Structure of PDB 4kpz Chain A Binding Site BS01

Receptor Information
>4kpz Chain A (length=450) Species: 727 (Haemophilus influenzae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KALSAVILAAGKGTRMYSDLPKVLHTIAGKPMVKHVIDTAHQLGSENIHL
IYGHGGDLMRTHLANEQVNWVLQTEQLGTAHAVQQAAPFFKDNENIVVLY
GDAPLITKETLEKLIEAKPENGIALLTVNLDNPTGYGRIIRENGNVVAIV
EQKDANAEQLNIKEVNTGVMVSDGASFKKWLARVGNNNAQGEYYLTDLIA
LANQDNCQVVAVQATDVMEVEGANNRLQLAALERYFQNKQASKLLLEGVM
IYDPARFDLRGTLEHGKDVEIDVNVIIEGNVKLGDRVKIGTGCVLKNVVI
GNDVEIKPYSVLEDSIVGEKAAIGPFSRLRPGAELAAETHVGNFVEIKKS
TVGKGSKVNHLTYVGDSEIGSNCNIGAGVITCNYDGANKFKTIIGDDVFV
GSDTQLVAPVKVANGATIGAGTTITRDVGENELVITRVAQRHIQGWQRPI
Ligand information
Ligand ID1SF
InChIInChI=1S/C10H9N3O4/c14-9-4-5-12(10(15)11-9)7-2-1-3-8(6-7)13(16)17/h1-3,6H,4-5H2,(H,11,14,15)
InChIKeyGMUGBPYYXAGNCT-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.370[O-][N+](=O)c1cccc(c1)N2CCC(=O)NC2=O
ACDLabs 12.01[O-][N+](=O)c1cc(ccc1)N2C(=O)NC(=O)CC2
OpenEye OEToolkits 1.7.6c1cc(cc(c1)[N+](=O)[O-])N2CCC(=O)NC2=O
FormulaC10 H9 N3 O4
Name1-(3-nitrophenyl)dihydropyrimidine-2,4(1H,3H)-dione
ChEMBL
DrugBank
ZINCZINC000212413206
PDB chain4kpz Chain A Residue 501 [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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PDB4kpz Rational design of inhibitors of the bacterial cell wall synthetic enzyme GlmU using virtual screening and lead-hopping.
Resolution2.09 Å
Binding residue
(original residue number in PDB)		L11 A12 A13 G14 V26 Q76 Q79 G81 D105
Binding residue
(residue number reindexed from 1)		L8 A9 A10 G11 V23 Q73 Q76 G78 D102
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=2.71,IC50=1950uM
Enzymatic activity
Catalytic site (original residue number in PDB) R18
Catalytic site (residue number reindexed from 1) R15
Enzyme Commision number 2.3.1.157: glucosamine-1-phosphate N-acetyltransferase.
2.7.7.23: UDP-N-acetylglucosamine diphosphorylase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0003977 UDP-N-acetylglucosamine diphosphorylase activity
GO:0016740 transferase activity
GO:0016746 acyltransferase activity
GO:0016779 nucleotidyltransferase activity
GO:0019134 glucosamine-1-phosphate N-acetyltransferase activity
GO:0046872 metal ion binding
Biological Process
GO:0000902 cell morphogenesis
GO:0006048 UDP-N-acetylglucosamine biosynthetic process
GO:0008360 regulation of cell shape
GO:0009245 lipid A biosynthetic process
GO:0009252 peptidoglycan biosynthetic process
GO:0071555 cell wall organization
Cellular Component
GO:0005737 cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4kpz, PDBe:4kpz, PDBj:4kpz
PDBsum4kpz
PubMed25262942
UniProtP43889|GLMU_HAEIN Bifunctional protein GlmU (Gene Name=glmU)

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