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Record Information

Version

2.0

Creation Date

2012-05-31 14:08:11 -0600

Update Date

2015-06-03 15:54:51 -0600

Secondary Accession Numbers

ECMDB06354

Identification

Name:

Deoxythymidine diphosphate-L-rhamnose

Description

Deoxythymidine diphosphate (dTDP)-L-rhamnose is the precursor of L-rhamnose, a saccharide required for the virulence of some pathogenic bacteria. In gram negative bacteria such as Salmonella enterica, Vibrio cholerae or Escherichia coli 075:K5, L-rhamnose is an important residue in the O-antigen of lipopolysaccharides, which are essential for resistance to serum killing and for colonization. dTDP-L-rhamnose is synthesized from glucose-1-phosphate and deoxythymidine triphosphate (dTTP) via a pathway involving four distinct enzymes. Whereas common sugars such as glucose, fructose and mannose are all D-configured, bacteria commonly utilize the L-configured carbohydrates in pharmacologically active compounds and in their cell-wall structures. The enzymes involved in dTDP-L-rhamnose synthesis are potential targets for the design of new therapeutic agents against bacteria. (PMID 10802738, 12773151)

Structure

MOL SDF 3D-SDF PDB SMILES InChI View 3D Structure

Synonyms:

Deoxythymidine diphosphoric acid-L-rhamnose
DTDP-6-Deoxy-L-mannose
DTDP-L-Rhamnose
DTDP-Rhamnose
TDP-Rhamnose
Thymidine diphosphate rhamnose
Thymidine diphosphate-L-rhamnose
Thymidine diphosphoric acid rhamnose
Thymidine diphosphoric acid-L-rhamnose

Chemical Formula:

C₁₆H₂₆N₂O₁₅P₂

Weight:

Average: 548.3296
Monoisotopic: 548.080841196

InChI Key:

ZOSQFDVXNQFKBY-CZRCVJRHSA-N

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)/t7-,8-,9+,10+,11-,12+,13+,15?/m0/s1

CAS number:

2147-59-3

IUPAC Name:

{[hydroxy({[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)oxolan-2-yl]methoxy})phosphoryl]oxy}({[(3R,4R,5R,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxy})phosphinic acid

Traditional IUPAC Name:

dtdp-L-rhamnose

SMILES:

C[C@@H]1OC(OP(O)(=O)OP(O)(=O)OC[C@H]2O[C@H](C[C@@H]2O)N2C=C(C)C(=O)NC2=O)[C@H](O)[C@H](O)[C@H]1O

Chemical Taxonomy

Description

belongs to the class of organic compounds known as pyrimidine nucleotide sugars. These are pyrimidine nucleotides bound to a saccharide derivative through the terminal phosphate group.

Kingdom

Organic compounds

Super Class

Nucleosides, nucleotides, and analogues

Class

Pyrimidine nucleotides

Sub Class

Pyrimidine nucleotide sugars

Direct Parent

Pyrimidine nucleotide sugars

Alternative Parents

Substituents

Pyrimidine nucleotide sugar
Pyrimidine 2'-deoxyribonucleoside diphosphate
Pentose phosphate
Monosaccharide phosphate
Organic pyrophosphate
Monoalkyl phosphate
Pyrimidone
Hydropyrimidine
Phosphoric acid ester
Monosaccharide
Organic phosphoric acid derivative
Oxane
Alkyl phosphate
Pyrimidine
Heteroaromatic compound
Vinylogous amide
Tetrahydrofuran
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

dTDP-rhamnose (CHEBI:35452 )

Physical Properties

State:

Solid

Charge:

-2

Melting point:

Not Available

Experimental Properties:

Property	Value	Source

Predicted Properties

Property	Value	Source
Water Solubility	11.6 g/L	ALOGPS
logP	-1.1	ALOGPS
logP	-2.7	ChemAxon
logS	-1.7	ALOGPS
pKa (Strongest Acidic)	1.73	ChemAxon
pKa (Strongest Basic)	-3.2	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	12	ChemAxon
Hydrogen Donor Count	7	ChemAxon
Polar Surface Area	251.08 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	107.76 m³·mol⁻¹	ChemAxon
Polarizability	46.26 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	0	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Biological Properties

Cellular Locations:

Cytoplasm

Reactions:

SMPDB Pathways:

Starch and sucrose metabolism

PW000941

KEGG Pathways:

Metabolic pathways eco01100
Novobiocin biosynthesis ec00401
Polyketide sugar unit biosynthesis ec00523
Starch and sucrose metabolism ec00500
Streptomycin biosynthesis ec00521

EcoCyc Pathways:

dTDP-L-rhamnose biosynthesis I DTDPRHAMSYN-PWY

Concentrations

Not Available

Spectra

Spectra:

Spectrum Type	Description	Splash Key
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-0036-6922340000-5b7bbefa46231e0401e7	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positive	splash10-00bc-8441509000-f72396e274d70b76dce1	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-004i-0900000000-a235a91a2d2afe7e5b0e	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-004i-3921000000-f27277a5a22d8b1a6e62	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-004i-4900000000-385a0d128de7afa0ef56	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0f6t-3303290000-8fb8bdb50a4d4dd37d52	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0ufu-5915010000-0710c988c191bfa8f10b	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0a6u-4901000000-ac82c124189fc9d5bf1d	View in MoNA
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer

References

References:

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. Pubmed: 12773151
Giraud, M. F., Leonard, G. A., Field, R. A., Berlind, C., Naismith, J. H. (2000). "RmlC, the third enzyme of dTDP-L-rhamnose pathway, is a new class of epimerase." Nat Struct Biol 7:398-402. Pubmed: 10802738
Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M. (2012). "KEGG for integration and interpretation of large-scale molecular data sets." Nucleic Acids Res 40:D109-D114. Pubmed: 22080510
Keseler, I. M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A. G., Mackie, A., Paulsen, I., Gunsalus, R. P., Karp, P. D. (2011). "EcoCyc: a comprehensive database of Escherichia coli biology." Nucleic Acids Res 39:D583-D590. Pubmed: 21097882

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

Links

External Links:

Resource	Link
CHEBI ID	35452
HMDB ID	HMDB06354
Pubchem Compound ID	439975
Kegg ID	C03319
ChemSpider ID	388998
Wikipedia ID	Not Available
BioCyc ID	DTDP-RHAMNOSE
EcoCyc ID	DTDP-RHAMNOSE

Enzymes

Protein Details

1. dTDP-4-dehydrorhamnose reductase

General function:: Involved in dTDP-4-dehydrorhamnose reductase activity
Specific function:: Catalyzes the reduction of dTDP-6-deoxy-L-lyxo-4- hexulose to yield dTDP-L-rhamnose. RmlD uses NADH and NADPH nearly equally well
Gene Name:: rfbD
Uniprot ID:: P37760
Molecular weight:: 32694

Reactions

dTDP-6-deoxy-L-mannose + NADP(+) = dTDP-4-dehydro-6-deoxy-L-mannose + NADPH.

Protein Details

2. Lipopolysaccharide core biosynthesis protein rfaS

General function:: Involved in protein binding
Specific function:: Specific function unknown
Gene Name:: rfaS
Uniprot ID:: P27126
Molecular weight:: 36730

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Deoxythymidine diphosphate-L-rhamnose (M2MDB000667)

Structure for #<Compound:0xab268080>

Enzymes

Reactions