Structure of PDB 1nop Chain B Binding Site BS02

Receptor Information
>1nop Chain B (length=433) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DKGNPFQFYLTRVSGVKPKYNSGALHIKDILSPLFGTLVSSAQFNYCFDV
DWLVKQYPPEFRKKPILLVHGDKREAKAHLHAQAKPYENISLCQAKLDIA
FGTHHTKMMLLLYEEGLRVVIHTSNLIHADWHQKTQGIWLSPLYPRIADG
THKSGESPTHFKANLISYLTAYNAPSLKEWIDVIHKHDLSETNVYLIGST
PGRFQGSQKDNWGHFRLKKLLKDHASSMPNAESWPVVGQFSSVGSLGADE
SKWLCSEFKESMLTLGSVPLYLIYPSVENVRTSLEGYPAGGSLPYSIQTA
EKQNWLHSYFHKWSAETSGRSNAMPHIKTYMRPSPDFSKIAWFLVTSANL
SKAAWGALEKNGTQLMIRSYELGVLFLPSALGLDSFKVKQKFMATFPVPY
DLPPELYGSKDRPWIWNIPYVKAPDTHGNMWVP
Ligand information
Ligand IDVO4
InChIInChI=1S/4O.V/q;3*-1;
InChIKeyLSGOVYNHVSXFFJ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04
CACTVS 3.341		[O-][V]([O-])([O-])=O
OpenEye OEToolkits 1.5.0[O-][V](=O)([O-])[O-]
FormulaO4 V
NameVANADATE ION
ChEMBL
DrugBank
ZINC
PDB chain1nop Chain B Residue 699 [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]
PDB1nop Crystal structure of a transition state mimic for Tdp1 assembled from vanadate, DNA, and a topoisomerase I-derived peptide
Resolution2.3 Å
Binding residue
(original residue number in PDB)		H263 K265 H493 K495
Binding residue
(residue number reindexed from 1)		H105 K107 H326 K328
Annotation score1
Binding affinityBindingDB: 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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:1nop, PDBe:1nop, PDBj:1nop
PDBsum1nop
PubMed12618186
UniProtQ9NUW8|TYDP1_HUMAN Tyrosyl-DNA phosphodiesterase 1 (Gene Name=TDP1)

[Back to BioLiP]