5EAM

Crystal structure of human WDR5 in complex with compound 9o

• PDB DOI:  https://doi.org/10.2210/pdb5EAM/pdb

• Classification: Transcription/Transcription inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-10-16 Released: 2015-11-04 
• Deposition Author(s): DONG, A., DOMBROVSKI, L., SMIL, D., GETLIK, M., BOLSHAN, Y., WALKER, J.R., SENISTERRA, G., PODA, G., AL-AWAR, R., SCHAPIRA, M., VEDADI, M., Bountra, C., Edwards, A.M., Arrowsmith, C.H., BROWN, P.J., WU, H., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.228 
• R-Value Work: 0.197 
• R-Value Observed: 0.197 

Literature

Structure-Based Optimization of a Small Molecule Antagonist of the Interaction Between WD Repeat-Containing Protein 5 (WDR5) and Mixed-Lineage Leukemia 1 (MLL1).

Getlik, M., Smil, D., Zepeda-Velazquez, C., Bolshan, Y., Poda, G., Wu, H., Dong, A., Kuznetsova, E., Marcellus, R., Senisterra, G., Dombrovski, L., Hajian, T., Kiyota, T., Schapira, M., Arrowsmith, C.H., Brown, P.J., Vedadi, M., Al-Awar, R.

(2016) J Med Chem 59: 2478-2496

• PubMed: 26958703 
• DOI: https://doi.org/10.1021/acs.jmedchem.5b01630
• Primary Citation of Related Structures:  
  5EAM, 5EAP, 5EAR


• PubMed Abstract: 
  

WD repeat-containing protein 5 (WDR5) is an important component of the multiprotein complex essential for activating mixed-lineage leukemia 1 (MLL1). Rearrangement of the MLL1 gene is associated with onset and progression of acute myeloid and lymphoblastic leukemias, and targeting the WDR5-MLL1 interaction may result in new cancer therapeutics. Our previous work showed that binding of small molecule ligands to WDR5 can modulate its interaction with MLL1, suppressing MLL1 methyltransferase activity. Initial structure-activity relationship studies identified N-(2-(4-methylpiperazin-1-yl)-5-substituted-phenyl) benzamides as potent and selective antagonists of this protein-protein interaction. Guided by crystal structure data and supported by in silico library design, we optimized the scaffold by varying the C-1 benzamide and C-5 substituents. This allowed us to develop the first highly potent (Kdisp < 100 nM) small molecule antagonists of the WDR5-MLL1 interaction and demonstrate that N-(4-(4-methylpiperazin-1-yl)-3'-(morpholinomethyl)-[1,1'-biphenyl]-3-yl)-6-oxo-4-(trifluoromethyl)-1,6-dihydropyridine-3-carboxamide 16d (OICR-9429) is a potent and selective chemical probe suitable to help dissect the biological role of WDR5.

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Organizational Affiliation: 

Department of Pharmacology and Toxicology, University of Toronto , Medical Sciences Building, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 70.04 kDa 
• Atom Count: 5,237 
• Modelled Residue Count: 608 
• 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

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5MN	C [auth A], P [auth B]	~{N}-[5-(1~{H}-indol-5-yl)-2-(4-methylpiperazin-1-yl)phenyl]-3-methyl-benzamide C27 H28 N4 O JXGJIPHOKSHSAC-UHFFFAOYSA-N
BTB	R [auth B]	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C8 H19 N O5 OWMVSZAMULFTJU-UHFFFAOYSA-N
SO4	Q [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	D [auth A], S [auth B], T [auth B], U [auth B], V [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
UNX	AA [auth B], BA [auth B], CA [auth B], DA [auth B], E [auth A], EA [auth B], F [auth A], FA [auth B], G [auth A], GA [auth B], H [auth A], HA [auth B], I [auth A], IA [auth B], J [auth A], JA [auth B], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], W [auth B], X [auth B], Y [auth B], Z [auth B]	UNKNOWN ATOM OR ION X

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.228 
• R-Value Work: 0.197 
• R-Value Observed: 0.197 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.939	α = 107.17
b = 54.779	β = 90.21
c = 64.011	γ = 112.61

Software Package:

Software Name	Purpose
HKL-3000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MOLREP	phasing
HKL-3000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-11-04 
Deposition Author(s): DONG, A., DOMBROVSKI, L., SMIL, D., GETLIK, M., BOLSHAN, Y., WALKER, J.R., SENISTERRA, G., PODA, G., AL-AWAR, R., SCHAPIRA, M., VEDADI, M., Bountra, C., Edwards, A.M., Arrowsmith, C.H., BROWN, P.J., WU, H., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2015-11-04
  Type: Initial release
  
• Version 1.1: 2018-05-23
  Changes: Data collection, Database references, Derived calculations
• Version 1.2: 2023-09-27
  Changes: Data collection, Database references, Refinement description