MiMeDB: Showing metabocard for coenzyme B (MMDBc0054402)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-06-05 23:10:55 UTC

Update Date

2025-10-07 16:04:18 UTC

Metabolite ID

MMDBc0054402

Metabolite Identification

Common Name

coenzyme B

Description

Coenzyme B is a thiol compound classified as a coenzyme involved in various biochemical pathways, particularly in methanogenic archaea and certain bacteria. Its chemical structure includes a reactive thiol group that participates in redox reactions, facilitating the transfer of electrons in metabolic processes. Coenzyme B plays a critical role in the reduction of heterodisulfides, specifically in the conversion of coenzyme M and coenzyme B to their reduced forms (CoM-SH and CoB-SH), which is essential during syntrophic interactions in the degradation of organic matter (PMID:40362433 ). Additionally, it is involved in the methyl-coenzyme M reductase (MCR) pathway, where it participates in the endergonic conversion of methane and is generated from the heterodisulfide adduct of coenzymes M and B (PMID:39911329 ). The biosynthesis of coenzyme B reflects evolutionary adaptations, as indicated by its balanced selection in various organisms (PMID:40051064 ). Furthermore, coenzyme B is implicated in C1 metabolism and the regulation of methyltransferases, highlighting its significance in cellular metabolic networks (PMID:39472004 ). Overall, coenzyme B's structural properties and involvement in key metabolic pathways underscore its importance in microbial energy conversion processes.

Structure

MOL SDF PDB SMILES InChI

 
  Mrv1533006041518282D          
 
 21 20  0  0  1  0            999 V2000
    7.1984  -10.0852    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.9095   -9.6670    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    8.6206  -10.0852    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    9.3735   -9.6670    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   10.0846  -10.0852    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.7957   -9.6670    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.5486  -10.0852    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.2597   -9.6670    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.9708  -10.0852    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.6819   -9.6670    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.4349  -10.0852    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.1460   -9.6670    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
   10.0846  -10.9218    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.6103  -10.9217    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.8885  -11.3267    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.3372  -11.3535    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.9097   -8.8158    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.9095   -7.9948    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    8.7461   -7.9948    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.0729   -7.9948    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.9095   -7.1582    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
  5 13  2  0  0  0  0
  3 14  1  6  0  0  0
 14 15  1  0  0  0  0
 14 16  2  0  0  0  0
  2 17  1  1  0  0  0
 18 19  1  0  0  0  0
 18 20  1  0  0  0  0
 18 21  2  0  0  0  0
 17 18  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0054402

> <DATABASE_NAME>
MIME

> <SMILES>
C[C@@H](OP(O)(O)=O)[C@H](NC(=O)CCCCCCS)C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C11H22NO7PS/c1-8(19-20(16,17)18)10(11(14)15)12-9(13)6-4-2-3-5-7-21/h8,10,21H,2-7H2,1H3,(H,12,13)(H,14,15)(H2,16,17,18)/t8-,10+/m1/s1

> <INCHI_KEY>
JBJSVEVEEGOEBZ-SCZZXKLOSA-N

> <FORMULA>
C11H22NO7PS

> <MOLECULAR_WEIGHT>
343.33

> <EXACT_MASS>
343.085460224

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
43

> <JCHEM_AVERAGE_POLARIZABILITY>
33.05852309707534

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(2S,3R)-3-(phosphonooxy)-2-(7-sulfanylheptanamido)butanoic acid

> <ALOGPS_LOGP>
1.24

> <JCHEM_LOGP>
0.7797356013333342

> <ALOGPS_LOGS>
-3.17

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-3

> <JCHEM_PKA>
3.846970985198939

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.3071573783229367

> <JCHEM_PKA_STRONGEST_BASIC>
-1.3780263645849726

> <JCHEM_POLAR_SURFACE_AREA>
133.16000000000003

> <JCHEM_REFRACTIVITY>
77.76469999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
11

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.30e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
MHTP

