Structure of PDB 3foe Chain B Binding Site BS02

Receptor Information
>3foe Chain B (length=433) Species: 1313 (Streptococcus pneumoniae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QNMSLEDIMGERFGRYSKYIIQDRALPDIRDGLKPVQRRILYSMNKDSNT
FDKSYRKSAKSVGNIMGNFHPHGDSSIYDAMVRMSQNWKNREILVEMHGN
NGSMDGDPPAAMRYTEARLSEIAGYLLQDIEKKTVPFAWNFDDTEKEPTV
LPAAFPNLLVNTDIPPHNLAEVIDAAVYMIDHPTAKIDKLMEFLPGPDFP
TIIQGRDEIKKAYETGKGRVVVRSEIEKLKGGKEQIVITEINKANLVKKI
DDVRVNNKVIELNTELVLNYLFKYTDLQINFNMVAIDNFTPRQVGIVPIL
SSYIAHRREVILARSRFDKEKAEKRLHIVEGLIRVISILDEVIALIRASE
NKADAKENLKVSYDFTEEQAEAIVTLQLYRLTNTDVVVLQEEEAELREKI
AMLAAIIGDERTMYNLMKKELREVKKKFATPRL
Ligand information
Ligand IDNFX
InChIInChI=1S/C17H17ClFN3O3/c18-13-14-10(5-12(19)15(13)21-4-3-8(20)6-21)16(23)11(17(24)25)7-22(14)9-1-2-9/h5,7-9H,1-4,6,20H2,(H,24,25)/t8-/m1/s1
InChIKeyQGPKADBNRMWEQR-MRVPVSSYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341N[C@@H]1CCN(C1)c2c(F)cc3C(=O)C(=CN(C4CC4)c3c2Cl)C(O)=O
OpenEye OEToolkits 1.5.0c1c2c(c(c(c1F)N3CCC(C3)N)Cl)N(C=C(C2=O)C(=O)O)C4CC4
ACDLabs 10.04Fc2c(c(Cl)c1N(C=C(C(=O)O)C(=O)c1c2)C3CC3)N4CCC(N)C4
CACTVS 3.341N[CH]1CCN(C1)c2c(F)cc3C(=O)C(=CN(C4CC4)c3c2Cl)C(O)=O
OpenEye OEToolkits 1.5.0c1c2c(c(c(c1F)N3CC[C@H](C3)N)Cl)N(C=C(C2=O)C(=O)O)C4CC4
FormulaC17 H17 Cl F N3 O3
Name7-[(3R)-3-aminopyrrolidin-1-yl]-8-chloro-1-cyclopropyl-6-fluoro-4-oxo-1,4-dihydroquinoline-3-carboxylic acid;
Clinafloxacin
ChEMBLCHEMBL113334
DrugBank
ZINCZINC000001278767
PDB chain3foe Chain F Residue 0 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3foe Structural insight into the quinolone-DNA cleavage complex of type IIA topoisomerases
Resolution4.001 Å
Binding residue
(original residue number in PDB)		G77 S79
Binding residue
(residue number reindexed from 1)		G73 S75
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:0006259 DNA metabolic process
GO:0006265 DNA topological change
Cellular Component
GO:0005694 chromosome

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3foe, PDBe:3foe, PDBj:3foe
PDBsum3foe
PubMed19448616
UniProtP72525|PARC_STRPN DNA topoisomerase 4 subunit A (Gene Name=parC)

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