Structure of PDB 5j3s Chain A Binding Site BS01

Receptor Information
>5j3s Chain A (length=236) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HMFSLITWNIDGLDLNNLSERARGVCSYLALYSPDVIFLQEVIPPYYSYL
KKRSSNYEIITGHEEGYFTAIMLKKSRVKLKSQEIIPFPSTKMMRNLLCV
HVNVSGNELCLMTSHLESTRGHAAERMNQLKMVLKKMQEAVIFAGDTNLR
DREVTRSGGLPNNIVDVWEFLGKPKHCQYTWDTQMNSNLGITAACKLRFD
RIFFRIIPRSLDLLGLEKLDCGRFPSDHWGLLCNLD
Ligand information
Ligand ID6FQ
InChIInChI=1S/C19H10N8O2/c20-9-10-4-5-11-8-14-17(21-19(29)22-18(14)28)27(15(11)6-10)13-3-1-2-12(7-13)16-23-25-26-24-16/h1-8H,(H,22,28,29)(H,23,24,25,26)
InChIKeyNDVGJTJBERLSGL-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.4c1cc(cc(c1)N2c3cc(ccc3C=C4C2=NC(=O)NC4=O)C#N)c5[nH]nnn5
CACTVS 3.385O=C1NC(=O)C2=Cc3ccc(cc3N(c4cccc(c4)c5[nH]nnn5)C2=N1)C#N
ACDLabs 12.01N2C(N=C1N(c3cc(C#N)ccc3C=C1C2=O)c5cc(c4nnnn4)ccc5)=O
FormulaC19 H10 N8 O2
Name2,4-dioxo-10-[3-(1H-tetrazol-5-yl)phenyl]-2,3,4,10-tetrahydropyrimido[4,5-b]quinoline-8-carbonitrile
ChEMBLCHEMBL2420480
DrugBank
ZINCZINC000096282687
PDB chain5j3s Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5j3s Mode of action of DNA-competitive small molecule inhibitors of tyrosyl DNA phosphodiesterase 2.
Resolution3.4 Å
Binding residue
(original residue number in PDB)		R231 R266 I307 C311
Binding residue
(residue number reindexed from 1)		R120 R150 I191 C195
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.72,IC50=19nM
BindingDB: IC50=590nM,EC50=40nM
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:5j3s, PDBe:5j3s, PDBj:5j3s
PDBsum5j3s
PubMed27099339
UniProtO95551|TYDP2_HUMAN Tyrosyl-DNA phosphodiesterase 2 (Gene Name=TDP2)

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