Structure of PDB 3smr Chain C Binding Site BS01

Receptor Information
>3smr Chain C (length=303) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VKPNYALKFTLAGHTKAVSSVKFSPNGEWLASSSADKLIKIWGAYDGKFE
KTISGHKLGISDVAWSSDSNLLVSASDDKTLKIWDVSSGKCLKTLKGHSN
YVFCCNFNPQSNLIVSGSFDESVRIWDVKTGKCLKTLPAHSDPVSAVHFN
RDGSLIVSSSYDGLCRIWDTASGQCLKTLIDDNPPVSFVKFSPNGKYILA
ATLDNTLKLWDYSKGKCLKTYTGHKNEKYCIFANFSVTGGKWIVSGSEDN
LVYIWNLQTKEIVQKLQGHTDVVISTACHPTENIIASAALENDKTIKLWK
SDC
Ligand information
Ligand IDNP7
InChIInChI=1S/C18H19ClN4O3/c1-21-8-10-22(11-9-21)17-7-6-13(23(25)26)12-16(17)20-18(24)14-4-2-3-5-15(14)19/h2-7,12H,8-11H2,1H3,(H,20,24)
InChIKeyWOGZFCMBPXJNFI-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01Clc1ccccc1C(=O)Nc3c(N2CCN(C)CC2)ccc([N+]([O-])=O)c3
OpenEye OEToolkits 1.7.2CN1CCN(CC1)c2ccc(cc2NC(=O)c3ccccc3Cl)[N+](=O)[O-]
CACTVS 3.370CN1CCN(CC1)c2ccc(cc2NC(=O)c3ccccc3Cl)[N+]([O-])=O
FormulaC18 H19 Cl N4 O3
Name2-chloro-N-[2-(4-methylpiperazin-1-yl)-5-nitrophenyl]benzamide
ChEMBLCHEMBL1609857
DrugBank
ZINC
PDB chain3smr Chain C Residue 1000 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3smr Small-molecule inhibition of MLL activity by disruption of its interaction with WDR5.
Resolution1.82 Å
Binding residue
(original residue number in PDB)		S49 S50 I90 S91 F133 C261
Binding residue
(residue number reindexed from 1)		S19 S20 I60 S61 F103 C230
Annotation score1
Binding affinityBindingDB: Kd=7000nM
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:3smr, PDBe:3smr, PDBj:3smr
PDBsum3smr
PubMed22989411
UniProtP61964|WDR5_HUMAN WD repeat-containing protein 5 (Gene Name=WDR5)

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