Cob(II)alamin (ECMDB06316) (M2MDB000664)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes (1)XML
Proteins (22)
Record Information
Version2.0
Creation Date2012-05-31 14:08:02 -0600
Update Date2015-06-03 15:54:51 -0600
Secondary Accession Numbers
  • ECMDB06316
Identification
Name:Cob(II)alamin
DescriptionCob(II)alamin is the product of reduction catalyzed by the microsomal enzyme. It is an intermediate of porphyrin and chlorophyll metabolism. (KEGG)
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms:
  • Cbl
  • Co(I)-Cobalamine
  • Cob(2)alamin
  • Cob(II)alamin
  • Cobalamin
  • Cobinamide-Co(1+)
  • Vitamin B12
  • Vitamin B12r
  • Vitamin B12
Chemical Formula:C62H89CoN13O14P
Weight:Average: 1330.3557
Monoisotopic: 1329.572156327
InChI Key:QDYKIIMTNDYRAM-UHFFFAOYSA-M
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;+4/p-1
CAS number:14463-33-3
IUPAC Name:λ⁴-cobalt(4+) ion 1-[(2S,3R,4S,5R)-4-[({[(2R)-1-({3-[(1R,3R,8S,13S,14S,18S,19S)-8,13-bis(2-carboximidatoethyl)-18-[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]-1-hydroxypropylidene}amino)propan-2-yl]oxy}(hydroxy)phosphoryl)oxy]-3-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-5,6-dimethyl-3H-1λ⁵,3-benzodiazol-1-ylium
Traditional IUPAC Name:λ⁴-cobalt(4+) ion 1-[(2S,3R,4S,5R)-4-({[(2R)-1-({3-[(1R,3R,8S,13S,14S,18S,19S)-8,13-bis(2-carboximidatoethyl)-18-[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]-1-hydroxypropylidene}amino)propan-2-yl]oxy(hydroxy)phosphoryl}oxy)-3-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-5,6-dimethyl-3H-1λ⁵,3-benzodiazol-1-ylium
SMILES:[Co+4].[H][C@@](C)(CN=C(O)CCC1(C)C2=NC([H])([C@]1([H])CC(O)=N)[C@]1(C)NC(=C(C)C3=NC(=CC4=NC(=C2C)[C@@]([H])(CCC([O-])=N)C4(C)C)[C@@]([H])(CCC([O-])=N)[C@]3(C)CC(O)=N)[C@@]([H])(CCC(O)=N)[C@]1(C)CC(O)=N)OP(O)(=O)O[C@]1([H])[C@@]([H])(CO)O[C@]([H])([N+]2=CNC3=C2C=C(C)C(C)=C3)[C@]1([H])O
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:Solid
Charge:3
Melting point:Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility0.027 g/LALOGPS
logP3.14ALOGPS
logP-3.1ChemAxon
logS-4.7ALOGPS
pKa (Strongest Acidic)1.81ChemAxon
pKa (Strongest Basic)9.07ChemAxon
Physiological Charge3ChemAxon
Hydrogen Acceptor Count23ChemAxon
Hydrogen Donor Count16ChemAxon
Polar Surface Area476.96 ŲChemAxon
Rotatable Bond Count26ChemAxon
Refractivity420.29 m³·mol⁻¹ChemAxon
Polarizability134.02 ųChemAxon
Number of Rings8ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Cytoplasm
Reactions:
NAD + 2 Cob(II)alamin + 2 Water + Hydrogen ion <> NADH +2 Aquacobalamin
2 Cob(II)alamin + NAD >2 Aquacobalamin + NADH
SMPDB Pathways:Not Available
KEGG Pathways:
EcoCyc Pathways:Not Available
Concentrations
Not Available
Spectra
Spectra:Not Available
References
References:
  • Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M. (2012). "KEGG for integration and interpretation of large-scale molecular data sets." Nucleic Acids Res 40:D109-D114. Pubmed: 22080510
Synthesis Reference:Kraeutler, 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
External Links:
ResourceLink
CHEBI ID16304
HMDB IDHMDB06316
Pubchem Compound ID5462226
Kegg IDC00541
ChemSpider IDNot Available
Wikipedia IDNot Available
BioCyc IDCPD-1829
EcoCyc IDCPD-1829

Enzymes

Protein Details
1. NAD(P)H-flavin reductase
General function:
Involved in oxidoreductase activity
Specific function:
Catalyzes the reduction of soluble flavins by reduced pyridine nucleotides. Seems to reduces the complexed Fe(3+) iron of siderophores to Fe(2+), thus releasing it from the chelator
Gene Name:
fre
Uniprot ID:
P0AEN1
Molecular weight:
26242
Reactions
Reduced riboflavin + NAD(P)(+) = riboflavin + NAD(P)H.
2 cob(II)alamin + NAD(+) = 2 aquacob(III)alamin + NADH.