Adenosylcobalamin 5'-phosphate (ECMDB23095) (M2MDB003485)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes (2)XML
Proteins (2)
Record Information
Version2.0
Creation Date2012-10-10 12:16:15 -0600
Update Date2015-06-03 17:25:55 -0600
Secondary Accession Numbers
  • ECMDB23095
Identification
Name:Adenosylcobalamin 5'-phosphate
DescriptionAdenosylcobalamin 5'-phosphate is an intermediate in the synthesis of vitamin B12. Until recently it was believed that the last reaction in the biosynthesis of coenzyme B12 was the linking of alpha-ribazole (a product of 5,6-dimethylbenzimidazole ) to adenosylcobinamide-GDP, in a reaction catalyzed by cobalamin synthase. However, it was recently shown that the true substrate for the enzyme is alpha-ribazole-5'-P, and not alpha-ribazole, and that the product of the reaction is actually adenosylcobalamin 5'-phosphate. The dephosphorylation of adenosylcobalamin 5'-phosphate by the CobC protein leads to coenzyme B12.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms:
  • Adenosylcobalamin 5'-phosphoric acid
Chemical Formula:C72H101CoN18O20P2
Weight:Average: 1659.5617
Monoisotopic: 1658.62467598
InChI Key:ZKESCEDFYCGFMC-UHFFFAOYSA-L
InChI:InChI=1S/C62H91N13O17P2.C10H12N5O3.Co/c1-29-20-39-40(21-30(29)2)75(28-70-39)57-52(83)53(41(90-57)27-89-93(84,85)86)92-94(87,88)91-31(3)26-69-49(82)18-19-59(8)37(22-46(66)79)56-62(11)61(10,25-48(68)81)36(14-17-45(65)78)51(74-62)33(5)55-60(9,24-47(67)80)34(12-15-43(63)76)38(71-55)23-42-58(6,7)35(13-16-44(64)77)50(72-42)32(4)54(59)73-56;1-4-6(16)7(17)10(18-4)15-3-14-5-8(11)12-2-13-9(5)15;/h20-21,23,28,31,34-37,41,52-53,56-57,83H,12-19,22,24-27H2,1-11H3,(H17,63,64,65,66,67,68,69,71,72,73,74,76,77,78,79,80,81,82,84,85,86,87,88);2-4,6-7,10,16-17H,1H2,(H2,11,12,13);/q;;+2/p-2
CAS number:Not Available
IUPAC Name:λ²-cobalt(2+) ion 1-[(2S,3R,4S,5R)-3-hydroxy-4-{[hydroxy({[(2R)-1-({1-hydroxy-3-[(1R,2R,3R,4R,8S,13S,14S,18S,19S)-8,13,18-tris(2-carboximidatoethyl)-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-[(phosphonooxy)methyl]oxolan-2-yl]-5,6-dimethyl-3H-1λ⁵,3-benzodiazol-1-ylium [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl
Traditional IUPAC Name:λ²-cobalt(2+) ion 1-[(2S,3R,4S,5R)-3-hydroxy-4-({hydroxy[(2R)-1-({1-hydroxy-3-[(1R,2R,3R,4R,8S,13S,14S,18S,19S)-8,13,18-tris(2-carboximidatoethyl)-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]oxyphosphoryl}oxy)-5-[(phosphonooxy)methyl]oxolan-2-yl]-5,6-dimethyl-3H-1λ⁵,3-benzodiazol-1-ylium [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl
SMILES:[Co++].[H][C@]1([CH2])O[C@@]([H])(N2C=NC3=C(N)N=CN=C23)[C@]([H])(O)[C@]1([H])O.[H][C@@](C)(CN=C(O)CC[C@@]1(C)C2=N[C@]([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])(COP(O)(O)=O)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-5-phosphate
  • Pentose phosphate
  • 5'-deoxyribonucleoside
  • N-glycosyl compound
  • Glycosyl compound
  • Monosaccharide phosphate
  • 6-aminopurine
  • Purine
  • Imidazopyrimidine
  • Benzimidazole
  • Phosphoethanolamine
  • Dialkyl phosphate
  • Monoalkyl phosphate
  • Aminopyrimidine
  • Fatty acyl
  • Imidolactam
  • Benzenoid
  • Alkyl phosphate
  • Pyrimidine
  • Phosphoric acid ester
  • Organic phosphoric acid derivative
