Structure of PDB 6g3y Chain A Binding Site BS01

Receptor Information
>6g3y Chain A (length=316) Species: 10090 (Mus musculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HMRHRTLSSSPALWASIPCPRSELRLDLVLASGQSFRWKEQSPAHWSGVL
ADQVWTLTQTEDQLYCTVYRGDDSQVSRPTLEELETLHKYFQLDVSLAQL
YSHWASVDSHFQRVAQKFQGVRLLRQDPTECLFSFICSSNNNIARITGMV
ERLCQAFGPRLIQLDDVTYHGFPNLHALAGPEAETHLRKLGLGYRARYVR
ASAKAILEEQGGPAWLQQLRVAPYEEAHKALCTLPGVGAKVADCICLMAL
DKPQAVPVDVHVWQIAHRDYGWHPKTSQAKGPSPLANKELGNFFRNLWGP
YAGWAQAVLFSADLRQ
Ligand information
Ligand IDELB
InChIInChI=1S/C19H20IN5O2/c20-12-4-6-13(7-5-12)22-18(26)24-10-8-14(9-11-24)25-16-3-1-2-15(21)17(16)23-19(25)27/h1-7,14H,8-11,21H2,(H,22,26)(H,23,27)
InChIKeyMCANHWLZFZFTAQ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Nc1cccc2N(C3CCN(CC3)C(=O)Nc4ccc(I)cc4)C(=O)Nc12
OpenEye OEToolkits 2.0.6c1cc(c2c(c1)N(C(=O)N2)C3CCN(CC3)C(=O)Nc4ccc(cc4)I)N
FormulaC19 H20 I N5 O2
Name4-(4-azanyl-2-oxidanylidene-3~{H}-benzimidazol-1-yl)-~{N}-(4-iodophenyl)piperidine-1-carboxamide;
TH5675
ChEMBL
DrugBank
ZINC
PDB chain6g3y Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6g3y Small-molecule inhibitor of OGG1 suppresses proinflammatory gene expression and inflammation.
Resolution2.51 Å
Binding residue
(original residue number in PDB)		G42 F45 N151 I152 K249 M257 H270 Q315 A316 F319 L323
Binding residue
(residue number reindexed from 1)		G33 F36 N142 I143 K240 M248 H261 Q306 A307 F310 L314
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.89,IC50=1.3uM
Enzymatic activity
Catalytic site (original residue number in PDB) K249 D268
Catalytic site (residue number reindexed from 1) K240 D259
Enzyme Commision number 3.2.2.-
4.2.99.18: DNA-(apurinic or apyrimidinic site) lyase.
Gene Ontology
Molecular Function
GO:0000702 oxidized base lesion DNA N-glycosylase activity
GO:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA binding
GO:0003677 DNA binding
GO:0003684 damaged DNA binding
GO:0003824 catalytic activity
GO:0008017 microtubule binding
GO:0008534 oxidized purine nucleobase lesion DNA N-glycosylase activity
GO:0016798 hydrolase activity, acting on glycosyl bonds
GO:0016829 lyase activity
GO:0019104 DNA N-glycosylase activity
GO:0019899 enzyme binding
GO:0032357 oxidized purine DNA binding
GO:0034039 8-oxo-7,8-dihydroguanine DNA N-glycosylase activity
GO:0140078 class I DNA-(apurinic or apyrimidinic site) endonuclease activity
GO:0140097 catalytic activity, acting on DNA
Biological Process
GO:0006281 DNA repair
GO:0006284 base-excision repair
GO:0006289 nucleotide-excision repair
GO:0006355 regulation of DNA-templated transcription
GO:0006974 DNA damage response
GO:0006979 response to oxidative stress
GO:0009314 response to radiation
GO:0009410 response to xenobiotic stimulus
GO:0009416 response to light stimulus
GO:0032355 response to estradiol
GO:0034614 cellular response to reactive oxygen species
GO:0043066 negative regulation of apoptotic process
GO:0044029 positive regulation of gene expression via chromosomal CpG island demethylation
GO:0045471 response to ethanol
GO:0045944 positive regulation of transcription by RNA polymerase II
GO:0051593 response to folic acid
GO:0071276 cellular response to cadmium ion
GO:1901291 negative regulation of double-strand break repair via single-strand annealing
Cellular Component
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005739 mitochondrion
GO:0016363 nuclear matrix
GO:0016607 nuclear speck
GO:0032991 protein-containing complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6g3y, PDBe:6g3y, PDBj:6g3y
PDBsum6g3y
PubMed30442810
UniProtO08760|OGG1_MOUSE N-glycosylase/DNA lyase (Gene Name=Ogg1)

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