Structure of PDB 6pib Chain A Binding Site BS03

Receptor Information
>6pib Chain A (length=245) Species: 573 (Klebsiella pneumoniae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VATLFIADLHLQTEEPAITAGFLRFLQGEARQADALYILGDLFEAWIGDD
DPNPLHQQIASAIKAVVDAGVPCYFIHGNRDFLVGQRFARQSGMILLAEE
ERLDLYGREVLIMHGDTLCTDDQGYLAFRAKVHTPWIQRLFLALPLFIRH
RIAARMRADSKAANSSKSMEIMDVNPQAVVDAMERHHVQWLIHGHTHRPA
VHELQANGQPAWRVVLGAWHSEGSMVKVTPDDVELIHFPFLLYFQ
Ligand information
Ligand IDOKV
InChIInChI=1S/C21H22F3N3O3S/c1-15(28)27-8-7-16-13-19(5-6-20(16)27)31(29,30)26-11-9-25(10-12-26)18-4-2-3-17(14-18)21(22,23)24/h2-6,13-14H,7-12H2,1H3
InChIKeyJRTCXCIMCOKGMN-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CC(=O)N1CCc2cc(ccc12)[S](=O)(=O)N3CCN(CC3)c4cccc(c4)C(F)(F)F
ACDLabs 12.01c2cc1N(C(=O)C)CCc1cc2S(N4CCN(c3cc(ccc3)C(F)(F)F)CC4)(=O)=O
OpenEye OEToolkits 2.0.7CC(=O)N1CCc2c1ccc(c2)S(=O)(=O)N3CCN(CC3)c4cccc(c4)C(F)(F)F
FormulaC21 H22 F3 N3 O3 S
Name1-[5-({4-[3-(trifluoromethyl)phenyl]piperazin-1-yl}sulfonyl)-2,3-dihydro-1H-indol-1-yl]ethan-1-one
ChEMBL
DrugBank
ZINCZINC000020181932
PDB chain6pib Chain A Residue 303 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6pib Structural basis of the UDP-diacylglucosamine pyrophosphohydrolase LpxH inhibition by sulfonyl piperazine antibiotics.
Resolution2.26 Å
Binding residue
(original residue number in PDB)		A45 W46 N79 R80 F82 Y125 F128 I137 F141 A153 M156 R157 S160
Binding residue
(residue number reindexed from 1)		A45 W46 N79 R80 F82 Y125 F128 I137 F141 A153 M156 R157 S160
Annotation score1
Binding affinityMOAD: ic50=0.36uM
Enzymatic activity
Enzyme Commision number 3.6.1.54: UDP-2,3-diacylglucosamine diphosphatase.
Gene Ontology
Molecular Function
GO:0008758 UDP-2,3-diacylglucosamine hydrolase activity
GO:0016462 pyrophosphatase activity
GO:0016787 hydrolase activity
GO:0030145 manganese ion binding
GO:0046872 metal ion binding
Biological Process
GO:0009245 lipid A biosynthetic process
Cellular Component
GO:0005737 cytoplasm
GO:0005886 plasma membrane
GO:0019897 extrinsic component of plasma membrane

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6pib, PDBe:6pib, PDBj:6pib
PDBsum6pib
PubMed32041866
UniProtA6T5R0|LPXH_KLEP7 UDP-2,3-diacylglucosamine hydrolase (Gene Name=lpxH)

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