8F1G

Crystal structure of human WDR5 in complex with compound WM662


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Discovery of Potent Small-Molecule Inhibitors of WDR5-MYC Interaction.

Ding, J.Li, G.Liu, H.Liu, L.Lin, Y.Gao, J.Zhou, G.Shen, L.Zhao, M.Yu, Y.Guo, W.Hommel, U.Ottl, J.Blank, J.Aubin, N.Wei, Y.He, H.Sage, D.R.Atadja, P.W.Li, E.Jain, R.K.Tallarico, J.A.Canham, S.M.Chiang, Y.L.Wang, H.

(2023) ACS Chem Biol 18: 34-40

  • DOI: https://doi.org/10.1021/acschembio.2c00843
  • Primary Citation of Related Structures:  
    8F1G

  • PubMed Abstract: 

    WD repeat domain 5 (WDR5) is a member of the WD40-repeat protein family that plays a critical role in multiple processes. It is also a prominent target for pharmacological inhibition in diseases such as cancer, aging, and neurodegenerative disorders. Interactions between WDR5 and various partners are essential for sustaining its function. Most drug discovery efforts center on the WIN (WDR5 interaction motif) site of WDR5 that is responsible for the recruitment of WDR5 to chromatin. Here, we describe the discovery of novel WDR5 inhibitors for the other WBM (WDR5 binding motif) pocket on this scaffold protein, to disrupt WDR5 interaction with its binding partner MYC by high-throughput biochemical screening, subsequent molecule optimization, and biological assessment. These new WDR5 inhibitors provide useful probes for future investigations of WDR5 and an avenue for targeting WDR5 as a therapeutic strategy.


  • Organizational Affiliation

    Novartis Institutes for BioMedical Research, Cambridge, Massachusetts02139, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
WD repeat-containing protein 5
A, B
316Homo sapiensMutation(s): 0 
Gene Names: WDR5BIG3
UniProt & NIH Common Fund Data Resources
Find proteins for P61964 (Homo sapiens)
Explore P61964 
Go to UniProtKB:  P61964
PHAROS:  P61964
GTEx:  ENSG00000196363 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61964
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
X8N (Subject of Investigation/LOI)
Query on X8N

Download Ideal Coordinates CCD File 
C [auth A],
J [auth B]
(2S)-2-({(2S)-3-(3'-chloro[1,1'-biphenyl]-4-yl)-1-oxo-1-[(1H-tetrazol-5-yl)amino]propan-2-yl}oxy)propanoic acid
C19 H18 Cl N5 O4
YSQNVTHQOQFUOS-ZBEGNZNMSA-N
PGE
Query on PGE

Download Ideal Coordinates CCD File 
I [auth A],
O [auth B]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
H [auth A],
N [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
K [auth B]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
K [auth B],
L [auth B],
M [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.966α = 90
b = 80.243β = 103.7
c = 64.183γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2023-01-11 
  • Deposition Author(s): Liu, H.

Funding OrganizationLocationGrant Number
Other private--

Revision History  (Full details and data files)

  • Version 1.0: 2023-01-11
    Type: Initial release
  • Version 1.1: 2023-02-01
    Changes: Database references
  • Version 1.2: 2023-10-25
    Changes: Data collection, Refinement description