Structure of PDB 6djd Chain B Binding Site BS01

Receptor Information
>6djd Chain B (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 IDGJP
InChIInChI=1S/C10H7NO3/c12-9-6-3-1-2-4-8(6)11-5-7(9)10(13)14/h1-5H,(H,11,12)(H,13,14)
InChIKeyILNJBIQQAIIMEY-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01c12ccccc1c(c(cn2)C(O)=O)O
OpenEye OEToolkits 2.0.6c1ccc2c(c1)c(c(cn2)C(=O)O)O
CACTVS 3.385OC(=O)c1cnc2ccccc2c1O
FormulaC10 H7 N O3
Name4-hydroxyquinoline-3-carboxylic acid
ChEMBLCHEMBL158890
DrugBank
ZINCZINC000008602789
PDB chain6djd Chain B Residue 701 [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]
PDB6djd 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.
Resolution1.777 Å
Binding residue
(original residue number in PDB)		Y204 H263 K265 N283 P461 H493 W590
Binding residue
(residue number reindexed from 1)		Y43 H102 K104 N122 P295 H327 W421
Annotation score1
Binding affinityMOAD: ic50=7.2mM
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6djd, PDBe:6djd, PDBj:6djd
PDBsum6djd
PubMed31199869
UniProtQ9NUW8|TYDP1_HUMAN Tyrosyl-DNA phosphodiesterase 1 (Gene Name=TDP1)

[Back to BioLiP]