adenosylcobinamide-GDP (PAMDB110423)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes Transporters
Proteins (3280)
Record Information
Version 1.0
Update Date 1/22/2018 11:54:54 AM
Metabolite IDPAMDB110423
Identification
Name: adenosylcobinamide-GDP
Description:An organophosphate oxoanion that is the anion of adenosylcobinamide guanosyl diphosphate with overall charge −1, arising from deprotonation of the phosphate OH groups; major species at pH 7.3.
Structure
Thumb
🔍MOLSDFPDBSMILESInChIView Structure
Synonyms:
  • Adenosine-GDP-cobinamide
Chemical Formula: C68H95N21O21P2Co
Average Molecular Weight: 1663.5
Monoisotopic Molecular Weight: 1664.597512507
InChI Key: IQTYKHRKNGVJEO-RRMAJTJESA-K
InChI: 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-3/t25-,28-,29-,30-,31+,33-,45-,46-,49-,52-,55-,56+,57+,58+;4-,6-,7-,10-;/m11./s1
CAS number: Not Available
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[15.2.1.1?,??1?????1??,???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 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-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[15.2.1.1?,??1?????1??,???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
SMILES:CC(OP([O-])(=O)OP([O-])(=O)OCC3(C(O)C(O)C(N2(C1(=C(C(=O)NC(N)=N1)N=C2)))O3))CNC(=O)CCC%11(C)(C(CC(=O)N)C%13(C%14(C)(C(C)(CC(N)=O)C(CCC(N)=O)C7(=[N+]([Co--]8%12(CC6(C(O)C(C(N5(C=NC4(C(N)=NC=NC=45)))O6)O))([N+]%10(C(=CC9(C(CCC(N)=O)C(C)(CC(N)=O)C(=C(C)7)[N+]8=9))C(C)(C)C(CCC(N)=O)C=%10C(C)=C%11N%12%13)))%14))))
Chemical Taxonomy
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.
Kingdom Chemical entities
Super ClassOrganic compounds
Class Nucleosides, nucleotides, and analogues
Sub ClassPurine nucleotides
Direct Parent Purine 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 Framework Aromatic heteropolycyclic compounds
External Descriptors Not Available
Physical Properties
State: Solid
Charge:-1
Melting point: Not Available
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
Biological Properties
Cellular Locations: Not Available
Reactions:
Pathways:
  • adenosylcobalamin biosynthesis II (late cobalt incorporation)P381-PWY
  • adenosylcobalamin salvage from cobinamide ICOBALSYN-PWY
  • adenosylcobalamin biosynthesis from cobyrinate a,c-diamide IPWY-5509
  • adenosylcobalamin biosynthesis from cobyrinate a,c-diamide IIPWY-5508
    Spectra
    Spectra: Not Available
    References
    References: Not Available
    Synthesis Reference: Not Available
    Material Safety Data Sheet (MSDS) Not Available
    External Links:
    ResourceLink
    ChEBI60487
    HMDBHMDB12185
    IAF126048463
    KEGGC06510
    PubChem51351658