Structure of PDB 6pgb Chain A Binding Site BS01

Receptor Information
>6pgb 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]
GSKPNYALKFTLAGHTKAVSSVKFSPNGEWLASSSADKLIKIWGAYDGKF
EKTISGHKLGISDVAWSSDSNLLVSASDDKTLKIWDVSSGKCLKTLKGHS
NYVFCCNFNPQSNLIVSGSFDESVRIWDVKTGKCLKTLPAHSDPVSAVHF
NRDGSLIVSSSYDGLCRIWDTASGQCLKTLIDDDNPPVSFVKFSPNGKYI
LAATLDNTLKLWDYSKGKCLKTYTGHKNEKYCIFANFSVTGGKWIVSGSE
DNLVYIWNLQTKEIVQKLQGHTDVVISTACHPTENIIASAALENDKTIKL
WKSDC
Ligand information
Ligand IDOJG
InChIInChI=1S/C16H21N3O2/c20-12-14-11-18-15(19-14)8-4-5-9-17-16(21)10-13-6-2-1-3-7-13/h1-3,6-7,11,20H,4-5,8-10,12H2,(H,17,21)(H,18,19)
InChIKeyNWJHGXOXPDGAJH-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7c1ccc(cc1)CC(=O)NCCCCc2[nH]c(cn2)CO
ACDLabs 12.01C(CNC(=O)Cc1ccccc1)CCc2ncc(CO)n2
CACTVS 3.385OCc1[nH]c(CCCCNC(=O)Cc2ccccc2)nc1
FormulaC16 H21 N3 O2
NameN-{4-[5-(hydroxymethyl)-1H-imidazol-2-yl]butyl}-2-phenylacetamide
ChEMBL
DrugBank
ZINC
PDB chain6pgb 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

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB6pgb Fragment screening for a protein-protein interaction inhibitor to WDR5.
Resolution1.73 Å
Binding residue
(original residue number in PDB)		S49 S91 F133 S175 A176 F219 K259 Y260 C261 F263 I305
Binding residue
(residue number reindexed from 1)		S20 S62 F104 S146 A147 F190 K230 Y231 C232 F234 I276
Annotation score1
Binding affinityMOAD: Kd=25uM
PDBbind-CN: -logKd/Ki=4.60,Kd=25uM
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6pgb, PDBe:6pgb, PDBj:6pgb
PDBsum6pgb
PubMed31768400
UniProtP61964|WDR5_HUMAN WD repeat-containing protein 5 (Gene Name=WDR5)

[Back to BioLiP]