dTDP-β-L-rhamnose (PAMDB110503)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes Transporters
Proteins (3280)
Record Information
Version 1.0
Update Date 1/22/2018 12:54:54 PM
Metabolite IDPAMDB110503
Identification
Name: dTDP-β-L-rhamnose
Description:Dianion of dTDP-6-deoxy-β-L-mannose arising from deprotonation of both free OH groups of the diphosphate.
Structure
Thumb
🔍MOLSDFPDBSMILESInChIView Structure
Synonyms:
  • dTDP-6-deoxy-β-L-mannose
Chemical Formula: C16H24N2O15P2
Average Molecular Weight: 546.32
Monoisotopic Molecular Weight: 548.0808411965
InChI Key: ZOSQFDVXNQFKBY-CGAXJHMRSA-L
InChI: InChI=1S/C16H26N2O15P2/c1-6-4-18(16(24)17-14(6)23)10-3-8(19)9(31-10)5-29-34(25,26)33-35(27,28)32-15-13(22)12(21)11(20)7(2)30-15/h4,7-13,15,19-22H,3,5H2,1-2H3,(H,25,26)(H,27,28)(H,17,23,24)/p-2/t7-,8-,9+,10+,11-,12+,13+,15+/m0/s1
CAS number: 2147-59-3
IUPAC Name:thymidine 5'-[3-(6-deoxy-β-L-mannopyranosyl) diphosphate]
Traditional IUPAC Name: dtdp-L-rhamnose
SMILES:CC1(=CN(C(=O)NC(=O)1)C3(CC(O)C(COP(=O)([O-])OP(=O)([O-])OC2(OC(C)C(O)C(O)C(O)2))O3))
Chemical Taxonomy
Taxonomy DescriptionThis compound belongs to the class of chemical entities known as pyrimidine nucleotide sugars. These are pyrimidine nucleotides bound to a saccharide derivative through the terminal phosphate group.
Kingdom Chemical entities
Super ClassOrganic compounds
Class Nucleosides, nucleotides, and analogues
Sub ClassPyrimidine nucleotides
Direct Parent Pyrimidine nucleotide sugars
Alternative Parents
Substituents
  • Pyrimidine nucleotide sugar
  • Pyrimidine 2'-deoxyribonucleoside diphosphate
  • Pentose phosphate
  • Monosaccharide phosphate
  • Organic pyrophosphate
  • Pyrimidone
  • Monoalkyl phosphate
  • Phosphoric acid ester
  • Hydropyrimidine
  • Monosaccharide
  • Pyrimidine
  • Organic phosphoric acid derivative
  • Alkyl phosphate
  • Oxane
  • Heteroaromatic compound
  • Vinylogous amide
  • Oxolane
  • Urea
  • Lactam
  • Secondary alcohol
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Polyol
  • Organonitrogen compound
  • Alcohol
  • Hydrocarbon derivative
  • Organic oxide
  • Organopnictogen compound
  • Organooxygen compound
  • Organic nitrogen compound
  • Organic oxygen compound
  • Aromatic heteromonocyclic compound
Molecular Framework Aromatic heteromonocyclic compounds
External Descriptors
Physical Properties
State: Solid
Charge:-2
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 Solubility11.6 mg/mLALOGPS
logP-1.1ALOGPS
logP-2.7ChemAxon
logS-1.7ALOGPS
pKa (Strongest Acidic)1.73ChemAxon
pKa (Strongest Basic)-3.2ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count12ChemAxon
Hydrogen Donor Count7ChemAxon
Polar Surface Area251.08 Å2ChemAxon
Rotatable Bond Count8ChemAxon
Refractivity107.76 m3·mol-1ChemAxon
Polarizability46.26 Å3ChemAxon
Number of Rings3ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations: Not Available
Reactions:
Pathways:
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-004i-0900000000-a235a91a2d2afe7e5b0eView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-004i-3921000000-f27277a5a22d8b1a6e62View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-004i-4900000000-385a0d128de7afa0ef56View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0f6t-3303290000-8fb8bdb50a4d4dd37d52View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0ufu-5915010000-0710c988c191bfa8f10bView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0a6u-4901000000-ac82c124189fc9d5bf1dView in MoNA
References
References:
  • Giraud MF, Leonard GA, Field RA, Berlind C, Naismith JH: RmlC, the third enzyme of dTDP-L-rhamnose pathway, is a new class of epimerase. Nat Struct Biol. 2000 May;7(5):398-402. [10802738 ]
  • Dong C, Beis K, Giraud MF, Blankenfeldt W, Allard S, Major LL, Kerr ID, Whitfield C, Naismith JH: A structural perspective on the enzymes that convert dTDP-d-glucose into dTDP-l-rhamnose. Biochem Soc Trans. 2003 Jun;31(Pt 3):532-6. [12773151 ]
Synthesis Reference: Shibaev, V. N.; Kusov, Yu. Yu.; Eliseeva, G. I.; Petrenko, V. A. Synthesis of thymidine diphosphate rhamnose analogs. Ref. Dokl. Soobshch. - Mendeleevsk. S'ezd Obshch. Prikl. Khim., 11th (1975), 6 111. CODEN: 37MOAO CAN 88:191313 AN 1978:191313
Material Safety Data Sheet (MSDS) Not Available
External Links:
ResourceLink
CAS572-96-3
ChEBI57510
HMDBHMDB06354
IAF126041621
KEGGC03319
PubChem25245982