Structure of PDB 6n17 Chain A Binding Site BS01

Receptor Information
>6n17 Chain A (length=438) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NPFQFYLTRVSGVKPKYNSGALHIKDILSPLFGTLVSSAQFNYCFDVDWL
VKQYPPEFRKKPILLVHGDKREAKAHLHAQAKPYENISLCQAKLDIAFGT
HHTKMMLLLYEEGLRVVIHTSNLIHADWHQKTQGIWLSPLYPRIADGTHK
SGESPTHFKADLISYLMAYNAPSLKEWIDVIHKHDLSETNVYLIGSTPGR
FQGSQKDNWGHFRLKKLLKDHASSMPNAESWPVVGQFSSVGSLGADESKW
LCSEFKESMLTLGKESSSVPLYLIYPSVENVRTSLEGYPAGGSLPYSIQT
AEKQNWLHSYFHKWSAETSGRSNAMPHIKTYMRPSPDFSKIAWFLVTSAN
LSKAAWGALEKNGTQLMIRSYELGVLFLPSAFGLDSFKVKQKFFAGPMAT
FPVPYDLPPELYGSKDRPWIWNIPYVKAPDTHGNMWVP
Ligand information
Ligand IDK8Y
InChIInChI=1S/C12H11NO7/c14-9(3-4-10(15)16)13-6-1-2-7(11(17)18)8(5-6)12(19)20/h1-2,5H,3-4H2,(H,13,14)(H,15,16)(H,17,18)(H,19,20)
InChIKeyJVZSGTXFIVTSIN-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385OC(=O)CCC(=O)Nc1ccc(C(O)=O)c(c1)C(O)=O
ACDLabs 12.01c1c(cc(C(O)=O)c(C(O)=O)c1)NC(CCC(O)=O)=O
OpenEye OEToolkits 2.0.6c1cc(c(cc1NC(=O)CCC(=O)O)C(=O)O)C(=O)O
FormulaC12 H11 N O7
Name4-[(3-carboxypropanoyl)amino]benzene-1,2-dicarboxylic acid
ChEMBL
DrugBank
ZINC
PDB chain6n17 Chain A Residue 701 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6n17 Identification of a ligand binding hot spot and structural motifs replicating aspects of tyrosyl-DNA phosphodiesterase I (TDP1) phosphoryl recognition by crystallographic fragment cocktail screening.
Resolution1.639 Å
Binding residue
(original residue number in PDB)
Y204 H263 K265 N283 S399 S400 P461 H493 K495 N516
Binding residue
(residue number reindexed from 1)
Y43 H102 K104 N122 S238 S239 P295 H327 K329 N350
Annotation score1
Binding affinityMOAD: ic50=1.01mM
PDBbind-CN: -logKd/Ki=3.00,IC50=1.01mM
Enzymatic activity
Enzyme Commision number 3.1.4.-
Gene Ontology
Molecular Function
GO:0008081 phosphoric diester hydrolase activity
Biological Process
GO:0006281 DNA repair
Cellular Component
GO:0005634 nucleus

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Molecular Function

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Biological Process

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Cellular Component
External links
PDB RCSB:6n17, PDBe:6n17, PDBj:6n17
PDBsum6n17
PubMed31199869
UniProtQ9NUW8|TYDP1_HUMAN Tyrosyl-DNA phosphodiesterase 1 (Gene Name=TDP1)

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