Structure of PDB 1kew Chain B Binding Site BS01

Receptor Information
>1kew Chain B (length=361) Species: 90371 (Salmonella enterica subsp. enterica serovar Typhimurium) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKILITGGAGFIGSAVVRHIIKNTQDTVVNIDKLTYAGNLESLSDISESN
RYNFEHADICDSAEITRIFEQYQPDAVMHLAAESHVDRSITGPAAFIETN
IVGTYALLEVARKYWSALGEDKKNNFRFHHISTDEVYGDLPHPDEVENSV
TLPLFTETTAYAPSSPYSASKASSDHLVRAWRRTYGLPTIVTNCSNNYGP
YHFPEKLIPLVILNALEGKPLPIYGKGDQIRDWLYVEDHARALHMVVTEG
KAGETYNIGGHNEKKNLDVVFTICDLLDEIVPKATSYREQITYVADRPGH
DRRYAIDAGKISRELGWKPLETFESGIRKTVEWYLANTQWVNNVKSGAYQ
SWIEQNYEGRQ
Ligand information
Ligand IDTYD
InChIInChI=1S/C10H16N2O11P2/c1-5-3-12(10(15)11-9(5)14)8-2-6(13)7(22-8)4-21-25(19,20)23-24(16,17)18/h3,6-8,13H,2,4H2,1H3,(H,19,20)(H,11,14,15)(H2,16,17,18)/t6-,7+,8+/m0/s1
InChIKeyUJLXYODCHAELLY-XLPZGREQSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P@](=O)(O)OP(=O)(O)O)O
OpenEye OEToolkits 1.5.0CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)OP(=O)(O)O)O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC2OC(N1C(=O)NC(=O)C(=C1)C)CC2O
CACTVS 3.341CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O
CACTVS 3.341CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P@@](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O
FormulaC10 H16 N2 O11 P2
NameTHYMIDINE-5'-DIPHOSPHATE
ChEMBLCHEMBL259724
DrugBankDB03103
ZINCZINC000008215882
PDB chain1kew Chain B Residue 2700 [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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PDB1kew Toward a structural understanding of the dehydratase mechanism.
Resolution1.8 Å
Binding residue
(original residue number in PDB)		E135 N196 K206 L207 P222 Y224 R231 N266 R297 H300 Y357
Binding residue
(residue number reindexed from 1)		E135 N196 K206 L207 P222 Y224 R231 N266 R297 H300 Y357
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) T133 D134 E135 L152 L154 F155 T158 Y167 K171
Catalytic site (residue number reindexed from 1) T133 D134 E135 L152 L154 F155 T158 Y167 K171
Enzyme Commision number 4.2.1.46: dTDP-glucose 4,6-dehydratase.
Gene Ontology
Molecular Function
GO:0008460 dTDP-glucose 4,6-dehydratase activity
GO:0016829 lyase activity
GO:0070404 NADH binding
Biological Process
GO:0009103 lipopolysaccharide biosynthetic process
GO:0009225 nucleotide-sugar metabolic process
GO:0009243 O antigen biosynthetic process
GO:0019305 dTDP-rhamnose biosynthetic process
GO:0045226 extracellular polysaccharide biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:1kew, PDBe:1kew, PDBj:1kew
PDBsum1kew
PubMed11796113
UniProtP26391|RMLB_SALTY dTDP-glucose 4,6-dehydratase (Gene Name=rfbB)

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