Structure of PDB 6rlw Chain CCC Binding Site BS01

Receptor Information

>6rlw Chain CCC (length=303) Species: 9606 (Homo sapiens)

MGHRTLASTPALWASIPCPRSELRLDLVLPSGQSFRWREQSPAHWSGVLA
DQVWTLTQTEEQLHCTVYRKSQASRPTPDELEAVRKYFQLDVTLAQLYHH
WGSVDSHFQEVAQKFQGVRLLRQDPIECLFSFICSSNNNIARITGMVERL
CQAFGPRLIQLDDVTYHGFPSLQALAGPEVEAHLRKLGLGYRARYVSASA
RAILEEQGGLAWLQQLRESSYEEAHKALCILPGVGTKVADCICLMALDKP
QAVPVDVHMWHIAQRDYSWHPSPQTNKELGNFFRSLWGPYAGWAQAVLFS
ADL

Ligand information

• Ligand ID: K8Q
• InChI: InChI=1S/C19H18BrIN4O2/c20-15-2-1-3-16-17(15)23-19(27)25(16)14-8-10-24(11-9-14)18(26)22-13-6-4-12(21)5-7-13/h1-7,14H,8-11H2,(H,22,26)(H,23,27)
• InChIKey: FZLKVWWPFOLPKF-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.385: Brc1cccc2N(C3CCN(CC3)C(=O)Nc4ccc(I)cc4)C(=O)Nc12
  OpenEye OEToolkits 2.0.7: c1cc2c(c(c1)Br)NC(=O)N2C3CCN(CC3)C(=O)Nc4ccc(cc4)I
• Formula: C19 H18 Br I N4 O2
• Name: 4-(4-bromanyl-2-oxidanylidene-3~{H}-benzimidazol-1-yl)-~{N}-(4-iodophenyl)piperidine-1-carboxamide
• PDB chain: 6rlw Chain CCC Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6rlw Targeting OGG1 arrests cancer cell proliferation by inducing replication stress.
• Resolution: 2.0 Å
• Binding residue (original residue number in PDB): G42 K249 M257 H270 Q315 A316 F319
• Binding residue (residue number reindexed from 1): G32 K237 M245 H258 Q295 A296 F299
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): K249 D268
• Catalytic site (residue number reindexed from 1): K237 D256
• Enzyme Commision number: 3.2.2.-
  4.2.99.18: DNA-(apurinic or apyrimidinic site) lyase.

Gene Ontology

Molecular Function

• 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:0004519 endonuclease activity
• GO:0005515 protein binding
• 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:0006285 base-excision repair, AP site formation
• 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:0045007 depurination
• GO:0045008 depyrimidination
• 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:0005759 mitochondrial matrix
• GO:0005829 cytosol
• GO:0016363 nuclear matrix
• GO:0016607 nuclear speck
• GO:0032991 protein-containing complex

External links

• PDB: RCSB:6rlw, PDBe:6rlw, PDBj:6rlw
• PDBsum: 6rlw
• PubMed: 33211885
• UniProt: O15527|OGG1_HUMAN N-glycosylase/DNA lyase (Gene Name=OGG1)