vitamin B12 (ECMDB23097) (M2MDB003487)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes (1)XML
Proteins (1)
Record Information
Version2.0
Creation Date2012-10-10 12:16:26 -0600
Update Date2015-09-17 15:41:14 -0600
Secondary Accession Numbers
  • ECMDB23097
Identification
Name:vitamin B12
DescriptionVitamin B12 is a cobalt-containing coordination compound produced by intestinal micro-organisms and found also in soil and water. Higher plants do not concentrate vitamin B 12 from the soil and so are a poor source of the substance as compared with animal tissues. INTRINSIC FACTOR is important for the assimilation of vitamin B 12.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms:Not Available
Chemical Formula:C62H88CoN13O14P
Weight:Average: 1329.3478
Monoisotopic: 1328.564331295
InChI Key:NSLAUEAQDBERRV-UHFFFAOYSA-L
InChI: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
CAS number:Not Available
IUPAC Name:cobalt(3+) ion 1-(3-hydroxy-4-{[hydroxy({1-[(1-hydroxy-3-{8,13,18-tris[2-(C-hydroxycarbonimidoyl)ethyl]-3,14,19-tris(C-hydroxycarbonimidoylmethyl)-1,4,6,9,9,14,16,19-octamethyl-20,21,22,23-tetraazapentacyclo[15.2.1.1²,⁵.1⁷,¹⁰.1¹²,¹⁵]tricosa-5(23),6,10(22),11,15(21),16-hexaen-4-yl}propylidene)amino]propan-2-yl}oxy)phosphoryl]oxy}-5-(hydroxymethyl)oxolan-2-yl)-5,6-dimethyl-3H-1λ⁵,3-benzodiazol-1-ylium
Traditional IUPAC Name:cobalt(3+) ion 1-(3-hydroxy-4-{[hydroxy({1-[(1-hydroxy-3-{8,13,18-tris[2-(C-hydroxycarbonimidoyl)ethyl]-3,14,19-tris(C-hydroxycarbonimidoylmethyl)-1,4,6,9,9,14,16,19-octamethyl-20,21,22,23-tetraazapentacyclo[15.2.1.1²,⁵.1⁷,¹⁰.1¹²,¹⁵]tricosa-5(23),6,10(22),11,15(21),16-hexaen-4-yl}propylidene)amino]propan-2-yl}oxy)phosphoryl]oxy}-5-(hydroxymethyl)oxolan-2-yl)-5,6-dimethyl-3H-1λ⁵,3-benzodiazol-1-ylium
SMILES:[Co+3].CC(CNC(=O)CCC1(C)C(CC(N)=O)C2[N-]\C1=C(C)/C1=N/C(=C\C3=N\C(=C(C)/C4=NC2(C)C(C)(CC(N)=O)C4CCC(N)=O)\C(C)(CC(N)=O)C3CCC(N)=O)/C(C)(C)C1CCC(N)=O)OP([O-])(=O)OC1C(CO)OC(C1O)N1C=NC2=C1C=C(C)C(C)=C2
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
  • Pentose monosaccharide
  • Monosaccharide phosphate
  • Benzimidazole
  • Dialkyl phosphate
  • Benzenoid
  • Alkyl phosphate
  • Phosphoric acid ester
  • Organic phosphoric acid derivative
  • N-substituted imidazole
  • Monosaccharide
  • Heteroaromatic compound
  • Tetrahydrofuran
  • Pyrroline
  • Pyrrolidine
  • Imidazole
  • Azole
  • Secondary alcohol
  • Ketimine
  • Oxacycle
  • Azacycle
  • Organic transition metal salt
  • Secondary amine
  • Enamine
  • Secondary aliphatic amine
  • Carboximidic acid derivative
  • Carboximidic acid
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organic cobalt salt
  • Organic salt
  • Primary alcohol
  • Organooxygen compound
  • Organonitrogen compound
  • Imine
  • Amine
  • Alcohol
  • Organic cation
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External DescriptorsNot Available
Physical Properties
State:Not Available
Charge:3
Melting point:Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
logP-3.1ChemAxon
pKa (Strongest Acidic)1.81ChemAxon
pKa (Strongest Basic)9.07ChemAxon
Physiological Charge3ChemAxon
Hydrogen Acceptor Count23ChemAxon
Hydrogen Donor Count18ChemAxon
Polar Surface Area471.3 ŲChemAxon
Rotatable Bond Count26ChemAxon
Refractivity399.19 m³·mol⁻¹ChemAxon
Polarizability134.77 ųChemAxon
Number of Rings8ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Cytoplasm
Reactions:
ADP + Phosphate + 4 Hydrogen ion + Heme + Nickel(2+) + Iron chelate + Taurine + Molybdate + Magnesium + Fe3+ + Potassium + Polyamine + vitamin B12 + Sulfate + glycerol-3-phosphate + Phosphonate + D-Maltose <> Adenosine triphosphate +3 Hydrogen ion + Water
Cobalamin + Adenosine triphosphate + vitamin B12 > coenzyme B12 + Triphosphate + Polyphosphate
Adenosine triphosphate + Cobalamin + vitamin B12 > Triphosphate + Adenosylcobalamin + Triphosphate
SMPDB Pathways:
adenosylcobalamin salvage from cobinamidePW001884 ThumbThumb?image type=greyscaleThumb?image type=simple
purine nucleotides de novo biosynthesisPW000910 ThumbThumb?image type=greyscaleThumb?image type=simple
purine nucleotides de novo biosynthesis 2PW002033 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways:
EcoCyc Pathways:Not Available
Concentrations
Not Available
Spectra
Spectra:Not Available
References
References:Not Available
Synthesis Reference:Not Available
Material Safety Data Sheet (MSDS)Not Available
External Links:
ResourceLink
CHEBI IDNot Available
HMDB IDNot Available
Pubchem Compound IDNot Available
Kegg IDC05776
ChemSpider IDNot Available
Wikipedia IDVitamin B12
BioCyc IDNot Available

Enzymes

Protein Details
1. Cob(I)yrinic acid a,c-diamide adenosyltransferase
General function:
Involved in ATP binding
Specific function:
Required for both de novo synthesis of the corrin ring for the assimilation of exogenous corrinoids. Participates in the adenosylation of a variety of incomplete and complete corrinoids
Gene Name:
btuR
Uniprot ID:
P0A9H5
Molecular weight:
21999
Reactions
ATP + cob(I)yrinic acid a,c-diamide = triphosphate + adenosylcob(III)yrinic acid a,c-diamide.
ATP + cobinamide = triphosphate + adenosylcobinamide.