Structure of PDB 1dzt Chain B Binding Site BS02

Receptor Information
>1dzt Chain B (length=183) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MMIVIKTAIPDVLILEPKVFGDERGFFFESYNQQTFEELIGRKVTFVQDN
HSKSKKNVLRGLHFQRGENAQGKLVRCAVGEVFDVAVDIRKESPTFGQWV
GVNLSAENKRQLWIPEGFAHGFVTLSEYAEFLYKATNYYSPSSEGSILWN
DEAIGIEWPFSQLPELSAKDAAAPLLDQALLTE
Ligand information
Ligand IDATY
InChIInChI=1S/C12H18N2O12P2/c1-6-4-14(12(17)13-11(6)16)10-3-8(24-7(2)15)9(25-10)5-23-28(21,22)26-27(18,19)20/h4,8-10H,3,5H2,1-2H3,(H,21,22)(H,13,16,17)(H2,18,19,20)/t8-,9+,10+/m0/s1
InChIKeyUWSIAAWKEICIJY-IVZWLZJFSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CC(=O)O[CH]1C[CH](O[CH]1CO[P](O)(=O)O[P](O)(O)=O)N2C=C(C)C(=O)NC2=O
OpenEye OEToolkits 1.5.0CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)OP(=O)(O)O)OC(=O)C
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC2OC(N1C(=O)NC(=O)C(=C1)C)CC2OC(=O)C
CACTVS 3.341CC(=O)O[C@H]1C[C@@H](O[C@@H]1CO[P@](O)(=O)O[P](O)(O)=O)N2C=C(C)C(=O)NC2=O
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)OC(=O)C
FormulaC12 H18 N2 O12 P2
Name3'-O-ACETYLTHYMIDINE-5'-DIPHOSPHATE
ChEMBL
DrugBankDB02549
ZINCZINC000012502259
PDB chain1dzt Chain B Residue 1000 [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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PDB1dzt Rmlc, the Third Enzyme of Dtdp-L-Rhamnose Pathway, is a New Class of Epimerase.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		Q48 H63 Y133 Y139 K169
Binding residue
(residue number reindexed from 1)		Q48 H63 Y133 Y139 K169
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) H63 K73 Y133 D170
Catalytic site (residue number reindexed from 1) H63 K73 Y133 D170
Enzyme Commision number 5.1.3.13: dTDP-4-dehydrorhamnose 3,5-epimerase.
Gene Ontology
Molecular Function
GO:0008830 dTDP-4-dehydrorhamnose 3,5-epimerase activity
GO:0016853 isomerase activity
Biological Process
GO:0009103 lipopolysaccharide biosynthetic process
GO:0009243 O antigen biosynthetic process
GO:0019305 dTDP-rhamnose biosynthetic process
GO:0045226 extracellular polysaccharide biosynthetic process
Cellular Component
GO:0005829 cytosol

View graph for
Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:1dzt, PDBe:1dzt, PDBj:1dzt
PDBsum1dzt
PubMed10802738
UniProtP26394|RMLC_SALTY dTDP-4-dehydrorhamnose 3,5-epimerase (Gene Name=rfbC)

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