Structure of PDB 8gl9 Chain A Binding Site BS03

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 305 [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)		Q38 S39 M40 H44 L47 L121 L126
Binding residue
(residue number reindexed from 1)		Q38 S39 M40 H44 L47 L117 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

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Molecular Function
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Biological Process
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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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