Structure of PDB 1kc3 Chain A Binding Site BS01

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 IDNDP
InChIInChI=1S/C21H30N7O17P3/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(44-46(33,34)35)14(30)11(43-21)6-41-48(38,39)45-47(36,37)40-5-10-13(29)15(31)20(42-10)27-3-1-2-9(4-27)18(23)32/h1,3-4,7-8,10-11,13-16,20-21,29-31H,2,5-6H2,(H2,23,32)(H,36,37)(H,38,39)(H2,22,24,25)(H2,33,34,35)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKeyACFIXJIJDZMPPO-NNYOXOHSSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)N5C=CCC(=C5)C(=O)N)O)O)O)OP(=O)(O)O)N
CACTVS 3.341NC(=O)C1=CN(C=CC1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O[P](O)(O)=O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
CACTVS 3.341NC(=O)C1=CN(C=CC1)[C@@H]2O[C@H](CO[P@@](O)(=O)O[P@](O)(=O)OC[C@H]3O[C@H]([C@H](O[P](O)(O)=O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)N5C=CCC(=C5)C(=O)N)O)O)O)OP(=O)(O)O)N
FormulaC21 H30 N7 O17 P3
NameNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
ChEMBLCHEMBL407009
DrugBankDB02338
ZINCZINC000008215411
PDB chain1kc3 Chain A Residue 901 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
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)		G10 Q11 V12 V31 F40 A61 A62 A63 T65 L80 Y102 S103 T104 Y128 K132 T151 V154
Binding residue
(residue number reindexed from 1)		G10 Q11 V12 V31 F40 A61 A62 A63 T65 L80 Y102 S103 T104 Y128 K132 T151 V154
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

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

[Back to BioLiP]