Structure of PDB 1rgt Chain B Binding Site BS02

Receptor Information
>1rgt Chain B (length=429) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NPFQFYLTRVSGVKPKYNSGALHIKDILSPLFGTLVSSAQFNYCFDVDWL
VKQYPPEFRKKPILLVHGDKREAKAHLHAQAKPYENISLCQAKLDIAFGT
HHTKMMLLLYEEGLRVVIHTSNLIHADWHQKTQGIWLSPLYPRIADGTHK
SGESPTHFKANLISYLTAYNAPSLKEWIDVIHKHDLSETNVYLIGSTPGR
FQGSQKDNWGHFRLKKLLKDHASSMPNAESWPVVGQFSSVGSLGADESKW
LCSEFKESMLTLGSVPLYLIYPSVENVRTSLEGYPAGGSLPYSIQTAEKQ
NWLHSYFHKWSAETSGRSNAMPHIKTYMRPSPDFSKIAWFLVTSANLSKA
AWGALEKNGTQLMIRSYELGVLFLPSALGLDSFKVKQKFFTFPVPYDLPP
ELYGSKDRPWIWNIPYVKAPDTHGNMWVP
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 chain1rgt Chain B Residue 699 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1rgt Explorations of peptide and oligonucleotide binding sites of tyrosyl-DNA phosphodiesterase using vanadate complexes.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		H263 K265 N283 H493 K495
Binding residue
(residue number reindexed from 1)		H102 K104 N122 H323 K325
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:1rgt, PDBe:1rgt, PDBj:1rgt
PDBsum1rgt
PubMed14761185
UniProtQ9NUW8|TYDP1_HUMAN Tyrosyl-DNA phosphodiesterase 1 (Gene Name=TDP1)

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