Showing metabocard for Cob(I)alamin (BMDB0003429)

IdentificationTaxonomyPhysical propertiesPathwaysSpectraConcentrationsLinksReferencesenzymes (1) Show 1 proteinXML
Record Information
Version1.0
Creation Date2016-09-30 23:04:36 UTC
Update Date2020-06-04 20:39:14 UTC
BMDB IDBMDB0003429
Secondary Accession Numbers
  • BMDB03429
Metabolite Identification
Common NameCob(I)alamin
DescriptionCob(I)alamin, also known as vitamin b-12S or hydrido-cobalamin, 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. Cob(I)alamin is possibly soluble (in water) and an extremely weak basic (essentially neutral) compound (based on its pKa). Cob(I)alamin has been found to be associated with the diseases known as dimethylglycine dehydrogenase deficiency; also cob(i)alamin has been linked to the inborn metabolic disorders including cobalamin malabsorption.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
ValueSource
Vitamin b-12SChEBI
Vitamin b12SChEBI
CyanocobalaminHMDB
Hydrido-cobalaminHMDB
HydridocobalaminHMDB
Chemical FormulaC62H89CoN13O14P
Average Molecular Weight1330.378
Monoisotopic Molecular Weight1329.572151
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-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)-1,1,1,1-tetrauide
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-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)-1,1,1,1-tetrauide
CAS Registry Number18534-66-2
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-4]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;+1/p-1/t31-,34-,35-,36-,37+,41-,52-,53-,56-,57+,59-,60+,61+,62+;/m1./s1
InChI KeyOMAOKVYASDIYQG-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
  • Glycosyl compound
  • N-glycosyl compound
  • Monosaccharide phosphate
  • Pentose monosaccharide
  • Benzimidazole
  • Dialkyl phosphate
  • Monosaccharide
  • N-substituted imidazole
  • Organic phosphoric acid derivative
  • Phosphoric acid ester
  • Alkyl phosphate
  • Benzenoid
  • Azole
  • Imidazole
  • Heteroaromatic compound
  • Pyrrolidine
  • Pyrroline
  • Tetrahydrofuran
  • Secondary alcohol
  • Ketimine
  • Propargyl-type 1,3-dipolar organic compound
  • Carboximidic acid
  • Secondary amine
  • Carboximidic acid derivative
  • Secondary aliphatic amine
  • Enamine
  • Oxacycle
  • Azacycle
  • Organic transition metal salt
  • Organic 1,3-dipolar compound
  • Primary alcohol
  • Imine
  • Amine
  • Organic oxide
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Organic zwitterion
  • Organic oxygen compound
  • Alcohol
  • Organonitrogen compound
  • Organooxygen compound
  • Organic cobalt salt
  • Organic salt
  • Organic nitrogen compound
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors
Ontology
StatusDetected and Quantified
Origin
  • Endogenous
BiofunctionNot Available
ApplicationNot Available
Cellular locationsNot Available
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP-14ChemAxon
pKa (Strongest Acidic)1.82ChemAxon
pKa (Strongest Basic)-0.55ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count13ChemAxon
Hydrogen Donor Count10ChemAxon
Polar Surface Area414.17 ŲChemAxon
Rotatable Bond Count16ChemAxon
Refractivity338.59 m³·mol⁻¹ChemAxon
Polarizability134.39 ųChemAxon
Number of Rings12ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
Spectrum TypeDescriptionSplash Key
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-01q0-0097000000-0021927d06a72e6704c3View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03xu-0093000000-2a92353bd428991e480fView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0007-0090000000-93430347c6ecec5d8cd3View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-01ti-0089000000-f49f5ec60e91e3af0114View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-01ox-1094000000-2defa0906339d10ef64dView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0006-8092000000-345ba89e7a43d9592f0fView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-03e9-0029000000-5ba3ede307aec5f3cdc0View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0il0-0094000000-04ee85a1354b2737544eView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0fa2-2292000000-b181211315ceb5efcd5eView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-004i-0009000000-35bd64cbc837fba1aaffView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-056r-2079000000-000e2e52473ee1bde9e5View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-00o0-0094000000-66f0381254255a3b7333View in MoNA
1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)Not AvailableView in JSpectraViewer
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Milk
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
MilkDetected and Quantified0.00286 uMNot SpecifiedNot Specified
Normal
    • Int. Dairy Journa...
 details
Abnormal Concentrations
Not Available
HMDB IDHMDB0003429
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB021826
KNApSAcK IDNot Available
Chemspider ID21864800
KEGG Compound IDC00853
BioCyc IDNot Available
BiGG ID36205
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound53477772
PDB IDNot Available
ChEBI ID15982
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Ingela Andersson, R. Öste (1994). Int. Dairy Journal 4 (1994) 161-172. International Dairy Journal.

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