6VYC

Crystal structure of WD-repeat domain of human WDR91


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.223 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Discovery of a First-in-Class Small-Molecule Ligand for WDR91 Using DNA-Encoded Chemical Library Selection Followed by Machine Learning.

Ahmad, S.Xu, J.Feng, J.A.Hutchinson, A.Zeng, H.Ghiabi, P.Dong, A.Centrella, P.A.Clark, M.A.Guie, M.A.Guilinger, J.P.Keefe, A.D.Zhang, Y.Cerruti, T.Cuozzo, J.W.von Rechenberg, M.Bolotokova, A.Li, Y.Loppnau, P.Seitova, A.Li, Y.Y.Santhakumar, V.Brown, P.J.Ackloo, S.Halabelian, L.

(2023) J Med Chem 66: 16051-16061

  • DOI: https://doi.org/10.1021/acs.jmedchem.3c01471
  • Primary Citation of Related Structures:  
    6VYC, 8SHJ, 8T55

  • PubMed Abstract: 

    WD40 repeat-containing protein 91 (WDR91) regulates early-to-late endosome conversion and plays vital roles in endosome fusion, recycling, and transport. WDR91 was recently identified as a potential host factor for viral infection. We employed DNA-encoded chemical library (DEL) selection against the WDR domain of WDR91, followed by machine learning to predict ligands from the synthetically accessible Enamine REAL database. Screening of predicted compounds identified a WDR91 selective compound 1 , with a K D of 6 ± 2 μM by surface plasmon resonance. The co-crystal structure confirmed the binding of 1 to the WDR91 side pocket, in proximity to cysteine 487, which led to the discovery of covalent analogues 18 and 19 . The covalent adduct formation for 18 and 19 was confirmed by intact mass liquid chromatography-mass spectrometry. The discovery of 1 , 18 , and 19 , accompanying structure-activity relationship, and the co-crystal structures provide valuable insights for designing potent and selective chemical tools against WDR91 to evaluate its therapeutic potential.


  • Organizational Affiliation

    Structural Genomics Consortium, University of Toronto, Ontario M5G 1L7, Canada.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
WD repeat-containing protein 91
A, B
374Homo sapiensMutation(s): 0 
Gene Names: WDR91HSPC049
UniProt & NIH Common Fund Data Resources
Find proteins for A4D1P6 (Homo sapiens)
Explore A4D1P6 
Go to UniProtKB:  A4D1P6
PHAROS:  A4D1P6
GTEx:  ENSG00000105875 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA4D1P6
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.223 
  • Space Group: P 21 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.004α = 90
b = 84.047β = 90
c = 110.165γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-25
    Type: Initial release
  • Version 1.1: 2023-10-11
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2024-05-01
    Changes: Database references