Structure of PDB 4lp0 Chain A Binding Site BS01

Receptor Information
>4lp0 Chain A (length=192) Species: 171101 (Streptococcus pneumoniae R6) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QVLEGLDAVRKRPGMYIGSTDGAGLHHLVWEIVDNAVDEALSGFGDRIDV
TINKDGSLTVQDHGRGMPTGMHAMGIPTVEVIFTILHVGSSVVNALSSWL
EVEITRDGAVYKQRFENGGKPVTTLKKIGTALKSKTGTKVTFMPDATIFS
TTDFKYNTISERLNESAFLLKNVTLSLTDKRTDEAIEFHYEN
Ligand information
Ligand ID1YM
InChIInChI=1S/C18H14F3N5O3S/c1-2-23-17(29)26-14-4-11(15-25-13(8-30-15)18(19,20)21)12(7-24-14)9-3-10(16(27)28)6-22-5-9/h3-8H,2H2,1H3,(H,27,28)(H2,23,24,26,29)
InChIKeyGLNFAHNABSNEAM-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C(O)c3cc(c1cnc(NC(=O)NCC)cc1c2nc(cs2)C(F)(F)F)cnc3
CACTVS 3.385CCNC(=O)Nc1cc(c2scc(n2)C(F)(F)F)c(cn1)c3cncc(c3)C(O)=O
OpenEye OEToolkits 1.7.6CCNC(=O)Nc1cc(c(cn1)c2cc(cnc2)C(=O)O)c3nc(cs3)C(F)(F)F
FormulaC18 H14 F3 N5 O3 S
Name6'-[(ethylcarbamoyl)amino]-4'-[4-(trifluoromethyl)-1,3-thiazol-2-yl]-3,3'-bipyridine-5-carboxylic acid
ChEMBLCHEMBL3235085
DrugBank
ZINCZINC000095921248
PDB chain4lp0 Chain A Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4lp0 Fragment-to-Hit-to-Lead Discovery of a Novel Pyridylurea Scaffold of ATP Competitive Dual Targeting Type II Topoisomerase Inhibiting Antibacterial Agents.
Resolution1.95 Å
Binding residue
(original residue number in PDB)		E55 D78 R81 M83 P84 I98
Binding residue
(residue number reindexed from 1)		E39 D62 R65 M67 P68 I82
Annotation score1
Binding affinityMOAD: ic50<10nM
PDBbind-CN: -logKd/Ki=8.00,IC50<0.01uM
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:4lp0, PDBe:4lp0, PDBj:4lp0
PDBsum4lp0
PubMed24098982
UniProtQ8DQB5

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