Structure of PDB 1wvg Chain A Binding Site BS02

Receptor Information
>1wvg Chain A (length=352) Species: 220341 (Salmonella enterica subsp. enterica serovar Typhi str. CT18) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SIDKNFWQGKRVFVTGHTGFKGSWLSLWLTEMGAIVKGYALDAPTVPSLF
EIVRLNDLMESHIGDIRDFEKLRSSIAEFKPEIVFHMAAQPLVRLSYEQP
IKTYSTNVMGTVHLLETVKQVGNIKAVVNITSDKCYDNREWVWGYRENEP
MGGYDPYSNSKGCAELVASAFRNSFFNPANYEQHGVGLASVRAGNVIGGG
DWAKDRLIPDILRSFENNQQVIIRNPYSIRPWQHVLEPLSGYIVVAQRLY
TEGAKFSEGWNFGPRDEDAKTVEFIVDKMVTLWGDDASWLLDPHEAHYLK
LDCSKANMQLGWHPRWGLTETLSRIVKWHKAWIRGEDMLICSKREISDYM
SA
Ligand information
Ligand IDCXY
InChIInChI=1S/C14H23N3O15P2/c15-7-1-2-17(14(23)16-7)12-10(21)9(20)6(30-12)4-29-33(24,25)32-34(26,27)31-13-11(22)8(19)5(18)3-28-13/h1-2,5-6,8-13,18-22H,3-4H2,(H,24,25)(H,26,27)(H2,15,16,23)/t5-,6-,8+,9-,10-,11-,12-,13-/m1/s1
InChIKeyNWSKPSPTJOAICE-OCIMBMBZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C1[C@H]([C@@H]([C@H]([C@H](O1)O[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)N3C=CC(=NC3=O)N)O)O)O)O)O
CACTVS 3.341NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)O[CH]3OC[CH](O)[CH](O)[CH]3O)[CH](O)[CH]2O
CACTVS 3.341NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P@@](O)(=O)O[P@](O)(=O)O[C@H]3OC[C@@H](O)[C@H](O)[C@H]3O)[C@@H](O)[C@H]2O
ACDLabs 10.04O=P(OC1OCC(O)C(O)C1O)(O)OP(=O)(O)OCC3OC(N2C=CC(=NC2=O)N)C(O)C3O
OpenEye OEToolkits 1.5.0C1C(C(C(C(O1)OP(=O)(O)OP(=O)(O)OCC2C(C(C(O2)N3C=CC(=NC3=O)N)O)O)O)O)O
FormulaC14 H23 N3 O15 P2
NameCYTIDINE-5'-DIPHOSPHO-BETA-D-XYLOSE
ChEMBL
DrugBankDB03069
ZINCZINC000016051634
PDB chain1wvg Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB1wvg Structure of CDP-D-glucose 4,6-dehydratase from Salmonella typhi complexed with CDP-D-xylose.
Resolution1.8 Å
Binding residue
(original residue number in PDB)		P93 K136 Y159 N197 D207 R208 L209 D212 I224 R226 N227 S230 R232 E301
Binding residue
(residue number reindexed from 1)		P91 K134 Y157 N195 D205 R206 L207 D210 I222 R224 N225 S228 R230 E295
Annotation score3
Enzymatic activity
Enzyme Commision number 4.2.1.45: CDP-glucose 4,6-dehydratase.
Gene Ontology
Molecular Function
GO:0016829 lyase activity
GO:0047733 CDP-glucose 4,6-dehydratase activity
Biological Process
GO:0009103 lipopolysaccharide biosynthetic process
GO:0009243 O antigen biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:1wvg, PDBe:1wvg, PDBj:1wvg
PDBsum1wvg
PubMed15805590
UniProtP26397|RFBG_SALTY CDP-glucose 4,6-dehydratase (Gene Name=rfbG)

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