Structure of PDB 6e1y Chain A Binding Site BS01

Receptor Information
>6e1y Chain A (length=299) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KPNYALKFTLAGHTKAVSSVKFSPNGEWLASSSADKLIKIWGAYDGKFEK
TISGHKLGISDVAWSSDSNLLVSASDDKTLKIWDVSSGKCLKTLKGHSNY
VFCCNFNPQSNLIVSGSFDESVRIWDVKTGKCLKTLPAHSDPVSAVHFNR
DGSLIVSSSYDGLCRIWDTASGQCLKTLNPPVSFVKFSPNGKYILAATLD
NTLKLWDYSKGKCLKTYTGHKNEKYCIFANFSVTGGKWIVSGSEDNLVYI
WNLQTKEIVQKLQGHTDVVISTACHPTENIIASAALENDKTIKLWKSDC
Ligand information
Ligand IDHLM
InChIInChI=1S/C19H21ClN4O/c1-13(15-5-3-7-17(20)11-15)24-18(25)16-6-2-4-14(10-16)12-23-19-21-8-9-22-19/h2-7,10-11,13H,8-9,12H2,1H3,(H,24,25)(H2,21,22,23)/t13-/m0/s1
InChIKeyZHGJIKXLESXIHK-ZDUSSCGKSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01c2(cc(C(=O)NC(C)c1cccc(c1)Cl)ccc2)CNC3=NCCN3
CACTVS 3.385C[CH](NC(=O)c1cccc(CNC2=NCCN2)c1)c3cccc(Cl)c3
OpenEye OEToolkits 2.0.6C[C@@H](c1cccc(c1)Cl)NC(=O)c2cccc(c2)CNC3=NCCN3
CACTVS 3.385C[C@H](NC(=O)c1cccc(CNC2=NCCN2)c1)c3cccc(Cl)c3
OpenEye OEToolkits 2.0.6CC(c1cccc(c1)Cl)NC(=O)c2cccc(c2)CNC3=NCCN3
FormulaC19 H21 Cl N4 O
NameN-[(1S)-1-(3-chlorophenyl)ethyl]-3-{[(4,5-dihydro-1H-imidazol-2-yl)amino]methyl}benzamide
ChEMBL
DrugBank
ZINC
PDB chain6e1y 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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PDB6e1y Displacement of WDR5 from Chromatin by a WIN Site Inhibitor with Picomolar Affinity.
Resolution1.219 Å
Binding residue
(original residue number in PDB)		S49 S91 F133 F149 S175 Y260 C261 F263 I305
Binding residue
(residue number reindexed from 1)		S18 S60 F102 F118 S144 Y225 C226 F228 I270
Annotation score1
Binding affinityMOAD: Kd=22nM
PDBbind-CN: -logKd/Ki=7.66,Kd=22nM
BindingDB: Ki=30.8nM
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:6e1y, PDBe:6e1y, PDBj:6e1y
PDBsum6e1y
PubMed30865883
UniProtP61964|WDR5_HUMAN WD repeat-containing protein 5 (Gene Name=WDR5)

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