Structure of PDB 6dai Chain A Binding Site BS02

Receptor Information
>6dai Chain A (length=305) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PVKPNYALKFTLAGHTKAVSSVKFSPNGEWLASSSADKLIKIWGAYDGKF
EKTISGHKLGISDVAWSSDSNLLVSASDDKTLKIWDVSSGKCLKTLKGHS
NYVFCCNFNPQSNLIVSGSFDESVRIWDVKTGKCLKTLPAHSDPVSAVHF
NRDGSLIVSSSYDGLCRIWDTASGQCLKTLIDDDNPPVSFVKFSPNGKYI
LAATLDNTLKLWDYSKGKCLKTYTGHKNEKYCIFANFSVTGGKWIVSGSE
DNLVYIWNLQTKEIVQKLQGHTDVVISTACHPTENIIASAALENDKTIKL
WKSDC
Ligand information
Ligand IDG2V
InChIInChI=1S/C15H17N3/c1-17-8-6-12-9-11(4-5-14(12)17)13-10-18-7-2-3-15(18)16-13/h4-5,9-10H,2-3,6-8H2,1H3
InChIKeyGANOSYHSDIPGSR-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6CN1CCc2c1ccc(c2)c3cn4c(n3)CCC4
CACTVS 3.385CN1CCc2cc(ccc12)c3cn4CCCc4n3
ACDLabs 12.01C1CN(c2c1cc(cc2)c4cn3c(CCC3)n4)C
FormulaC15 H17 N3
Name6-(6,7-dihydro-5H-pyrrolo[1,2-a]imidazol-2-yl)-1-methylindoline;
5-(6,7-dihydro-5H-pyrrolo[1,2-a]imidazol-2-yl)-1-methyl-2,3-dihydro-1H-indole
ChEMBLCHEMBL4281112
DrugBank
ZINC
PDB chain6dai Chain A Residue 504 [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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PDB6dai Discovery of Potent 2-Aryl-6,7-dihydro-5 H-pyrrolo[1,2- a]imidazoles as WDR5-WIN-Site Inhibitors Using Fragment-Based Methods and Structure-Based Design.
Resolution1.63 Å
Binding residue
(original residue number in PDB)		Y131 F133 F149 P173 V174 S175 Y191
Binding residue
(residue number reindexed from 1)		Y102 F104 F120 P144 V145 S146 Y162
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=4.07,Ki=85.2uM
BindingDB: Ki=85200nM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0005515 protein binding
GO:0035064 methylated histone binding
GO:0042393 histone binding
GO:0042800 histone H3K4 methyltransferase activity
Biological Process
GO:0000122 negative regulation of transcription by RNA polymerase II
GO:0001501 skeletal system development
GO:0006094 gluconeogenesis
GO:0006325 chromatin organization
GO:0006355 regulation of DNA-templated transcription
GO:0006357 regulation of transcription by RNA polymerase II
GO:0045722 positive regulation of gluconeogenesis
GO:0045815 transcription initiation-coupled chromatin remodeling
GO:0045893 positive regulation of DNA-templated transcription
GO:0045995 regulation of embryonic development
GO:0051302 regulation of cell division
GO:0051726 regulation of cell cycle
GO:0090043 regulation of tubulin deacetylation
Cellular Component
GO:0000123 histone acetyltransferase complex
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0035097 histone methyltransferase complex
GO:0044545 NSL complex
GO:0044665 MLL1/2 complex
GO:0044666 MLL3/4 complex
GO:0048188 Set1C/COMPASS complex
GO:0071339 MLL1 complex
GO:0072686 mitotic spindle
GO:0140672 ATAC complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6dai, PDBe:6dai, PDBj:6dai
PDBsum6dai
PubMed29889518
UniProtP61964|WDR5_HUMAN WD repeat-containing protein 5 (Gene Name=WDR5)

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