10   25                                                       
CONECT   25   18   19   20   24                                             
CONECT   26    7   27                                                       
CONECT   27    8   26                                                       
CONECT   28    9   21   22   23                                             
CONECT   29   10                                                            
CONECT   30   12                                                            
MASTER        0    0    0    0    0    0    0    0   30    0   58    0
END

Synonyms

Value	Source
(2S,3S)-3-(Phosphonatooxy)-2-({7-[(2-sulfonatoethyl)disulfanyl]heptanoyl}amino)butanoate	ChEBI
Coenzyme m-coenzyme b heterodisulfide	ChEBI
(2S,3S)-3-(Phosphonatooxy)-2-({7-[(2-sulfonatoethyl)disulfanyl]heptanoyl}amino)butanoic acid	Generator
(2S,3S)-3-(Phosphonatooxy)-2-({7-[(2-sulphonatoethyl)disulphanyl]heptanoyl}amino)butanoate	Generator
(2S,3S)-3-(Phosphonatooxy)-2-({7-[(2-sulphonatoethyl)disulphanyl]heptanoyl}amino)butanoic acid	Generator
Coenzyme m-coenzyme b heterodisulphide	Generator
12-Aza-13-carboxy-14-hydroxy-11-oxo-3,4-dithiapentadecanesulfonic acid 14-phosphate	MeSH
CoB-S-S-com	MeSH

Chemical Formula

C₁₃H₂₂NO₁₀PS₃

Average Molecular Weight

479.47

Monoisotopic Molecular Weight

479.016540752

IUPAC Name

(2S,3R)-2-({1-oxido-7-[(2-sulfoethyl)disulfanyl]heptylidene}amino)-3-(phosphonooxy)butanoate

Traditional Name

(2S,3R)-2-({1-oxido-7-[(2-sulfoethyl)disulfanyl]heptylidene}amino)-3-(phosphonooxy)butanoate

CAS Registry Number

Not Available

SMILES

[H][C@](C)(OP([O-])([O-])=O)[C@]([H])(N=C([O-])CCCCCCSSCCS(O)(=O)=O)C([O-])=O

InChI Identifier

InChI=1S/C13H26NO10PS3/c1-10(24-25(18,19)20)12(13(16)17)14-11(15)6-4-2-3-5-7-26-27-8-9-28(21,22)23/h10,12H,2-9H2,1H3,(H,14,15)(H,16,17)(H2,18,19,20)(H,21,22,23)/p-4/t10-,12+/m1/s1

InChI Key

OBGQLHXSMIBYLN-PWSUYJOCSA-J

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as n-acyl-l-alpha-amino acids. These are n-acylated alpha amino acids which have the L-configuration of the alpha-carbon atom.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Carboxylic acids and derivatives

Sub Class

Amino acids, peptides, and analogues

Direct Parent

N-acyl-L-alpha-amino acids

Alternative Parents

Substituents

N-acyl-l-alpha-amino acid
Phosphoethanolamine
Fatty amide
N-acyl-amine
Organic phosphoric acid derivative
Phosphoric acid ester
Alkyl phosphate
Fatty acid
Fatty acyl
Alkanesulfonic acid
Sulfonyl
Organosulfonic acid
Organosulfonic acid or derivatives
Organic sulfonic acid or derivatives
Dialkyldisulfide
Secondary carboxylic acid amide
Organic disulfide
Carboxamide group
Monocarboxylic acid or derivatives
Sulfenyl compound
Carboxylic acid
Organopnictogen compound
Organic oxide
Organooxygen compound
Organonitrogen compound
Organosulfur compound
Organic nitrogen compound
Carbonyl group
Organic oxygen compound
Hydrocarbon derivative
Organic anion
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

organophosphate oxoanion (CHEBI:58411 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
logP	-0.28	ChemAxon
pKa (Strongest Acidic)	-0.92	ChemAxon
pKa (Strongest Basic)	0.24	ChemAxon
Physiological Charge	-4	ChemAxon
Hydrogen Acceptor Count	10	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	202.34 Å²	ChemAxon
Rotatable Bond Count	16	ChemAxon
Refractivity	125.03 m³·mol⁻¹	ChemAxon
Polarizability	43.38 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Not Available

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Proteins

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Related Health Condition	Evidence Type	Measured in Matrix	Data Source	Reference

Microbial Sources

Kingdom	Phylum	Total species
Archaea	Euryarchaeota	8
	Euryarchaeota	3
Archaea		2

Exposure Sources

Source Type	Source Sub-type	Species	Data Source	Reference	Details

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

26331163

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

25246009

PDB ID

Not Available

ChEBI ID

58411

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 coenzyme M-coenzyme B heterodisulfide (MMDBc0055827)

MOL for #<Metabolite:0x0000564abfa453c0>

3D MOL for #<Metabolite:0x0000564abfa453c0>

3D SDF for #<Metabolite:0x0000564abfa453c0>

3D-SDF for #<Metabolite:0x0000564abfa453c0>

PDB for #<Metabolite:0x0000564abfa453c0>

3D PDB for #<Metabolite:0x0000564abfa453c0>

SMILES for #<Metabolite:0x0000564abfa453c0>

INCHI for #<Metabolite:0x0000564abfa453c0>

Structure for #<Metabolite:0x0000564abfa453c0>

3D Structure for #<Metabolite:0x0000564abfa453c0>