Structure of PDB 4pdi Chain A Binding Site BS03

Receptor Information
>4pdi Chain A (length=268) Species: 1359 (Lactococcus cremoris) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PELPEVETVRRELEKRIVGQKIISIEATYPRMVLTGFEQLKKELTGKTIQ
GISRRGKYLIFEIGDDFRLISHLRMEGKYRLATLDAPREKHDHLTMKFAD
GQLIYADVRKFGTWELISTDQVLPYFLKKKIGPEPTYEDFDEKLFREKLR
KSTKKIKPYLLEQTLVAGLGNIYVDEVLWLAKIHPEKETNQLIESSIHLL
HDSIIEILQKAIKLGGSSIRALGSTGKMQNELQVYGKTGEKCSRCGAEIQ
KIKVAGRGTHFCPVCQQK
Ligand information
Ligand ID2ON
InChIInChI=1S/C5H4N4OS/c10-4-2-3(7-1-6-2)8-5(11)9-4/h1H,(H3,6,7,8,9,10,11)
InChIKeyXNHFAGRBSMMFKL-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C1c2ncnc2N=C(S)N1
CACTVS 3.370SC1=Nc2[nH]cnc2C(=O)N1
OpenEye OEToolkits 1.7.6c1[nH]c2c(n1)C(=O)NC(=N2)S
FormulaC5 H4 N4 O S
Name2-sulfanyl-1,9-dihydro-6H-purin-6-one
ChEMBLCHEMBL218762
DrugBank
ZINCZINC000018127213
PDB chain4pdi Chain A Residue 300 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4pdi Zinc finger oxidation of Fpg/Nei DNA glycosylases by 2-thioxanthine: biochemical and X-ray structural characterization.
Resolution2.1 Å
Binding residue
(original residue number in PDB)		W179 K182 C268
Binding residue
(residue number reindexed from 1)		W179 K182 C265
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) P1 E2
Catalytic site (residue number reindexed from 1) P1 E2
Enzyme Commision number 3.2.2.23: DNA-formamidopyrimidine glycosylase.
4.2.99.18: DNA-(apurinic or apyrimidinic site) lyase.
Gene Ontology
Molecular Function
GO:0003676 nucleic acid binding
GO:0003677 DNA binding
GO:0003684 damaged DNA binding
GO:0003906 DNA-(apurinic or apyrimidinic site) endonuclease activity
GO:0008270 zinc ion binding
GO:0008534 oxidized purine nucleobase lesion DNA N-glycosylase activity
GO:0016787 hydrolase activity
GO:0016798 hydrolase activity, acting on glycosyl bonds
GO:0016799 hydrolase activity, hydrolyzing N-glycosyl compounds
GO:0016829 lyase activity
GO:0019104 DNA N-glycosylase activity
GO:0034039 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity
GO:0046872 metal ion binding
GO:0140078 class I DNA-(apurinic or apyrimidinic site) endonuclease activity
Biological Process
GO:0006281 DNA repair
GO:0006284 base-excision repair

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:4pdi, PDBe:4pdi, PDBj:4pdi
PDBsum4pdi
PubMed25143530
UniProtP42371|FPG_LACLC Formamidopyrimidine-DNA glycosylase (Gene Name=mutM)

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