Showing metabocard for Adenosylcobinamide-GDP (BMDB0012185)

IdentificationTaxonomyPhysical propertiesPathwaysSpectraConcentrationsLinksReferencesXML
Record Information
Version1.0
Creation Date2016-10-03 18:33:50 UTC
Update Date2020-04-22 15:48:56 UTC
BMDB IDBMDB0012185
Secondary Accession Numbers
  • BMDB12185
Metabolite Identification
Common NameAdenosylcobinamide-GDP
DescriptionAdenosylcobinamide-GDP, also known as adenosine-GDP-cobinamide, belongs to the class of organic compounds known as purine ribonucleoside diphosphates. These are purine ribobucleotides with diphosphate group linked to the ribose moiety. Adenosylcobinamide-GDP exists in all living organisms, ranging from bacteria to humans. Based on a literature review a small amount of articles have been published on Adenosylcobinamide-GDP.
Structure
Thumb
MOLSDFPDBSMILESInChI
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
StatusExpected but not Quantified
Origin
  • Endogenous
  • Exogenous
BiofunctionNot Available
ApplicationNot Available
Cellular locations
  • Cell membrane
  • Membrane
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
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
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
Spectrum TypeDescriptionSplash Key
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0udi-0900004000-b99417703a97697aab48View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0udi-0820029000-f0beaa26df346053a517View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03di-0930000000-ef31295f338a08f3c804View in MoNA
Biological Properties
Cellular Locations
  • Cell membrane
  • Membrane
Biospecimen LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
HMDB IDHMDB0012185
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
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available