Bovine Metabolome Database: Showing metabocard for Cobalamin (BMDB0002174)

Identification Taxonomy Physical properties Pathways Spectra Concentrations Links References enzymes (8) Show 8 proteins XML

Record Information

Version

1.0

Creation Date

2016-09-30 22:52:05 UTC

Update Date

2020-06-04 20:39:44 UTC

BMDB ID

BMDB0002174

Secondary Accession Numbers

BMDB02174

Metabolite Identification

Common Name

Cobalamin

Description

Cobalamin, also known as cobalamin (iii) or vitamin B12, belongs to the class of organic compounds known as cobalamin derivatives. These are organic compounds containing a corrin ring, a cobalt atom, an a nucleotide moiety. Cobalamin Derivatives are actually derived from vitamin B12. Cobalamin is possibly soluble (in water) and an extremely weak basic (essentially neutral) compound (based on its pKa). Cobalamin exists in all eukaryotes, ranging from yeast to humans.

Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
alpha-(5,6-Dimethylbenzimidazolyl)cobamide	ChEBI
Cbl	ChEBI
Cobalamin (III)	ChEBI
Cobalamin(1+)	ChEBI
Cobalamin(III)	ChEBI
a-(5,6-Dimethylbenzimidazolyl)cobamide	Generator
Α-(5,6-dimethylbenzimidazolyl)cobamide	Generator
5,6-Dimethyl-1-a-D-ribofuranosyl-1H-benzimidazole	HMDB
5,6-Dimethyl-1-a-D-ribofuranosylbenzimidazole	HMDB
5,6-Dimethyl-1-alpha-delta-ribofuranosyl-1H-benzimidazole	HMDB
5,6-Dimethyl-1-alpha-delta-ribofuranosylbenzimidazole	HMDB
Cob(III)alamin	HMDB
Cobalamine	HMDB
Cobinamide ion(1+) dihydrogen phosphate (ester) inner salt 3'-ester	HMDB
Cobinamide ion(1+) dihydrogen phosphate (ester) inner salt 3'-ester with 5,6-dimethyl-1-alpha-delta-ribofuranosyl-1H-benzimidazole	HMDB
Hydroxomin	HMDB
Rubivite	HMDB
Rubratope-57	HMDB
Rubratope-60	HMDB
Ruvite	HMDB
Vitamin b12	HMDB
b 12, Vitamin	HMDB
b12, Vitamin	HMDB
Cobalamins	HMDB
Cyanocobalamin	HMDB
Eritron	HMDB
Vitamin b 12	HMDB

Chemical Formula

C₆₂H₈₈CoN₁₃O₁₄P

Average Molecular Weight

1329.369

Monoisotopic Molecular Weight

1328.563777

IUPAC Name

(10S,12R,13S,17R,23R,24R,25R,30S,35S,36S,40S,41S,42R,46R)-30,35,40-tris(2-carbamoylethyl)-24,36,41-tris(carbamoylmethyl)-46-hydroxy-12-(hydroxymethyl)-5,6,17,23,28,31,31,36,38,41,42-undecamethyl-15,20-dioxo-11,14,16-trioxa-2lambda5,9,19,26,43lambda5,44lambda5,45lambda5-heptaaza-15lambda5-phospha-1-cobaltadodecacyclo[27.14.1.1^{1,34}.1^{2,9}.1^{10,13}.0^{1,26}.0^{3,8}.0^{23,27}.0^{25,42}.0^{32,44}.0^{39,43}.0^{37,45}]heptatetraconta-2(47),3,5,7,27,29(44),32,34(45),37,39(43)-decaene-2,43,44,45-tetrakis(ylium)-1,1-diuid-15-olate

Traditional Name

CAS Registry Number

13408-78-1

SMILES

[H][C@]12[C@H](CC(N)=O)[C@@]3(C)CCC(=O)NC[C@@H](C)OP([O-])(=O)O[C@H]4[C@@H](O)[C@H](O[C@@H]4CO)N4C=[N+](C5=CC(C)=C(C)C=C45)[Co--]456N1C3=C(C)C1=[N+]4C(=CC3=[N+]5C(=C(C)C4=[N+]6[C@]2(C)[C@@](C)(CC(N)=O)[C@@H]4CCC(N)=O)[C@@](C)(CC(N)=O)[C@@H]3CCC(N)=O)C(C)(C)[C@@H]1CCC(N)=O

InChI Identifier

InChI=1S/C62H90N13O14P.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;/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);/q;+3/p-2/t31-,34-,35-,36-,37+,41-,52-,53-,56-,57+,59-,60+,61+,62+;/m1./s1

