5EAM

Crystal structure of human WDR5 in complex with compound 9o


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

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

  • DOI: 10.1021/acs.jmedchem.5b01630
  • Primary Citation of Related Structures:  

  • 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 lymphob ...

    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.


    Organizational Affiliation

    Drug Discovery Program, Ontario Institute for Cancer Research , 661 University Avenue, MaRS Centre, West Tower, Toronto, Ontario M5G 0A3, Canada.




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 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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Download CCD File 
B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 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

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A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
BTB
Query on BTB

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Download CCD File 
B
2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
BIS-TRIS BUFFER
C8 H19 N O5
OWMVSZAMULFTJU-UHFFFAOYSA-N
 Ligand Interaction
5MN
Query on 5MN

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Download CCD File 
A, B
~{N}-[5-(1~{H}-indol-5-yl)-2-(4-methylpiperazin-1-yl)phenyl]-3-methyl-benzamide
C27 H28 N4 O
JXGJIPHOKSHSAC-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.197 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 46.939α = 107.17
b = 54.779β = 90.21
c = 64.011γ = 112.61
Software Package:
Software NamePurpose
HKL-3000data scaling
PDB_EXTRACTdata extraction
MOLREPphasing
REFMACrefinement
HKL-3000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2015-11-04
    Type: Initial release
  • Version 1.1: 2018-05-23
    Type: Data collection, Database references, Derived calculations