Structure of PDB 5vfc Chain A Binding Site BS01

Receptor Information
>5vfc Chain A (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 ID9BA
InChIInChI=1S/C28H44N8O5/c1-6-19-23(38)35-21(18-11-8-7-9-12-18)25(40)31-16-14-28(4,36-22(37)17(2)3)26(41)34-20(24(39)33-19)13-10-15-32-27(29)30-5/h7-9,11-12,17,19-21H,6,10,13-16H2,1-5H3,(H,31,40)(H,33,39)(H,34,41)(H,35,38)(H,36,37)(H3,29,30,32)/t19-,20-,21+,28+/m0/s1
InChIKeyZAIPJVQTYUSDTG-LDFBIXNTSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01CN/C(NCCCC1NC(=O)C(C)(NC(=O)C(C)C)CCNC(C(NC(C(NC1=O)CC)=O)c2ccccc2)=O)=N
CACTVS 3.385CC[C@@H]1NC(=O)[C@H](CCCNC(=N)NC)NC(=O)[C@@](C)(CCNC(=O)[C@H](NC1=O)c2ccccc2)NC(=O)C(C)C
OpenEye OEToolkits 2.0.6[H]/N=C(\NC)/NCCC[C@H]1C(=O)N[C@H](C(=O)N[C@@H](C(=O)NCC[C@@](C(=O)N1)(C)NC(=O)C(C)C)c2ccccc2)CC
CACTVS 3.385CC[CH]1NC(=O)[CH](CCCNC(=N)NC)NC(=O)[C](C)(CCNC(=O)[CH](NC1=O)c2ccccc2)NC(=O)C(C)C
OpenEye OEToolkits 2.0.6CCC1C(=O)NC(C(=O)NCCC(C(=O)NC(C(=O)N1)CCCNC(=N)NC)(C)NC(=O)C(C)C)c2ccccc2
FormulaC28 H44 N8 O5
NameN-{(3R,6S,9S,12R)-6-ethyl-12-methyl-9-[3-(N'-methylcarbamimidamido)propyl]-2,5,8,11-tetraoxo-3-phenyl-1,4,7,10-tetraazacyclotetradecan-12-yl}-2-methylpropanamide
ChEMBLCHEMBL4116919
DrugBank
ZINC
PDB chain5vfc 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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PDB5vfc Discovery of a Highly Potent, Cell-Permeable Macrocyclic Peptidomimetic (MM-589) Targeting the WD Repeat Domain 5 Protein (WDR5)-Mixed Lineage Leukemia (MLL) Protein-Protein Interaction.
Resolution1.64 Å
Binding residue
(original residue number in PDB)		A47 S49 A65 I90 S91 D107 F133 Y260 C261 F263
Binding residue
(residue number reindexed from 1)		A17 S19 A35 I60 S61 D77 F103 Y230 C231 F233
Annotation score1
Binding affinityMOAD: ic50=0.9nM
PDBbind-CN: -logKd/Ki=9.05,IC50=0.90nM
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
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5vfc, PDBe:5vfc, PDBj:5vfc
PDBsum5vfc
PubMed28603984
UniProtP61964|WDR5_HUMAN WD repeat-containing protein 5 (Gene Name=WDR5)

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