Metabolomics Structure Database

MDLMOL SDF CSV TSV

MW REGNO:	37740
Common Name:	GDP-4-Dehydro-6-deoxy-D-mannose
Systematic Name:	{[(2R,3S,4R,5R)-5-(2-amino-6-oxo-6,9-dihydro-1H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}[({[(2R,3S,4R,6R)-3,4-dihydroxy-6-methyl-5-oxooxan-2-yl]oxy}(hydroxy)phosphoryl)oxy]phosphinic acid
RefMet Name:	GDP-4-Dehydro-6-deoxy-D-mannose
Synonyms:	[PubChem Synonyms]
Exact Mass:	587.0666 (neutral)    Calculate m/z: (Choose adduct) [M+H]+ [M+H-H2O]+ [M.]+ [M+2H]2+ [M+3H]3+ [M+4H]4+ [M+K]+ [M+2K]2+ [M-H+2K]+ [M+Na]+ [M+2Na]2+ [M-H+2Na]+ [M+Li]+ [M+2Li]2+ [M+NH4]+ [M-H]- [M-2H]2- [M-3H]3- [M-4H]4- [M+Cl]- [M+OAc]- [M+HCOO]- M(neutral)
Formula:	C16H23N5O15P2
InChIKey:	PNHLMHWWFOPQLK-BKUUWRAGSA-N
ClassyFire superclass:	Nucleosides, nucleotides, and analogues [C0000289]
ClassyFire class:	Purine nucleotides [C0001506]
ClassyFire subclass:	Purine nucleotide sugars [C0001293]
ClassyFire direct parent:	Purine nucleotide sugars [C0001293]
SMILES:	C[C@@H]1C(=O)[C@@H]([C@@H]([C@H](O1)OP(=O)(O)OP(=O)(O)OC[C@@H]1[C@H]([C@H]([C@H](n2cnc3c2nc(N)[nH]c3=O)O1)O)O)O)O
Studies:	Available studies (via RefMet name)

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All Database Links Calculated Properties Human Pathways

External database links:

PubChem CID:	135398621
CHEBI ID:	16955
HMDB ID:	HMDB0001346
KEGG ID:	C01222
Chemspider ID:	388554
METLIN ID:	6180
MetaCyc ID:	GDP-4-DEHYDRO-6-DEOXY-D-MANNOSE
Plant Metabolite Hub(Pmhub):	MS000017159

Calculated physicochemical properties (?):

Heavy Atoms:	38
Rings:	4
Aromatic Rings:	2
Rotatable Bonds:	8
van der Waals Molecular volume:	427.43 Å3 molecule-1
Toplogical Polar Sufrace Area:	312.47 Å2 molecule-1
Hydrogen Bond Donors:	8
Hydrogen Bond Acceptors:	18
logP:	-0.02
Molar Refractivity:	121.45
Fraction sp3 Carbons:	0.62
sp3 Carbons:	10

Human Pathway links:

HMDB and KEGG pathways containing this metabolite

References

LIPID MAPS classification: "Update of the LIPID MAPS comprehensive classification system for lipids", Fahy E, Subramaniam S, Murphy RC, Nishijima M, Raetz CR, Shimizu T, Spener F, van Meer G, Wakelam MJ, and Dennis EA, J. Lipid Res. (2009) 50: S9-S14. DOI: 10.1194/jlr.R800095-JLR200
ClassyFire classification: "ClassyFire: automated chemical classification with a comprehensive, computable taxonomy", Djoumbou Feunang Y, Eisner R, Knox C, Chepelev L, Hastings J, Owen G, Fahy E, Steinbeck C, Subramanian S, Bolton E, Greiner R, and Wishart DS, J. Cheminformatics (2016) 8:61. DOI: 10.1186/s13321-016-0174-y