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 04-JUN-15   NONE
TITLE     NULL                                                        
COMPND    MOLECULE:                                                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-JUN-15         0                                  
HETATM    1  C   UNK     0      13.437 -18.826   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      14.764 -18.045   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      16.092 -18.826   0.000  0.00  0.00           C+0
HETATM    4  N   UNK     0      17.497 -18.045   0.000  0.00  0.00           N+0
HETATM    5  C   UNK     0      18.825 -18.826   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      20.152 -18.045   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      21.557 -18.826   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      22.885 -18.045   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      24.212 -18.826   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      25.540 -18.045   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      26.945 -18.826   0.000  0.00  0.00           C+0
HETATM   12  S   UNK     0      28.272 -18.045   0.000  0.00  0.00           S+0
HETATM   13  O   UNK     0      18.825 -20.387   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0      16.073 -20.387   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      14.725 -21.143   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0      17.429 -21.193   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0      14.765 -16.456   0.000  0.00  0.00           O+0
HETATM   18  P   UNK     0      14.764 -14.924   0.000  0.00  0.00           P+0
HETATM   19  O   UNK     0      16.326 -14.924   0.000  0.00  0.00           O+0
HETATM   20  O   UNK     0      13.203 -14.924   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0      14.764 -13.362   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   17                                                  
CONECT    3    2    4   14                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6   13                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11                                                            
CONECT   13    5                                                            
CONECT   14    3   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14                                                            
CONECT   17    2   18                                                       
CONECT   18   19   20   21   17                                             
CONECT   19   18                                                            
CONECT   20   18                                                            
CONECT   21   18                                                            
MASTER        0    0    0    0    0    0    0    0   21    0   40    0
END

Synonyms

Value	Source
(2S,3R)-2-[(7-Mercaptoheptanoyl)amino]-3-(phosphonooxy)butanoic acid	ChEBI
(2S,3R)-3-Phosphonooxy-2-[(7-sulfanylheptanoyl)amino]butanoic acid	ChEBI
7-Mercaptoheptanoyl-O-phospho-L-threonine	ChEBI
7-Mercaptoheptanoylthreonine phosphate	ChEBI
7-Thioheptanoyl-threonine O-phosphate	ChEBI
HTP	ChEBI
MHTP	ChEBI
N-(7-Mercaptoheptanoyl)-L-threonine 3-O-phosphate	ChEBI
N-(7-Mercaptoheptanoyl)threonine 3-O-phosphate	ChEBI
N-(7-Mercaptoheptanoyl)threonine O3-phosphate	ChEBI
N-(7-Sulfanylheptanoyl)-3-O-phosphono-L-threonine	ChEBI
N-(7-Sulfanylheptanoyl)-3-phospho-L-threonine	ChEBI
CoB	Kegg
(2S,3R)-2-[(7-Mercaptoheptanoyl)amino]-3-(phosphonooxy)butanoate	Generator
(2S,3R)-3-Phosphonooxy-2-[(7-sulfanylheptanoyl)amino]butanoate	Generator
(2S,3R)-3-Phosphonooxy-2-[(7-sulphanylheptanoyl)amino]butanoate	Generator
(2S,3R)-3-Phosphonooxy-2-[(7-sulphanylheptanoyl)amino]butanoic acid	Generator
7-Mercaptoheptanoylthreonine phosphoric acid	Generator
7-Thioheptanoyl-threonine O-phosphoric acid	Generator
N-(7-Mercaptoheptanoyl)-L-threonine 3-O-phosphoric acid	Generator
N-(7-Mercaptoheptanoyl)threonine 3-O-phosphoric acid	Generator
N-(7-Mercaptoheptanoyl)threonine O3-phosphoric acid	Generator
N-(7-Sulphanylheptanoyl)-3-O-phosphono-L-threonine	Generator
N-(7-Sulphanylheptanoyl)-3-phospho-L-threonine	Generator

