Metabolomics Structure Database

MDLMOL SDF CSV TSV

MW REGNO:	56637
Common Name:	dTDP-4-dehydro-beta-L-rhamnose
Systematic Name:	thymidine 5'-[3-(6-deoxy-beta-L-lyxo-hexopyranosyl-4-ulose) dihydrogen diphosphate]
RefMet Name:	dTDP-4-dehydro-beta-L-rhamnose
Synonyms:	DTDP-4-KETO-L-RHAMNOSE; dTDP-6-deoxy-beta-L-lyxo-hex-4-ulose [PubChem Synonyms]
Exact Mass:	546.0652 (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:	C16H24N2O15P2
InChIKey:	PSXWNITXWWECNY-LPVGZGSHSA-N
ClassyFire superclass:	Nucleosides, nucleotides, and analogues
ClassyFire class:	Pyrimidine nucleotides
ClassyFire subclass:	Pyrimidine nucleotide sugars
ClassyFire direct parent:	Pyrimidine nucleotide sugars
SMILES:	Cc1cn([C@H]2C[C@@H]([C@@H](COP(=O)(O)OP(=O)(O)O[C@@H]3[C@@H]([C@@H](C(=O)[C@H](C)O3)O)O)O2)O)c(=O)[nH]c1=O
Studies:	Available studies (via RefMet name)

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All Database Links Calculated Properties Human Pathways

External database links:

PubChem CID:	443211
CHEBI ID:	45868
HMDB ID:	HMDB0304343

Calculated physicochemical properties (?):

Heavy Atoms:	35
Rings:	3
Aromatic Rings:	1
Rotatable Bonds:	8
van der Waals Molecular volume:	420.33 Å3 molecule-1
Toplogical Polar Sufrace Area:	257.51 Å2 molecule-1
Hydrogen Bond Donors:	6
Hydrogen Bond Acceptors:	16
logP:	1.77
Molar Refractivity:	113.16
Fraction sp3 Carbons:	0.69
sp3 Carbons:	11

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
NPClassifier classification: "NPClassifier: A Deep Neural Network-Based Structural Classification Tool for Natural Products", Kim HW, Wang M, Leber CA, Nothias LF, Reher R, Kang KB, van der Hooft JJJ, Dorrestein PC, Gerwick WH and Cottrell GW. J Nat Prod. 2021 Nov 26;84(11):2795-2807.DOI: 10.1021/acs.jnatprod.1c00399.