Structure of PDB 5l3j Chain A Binding Site BS01

Receptor Information
>5l3j Chain A (length=360) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GLDAVRKRPGMYIGDTDDGTGLHHMVFEVVDNAIDEALAGHCKEIIVTIH
ADNSVSVQDDGRGIPTGIHPEEGVSAAEVIMTVLHVGVSVVNALSQKLEL
VIQREGKIHRQIYEHGVPQAPLAVTGETEKTGTMVRFWPSLETFTNVTEF
EYEILAKRLRELSFLNSGVSIRLRDKRDGKEDHFHYEGGIKAFVEYLNKN
KTPIHPNIFYFSTEKDGIGVEVALQWNDGFQENIYCFTNNIPQRDGGTHL
AGFRAAMTRTLNAYMDKEGYSKKAKVSATGDDAREGLIAVVSVKVPDPKF
SSQTKDKLVSSEVKSAVEQQMNELLAEYLLENPTDAKIVVGKIIDAARAR
EAARRAREMT
Ligand information
Ligand ID6G9
InChIInChI=1S/C14H8Br2N4O4S/c15-6-4-8(18-10(6)16)11(21)20-14-19-7-2-1-5(3-9(7)25-14)17-12(22)13(23)24/h1-4,18H,(H,17,22)(H,23,24)(H,19,20,21)
InChIKeyZDVZBRWEKLWNNU-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.5c1cc2c(cc1NC(=O)C(=O)O)sc(n2)NC(=O)c3cc(c([nH]3)Br)Br
CACTVS 3.385OC(=O)C(=O)Nc1ccc2nc(NC(=O)c3[nH]c(Br)c(Br)c3)sc2c1
FormulaC14 H8 Br2 N4 O4 S
Name2-[[2-[[4,5-bis(bromanyl)-1~{H}-pyrrol-2-yl]carbonylamino]-1,3-benzothiazol-6-yl]amino]-2-oxidanylidene-ethanoic acid
ChEMBLCHEMBL3908487
DrugBank
ZINCZINC000584904990
PDB chain5l3j Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB5l3j Discovery of Benzothiazole Scaffold-Based DNA Gyrase B Inhibitors.
Resolution2.83 Å
Binding residue
(original residue number in PDB)		V43 N46 E50 V71 D73 R76 G77 I78 P79 V120 T165
Binding residue
(residue number reindexed from 1)		V29 N32 E36 V57 D59 R62 G63 I64 P65 V88 T133
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.64,Kd=0.23uM
BindingDB: IC50=58nM,Kd=230nM
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
View graph for
Biological Process
External links
PDB RCSB:5l3j, PDBe:5l3j, PDBj:5l3j
PDBsum5l3j
PubMed27541007
UniProtP0AES6|GYRB_ECOLI DNA gyrase subunit B (Gene Name=gyrB)

[Back to BioLiP]