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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2009-04-06 16:20:39 UTC
Update Date2022-03-07 02:51:22 UTC
HMDB IDHMDB0012185
Secondary Accession Numbers
  • HMDB12185
Metabolite Identification
Common NameAdenosylcobinamide-GDP
DescriptionAdenosylcobinamide-GDP,a known de novo intermediate, is involved in Porphyrin and chlorophyll metabolism.In Salmonella typhimurium LT2, under anaerobic conditions, CobU (EC 2.7.7.62 and EC 2.7.1.156), CobT (EC 2.4.2.21), CobC (EC 3.1.3.73) and CobS (EC 2.7.8.26) catalyse reactions in the nucleotide loop. assembly pathway, which convert adenosylcobinamide (AdoCbi) into. adenosylcobalamin (AdoCbl). CobT and CobC are involved in 5,6-dimethylbenzimidazole activation whereby. 5,6-dimethylbenzimidazole is converted to its riboside,. alpha-ribazole. The second branch of the nuclotide loop assembly. pathway is the cobinamide (Cbi) activation branch where AdoCbi or. adenosylcobinamide-phosphate is converted to the activated. intermediate AdoCbi-GDP by the bifunctional enzyme Cob U. The final. step in adenosylcobalamin biosynthesis is the condensation of. AdoCbi-GDP with alpha-ribazole, which is catalysed by EC 2.7.8.26,. cobalamin synthase (CobS), to yield adenosylcobalamin.
Structure
Data?1582753025
Synonyms
ValueSource
Adenosine-GDP-cobinamideChEBI
Chemical FormulaC68H97CoN21O21P2
Average Molecular Weight1665.5066
Monoisotopic Molecular Weight1664.597512489
IUPAC Name(3R,4S,5S,9S,10S,15S,19R,20R,21R)-19-(2-{[(2R)-2-({[({[(2R,3S,4R,5R)-5-(2-amino-6-oxo-6,9-dihydro-1H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy](hydroxy)phosphoryl}oxy)propyl]carbamoyl}ethyl)-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)-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)-19-(2-{[(2R)-2-[({[(2R,3S,4R,5R)-5-(2-amino-6-oxo-1H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy(hydroxy)phosphoryl)oxy]propyl]carbamoyl}ethyl)-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)-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)OP(O)(=O)OP(O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)N3C=NC4=C3N=C(N)NC4=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/C58H86N16O18P2.C10H12N5O3.Co/c1-25(91-94(87,88)92-93(85,86)89-23-33-45(82)46(83)52(90-33)74-24-67-44-50(74)71-53(65)72-51(44)84)22-66-41(81)16-17-55(6)31(18-38(62)78)49-58(9)57(8,21-40(64)80)30(12-15-37(61)77)43(73-58)27(3)48-56(7,20-39(63)79)28(10-13-35(59)75)32(68-48)19-34-54(4,5)29(11-14-36(60)76)42(69-34)26(2)47(55)70-49;1-4-6(16)7(17)10(18-4)15-3-14-5-8(11)12-2-13-9(5)15;/h19,24-25,28-31,33,45-46,49,52,82-83H,10-18,20-23H2,1-9H3,(H19,59,60,61,62,63,64,65,66,68,69,70,71,72,73,75,76,77,78,79,80,81,84,85,86,87,88);2-4,6-7,10,16-17H,1H2,(H2,11,12,13);/q;;+2/p-1/t25-,28-,29-,30-,31+,33-,45-,46-,49-,52-,55-,56+,57+,58+;4-,6-,7-,10-;/m11./s1
InChI KeyIQTYKHRKNGVJEO-RRMAJTJESA-M
Chemical Taxonomy
Description Belongs to the class of organic compounds known as purine ribonucleoside diphosphates. These are purine ribobucleotides with diphosphate group linked to the ribose moiety.
KingdomOrganic compounds
Super ClassNucleosides, nucleotides, and analogues
ClassPurine nucleotides
Sub ClassPurine ribonucleotides
Direct ParentPurine ribonucleoside diphosphates
Alternative Parents
Substituents
  • Purine ribonucleoside diphosphate
  • Metallotetrapyrrole skeleton
  • Purine ribonucleoside monophosphate
  • Tetrapyrrole skeleton
  • Pentose phosphate
  • Pentose-5-phosphate
  • 5'-deoxyribonucleoside
  • N-glycosyl compound
  • Glycosyl compound
  • Organic pyrophosphate
  • 6-oxopurine
  • Hypoxanthine
  • 6-aminopurine
  • Monosaccharide phosphate
  • Purine
  • Imidazopyrimidine
  • Phosphoethanolamine
  • Monoalkyl phosphate
  • Aminopyrimidine
  • Hydroxypyrimidine
  • Pyrimidone
  • Phosphoric acid ester
  • Fatty amide
  • Fatty acyl
  • Imidolactam
  • Pyrimidine
  • Alkyl phosphate
  • Monosaccharide
  • Organic phosphoric acid derivative
  • N-substituted imidazole
  • Pyrrolidine
  • Pyrroline
  • Vinylogous amide
  • Azole
  • Heteroaromatic compound
  • Tetrahydrofuran
  • Imidazole
  • Primary carboxylic acid amide
  • Secondary alcohol
  • Amino acid or derivatives
  • Secondary carboxylic acid amide
  • Ketimine
  • Carboxamide group
  • Carboximidic acid
  • Carboximidic acid derivative
  • Oxacycle
  • Carboxylic acid derivative
  • Secondary aliphatic amine
  • Enamine
  • Azacycle
  • Organic transition metal salt
  • Organoheterocyclic compound
  • Carbene-type 1,3-dipolar compound
  • Secondary amine
  • Organic oxide
  • Organopnictogen compound
  • Amine
  • Alcohol
  • Hydrocarbon derivative
  • Organic cobalt salt
  • Carbonyl group
  • Organic salt
  • Organic nitrogen compound
  • Imine
  • Organic oxygen compound
  • Primary amine
  • Organooxygen compound
  • Organonitrogen compound
  • Organic cation
  • Aromatic heteropolycyclic compound
Molecular FrameworkNot Available
External Descriptors
Ontology
Disposition

Biological location

Source

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 Solubility0.15 g/LALOGPS
logP0.07ALOGPS
logP-16ChemAxon
logS-4.7ALOGPS
pKa (Strongest Acidic)1.85ChemAxon
pKa (Strongest Basic)4.01ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count26ChemAxon
Hydrogen Donor Count16ChemAxon
Polar Surface Area656.5 ŲChemAxon
Rotatable Bond Count31ChemAxon
Refractivity401.91 m³·mol⁻¹ChemAxon
Polarizability161.78 ųChemAxon
Number of Rings14ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
Predicted Chromatographic Properties

Predicted Kovats Retention Indices

Not Available
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Adenosylcobinamide-GDP 10V, Positive-QTOFsplash10-0udi-0900004000-b99417703a97697aab482021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Adenosylcobinamide-GDP 20V, Positive-QTOFsplash10-0udi-0820029000-f0beaa26df346053a5172021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Adenosylcobinamide-GDP 40V, Positive-QTOFsplash10-03di-0930000000-ef31295f338a08f3c8042021-09-25Wishart LabView Spectrum
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 ID29368592
KEGG Compound IDNot Available
BioCyc IDADENOSYLCOBINAMIDE-GDP
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI ID2479
Food Biomarker OntologyNot Available
VMH IDAGDPCBI
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available