Structure of PDB 6dya Chain A Binding Site BS01
Receptor Information
>6dya Chain A (length=305) Species:
9606
(Homo sapiens) [
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PVKPNYALKFTLAGHTKAVSSVKFSPNGEWLASSSADKLIKIWGAYDGKF
EKTISGHKLGISDVAWSSDSNLLVSASDDKTLKIWDVSSGKCLKTLKGHS
NYVFCCNFNPQSNLIVSGSFDESVRIWDVKTGKCLKTLPAHSDPVSAVHF
NRDGSLIVSSSYDGLCRIWDTASGQCLKTLIDDDNPPVSFVKFSPNGKYI
LAATLDNTLKLWDYSKGKCLKTYTGHKNEKYCIFANFSVTGGKWIVSGSE
DNLVYIWNLQTKEIVQKLQGHTDVVISTACHPTENIIASAALENDKTIKL
WKSDC
Ligand information
Ligand ID
HHM
InChI
InChI=1S/C18H15Cl2N3O/c19-16-7-14(8-17(20)9-16)10-22-18(24)15-3-1-2-13(6-15)11-23-5-4-21-12-23/h1-9,12H,10-11H2,(H,22,24)
InChIKey
JZXCLJKOXUVFTA-UHFFFAOYSA-N
SMILES
Software
SMILES
OpenEye OEToolkits 2.0.6
c1cc(cc(c1)C(=O)NCc2cc(cc(c2)Cl)Cl)Cn3ccnc3
ACDLabs 12.01
c3(cc(CNC(c1cc(ccc1)Cn2ccnc2)=O)cc(c3)Cl)Cl
CACTVS 3.385
Clc1cc(Cl)cc(CNC(=O)c2cccc(Cn3ccnc3)c2)c1
Formula
C18 H15 Cl2 N3 O
Name
N-[(3,5-dichlorophenyl)methyl]-3-[(1H-imidazol-1-yl)methyl]benzamide
ChEMBL
CHEMBL5176836
DrugBank
ZINC
PDB chain
6dya Chain A Residue 401 [
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Receptor-Ligand Complex Structure
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PDB
6dya
Displacement of WDR5 from Chromatin by a WIN Site Inhibitor with Picomolar Affinity.
Resolution
2.56 Å
Binding residue
(original residue number in PDB)
S49 F133 F149 Y191 Y260 C261 F263 I305
Binding residue
(residue number reindexed from 1)
S20 F104 F120 Y162 Y231 C232 F234 I276
Annotation score
1
Binding affinity
PDBbind-CN
: -logKd/Ki=6.17,Kd=681nM
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:6dya
,
PDBe:6dya
,
PDBj:6dya
PDBsum
6dya
PubMed
30865883
UniProt
P61964
|WDR5_HUMAN WD repeat-containing protein 5 (Gene Name=WDR5)
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