Structure of PDB 8f93 Chain B Binding Site BS01

Receptor Information
>8f93 Chain B (length=304) 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
KSDC
Ligand information
Ligand IDXKN
InChIInChI=1S/C30H29FN4O4S/c1-4-22-13-23(15-26(14-22)40(31,37)38)18-33-11-12-35(21(2)17-33)30(36)24-9-10-28-27(16-24)32-20-34(28)19-25-7-5-6-8-29(25)39-3/h1,5-10,13-16,20-21H,11-12,17-19H2,2-3H3/t21-/m1/s1
InChIKeyADWDKRWBNOJKEH-OAQYLSRUSA-N
SMILES
SoftwareSMILES
CACTVS 3.385COc1ccccc1Cn2cnc3cc(ccc23)C(=O)N4CCN(C[CH]4C)Cc5cc(cc(c5)[S](F)(=O)=O)C#C
OpenEye OEToolkits 2.0.7C[C@@H]1CN(CCN1C(=O)c2ccc3c(c2)ncn3Cc4ccccc4OC)Cc5cc(cc(c5)S(=O)(=O)F)C#C
CACTVS 3.385COc1ccccc1Cn2cnc3cc(ccc23)C(=O)N4CCN(C[C@H]4C)Cc5cc(cc(c5)[S](F)(=O)=O)C#C
ACDLabs 12.01COc1ccccc1Cn1cnc2cc(ccc12)C(=O)N1CCN(Cc2cc(cc(C#C)c2)S(F)(=O)=O)CC1C
OpenEye OEToolkits 2.0.7CC1CN(CCN1C(=O)c2ccc3c(c2)ncn3Cc4ccccc4OC)Cc5cc(cc(c5)S(=O)(=O)F)C#C
FormulaC30 H29 F N4 O4 S
Name3-ethynyl-5-{[(3R)-4-{1-[(2-methoxyphenyl)methyl]-1H-benzimidazole-5-carbonyl}-3-methylpiperazin-1-yl]methyl}benzene-1-sulfonyl fluoride
ChEMBL
DrugBank
ZINC
PDB chain8f93 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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PDB8f93 Direct mapping of ligandable tyrosines and lysines in cells with chiral sulfonyl fluoride probes.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		R181 P224
Binding residue
(residue number reindexed from 1)		R151 P194
Annotation score1
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
View graph for
Cellular Component
External links
PDB RCSB:8f93, PDBe:8f93, PDBj:8f93
PDBsum8f93
PubMed37460812
UniProtP61964|WDR5_HUMAN WD repeat-containing protein 5 (Gene Name=WDR5)

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