Structure of PDB 5z9e Chain A Binding Site BS01

Receptor Information
>5z9e Chain A (length=185) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LDAVRKRPGMYIGDTDDGTGLHHMVFEVVDNAIDEALAGHCKEIIVTIHA
DNSVSVQDDGRGIPTGIHPEEGVSAAEVIMTVLGVGVSVVNALSQKLELV
IQREGKIHRQIYEHGVPQAPLAVTGETEKTGTMVRFWPSLETFTNVTEFE
YEILAKRLRELSFLNSGVSIRLRDKRDGKEDHFHY
Ligand information
Ligand ID27K
InChIInChI=1S/C11H14O3/c1-2-3-8-14-11(13)9-4-6-10(12)7-5-9/h4-7,12H,2-3,8H2,1H3
InChIKeyQFOHBWFCKVYLES-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6CCCCOC(=O)c1ccc(cc1)O
CACTVS 3.385CCCCOC(=O)c1ccc(O)cc1
ACDLabs 12.01O=C(OCCCC)c1ccc(O)cc1
FormulaC11 H14 O3
Namebutyl 4-hydroxybenzoate
ChEMBLCHEMBL459008
DrugBankDB14084
ZINCZINC000001586769
PDB chain5z9e Chain A Residue 304 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5z9e Identification of an auxiliary druggable pocket in the DNA gyrase ATPase domain using fragment probes
Resolution1.8 Å
Binding residue
(original residue number in PDB)		N46 I78
Binding residue
(residue number reindexed from 1)		N31 I63
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=3.48,IC50=0.33mM
Enzymatic activity
Enzyme Commision number 5.6.2.2: DNA topoisomerase (ATP-hydrolyzing).
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003918 DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity
GO:0005524 ATP binding
Biological Process
GO:0006265 DNA topological change

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Molecular Function
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Biological Process
External links
PDB RCSB:5z9e, PDBe:5z9e, PDBj:5z9e
PDBsum5z9e
PubMed30429968
UniProtP0AES6|GYRB_ECOLI DNA gyrase subunit B (Gene Name=gyrB)

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