InChI Key

NSLAUEAQDBERRV-DSRCUDDDSA-L

Chemical Taxonomy

Description

belongs to the class of organic compounds known as cobalamin derivatives. These are organic compounds containing a corrin ring, a cobalt atom, an a nucleotide moiety. Cobalamin Derivatives are actually derived from vitamin B12.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Tetrapyrroles and derivatives

Sub Class

Corrinoids

Direct Parent

Cobalamin derivatives

Alternative Parents

Substituents

Cobalamin
Metallotetrapyrrole skeleton
1-ribofuranosylbenzimidazole
Pentose phosphate
N-glycosyl compound
Glycosyl compound
Monosaccharide phosphate
Pentose monosaccharide
Benzimidazole
Phosphoethanolamine
Dialkyl phosphate
Monosaccharide
N-substituted imidazole
Organic phosphoric acid derivative
Phosphoric acid ester
Alkyl phosphate
Benzenoid
Fatty amide
Fatty acyl
Pyrroline
Pyrrolidine
Imidazole
Azole
Tetrahydrofuran
Heteroaromatic compound
Secondary carboxylic acid amide
Secondary alcohol
Primary carboxylic acid amide
Carboxamide group
Ketimine
Oxacycle
Azacycle
Organic transition metal salt
Carbene-type 1,3-dipolar compound
Carboxylic acid derivative
Alcohol
Organic nitrogen compound
Organonitrogen compound
Organooxygen compound
Imine
Primary alcohol
Organic salt
Organic cobalt salt
Hydrocarbon derivative
Organic oxide
Organopnictogen compound
Carbonyl group
Organic oxygen compound
Organic cation
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

cobalamin (CHEBI:28911 )

Ontology

Status

Detected and Quantified

Origin

Exogenous

Biofunction

Not Available

Application

Not Available

Cellular locations

Cell membrane
Membrane
Myelin sheath

Physical Properties

State

Solid

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
logP	0.61	ALOGPS
logP	-14	ChemAxon
logS	-5.9	ALOGPS
pKa (Strongest Acidic)	1.82	ChemAxon
pKa (Strongest Basic)	-0.55	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	13	ChemAxon
Hydrogen Donor Count	9	ChemAxon
Polar Surface Area	417 Å²	ChemAxon
Rotatable Bond Count	16	ChemAxon
Refractivity	337.47 m³·mol⁻¹	ChemAxon
Polarizability	132.05 Å³	ChemAxon
Number of Rings	12	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Spectra

Spectrum Type	Description	Splash Key
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0002-2031000095-b9bf39827ae83761ccb6	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0a4j-2393000063-424c175511ddc5e4d2fe	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0a4i-9740000051-7d6903b2dd8881008344	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-03di-0059000000-dec49680276dd7d5a080	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0i00-0092000000-2a13d3fd995ffd79ff7f	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-004i-3191000000-20e008a7f11bbe916e61	View in MoNA
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Not Available	View in JSpectraViewer

