Structure of PDB 1kc3 Chain A Binding Site BS02

Receptor Information
>1kc3 Chain A (length=298) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MNILLFGKTGQVGWELQRSLAPVGNLIALDVHSKEFCGDFSNPKGVAETV
RKLRPDVIVNAAAHTAVDKAESEPELAQLLNATSVEAIAKAANETGAWVV
HYSTDYVFPGTGDIPWQETDATSPLNVYGKTKLAGEKALQDNCPKHLIFR
TSWVYAGKGNNFAKTMLRLAKERQTLSVINDQYGAPTGAELLADCTAHAI
RVALNKPEVAGLYHLVAGGTTTWHDYAALVFDEARKAGITLALTELNAVP
TSAYPTPASRPGNSRLNTEKFQRNFDLILPQWELGVKRMLTEMFTTTT
Ligand information
Ligand IDTRH
InChIInChI=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
InChIKeyZOSQFDVXNQFKBY-CGAXJHMRSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC1C(C(C(C(O1)OP(=O)(O)OP(=O)(O)OCC2C(CC(O2)N3C=C(C(=O)NC3=O)C)O)O)O)O
CACTVS 3.341C[CH]1O[CH](O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH](C[CH]2O)N3C=C(C)C(=O)NC3=O)[CH](O)[CH](O)[CH]1O
CACTVS 3.341C[C@@H]1O[C@H](O[P@@](O)(=O)O[P@](O)(=O)OC[C@H]2O[C@H](C[C@@H]2O)N3C=C(C)C(=O)NC3=O)[C@H](O)[C@H](O)[C@H]1O
ACDLabs 10.04O=P(OC1OC(C(O)C(O)C1O)C)(O)OP(=O)(O)OCC3OC(N2C=C(C(=O)NC2=O)C)CC3O
OpenEye OEToolkits 1.5.0C[C@H]1[C@@H]([C@H]([C@H]([C@H](O1)O[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]2[C@H](C[C@@H](O2)N3C=C(C(=O)NC3=O)C)O)O)O)O
FormulaC16 H26 N2 O15 P2
Name2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE
ChEMBL
DrugBankDB03723
ZINCZINC000008218444
PDB chain1kc3 Chain A Residue 601 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1kc3 Variation on a theme of SDR. dTDP-6-deoxy-L- lyxo-4-hexulose reductase (RmlD) shows a new Mg2+-dependent dimerization mode.
Resolution2.7 Å
Binding residue
(original residue number in PDB)		V67 T104 Y106 Y128 S152 W153 F162 V178 I179 W223 R260
Binding residue
(residue number reindexed from 1)		V67 T104 Y106 Y128 S152 W153 F162 V178 I179 W223 R260
Annotation score4
Enzymatic activity
Enzyme Commision number 1.1.1.133: dTDP-4-dehydrorhamnose reductase.
Gene Ontology
Molecular Function
GO:0008831 dTDP-4-dehydrorhamnose reductase activity
GO:0016491 oxidoreductase activity
GO:0046872 metal ion binding
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:1kc3, PDBe:1kc3, PDBj:1kc3
PDBsum1kc3
PubMed12057193
UniProtP26392|RMLD_SALTY dTDP-4-dehydrorhamnose reductase (Gene Name=rfbD)

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