Structure of PDB 3fv5 Chain A Binding Site BS01

Receptor Information
>3fv5 Chain A (length=180) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GLEPVRRRPGMYTDTTRPNHLGQEVIDNSVDEALAGHAKRVDVILHADQS
LEVIDDGRGMPVDIHPEEGVPAVELILCRLISVVNALSKRVEVNVRRDGQ
VYNIAFENGEKVQDLQVVGTCGKRNTGTSVHFWPDETFFDSPRFSVSRLT
HVLKAKAVLCPGVEITFKDEINNTEQRWCY
Ligand information
Ligand ID1EU
InChIInChI=1S/C17H17N5O2/c1-3-19-17(24)22-16-20-14-8-12(11-5-4-6-18-9-11)7-13(10(2)23)15(14)21-16/h4-9H,3H2,1-2H3,(H3,19,20,21,22,24)
InChIKeyKDHATIBQZJAMKQ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CCNC(=O)Nc1[nH]c2cc(cc(c2n1)C(=O)C)c3cccnc3
CACTVS 3.341CCNC(=O)Nc1[nH]c2cc(cc(C(C)=O)c2n1)c3cccnc3
ACDLabs 10.04O=C(c2cc(cc1c2nc(n1)NC(=O)NCC)c3cccnc3)C
FormulaC17 H17 N5 O2
Name1-(4-acetyl-6-pyridin-3-yl-1H-benzimidazol-2-yl)-3-ethylurea
ChEMBL
DrugBank
ZINCZINC000058631644
PDB chain3fv5 Chain A Residue 2 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3fv5 Design and syntheses of novel C7-derived-aminobenzimidazole ureas: bacterial gyrase/topoisomerase IV inhibitors with potent Gram-positve antibacterial activity
Resolution1.8 Å
Binding residue
(original residue number in PDB)		V39 S43 E46 V67 D69 R72 G73 M74 P75 R132 T163 V165
Binding residue
(residue number reindexed from 1)		V25 S29 E32 V53 D55 R58 G59 M60 P61 R97 T128 V130
Annotation score1
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
Cellular Component
GO:0005694 chromosome

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Cellular Component
External links
PDB RCSB:3fv5, PDBe:3fv5, PDBj:3fv5
PDBsum3fv5
PubMed
UniProtP20083|PARE_ECOLI DNA topoisomerase 4 subunit B (Gene Name=parE)

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