Biological Properties

Cellular Locations

Cell membrane
Membrane
Myelin sheath

Biospecimen Locations

Erythrocyte
Fibroblasts
Intestine
Liver
Milk
Neuron
Placenta

Pathways

Not Available

Name	SMPDB/Pathwhiz	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Erythrocyte	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Fibroblasts	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Intestine	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Liver	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Milk	Detected and Quantified	0.00256 uM	Not Specified	Not Specified	Normal	USDA Food Co...	details
Milk	Detected and Quantified	0.00256 uM	Not Specified	Not Specified	Normal	USDA Food Co...	details
Milk	Detected and Quantified	0.00354 uM	Not Specified	Not Specified	Normal	USDA Food Co...	details
Milk	Detected and Quantified	0.00286 uM	Not Specified	Not Specified	Normal	USDA Food Co...	details
Milk	Detected and Quantified	0.00271 uM	Not Specified	Not Specified	Normal	USDA Food Co...	details
Milk	Detected and Quantified	0.00323 uM	Not Specified	Not Specified	Normal	USDA Food Co...	details
Milk	Detected and Quantified	0.00286 uM	Not Specified	Not Specified	Normal	USDA Food Co...	details
Milk	Detected and Quantified	0.00354 uM	Not Specified	Not Specified	Normal	USDA Food Co...	details
Milk	Detected and Quantified	0.00323 uM	Not Specified	Not Specified	Normal	USDA Food Co...	details
Milk	Detected and Quantified	0.00293 uM	Not Specified	Not Specified	Normal	USDA Food Co...	details
Milk	Detected and Quantified	0.00376 uM	Not Specified	Not Specified	Normal	USDA Food Co...	details
Milk	Detected and Quantified	0.00376 uM	Not Specified	Not Specified	Normal	USDA Food Co...	details
Milk	Detected and Quantified	0.00271 uM	Not Specified	Not Specified	Normal	USDA Food Co...	details
Milk	Detected and Quantified	0.00323 uM	Not Specified	Not Specified	Normal	USDA Food Co...	details
Milk	Detected and Quantified	0.00286 uM	Not Specified	Not Specified	Normal	USDA Food Co...	details
Milk	Detected and Quantified	0.00293 uM	Not Specified	Not Specified	Normal	USDA Food Co...	details
Milk	Detected and Quantified	0.00399 uM	Not Specified	Not Specified	Normal	USDA Food Co...	details
Milk	Detected and Quantified	0.00399 uM	Not Specified	Not Specified	Normal	USDA Food Co...	details
Milk	Detected and Quantified	0.00339 uM	Not Specified	Not Specified	Normal	USDA Food Co...	details
Milk	Detected and Quantified	0.00339 uM	Not Specified	Not Specified	Normal	USDA Food Co...	details
Milk	Detected and Quantified	0.00329 uM	Not Specified	Not Specified	Normal	Fooddata+, T...	details
Milk	Detected and Quantified	0.00286 uM	Not Specified	Not Specified	Normal	Fooddata+, T...	details
Milk	Detected and Quantified	0.00361 uM	Not Specified	Not Specified	Normal	Fooddata+, T...	details
Milk	Detected and Quantified	0.00363 uM	Not Specified	Not Specified	Normal	Fooddata+, T...	details
Milk	Detected and Quantified	0.00361 uM	Not Specified	Not Specified	Normal	Fooddata+, T...	details
Milk	Detected and Quantified	0.00339 uM	Not Specified	Not Specified	Normal	Fooddata+, T...	details
Milk	Detected and Quantified	0.00336 uM	Not Specified	Not Specified	Normal	Fooddata+, T...	details
Milk	Detected and Quantified	0.0029 uM	Not Specified	Not Specified	Normal	Fooddata+, T...	details
Milk	Detected and Quantified	0.00269 - 0.00284 uM	Not Specified	Not Specified	Normal	PMID: 22081685	details
Milk	Detected and Quantified	0.00269 uM	Not Specified	Not Specified	Normal	Park, Y. W; Juáre...	details
Milk	Detected and Quantified	0.0037 +/- 0.0001 uM	Not Specified	Not Specified	Normal	PMID: 30994344	details
Milk	Detected and Quantified	0.0037 +/- 0.0001 uM	Not Specified	Not Specified	Normal	PMID: 30994344	details
Milk	Detected and Quantified	0.0037 +/- 0.0001 uM	Not Specified	Not Specified	Normal	PMID: 30994344	details
Milk	Detected and Quantified	0.0046 +/- 0.0001 uM	Not Specified	Not Specified	Normal	PMID: 30994344	details
Milk	Detected and Quantified	0.00534 - 0.0120 uM	Not Specified	Not Specified	Normal	R. A. Collins A. ...	details
Neuron	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Placenta	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details

Abnormal Concentrations

Not Available

External Links

HMDB ID

HMDB0002174

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Cobalamin

METLIN ID

6527

PubChem Compound

6857388

PDB ID

Not Available

ChEBI ID

28911

References

Synthesis Reference

Abou-Zeid, A. A.; El-Sherbeeny, M. R. Production of cobalamin by Streptomyces olivaceus. Indian Journal of Technology (1976), 14(7), 357-9.

Material Safety Data Sheet (MSDS)

