Structure of PDB 1rfi Chain B Binding Site BS03

Receptor Information

>1rfi Chain B (length=429) Species: 9606 (Homo sapiens)

NPFQFYLTRVSGVKPKYNSGALHIKDILSPLFGTLVSSAQFNYCFDVDWL
VKQYPPEFRKKPILLVHGDKREAKAHLHAQAKPYENISLCQAKLDIAFGT
HHTKMMLLLYEEGLRVVIHTSNLIHADWHQKTQGIWLSPLYPRIADGTHK
SGESPTHFKANLISYLTAYNAPSLKEWIDVIHKHDLSETNVYLIGSTPGR
FQGSQKDNWGHFRLKKLLKDHASSMPNAESWPVVGQFSSVGSLGADESKW
LCSEFKESMLTLGSVPLYLIYPSVENVRTSLEGYPAGGSLPYSIQTAEKQ
NWLHSYFHKWSAETSGRSNAMPHIKTYMRPSPDFSKIAWFLVTSANLSKA
AWGALEKNGTQLMIRSYELGVLFLPSALGLDSFKVKQKFFTFPVPYDLPP
ELYGSKDRPWIWNIPYVKAPDTHGNMWVP

Ligand information

• Ligand ID: VO4
• InChI: InChI=1S/4O.V/q;3*-1;
• InChIKey: LSGOVYNHVSXFFJ-UHFFFAOYSA-N
• SMILES:
  ACDLabs 10.04
  CACTVS 3.341: [O-][V]([O-])([O-])=O
  OpenEye OEToolkits 1.5.0: [O-][V](=O)([O-])[O-]
• Formula: O4 V
• Name: VANADATE ION
• PDB chain: 1rfi Chain B Residue 699

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1rfi Explorations of peptide and oligonucleotide binding sites of tyrosyl-DNA phosphodiesterase using vanadate complexes.
• Resolution: 2.2 Å
• Binding residue (original residue number in PDB): H263 K265 H493 K495
• Binding residue (residue number reindexed from 1): H102 K104 H323 K325
• Annotation score: 1
• Binding affinity: BindingDB: IC50=4000nM

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:1rfi, PDBe:1rfi, PDBj:1rfi
• PDBsum: 1rfi
• PubMed: 14761185
• UniProt: Q9NUW8|TYDP1_HUMAN Tyrosyl-DNA phosphodiesterase 1 (Gene Name=TDP1)