4QL1

Crystal structure of human WDR5 in complex with compound OICR-9429


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Pharmacological targeting of the Wdr5-MLL interaction in C/EBP alpha N-terminal leukemia.

Grebien, F.Vedadi, M.Getlik, M.Giambruno, R.Grover, A.Avellino, R.Skucha, A.Vittori, S.Kuznetsova, E.Smil, D.Barsyte-Lovejoy, D.Li, F.Poda, G.Schapira, M.Wu, H.Dong, A.Senisterra, G.Stukalov, A.Huber, K.V.Schonegger, A.Marcellus, R.Bilban, M.Bock, C.Brown, P.J.Zuber, J.Bennett, K.L.Al-Awar, R.Delwel, R.Nerlov, C.Arrowsmith, C.H.Superti-Furga, G.

(2015) Nat.Chem.Biol. 11: 571-578

  • DOI: 10.1038/nchembio.1859

  • PubMed Abstract: 
  • The CEBPA gene is mutated in 9% of patients with acute myeloid leukemia (AML). Selective expression of a short (30-kDa) CCAAT-enhancer binding protein-α (C/EBPα) translational isoform, termed p30, represents the most common type of CEBPA mutation in ...

    The CEBPA gene is mutated in 9% of patients with acute myeloid leukemia (AML). Selective expression of a short (30-kDa) CCAAT-enhancer binding protein-α (C/EBPα) translational isoform, termed p30, represents the most common type of CEBPA mutation in AML. The molecular mechanisms underlying p30-mediated transformation remain incompletely understood. We show that C/EBPα p30, but not the normal p42 isoform, preferentially interacts with Wdr5, a key component of SET/MLL (SET-domain/mixed-lineage leukemia) histone-methyltransferase complexes. Accordingly, p30-bound genomic regions were enriched for MLL-dependent H3K4me3 marks. The p30-dependent increase in self-renewal and inhibition of myeloid differentiation required Wdr5, as downregulation of the latter inhibited proliferation and restored differentiation in p30-dependent AML models. OICR-9429 is a new small-molecule antagonist of the Wdr5-MLL interaction. This compound selectively inhibited proliferation and induced differentiation in p30-expressing human AML cells. Our data reveal the mechanism of p30-dependent transformation and establish the essential p30 cofactor Wdr5 as a therapeutic target in CEBPA-mutant AML.


    Organizational Affiliation

    Department of Hematology, Erasmus University Medical Center, Rotterdam 3015 GE, The Netherlands.,Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 2M9, Canada.,Ludwig Boltzmann Institute for Cancer Research, Vienna 1090, Austria.,MRC Molecular Hematology Unit, Weatherall Institute of Molecular Medicine, Oxford OX3 9DS, United Kingdom.,Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, M5S 3M2, Canada.,CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna 1090, Austria.,Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, M5S 1A8, Canada.,Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, ON, M5G 0A3, Canada.,Department of Laboratory Medicine & Core Facility Genomics, Core Facilities, Medical University Vienna, Vienna 1090, Austria.,Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada.,Research Institute of Molecular Pathology (IMP), Vienna 1030, Austria.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
WD repeat-containing protein 5
A, B
312Homo sapiensMutation(s): 0 
Gene Names: WDR5 (BIG3)
Find proteins for P61964 (Homo sapiens)
Go to Gene View: WDR5
Go to UniProtKB:  P61964
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
35Q
Query on 35Q

Download SDF File 
Download CCD File 
A, B
N-(4-(4-methylpiperazin-1-yl)-3'-(morpholinomethyl)-[1,1'-biphenyl]-3-yl)-6-oxo-4-(trifluoromethyl)-1,6-dihydropyridine-3-carboxamide
C29 H32 F3 N5 O3
DJOVLOYCGXNVPI-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
UNX
Query on UNX

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Download CCD File 
A, B
UNKNOWN ATOM OR ION
X
*
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
35QKd: 30 - 93 nM (99) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.195 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 46.843α = 71.45
b = 56.628β = 88.94
c = 64.688γ = 65.43
Software Package:
Software NamePurpose
Cootmodel building
PDB_EXTRACTdata extraction
REFMACrefinement
SCALEPACKdata scaling
MxDCdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2014-12-17
    Type: Initial release
  • Version 1.1: 2015-04-15
    Type: Non-polymer description
  • Version 1.2: 2015-07-15
    Type: Database references
  • Version 1.3: 2015-07-29
    Type: Database references
  • Version 1.4: 2016-02-24
    Type: Database references