Molecular Formula

C₁₁H₂₂NO₇PS

Average Mass

343.33

Monoisotopic Mass

343.085460224

IUPAC Name

(2S,3R)-3-(phosphonooxy)-2-(7-sulfanylheptanamido)butanoic acid

Traditional Name

MHTP

CAS Registry Number

Not Available

SMILES

C[C@@H](OP(O)(O)=O)[C@H](NC(=O)CCCCCCS)C(O)=O

InChI Identifier

InChI=1S/C11H22NO7PS/c1-8(19-20(16,17)18)10(11(14)15)12-9(13)6-4-2-3-5-7-21/h8,10,21H,2-7H2,1H3,(H,12,13)(H,14,15)(H2,16,17,18)/t8-,10+/m1/s1

InChI Key

JBJSVEVEEGOEBZ-SCZZXKLOSA-N

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
Monoalkyl phosphate
Fatty amide
N-acyl-amine
Organic phosphoric acid derivative
Phosphoric acid ester
Alkyl phosphate
Fatty acid
Fatty acyl
Secondary carboxylic acid amide
Carboxamide group
Alkylthiol
Carboxylic acid
Monocarboxylic acid or derivatives
Organic nitrogen compound
Organosulfur compound
Organooxygen compound
Organonitrogen compound
Carbonyl group
Organic oxygen compound
Organopnictogen compound
Hydrocarbon derivative
Organic oxide
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

L-threonine derivative (CHEBI:28890 )
Coenzymes (C04628 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	0.23 g/L	ALOGPS
logP	1.24	ALOGPS
logP	0.78	ChemAxon
logS	-3.2	ALOGPS
pKa (Strongest Acidic)	1.31	ChemAxon
pKa (Strongest Basic)	-1.4	ChemAxon
Physiological Charge	-3	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	133.16 Å²	ChemAxon
Rotatable Bond Count	11	ChemAxon
Refractivity	77.76 m³·mol⁻¹	ChemAxon
Polarizability	33.06 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_5) - 70eV, Positive	Not Available	2022-08-08	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0002-0390000000-851c5b88e898cc9e6b7a	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0udj-1980000000-7ab95bfedcf15beec5d0	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0udi-2930000000-f31eb664b73257871e2d	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0005-9167000000-4fecec8b161b6731279a	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9351000000-c561e7d7562e6a535e2e	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-8db5547e459b267f2e7b	2019-02-23	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

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	Species

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
MMDBr0025560	di-mu-Sulfido-diiron(2+)	di-mu-Sulfido-diiron(1+)	Ferredoxin:CoB-CoM heterodisulfide reductase subunit B	Reduction	RHEA	34755880
MMDBr0025576	di-mu-Sulfido-diiron(1+)	di-mu-Sulfido-diiron(2+)	Ferredoxin/F(420)H(2)-dependent CoB-CoM heterodisulfide reductase subunit B	Reduction	RHEA	34755880
MMDBr0025577	di-mu-Sulfido-diiron(1+)	Hydrogen	H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A	Reduction	RHEA	34755880
MMDBr0025578	di-mu-Sulfido-diiron(1+)	formate	H(2)/formate:CoB-CoM heterodisulfide,ferredoxin reductase subunit A	Reduction	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
Archaea/Archaea	Euryarchaeota	8
Archaea	Euryarchaeota	3
Archaea/Archaea	nah	3

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

C00000760

Chemspider ID

Not Available

KEGG Compound ID

C04628

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Coenzyme B

METLIN ID

Not Available

PubChem Compound

5462265

PDB ID

Not Available

ChEBI ID

28890

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

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 B (MMDBc0054402)

MOL for #<Metabolite:0x00007fb4a8501400>

3D MOL for #<Metabolite:0x00007fb4a8501400>

3D SDF for #<Metabolite:0x00007fb4a8501400>

3D-SDF for #<Metabolite:0x00007fb4a8501400>

PDB for #<Metabolite:0x00007fb4a8501400>

3D PDB for #<Metabolite:0x00007fb4a8501400>

SMILES for #<Metabolite:0x00007fb4a8501400>

INCHI for #<Metabolite:0x00007fb4a8501400>

Structure for #<Metabolite:0x00007fb4a8501400>

3D Structure for #<Metabolite:0x00007fb4a8501400>