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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2008-08-15 14:47:48 UTC
Update Date2022-03-07 02:49:34 UTC
HMDB IDHMDB0006903
Secondary Accession Numbers
  • HMDB0006964
  • HMDB06903
  • HMDB06964
Metabolite Identification
Common NameAdenosyl cobinamide
DescriptionAdenosyl cobinamide is an intermediate in vitamin B12 cofactor biosynthesis and adenosylcobalamin synthesis. It is a substrate for the enzyme Cob(I)yrinic acid a,c-diamide adenosyltransferase which is found in the mitochondria. The enzyme is responsible for the following 2 step reaction: ATP + cob(I)yrinic acid a,c-diamide = triphosphate + adenosylcob(III)yrinic acid a,c-diamide and then ATP + cobinamide = triphosphate + adenosylcobinamide.
Structure
Data?1582752415
Synonyms
ValueSource
5'-Deoxy-5'-adenosylcobinamideChEBI
Adenosylcob(III)inamideChEBI
Chemical FormulaC58H84CoN16O11
Average Molecular Weight1240.3214
Monoisotopic Molecular Weight1239.583747804
IUPAC Name(3R,4S,5S,9S,10S,15S,19R,20R,21R)-1-{[(2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl}-5,10,15-tris(2-carbamoylethyl)-4,9,20-tris(carbamoylmethyl)-19-(2-{[(2R)-2-hydroxypropyl]carbamoyl}ethyl)-3,4,7,9,14,14,17,19-octamethyl-2lambda5,22,23lambda5,24lambda5-tetraaza-1-cobaltaoctacyclo[11.9.1.1^{1,8}.0^{2,6}.0^{3,21}.0^{16,23}.0^{18,22}.0^{11,24}]tetracosa-2(6),7,11(24),12,16(23),17-hexaene-2,23,24-tris(ylium)-1,1-diuide
Traditional Name(3R,4S,5S,9S,10S,15S,19R,20R,21R)-1-{[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl}-5,10,15-tris(2-carbamoylethyl)-4,9,20-tris(carbamoylmethyl)-19-(2-{[(2R)-2-hydroxypropyl]carbamoyl}ethyl)-3,4,7,9,14,14,17,19-octamethyl-2lambda5,22,23lambda5,24lambda5-tetraaza-1-cobaltaoctacyclo[11.9.1.1^{1,8}.0^{2,6}.0^{3,21}.0^{16,23}.0^{18,22}.0^{11,24}]tetracosa-2(6),7,11(24),12,16(23),17-hexaene-2,23,24-tris(ylium)-1,1-diuide
CAS Registry NumberNot Available
SMILES
[H][C@@]12[C@H](CC(N)=O)[C@@](C)(CCC(=O)NC[C@@H](C)O)C3=C(C)C4=[N+]5C(=CC6=[N+]7C(=C(C)C8=[N+]([C@]1(C)[C@@](C)(CC(N)=O)[C@@H]8CCC(N)=O)[Co--]57(C[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1C=NC5=C1N=CN=C5N)N23)[C@@](C)(CC(N)=O)[C@@H]6CCC(N)=O)C(C)(C)[C@@H]4CCC(N)=O
InChI Identifier
InChI=1S/C48H73N11O8.C10H12N5O3.Co/c1-23(60)22-55-38(67)16-17-45(6)29(18-35(52)64)43-48(9)47(8,21-37(54)66)28(12-15-34(51)63)40(59-48)25(3)42-46(7,20-36(53)65)26(10-13-32(49)61)30(56-42)19-31-44(4,5)27(11-14-33(50)62)39(57-31)24(2)41(45)58-43;1-4-6(16)7(17)10(18-4)15-3-14-5-8(11)12-2-13-9(5)15;/h19,23,26-29,43,60H,10-18,20-22H2,1-9H3,(H14,49,50,51,52,53,54,55,56,57,58,59,61,62,63,64,65,66,67);2-4,6-7,10,16-17H,1H2,(H2,11,12,13);/q;;+2/p-1/t23-,26-,27-,28-,29+,43-,45-,46+,47+,48+;4-,6-,7-,10-;/m11./s1
InChI KeyKQXSPGAEBZWHMC-QMUWONGRSA-M
Chemical Taxonomy
Description Belongs to the class of organic compounds known as phenylpyruvic acid derivatives. Phenylpyruvic acid derivatives are compounds containing a phenylpyruvic acid moiety, which consists of a phenyl group substituted at the second position by an pyruvic acid.
KingdomOrganic compounds
Super ClassBenzenoids
ClassBenzene and substituted derivatives
Sub ClassPhenylpyruvic acid derivatives
Direct ParentPhenylpyruvic acid derivatives
Alternative Parents
Substituents
  • Cinnamic acid
  • Cinnamic acid or derivatives
  • Coumaric acid
  • Coumaric acid or derivatives
  • Hydroxycinnamic acid
  • Hydroxycinnamic acid or derivatives
  • Enol-phenylpyruvate
  • Phenol
  • 1-hydroxy-2-unsubstituted benzenoid
  • Monocarboxylic acid or derivatives
  • Enol
  • Carboxylic acid
  • Carboxylic acid derivative
  • Carbonyl group
  • Organooxygen compound
  • Hydrocarbon derivative
  • Organic oxide
  • Organic oxygen compound
  • Aromatic homomonocyclic compound
Molecular FrameworkAromatic homomonocyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Process
RoleNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility0.019 g/LALOGPS
logP-0.28ALOGPS
logP-14ChemAxon
logS-5.3ALOGPS
pKa (Strongest Acidic)12.49ChemAxon
pKa (Strongest Basic)3.92ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count16ChemAxon
Hydrogen Donor Count11ChemAxon
Polar Surface Area439.45 ŲChemAxon
Rotatable Bond Count23ChemAxon
Refractivity319.33 m³·mol⁻¹ChemAxon
Polarizability127.45 ųChemAxon
Number of Rings11ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
Predicted Chromatographic Properties

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid358.5 seconds40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid3083.9 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid113.5 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid229.6 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid160.2 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid153.8 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid478.3 seconds40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid519.5 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)1117.8 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid1047.3 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid520.6 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid1658.2 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid368.9 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid319.1 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate356.6 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA907.3 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water170.3 seconds40023050

Predicted Kovats Retention Indices

Not Available
Spectra
Biological Properties
Cellular Locations
  • Extracellular
  • Membrane
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 IDNot Available
KNApSAcK IDNot Available
Chemspider ID21864727
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI ID2480
Food Biomarker OntologyNot Available
VMH IDADOCBI
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available

Enzymes

General function:
Involved in ATP binding
Specific function:
Not Available
Gene Name:
MMAB
Uniprot ID:
Q96EY8
Molecular weight:
27387.975
Reactions
Adenosine triphosphate + Cobinamide → Triphosphate + Adenosyl cobinamidedetails
Adenosine triphosphate + Cobinamide → Triphosphate + Adenosyl cobinamidedetails