Structure of PDB 5z4h Chain A Binding Site BS01

Receptor Information
>5z4h Chain A (length=186) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LDAVRKRPGMYIGDTDDGTGLHHMVFEVVDNAIDEALAGHCKEIIVTIHA
DNSVSVQDDGRGIPTGIHPEEGVSAAEVIMTVLHGVGVSVVNALSQKLEL
VIQREGKIHRQIYEHGVPQAPLAVTGETEKTGTMVRFWPSLETFTNVTEF
EYEILAKRLRELSFLNSGVSIRLRDKRDGKEDHFHY
Ligand information
Ligand IDA8K
InChIInChI=1S/C12H10O2S/c13-9-1-5-11(6-2-9)15-12-7-3-10(14)4-8-12/h1-8,13-14H
InChIKeyVWGKEVWFBOUAND-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Oc1ccc(Sc2ccc(O)cc2)cc1
OpenEye OEToolkits 2.0.6c1cc(ccc1O)Sc2ccc(cc2)O
FormulaC12 H10 O2 S
Name4-(4-hydroxyphenyl)sulfanylphenol
ChEMBLCHEMBL3183502
DrugBank
ZINCZINC000000136154
PDB chain5z4h 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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PDB5z4h Identification of an auxiliary druggable pocket in the DNA gyrase ATPase domain using fragment probes
Resolution2.0 Å
Binding residue
(original residue number in PDB)		N46 A47 Q72 D73 I78 A91 I94 M95 T165 V167
Binding residue
(residue number reindexed from 1)		N31 A32 Q57 D58 I63 A76 I79 M80 T133 V135
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=3.02,IC50=0.95mM
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:5z4h, PDBe:5z4h, PDBj:5z4h
PDBsum5z4h
PubMed30429968
UniProtP0AES6|GYRB_ECOLI DNA gyrase subunit B (Gene Name=gyrB)

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