Structure of PDB 6dih Chain B Binding Site BS01

Receptor Information

>6dih Chain B (length=438) Species: 9606 (Homo sapiens)

NPFQFYLTRVSGVKPKYNSGALHIKDILSPLFGTLVSSAQFNYCFDVDWL
VKQYPPEFRKKPILLVHGDKREAKAHLHAQAKPYENISLCQAKLDIAFGT
HHTKMMLLLYEEGLRVVIHTSNLIHADWHQKTQGIWLSPLYPRIADGTHK
SGESPTHFKADLISYLMAYNAPSLKEWIDVIHKHDLSETNVYLIGSTPGR
FQGSQKDNWGHFRLKKLLKDHASSMPNAESWPVVGQFSSVGSLGADESKW
LCSEFKESMLTLGKESSSVPLYLIYPSVENVRTSLEGYPAGGSLPYSIQT
AEKQNWLHSYFHKWSAETSGRSNAMPHIKTYMRPSPDFSKIAWFLVTSAN
LSKAAWGALEKNGTQLMIRSYELGVLFLPSAFGLDSFKVKQKFFAGPMAT
FPVPYDLPPELYGSKDRPWIWNIPYVKAPDTHGNMWVP

Ligand information

• Ligand ID: GJS
• InChI: InChI=1S/C8H6O5/c9-4-1-2-5(7(10)11)6(3-4)8(12)13/h1-3,9H,(H,10,11)(H,12,13)
• InChIKey: MWRVRCAFWBBXTL-UHFFFAOYSA-N
• SMILES:
  OpenEye OEToolkits 2.0.6: c1cc(c(cc1O)C(=O)O)C(=O)O
  ACDLabs 12.01: c1(C(O)=O)c(C(O)=O)ccc(c1)O
  CACTVS 3.385: OC(=O)c1ccc(O)cc1C(O)=O
• Formula: C8 H6 O5
• Name: 4-hydroxybenzene-1,2-dicarboxylic acid
• ZINC: ZINC000000226728
• PDB chain: 6dih Chain B Residue 701

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6dih 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.
• Resolution: 1.78 Å
• Binding residue (original residue number in PDB): Y204 H263 K265 S399 P461 H493 K495 N516
• Binding residue (residue number reindexed from 1): Y43 H102 K104 S238 P295 H327 K329 N350
• Annotation score: 1
• Binding affinity: MOAD: ic50=1.9mM

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

External links

• PDB: RCSB:6dih, PDBe:6dih, PDBj:6dih
• PDBsum: 6dih
• PubMed: 31199869
• UniProt: Q9NUW8|TYDP1_HUMAN Tyrosyl-DNA phosphodiesterase 1 (Gene Name=TDP1)