Not Available

General References

Gaucheron F: Milk and dairy products: a unique micronutrient combination. J Am Coll Nutr. 2011 Oct;30(5 Suppl 1):400S-9S. [PubMed:22081685 ]
A. Foroutan et al. (2019). A. Foroutan et al. The Chemical Composition of Commercial Cow's Milk (in preparation). Journal of Agricultural and Food Chemistry.
Park, Y. W; Juárez, Manuela ; Ramos, M.; Haenlein, G. F. W. (2007). Park, Y. W; Juárez, Manuela ; Ramos, M.; Haenlein, G. F. W. Physico-chemical characteristics of goat and sheep milk. Small Ruminant Res.(2007) 68:88-113 doi: 10.1016/j.smallrumres.2006.09.013. Small Ruminant Research.
R. A. Collins A. E. Harper M. Schreiber C. A. Elvehjem (1951). R. A. Collins A. E. Harper M. Schreiber C. A. Elvehjem. 1951. The Folic Acid and Vitamin B12 Content of the Milk of Various Species. The Journal of Nutrition, Volume 43, Issue 2 Pages 313–321,. The Journal of Nutrition.
USDA Food Composition Databases [Link]
Fooddata+, The Technical University of Denmark (DTU) [Link]
Fooddata+, The Technical University of Denmark (DTU) [Link]
Fooddata+, The Technical University of Denmark (DTU) [Link]
Fooddata+, The Technical University of Denmark (DTU) [Link]
Fooddata+, The Technical University of Denmark (DTU) [Link]
Fooddata+, The Technical University of Denmark (DTU) [Link]
Fooddata+, The Technical University of Denmark (DTU) [Link]
Fooddata+, The Technical University of Denmark (DTU) [Link]

Enzymes

Enzyme Details

1. Methionine synthase

General function:: Amino acid transport and metabolism
Specific function:: Catalyzes the transfer of a methyl group from methyl-cobalamin to homocysteine, yielding enzyme-bound cob(I)alamin and methionine. Subsequently, remethylates the cofactor using methyltetrahydrofolate (By similarity).
Gene Name:: MTR
Uniprot ID:: Q4JIJ3
Molecular weight:: 140478.0

Enzyme Details

2. Methylmalonyl-CoA mutase, mitochondrial

General function:: Lipid transport and metabolism
Specific function:: Involved in the degradation of several amino acids, odd-chain fatty acids and cholesterol via propionyl-CoA to the tricarboxylic acid cycle.
Gene Name:: MMUT
Uniprot ID:: Q9GK13
Molecular weight:: 83235.0

Enzyme Details

3. Methylmalonyl Coenzyme A mutase

General function:: Lipid transport and metabolism
Specific function:: Not Available
Gene Name:: MMUT
Uniprot ID:: Q0III1
Molecular weight:: 83257.0

Enzyme Details

4. Transcobalamin-2

General function:: Involved in cobalamin binding
Specific function:: Primary vitamin B12-binding and transport protein. Delivers cobalamin to cells.
Gene Name:: TCN2
Uniprot ID:: Q9XSC9
Molecular weight:: 47958.0

Enzyme Details

5. Methylmalonic aciduria and homocystinuria type C protein homolog

General function:: Involved in cobalamin binding
Specific function:: Catalyzes the reductive dealkylation of cyanocobalamin to cob(II)alamin, using FAD or FMN as cofactor and NADPH as cosubstrate. Can also catalyze the glutathione-dependent reductive demethylation of methylcobalamin, and, with much lower efficiency, the glutathione-dependent reductive demethylation of adenosylcobalamin. Under anaerobic conditions cob(I)alamin is the first product; it is highly reactive and is converted to aquocob(II)alamin in the presence of oxygen. Binds cyanocobalamin, adenosylcobalamin, methylcobalamin and other, related vitamin B12 derivatives.
Gene Name:: MMACHC
Uniprot ID:: Q5E9C8
Molecular weight:: 31633.0

Enzyme Details

6. Probable lysosomal cobalamin transporter

General function:: Involved in cobalamin binding
Specific function:: Probable lysosomal cobalamin transporter. Required to export cobalamin from lysosomes allowing its conversion to cofactors (By similarity).
Gene Name:: LMBRD1
Uniprot ID:: Q3SYY9
Molecular weight:: 62022.0

Enzyme Details

7. Transcobalamin II

General function:: Involved in cobalamin binding
Specific function:: Not Available
Gene Name:: TCN2
Uniprot ID:: Q58CU1
Molecular weight:: 32235.0

Enzyme Details

8. CD320 antigen

General function:: Involved in growth factor activity
Specific function:: Receptor for transcobalamin saturated with cobalamin (TCbl). Plays an important role in cobalamin uptake. Plasma membrane protein that is expressed on follicular dendritic cells (FDC) and mediates interaction with germinal center B cells. Functions as costimulator to promote B cell responses to antigenic stimuli; promotes B cell differentiation and proliferation. Germinal center-B (GC-B) cells differentiate into memory B-cells and plasma cells (PC) through interaction with T-cells and follicular dendritic cells (FDC). CD320 augments the proliferation of PC precursors generated by IL-10.
Gene Name:: CD320
Uniprot ID:: A6QNY1
Molecular weight:: 26935.0

Showing metabocard for Cobalamin (BMDB0002174)

Structure for BMDB0002174 (Cobalamin)

Enzymes