Structure of PDB 6dar Chain A Binding Site BS01

Receptor Information
>6dar Chain A (length=302) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VKPNYALKFTLAGHTKAVSSVKFSPNGEWLASSSADKLIKIWGAYDGKFE
KTISGHKLGISDVAWSSDSNLLVSASDDKTLKIWDVSSGKCLKTLKGHSN
YVFCCNFNPQSNLIVSGSFDESVRIWDVKTGKCLKTLPAHSDPVSAVHFN
RDGSLIVSSSYDGLCRIWDTASGQCLKTLIDDDNPPVSFVKFSPNGKYIL
AATLDNTLKLWDYSKGKCLKTYTGHKNEKYCIFANFSVTGGKWIVSGSED
NLVYIWNLQTKEIVQKLQGHTDVVISTACHPTENIIASAALENDKTIKLW
KS
Ligand information
Ligand IDG2J
InChIInChI=1S/C25H27N3O2/c1-30-22-8-3-7-21(14-22)25(29)28(15-18-10-11-18)16-19-5-2-6-20(13-19)23-17-27-12-4-9-24(27)26-23/h2-3,5-8,13-14,17-18H,4,9-12,15-16H2,1H3
InChIKeyUVWAIBUOXKRXQY-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385COc1cccc(c1)C(=O)N(CC2CC2)Cc3cccc(c3)c4cn5CCCc5n4
OpenEye OEToolkits 2.0.6COc1cccc(c1)C(=O)N(Cc2cccc(c2)c3cn4c(n3)CCC4)CC5CC5
ACDLabs 12.01O=C(N(CC1CC1)Cc4cccc(c3cn2CCCc2n3)c4)c5cccc(c5)OC
FormulaC25 H27 N3 O2
NameN-(cyclopropylmethyl)-N-{[3-(6,7-dihydro-5H-pyrrolo[1,2-a]imidazol-2-yl)phenyl]methyl}-3-methoxybenzamide
ChEMBLCHEMBL4294825
DrugBank
ZINC
PDB chain6dar 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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PDB6dar 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.
Resolution1.88 Å
Binding residue
(original residue number in PDB)		S49 S91 F133 F149 S175 Y191 F219 Y260 C261 F263 I305
Binding residue
(residue number reindexed from 1)		S19 S61 F103 F119 S145 Y161 F189 Y230 C231 F233 I275
Annotation score1
Binding affinityMOAD: Ki=0.219uM
PDBbind-CN: -logKd/Ki=6.66,Ki=0.219uM
BindingDB: Ki=219nM
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:6dar, PDBe:6dar, PDBj:6dar
PDBsum6dar
PubMed29889518
UniProtP61964|WDR5_HUMAN WD repeat-containing protein 5 (Gene Name=WDR5)

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