Structure of PDB 4zvi Chain A Binding Site BS01

Receptor Information
>4zvi Chain A (length=357) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LDAVRKRPGMYIGDTDDGTGLHHMVFEVVDNAIDEALAGHCKEIIVTIHA
DNSVSVQDDGRGIPTGIHPEEGVSAAEVIMTVLVGVSVVNALSQKLELVI
QRGKIHRQIYEHGVPQAPLAVTGETEKTGTMVRFWPSLETFTNVTEFEYE
ILAKRLRELSFLNSGVSIRLRDKRDGKEDHFHYEGGIKAFVEYLNKNKTP
IHPNIFYFSTEKDGIGVEVALQWNDGFQENIYCFTNNIPQRDGGTHLAGF
RAAMTRTLNAYMDKEGYSKKAKVSATGDDAREGLIAVVSVKVPDPKFSSQ
TKDKLVSSEVKSAVEQQMNELLAEYLLENPTDAKIVVGKIIDAARAREAA
RRAREMT
Ligand information
Ligand ID4S4
InChIInChI=1S/C14H11Br2N3O4/c15-9-5-10(19-12(9)16)14(23)18-8-3-1-7(2-4-8)13(22)17-6-11(20)21/h1-5,19H,6H2,(H,17,22)(H,18,23)(H,20,21)
InChIKeyGVWXWAOQVXYEQC-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01C(=O)(c1nc(c(c1)Br)Br)Nc2ccc(C(=O)NCC(O)=O)cc2
OpenEye OEToolkits 1.9.2c1cc(ccc1C(=O)NCC(=O)O)NC(=O)c2cc(c([nH]2)Br)Br
CACTVS 3.385OC(=O)CNC(=O)c1ccc(NC(=O)c2[nH]c(Br)c(Br)c2)cc1
FormulaC14 H11 Br2 N3 O4
NameN-(4-{[(4,5-dibromo-1H-pyrrol-2-yl)carbonyl]amino}benzoyl)glycine
ChEMBL
DrugBank
ZINCZINC000263620482
PDB chain4zvi Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4zvi N-Phenyl-4,5-dibromopyrrolamides and N-Phenylindolamides as ATP Competitive DNA Gyrase B Inhibitors: Design, Synthesis, and Evaluation.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		N46 E50 D73 R76 P79 V120
Binding residue
(residue number reindexed from 1)		N31 E35 D58 R61 P64 V86
Annotation score1
Binding affinityMOAD: Kd=0.47uM
PDBbind-CN: -logKd/Ki=6.33,Kd=0.47uM
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

View graph for
Molecular Function
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Biological Process
External links
PDB RCSB:4zvi, PDBe:4zvi, PDBj:4zvi
PDBsum4zvi
PubMed26126187
UniProtP0AES7|GYRB_ECO57 DNA gyrase subunit B (Gene Name=gyrB)

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