Hmdb loader
You are using an unsupported browser. Please upgrade your browser to a newer version to get the best experience on Human Metabolome Database.
Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2007-05-23 00:07:35 UTC
Update Date2021-09-14 15:17:03 UTC
HMDB IDHMDB0006316
Secondary Accession Numbers
  • HMDB06316
Metabolite Identification
Common NameCob(II)alamin
DescriptionCob(II)alamin, also known as vitamin B12R or co(i)-cobalamine, 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. Based on a literature review a significant number of articles have been published on Cob(II)alamin.
Structure
Data?1582752380
Synonyms
ValueSource
Co(I)-cobalamineHMDB
Cob(2)alaminHMDB
Cobinamide-co(1+)HMDB
Vitamin b12RHMDB
b12RHMDB
Reduced vitamin b12HMDB
Cob(II)alaminHMDB
Chemical FormulaC62H89CoN13O14P
Average Molecular Weight1330.377
Monoisotopic Molecular Weight1329.571053
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)-15,46-dihydroxy-12-(hydroxymethyl)-5,6,17,23,28,31,31,36,38,41,42-undecamethyl-15,20-dioxo-11,14,16-trioxa-2lambda4,9,19,26,43lambda4,44lambda4,45lambda4-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-1,1-bis(ylium)
Traditional 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)-15,46-dihydroxy-12-(hydroxymethyl)-5,6,17,23,28,31,31,36,38,41,42-undecamethyl-15,20-dioxo-11,14,16-trioxa-2lambda4,9,19,26,43lambda4,44lambda4,45lambda4-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-1,1-bis(ylium)
CAS Registry Number14463-33-3
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](CO)O[C@@H]([C@@H]4O)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-1/t31-,34-,35-,36-,37+,41-,52-,53-,56-,57+,59-,60+,61+,62+;/m1./s1
InChI KeyNSLAUEAQDBERRV-DSRCUDDDSA-M
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.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassTetrapyrroles and derivatives
Sub ClassCorrinoids
Direct ParentCobalamin 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 FrameworkAromatic heteropolycyclic compounds
External DescriptorsNot Available
Ontology
Disposition

Biological location

Source

Route of exposure

Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Spectral PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
logP10(1.14) g/LALOGPS
logS10(-5.4) g/LALOGPS
Hydrogen Acceptor Count0ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area476.41 ŲChemAxon
Rotatable Bond Count16ChemAxon
Refractivity349.57 m³·mol⁻¹ChemAxon
Polarizability132.72 ųChemAxon
Number of Rings12ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
Predicted Spectral Properties

Predicted Kovats Retention Indices

Not Available
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm
  • Mitochondria
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB023883
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDC00541
BioCyc IDCPD-1829
BiGG ID35292
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI ID16304
Food Biomarker OntologyNot Available
VMH IDCBL2
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceKraeutler, Bernhard; Keller, Walter; Kratky, Christoph. Coenzyme B12 chemistry: the crystal and molecular structure of cob(II)alamin. Journal of the American Chemical Society (1989), 111(24), 8936-8.
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Kolhouse JF, Utley C, Stabler SP, Allen RH: Mechanism of conversion of human apo- to holomethionine synthase by various forms of cobalamin. J Biol Chem. 1991 Dec 5;266(34):23010-5. [PubMed:1744096 ]
  2. Pezacka EH: Identification and characterization of two enzymes involved in the intracellular metabolism of cobalamin. Cyanocobalamin beta-ligand transferase and microsomal cob(III)alamin reductase. Biochim Biophys Acta. 1993 Jun 11;1157(2):167-77. [PubMed:8507652 ]

Enzymes

General function:
Involved in cobalamin binding
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:
Q99707
Molecular weight:
140525.91
General function:
Involved in oxidoreductase activity
Specific function:
Involved in the reductive regeneration of cob(I)alamin cofactor required for the maintenance of methionine synthase in a functional state.
Gene Name:
MTRR
Uniprot ID:
Q9UBK8
Molecular weight:
77672.995
General function:
Involved in histone-arginine N-methyltransferase activity
Specific function:
Arginine methyltransferase that can both catalyze the formation of omega-N monomethylarginine (MMA) and symmetrical dimethylarginine (sDMA), with a preference for the formation of MMA. Specifically mediates the symmetrical dimethylation of arginine residues in the small nuclear ribonucleoproteins Sm D1 (SNRPD1) and Sm D3 (SNRPD3); such methylation being required for the assembly and biogenesis of snRNP core particles. Methylates SUPT5H. Mono- and dimethylates arginine residues of myelin basic protein (MBP) in vitro. Plays a role in the assembly of snRNP core particles. May play a role in cytokine-activated transduction pathways. Negatively regulates cyclin E1 promoter activity and cellular proliferation. May regulate the SUPT5H transcriptional elongation properties. May be part of a pathway that is connected to a chloride current, possibly through cytoskeletal rearrangement. Methylates histone H2A and H4 'Arg-3' during germ cell development. Methylates histone H3 'Arg-8', which may repress transcription. Methylates the Piwi proteins (PIWIL1, PIWIL2 and PIWIL4), methylation of Piwi proteins being required for the interaction with Tudor domain-containing proteins and subsequent localization to the meiotic nuage. Methylates RPS10. Attenuates EGF signaling through the MAPK1/MAPK3 pathway acting at 2 levels. First, monomethylates EGFR; this enhances EGFR 'Tyr-1197' phosphorylation and PTPN6 recruitment, eventually leading to reduced SOS1 phosphorylation. Second, methylates RAF1 and probably BRAF, hence destabilizing these 2 signaling proteins and reducing their catalytic activity. Required for induction of E-selectin and VCAM-1, on the endothelial cells surface at sites of inflammation. Methylates HOXA9. Methylates and regulates SRGAP2 which is involved in cell migration and differentiation.
Gene Name:
PRMT5
Uniprot ID:
O14744
Molecular weight:
71319.755