Structure of PDB 3raf Chain D Binding Site BS04

Receptor Information
>3raf Chain D (length=210) Species: 1313 (Streptococcus pneumoniae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KLTPAQSKNPAKNELYLVEGDSAGGSAKQGRDRKFQAILPLRGKVINTAK
AKMADILKNEEINTMIYTIGAGVGADFSIEDANYDKIIIMTDADTDGAHI
QTLLLTFFYRYMRPLVEAGHVYIALPPLYKMAYAWTDGELEELRKQLQRY
KGLGEMNADQLWETTMNPETRTLIRVTIEDLARAERRVNVLMGDKVEPRR
KWIEDNVKFT
Ligand information
Ligand IDPDQ
InChIInChI=1S/C18H24FN5O2/c1-9-15-13(17(25)24(21)18(26)23(15)12-3-4-12)7-14(19)16(9)22-6-5-11(8-22)10(2)20/h7,10-12H,3-6,8,20-21H2,1-2H3/t10-,11+/m0/s1
InChIKeySMONLCFJGCJROJ-WDEREUQCSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0Cc1c2c(cc(c1N3CC[C@H](C3)[C@H](C)N)F)C(=O)N(C(=O)N2C4CC4)N
ACDLabs 12.01O=C2c1cc(F)c(c(c1N(C(=O)N2N)C3CC3)C)N4CCC(C(N)C)C4
CACTVS 3.370C[CH](N)[CH]1CCN(C1)c2c(C)c3N(C4CC4)C(=O)N(N)C(=O)c3cc2F
CACTVS 3.370C[C@H](N)[C@@H]1CCN(C1)c2c(C)c3N(C4CC4)C(=O)N(N)C(=O)c3cc2F
OpenEye OEToolkits 1.7.0Cc1c2c(cc(c1N3CCC(C3)C(C)N)F)C(=O)N(C(=O)N2C4CC4)N
FormulaC18 H24 F N5 O2
Name3-amino-7-{(3R)-3-[(1S)-1-aminoethyl]pyrrolidin-1-yl}-1-cyclopropyl-6-fluoro-8-methylquinazoline-2,4(1H,3H)-dione
ChEMBLCHEMBL383917
DrugBank
ZINC
PDB chain3raf Chain H Residue 0 [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]
PDB3raf Inhibitor-stabilised cleavage complexes of topoisomerase IIa: structural analysis of drug-dependent inter- and intramolecular interactions
Resolution3.24 Å
Binding residue
(original residue number in PDB)		R456 E475
Binding residue
(residue number reindexed from 1)		R42 E61
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

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3raf, PDBe:3raf, PDBj:3raf
PDBsum3raf
PubMed
UniProtQ59961|PARE_STRPN DNA topoisomerase 4 subunit B (Gene Name=parE)

[Back to BioLiP]