Structure of PDB 5m23 Chain A Binding Site BS01

Receptor Information
>5m23 Chain A (length=300) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PNYALKFTLAGHTKAVSSVKFSPNGEWLASSSADKLIKIWGAYDGKFEKT
ISGHKLGISDVAWSSDSNLLVSASDDKTLKIWDVSSGKCLKTLKGHSNYV
FCCNFNPQSNLIVSGSFDESVRIWDVKTGKCLKTLPAHSDPVSAVHFNRD
GSLIVSSSYDGLCRIWDTASGQCLKTLIDDDNPPVSFVKFSPNGKYILAA
TLDNTLKLWDYSKGKCLKTYTGHKNEKYCIFANFSVTGGKWIVSGSEDNL
VYIWNLQTKEIVQKLQGHTDVVISTACHPTENIIASAALENDKTIKLWKS
Ligand information
Ligand ID7DC
InChIInChI=1S/C34H49N11O7/c1-19(2)28(18-47)43-31(50)23-9-13-25(14-10-23)45-44-24-11-7-22(8-12-24)16-39-29(48)20(3)41-33(52)27(6-5-15-38-34(36)37)42-30(49)21(4)40-32(51)26(35)17-46/h7-14,18-21,26-28,46H,5-6,15-17,35H2,1-4H3,(H,39,48)(H,40,51)(H,41,52)(H,42,49)(H,43,50)(H4,36,37,38)/b45-44+/t20-,21-,26-,27-,28+/m0/s1
InChIKeyZYZPAXPFTDDNJW-KERJXBJTSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6[H]/N=C(\N)/NCCC[C@@H](C(=O)N[C@@H](C)C(=O)NCc1ccc(cc1)/N=N/c2ccc(cc2)C(=O)N[C@H](C=O)C(C)C)NC(=O)[C@H](C)NC(=O)[C@H](CO)N
CACTVS 3.385CC(C)[C@H](NC(=O)c1ccc(cc1)N=Nc2ccc(CNC(=O)[C@H](C)NC(=O)[C@H](CCCNC(N)=N)NC(=O)[C@H](C)NC(=O)[C@@H](N)CO)cc2)C=O
CACTVS 3.385CC(C)[CH](NC(=O)c1ccc(cc1)N=Nc2ccc(CNC(=O)[CH](C)NC(=O)[CH](CCCNC(N)=N)NC(=O)[CH](C)NC(=O)[CH](N)CO)cc2)C=O
OpenEye OEToolkits 2.0.6CC(C)C(C=O)NC(=O)c1ccc(cc1)N=Nc2ccc(cc2)CNC(=O)C(C)NC(=O)C(CCCNC(=N)N)NC(=O)C(C)NC(=O)C(CO)N
FormulaC34 H49 N11 O7
Name
ChEMBL
DrugBank
ZINC
PDB chain5m23 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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PDB5m23 Controlled inhibition of methyltransferases using photoswitchable peptidomimetics: towards an epigenetic regulation of leukemia.
Resolution1.97 Å
Binding residue
(original residue number in PDB)		S49 A65 G89 I90 S91 D107 F133 K259 Y260 C261 F263 I305
Binding residue
(residue number reindexed from 1)		S17 A33 G57 I58 S59 D75 F101 K227 Y228 C229 F231 I273
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=8.90,Ki=1.25nM
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:5m23, PDBe:5m23, PDBj:5m23
PDBsum5m23
PubMed28970883
UniProtP61964|WDR5_HUMAN WD repeat-containing protein 5 (Gene Name=WDR5)

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