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Record Information
Version3.6
Creation Date2009-04-06 16:20:39 UTC
Update Date2017-03-02 21:32:21 UTC
HMDB IDHMDB12185
Secondary Accession NumbersNone
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
Thumb
Synonyms
ValueSource
Adenosine-GDP-cobinamideHMDB
Chemical FormulaC68H97CoN21O21P2
Average Molecular Weight1665.5066
Monoisotopic Molecular Weight1664.597512489
IUPAC Name[(1R,3R,4R,6Z,8S,11Z,13S,14S,16Z,18S,19S)-4-(2-{[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)-8,13,18-tris(2-carbamoylethyl)-3,14,19-tris(carbamoylmethyl)-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-20-yl]({[(2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl})cobaltylium
Traditional Name[(1R,3R,4R,6Z,8S,11Z,13S,14S,16Z,18S,19S)-4-[2-({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]-8,13,18-tris(2-carbamoylethyl)-3,14,19-tris(carbamoylmethyl)-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-20-yl]({[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl})cobaltylium
CAS Registry NumberNot Available
SMILES
CC(CNC(=O)CC[C@]1(C)[C@@H](CC(N)=O)C2N=C1\C(C)=C1/N=C(/C=C3\N=C(\C(\C)=C4\[C@@H](CCC(N)=O)[C@](C)(CC(N)=O)[C@@]2(C)N4[Co+]C[C@H]2O[C@H]([C@H](O)[C@@H]2O)N2C=NC4=C2N=CN=C4N)[C@@](C)(CC(N)=O)[C@@H]3CCC(N)=O)C(C)(C)[C@@H]1CCC(N)=O)OP(O)(=O)OP(O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1C=NC2=C1N=C(N)NC2=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-FGHWVWCISA-M
Chemical Taxonomy
DescriptionThis compound belongs to the class of chemical entities known as purine ribonucleoside diphosphates. These are purine ribobucleotides with diphosphate group linked to the ribose moiety.
KingdomChemical entities
Super ClassOrganic compounds
ClassNucleosides, nucleotides, and analogues
Sub ClassPurine nucleotides
Direct ParentPurine ribonucleoside diphosphates
Alternative Parents
Substituents
  • Purine ribonucleoside diphosphate
  • Metallotetrapyrrole skeleton
  • Purine ribonucleoside monophosphate
  • Tetrapyrrole skeleton
  • Pentose-5-phosphate
  • Pentose phosphate
  • 5'-deoxyribonucleoside
  • Glycosyl compound
  • N-glycosyl compound
  • 6-aminopurine
  • 6-oxopurine
  • Monosaccharide phosphate
  • Organic pyrophosphate
  • Hypoxanthine
  • Purine
  • Imidazopyrimidine
  • Phosphoethanolamine
  • Aminopyrimidine
  • Pyrimidone
  • Monoalkyl phosphate
  • Fatty amide
  • Imidolactam
  • Primary aromatic amine
  • Monosaccharide
  • N-substituted imidazole
  • Organic phosphoric acid derivative
  • Pyrimidine
  • Alkyl phosphate
  • Fatty acyl
  • Phosphoric acid ester
  • Pyrrolidine
  • Pyrroline
  • Heteroaromatic compound
  • Imidazole
  • Tetrahydrofuran
  • Vinylogous amide
  • Azole
  • Lactam
  • Amino acid or derivatives
  • Carboxamide group
  • Ketimine
  • Secondary carboxylic acid amide
  • Secondary alcohol
  • Primary carboxylic acid amide
  • Oxacycle
  • Carboxylic acid derivative
  • Organoheterocyclic compound
  • Azacycle
  • Organic metal salt
  • Organic transition metal salt
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organic transition metal moeity
  • Imine
  • Organometallic compound
  • Organonitrogen compound
  • Organooxygen compound
  • Primary amine
  • Organic salt
  • Organic cobalt salt
  • Hydrocarbon derivative
  • Carbonyl group
  • Organic oxide
  • Transition metal alkyl
  • Organopnictogen compound
  • Amine
  • Alcohol
  • Organic cation
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External DescriptorsNot Available
Ontology
StatusExpected but not Quantified
Origin
  • Endogenous
  • Food
Biofunction
  • Cell signaling
  • Fuel and energy storage
  • Fuel or energy source
  • Membrane integrity/stability
Application
  • Nutrients
  • Stabilizers
  • Surfactants and Emulsifiers
Cellular locations
  • Extracellular
  • 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
Water Solubility0.15 mg/mLALOGPS
logP0.71ALOGPS
logP-11ChemAxon
logS-4.1ALOGPS
pKa (Strongest Acidic)1.85ChemAxon
pKa (Strongest Basic)8.77ChemAxon
Physiological Charge2ChemAxon
Hydrogen Acceptor Count29ChemAxon
Hydrogen Donor Count16ChemAxon
Polar Surface Area684.55 Å2ChemAxon
Rotatable Bond Count32ChemAxon
Refractivity396.59 m3·mol-1ChemAxon
Polarizability159.94 Å3ChemAxon
Number of Rings11ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
SpectraNot Available
Biological Properties
Cellular Locations
  • Extracellular
  • Membrane
Biofluid LocationsNot Available
Tissue LocationNot Available
PathwaysNot Available
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
DrugBank Metabolite IDNot Available
Phenol Explorer Compound IDNot Available
Phenol Explorer Metabolite IDNot Available
FoodDB IDFDB028838
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDC06510
BioCyc IDADENOSYLCOBINAMIDE-GDP
BiGG IDNot Available
Wikipedia LinkNot Available
NuGOwiki LinkHMDB12185
Metagene LinkHMDB12185
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available