Structure of PDB 5j42 Chain B Binding Site BS01

Receptor Information
>5j42 Chain B (length=249) Species: 10090 (Mus musculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
STISFITWNIDGLDGCNLPERARGVCSCLALYSPDVVFLQEVIPPYCAYL
KKRAASYTIITGNEEGYFTAILLKKGRVKFKSQEIIPFPNTKMMRNLLCV
NVSLGGNEFCLMTSHLESTRGHSAERIRQLKTVLGKMQEAPDSTTVIFAG
DTNLRDREVIKCGGLPDNVFDAWEFLGKPKHCQYTWDTKANNNLRIPAAC
KLRFDRIFFRAEEGHLIPQSLDLVGLEKLDCGRFPSDHWGLLCTLNVVL
Ligand information
Ligand ID6FV
InChIInChI=1S/C18H10N4O3/c19-9-10-1-2-11-8-14-16(20-18(25)21-17(14)24)22(15(11)7-10)12-3-5-13(23)6-4-12/h1-8,23H,(H,21,24,25)
InChIKeyJAOMIQIQBBRLQX-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Oc1ccc(cc1)N2c3cc(ccc3C=C4C(=O)NC(=O)N=C24)C#N
OpenEye OEToolkits 2.0.4c1cc(ccc1N2c3cc(ccc3C=C4C2=NC(=O)NC4=O)C#N)O
ACDLabs 12.01N3C(C2=Cc4c(N(c1ccc(cc1)O)C2=NC3=O)cc(cc4)C#N)=O
FormulaC18 H10 N4 O3
Name10-(4-hydroxyphenyl)-2,4-dioxo-2,3,4,10-tetrahydropyrimido[4,5-b]quinoline-8-carbonitrile
ChEMBLCHEMBL2420465
DrugBank
ZINCZINC000096282702
PDB chain5j42 Chain B 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]
PDB5j42 Mode of action of DNA-competitive small molecule inhibitors of tyrosyl DNA phosphodiesterase 2.
Resolution1.7 Å
Binding residue
(original residue number in PDB)		R241 R276 W307 C321 L323
Binding residue
(residue number reindexed from 1)		R120 R155 W186 C200 L202
Annotation score1
Binding affinityBindingDB: IC50=>1.11e+5nM
Enzymatic activity
Enzyme Commision number 3.1.4.-
Gene Ontology
Molecular Function
GO:0003824 catalytic activity

View graph for
Molecular Function
External links
PDB RCSB:5j42, PDBe:5j42, PDBj:5j42
PDBsum5j42
PubMed27099339
UniProtQ9JJX7|TYDP2_MOUSE Tyrosyl-DNA phosphodiesterase 2 (Gene Name=Tdp2)

[Back to BioLiP]