3SMR

Crystal structure of human WD repeat domain 5 with compound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Small-molecule inhibition of MLL activity by disruption of its interaction with WDR5.

Senisterra, G.Wu, H.Allali-Hassani, A.Wasney, G.A.Barsyte-Lovejoy, D.Dombrovski, L.Dong, A.Nguyen, K.T.Smil, D.Bolshan, Y.Hajian, T.He, H.Seitova, A.Chau, I.Li, F.Poda, G.Couture, J.F.Brown, P.J.Al-Awar, R.Schapira, M.Arrowsmith, C.H.Vedadi, M.

(2013) Biochem J 449: 151-159

  • DOI: 10.1042/BJ20121280
  • Primary Citation of Related Structures:  
    3UR4, 3SMR

  • PubMed Abstract: 
  • WDR5 (WD40 repeat protein 5) is an essential component of the human trithorax-like family of SET1 [Su(var)3-9 enhancer-of-zeste trithorax 1] methyltransferase complexes that carry out trimethylation of histone 3 Lys4 (H3K4me3), play key roles in deve ...

    WDR5 (WD40 repeat protein 5) is an essential component of the human trithorax-like family of SET1 [Su(var)3-9 enhancer-of-zeste trithorax 1] methyltransferase complexes that carry out trimethylation of histone 3 Lys4 (H3K4me3), play key roles in development and are abnormally expressed in many cancers. In the present study, we show that the interaction between WDR5 and peptides from the catalytic domain of MLL (mixed-lineage leukaemia protein) (KMT2) can be antagonized with a small molecule. Structural and biophysical analysis show that this antagonist binds in the WDR5 peptide-binding pocket with a Kd of 450 nM and inhibits the catalytic activity of the MLL core complex in vitro. The degree of inhibition was enhanced at lower protein concentrations consistent with a role for WDR5 in directly stabilizing the MLL multiprotein complex. Our data demonstrate inhibition of an important protein-protein interaction and form the basis for further development of inhibitors of WDR5-dependent enzymes implicated in MLL-rearranged leukaemias or other cancers.


    Organizational Affiliation

    Structural Genomics Consortium, 101 College Street, Toronto, Ontario, Canada.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
WD repeat-containing protein 5ABCD312Homo sapiensMutation(s): 0 
Gene Names: WDR5BIG3
Find proteins for P61964 (Homo sapiens)
Explore P61964 
Go to UniProtKB:  P61964
NIH Common Fund Data Resources
PHAROS  P61964
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NP7
Query on NP7

Download CCD File 
A, B, C, D
2-chloro-N-[2-(4-methylpiperazin-1-yl)-5-nitrophenyl]benzamide
C18 H19 Cl N4 O3
WOGZFCMBPXJNFI-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download CCD File 
A, B, C, D
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
UNX
Query on UNX

Download CCD File 
A, B, C, D
UNKNOWN ATOM OR ION
X
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
NP7Kd:  6900   nM  BindingDB
NP7Kd:  7000   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 204.171α = 90
b = 93.467β = 107.24
c = 64.786γ = 90
Software Package:
Software NamePurpose
StructureStudiodata collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Revision History 

  • Version 1.0: 2011-08-31
    Type: Initial release
  • Version 1.1: 2018-05-16
    Changes: Data collection, Database references