Structure of PDB 8gl9 Chain A Binding Site BS01

Receptor Information
>8gl9 Chain A (length=240) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MFEARLVQGSILKKVLEALKDLINEACWDISSSGVNLQSMDSSHVSLVQL
TLRSEGFDTYRCDRNLAMGVNLTSMSKILKCAGNEDIITLRAEDDTLALV
FEAQEKVSDYEMKLMDLDVEQLGIPEQEYSCVVKMPSGEFARICRDLSHI
GDAVVISCAVKFSASGELGNGNIKLSQTEAVTIEMNEPVQLTFALRYLNF
FTKATPLSSTVTLSMSADVPLVVEYKIADMGHLKYYLAPK
Ligand information
Ligand IDZQW
InChIInChI=1S/C28H24N2O5/c31-26(32)18-17-24(30-27(33)22-14-8-10-19-9-4-5-13-21(19)22)28(34)29-23-15-6-7-16-25(23)35-20-11-2-1-3-12-20/h1-16,24H,17-18H2,(H,29,34)(H,30,33)(H,31,32)/t24-/m0/s1
InChIKeyIIQXEGLQYMXTEV-DEOSSOPVSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7c1ccc(cc1)Oc2ccccc2NC(=O)C(CCC(=O)O)NC(=O)c3cccc4c3cccc4
CACTVS 3.385OC(=O)CC[CH](NC(=O)c1cccc2ccccc12)C(=O)Nc3ccccc3Oc4ccccc4
ACDLabs 12.01O=C(O)CCC(NC(=O)c1cccc2ccccc21)C(=O)Nc1ccccc1Oc1ccccc1
CACTVS 3.385OC(=O)CC[C@H](NC(=O)c1cccc2ccccc12)C(=O)Nc3ccccc3Oc4ccccc4
OpenEye OEToolkits 2.0.7c1ccc(cc1)Oc2ccccc2NC(=O)[C@H](CCC(=O)O)NC(=O)c3cccc4c3cccc4
FormulaC28 H24 N2 O5
NameN~2~-(naphthalene-1-carbonyl)-N-(2-phenoxyphenyl)-L-alpha-glutamine
ChEMBL
DrugBank
ZINC
PDB chain8gl9 Chain A Residue 303 [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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PDB8gl9 Small molecule targeting of transcription-replication conflict for selective chemotherapy.
Resolution2.81 Å
Binding residue
(original residue number in PDB)		M40 H44 V45 L126
Binding residue
(residue number reindexed from 1)		M40 H44 V45 L122
Annotation score1
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0000701 purine-specific mismatch base pair DNA N-glycosylase activity
GO:0003677 DNA binding
GO:0003682 chromatin binding
GO:0003684 damaged DNA binding
GO:0005515 protein binding
GO:0019899 enzyme binding
GO:0030331 nuclear estrogen receptor binding
GO:0030337 DNA polymerase processivity factor activity
GO:0030971 receptor tyrosine kinase binding
GO:0032139 dinucleotide insertion or deletion binding
GO:0032405 MutLalpha complex binding
GO:0035035 histone acetyltransferase binding
GO:0042802 identical protein binding
GO:0044877 protein-containing complex binding
GO:0070182 DNA polymerase binding
Biological Process
GO:0000122 negative regulation of transcription by RNA polymerase II
GO:0006260 DNA replication
GO:0006272 leading strand elongation
GO:0006275 regulation of DNA replication
GO:0006281 DNA repair
GO:0006287 base-excision repair, gap-filling
GO:0006298 mismatch repair
GO:0006979 response to oxidative stress
GO:0007507 heart development
GO:0019985 translesion synthesis
GO:0030855 epithelial cell differentiation
GO:0031297 replication fork processing
GO:0032077 positive regulation of deoxyribonuclease activity
GO:0032355 response to estradiol
GO:0033993 response to lipid
GO:0034644 cellular response to UV
GO:0044849 estrous cycle
GO:0045739 positive regulation of DNA repair
GO:0045740 positive regulation of DNA replication
GO:0046686 response to cadmium ion
GO:0070301 cellular response to hydrogen peroxide
GO:0071466 cellular response to xenobiotic stimulus
GO:0071548 response to dexamethasone
GO:0097421 liver regeneration
GO:1900264 positive regulation of DNA-directed DNA polymerase activity
GO:1902065 response to L-glutamate
GO:1902990 mitotic telomere maintenance via semi-conservative replication
Cellular Component
GO:0000307 cyclin-dependent protein kinase holoenzyme complex
GO:0000781 chromosome, telomeric region
GO:0000785 chromatin
GO:0001673 male germ cell nucleus
GO:0005634 nucleus
GO:0005652 nuclear lamina
GO:0005654 nucleoplasm
GO:0005657 replication fork
GO:0005813 centrosome
GO:0016604 nuclear body
GO:0030894 replisome
GO:0043596 nuclear replication fork
GO:0043626 PCNA complex
GO:0070062 extracellular exosome
GO:0070557 PCNA-p21 complex

View graph for
Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8gl9, PDBe:8gl9, PDBj:8gl9
PDBsum8gl9
PubMed37531956
UniProtP12004|PCNA_HUMAN Proliferating cell nuclear antigen (Gene Name=PCNA)

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