Structure of PDB 6djf Chain A Binding Site BS01

Receptor Information
>6djf 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 IDGNV
InChIInChI=1S/C11H7NO5/c13-9-5-2-1-3-6(10(14)15)8(5)12-4-7(9)11(16)17/h1-4H,(H,12,13)(H,14,15)(H,16,17)
InChIKeyYYLVBIBWUBXXRA-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6c1cc2c(c(c1)C(=O)O)ncc(c2O)C(=O)O
CACTVS 3.385OC(=O)c1cccc2c(O)c(cnc12)C(O)=O
ACDLabs 12.01c2cc(c1c(c(c(C(O)=O)cn1)O)c2)C(O)=O
FormulaC11 H7 N O5
Name4-hydroxyquinoline-3,8-dicarboxylic acid
ChEMBLCHEMBL386243
DrugBank
ZINCZINC000000117354
PDB chain6djf Chain A Residue 702 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6djf 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.
Resolution1.67 Å
Binding residue
(original residue number in PDB)		Y204 H263 K265 N283 S459 P461 H493 W590
Binding residue
(residue number reindexed from 1)		Y43 H102 K104 N122 S293 P295 H327 W421
Annotation score1
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:6djf, PDBe:6djf, PDBj:6djf
PDBsum6djf
PubMed31199869
UniProtQ9NUW8|TYDP1_HUMAN Tyrosyl-DNA phosphodiesterase 1 (Gene Name=TDP1)

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