Structure of PDB 7pkm Chain A Binding Site BS02

Receptor Information
>7pkm Chain A (length=297) Species: 208964 (Pseudomonas aeruginosa PAO1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MIKQRTLKNIIRATGVGLHSGEKVYLTLKPAPVDTGIVFSRTDLDPVVEI
PARAENVGETTMSTTLVKGDVKVDTVEHLLSAMAGLGIDNAYVELSASEV
PIMDGSAGPFVFLIQSAGLQEQEAAKKFIRIKREVSVEEGDKRAVFVPFD
GFKVSFEIDFDHPVFRTQQASVDFSSTSFVKEVSRARTFGFMRDIEYLRS
QNLALGGSVENAIVVDENRVLNEDGLRYEDEFVKHKILDAIGDLYLLGNS
LIGEFRGFKSGHALNNQLLRTLIADKDAWEVVTFEDARTAPISYMRP
Ligand information
Ligand ID6G8
InChIInChI=1S/C35H42FN5O4/c1-23-16-25(5-2-24-3-6-26(7-4-24)21-40-12-14-45-15-13-40)8-11-31(23)33(42)38-20-30-18-29(22-41(30)35(44)27-9-10-27)39-34(43)32-17-28(36)19-37-32/h3-4,6-8,11,16,27-30,32,37H,9-10,12-15,17-22H2,1H3,(H,38,42)(H,39,43)/t28-,29+,30+,32-/m0/s1
InChIKeyVANITAVOZBNWHX-TWXNZYBRSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7Cc1cc(ccc1C(=O)NC[C@H]2C[C@H](CN2C(=O)C3CC3)NC(=O)[C@@H]4C[C@@H](CN4)F)C#Cc5ccc(cc5)CN6CCOCC6
OpenEye OEToolkits 2.0.7Cc1cc(ccc1C(=O)NCC2CC(CN2C(=O)C3CC3)NC(=O)C4CC(CN4)F)C#Cc5ccc(cc5)CN6CCOCC6
CACTVS 3.385Cc1cc(ccc1C(=O)NC[C@H]2C[C@H](CN2C(=O)C3CC3)NC(=O)[C@@H]4C[C@H](F)CN4)C#Cc5ccc(CN6CCOCC6)cc5
CACTVS 3.385Cc1cc(ccc1C(=O)NC[CH]2C[CH](CN2C(=O)C3CC3)NC(=O)[CH]4C[CH](F)CN4)C#Cc5ccc(CN6CCOCC6)cc5
FormulaC35 H42 F N5 O4
Name(2S,4S)-N-[(3R,5R)-1-cyclopropylcarbonyl-5-[[[2-methyl-4-[2-[4-(morpholin-4-ylmethyl)phenyl]ethynyl]phenyl]carbonylamino]methyl]pyrrolidin-3-yl]-4-fluoranyl-pyrrolidine-2-carboxamide
ChEMBL
DrugBank
ZINC
PDB chain7pkm Chain A Residue 502 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB7pkm LpxC Inhibitors With Fluoroproline As A Novel Zinc-Binding Group Can Serve As A Novel Class of Antibiotic With Activity Against Multidrug-Resistant Gram-Negative Bacteria
Resolution2.1 Å
Binding residue
(original residue number in PDB)		L18 E77 H78 F160 T190 F191 F193 I197 G209 S210 V216 H237 D241
Binding residue
(residue number reindexed from 1)		L18 E77 H78 F160 T188 F189 F191 I195 G207 S208 V214 H235 D239
Annotation score1
Enzymatic activity
Enzyme Commision number 3.5.1.108: UDP-3-O-acyl-N-acetylglucosamine deacetylase.
Gene Ontology
Molecular Function
GO:0016787 hydrolase activity
GO:0046872 metal ion binding
GO:0103117 UDP-3-O-acyl-N-acetylglucosamine deacetylase activity
Biological Process
GO:0006796 phosphate-containing compound metabolic process
GO:0009245 lipid A biosynthetic process
GO:0019637 organophosphate metabolic process
GO:1901135 carbohydrate derivative metabolic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:7pkm, PDBe:7pkm, PDBj:7pkm
PDBsum7pkm
PubMed
UniProtP47205|LPXC_PSEAE UDP-3-O-acyl-N-acetylglucosamine deacetylase (Gene Name=lpxC)

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