4QL1 | pdb_00004ql1

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

• PDB DOI: https://doi.org/10.2210/pdb4QL1/pdb

• Classification: TRANSCRIPTION/INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-06-10 Released: 2014-12-17 
• Deposition Author(s): Dong, A., Dombrovski, L., Walker, J.R., Getlik, M., Kuznetsova, E., Smil, D., Barsyte, D., Li, F., Poda, G., Senisterra, G., Marcellus, R., Al-Awar, R., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Brown, P.J., Schapira, M., Vedadi, M., Wu, H., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.227 (Depositor), 0.228 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

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

• PubMed: 26167872 
• DOI: https://doi.org/10.1038/nchembio.1859
• Primary Citation Related Structures: 
  4QL1


• 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 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.

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 69.85 kDa 
• Atom Count: 5,115 
• Modeled Residue Count: 606 
• Deposited Residue Count: 624 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
WD repeat-containing protein 5	A, B	312	Homo sapiens	Mutation(s): 0  Gene Names: WDR5, BIG3
UniProt & NIH Common Fund Data Resources
Find proteins for P61964 (Homo sapiens) Explore P61964  Go to UniProtKB:  P61964
PHAROS:  P61964 GTEx:  ENSG00000196363

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
35Q	C [auth A], E [auth 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
GOL	G [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	F [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
UNX	D [auth A], H [auth B]	UNKNOWN ATOM OR ION X

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.227 (Depositor), 0.228 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.843	α = 71.45
b = 56.628	β = 88.94
c = 64.688	γ = 65.43

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MxDC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-12-17 
Deposition Author(s): Dong, A., Dombrovski, L., Walker, J.R., Getlik, M., Kuznetsova, E., Smil, D., Barsyte, D., Li, F., Poda, G., Senisterra, G., Marcellus, R., Al-Awar, R., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Brown, P.J., Schapira, M., Vedadi, M., Wu, H., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2014-12-17
  Type: Initial release
  
• Version 1.1: 2015-04-15
  Changes: Non-polymer description
• Version 1.2: 2015-07-15
  Changes: Database references
• Version 1.3: 2015-07-29
  Changes: Database references
• Version 1.4: 2016-02-24
  Changes: Database references
• Version 1.5: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description