  • N-substituted imidazole
  • Monosaccharide
  • Fatty amide
  • Heteroaromatic compound
  • Tetrahydrofuran
  • Pyrroline
  • Pyrrolidine
  • Oxolane
  • Imidazole
  • Azole
  • Secondary carboxylic acid amide
  • Secondary alcohol
  • Primary carboxylic acid amide
  • Ketimine
  • Carboxamide group
  • Oxacycle
  • Azacycle
  • Organic transition metal salt
  • Organic 1,3-dipolar compound
  • Carbene-type 1,3-dipolar compound
  • Propargyl-type 1,3-dipolar organic compound
  • Secondary amine
  • Enamine
  • Secondary aliphatic amine
  • Carboxylic acid derivative
  • Carboximidic acid derivative
  • Carboximidic acid
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organic cobalt salt
  • Organic salt
  • Organic zwitterion
  • Primary amine
  • Organooxygen compound
  • Organonitrogen compound
  • Imine
  • Carbonyl group
  • Amine
  • Alcohol
  • Aromatic heteropolycyclic compound
Molecular FrameworkNot Available
External DescriptorsNot Available
Physical Properties
State:Not Available
Charge:2
Melting point:Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
logP0.99ChemAxon
pKa (Strongest Acidic)1.11ChemAxon
pKa (Strongest Basic)8.97ChemAxon
Physiological Charge2ChemAxon
Hydrogen Acceptor Count25ChemAxon
Hydrogen Donor Count16ChemAxon
Polar Surface Area526.32 ŲChemAxon
Rotatable Bond Count29ChemAxon
Refractivity441.71 m³·mol⁻¹ChemAxon
Polarizability137.62 ųChemAxon
Number of Rings11ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Cytoplasm
Reactions:
Adenosylcobinamide-GDP + N1-(alpha-D-ribosyl)-5,6-dimethyl-benzimidazole + N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole <> Guanosine monophosphate + Adenosylcobalamin + Adenosylcobalamin 5'-phosphate
N1-(5-Phospho-a-D-ribosyl)-5,6-dimethylbenzimidazole + Adenosylcobinamide-GDP + Adenosylcobinamide-GDP > Hydrogen ion + GMP + Adenosylcobalamin 5'-phosphate
Adenosylcobalamin 5'-phosphate + Water > Phosphate + coenzyme B12
SMPDB Pathways:
adenosylcobalamin salvage from cobinamidePW001884 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways:
EcoCyc Pathways:Not Available
Concentrations
Not Available
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_2) - 70eV, PositiveNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
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 IDNot Available
ChemSpider IDNot Available
Wikipedia IDNot Available
BioCyc IDNot Available

Enzymes

Protein Details
1. Cobalamin synthase
General function:
Involved in cobalamin 5'-phosphate synthase activity
Specific function:
Joins Ado-cobinamide-GDP and alpha-ribazole to generate adenosylcobalamin (Ado-cobalamin)
Gene Name:
cobS
Uniprot ID:
P36561
Molecular weight:
26385
Reactions
GDP-cobinamide + alpha-ribazole = cobalamin + GMP.
Protein Details
2. Alpha-ribazole phosphatase
General function:
Involved in catalytic activity
Specific function:
Converts N1-(5-phospho-alpha-D-ribosyl)-5,6- dimethylbenzimidazole into N1-alpha-D-ribosyl-5,6- dimethylbenzimidazole; involved in the assembly of the nucleotide loop of cobalamin
Gene Name:
cobC
Uniprot ID:
P52086
Molecular weight:
23308
Reactions
Adenosylcobalamin 5'-phosphate + H(2)O = coenzyme B12 + phosphate.
Alpha-ribazole 5'-phosphate + H(2)O = alpha-ribazole + phosphate.