9BA2 | pdb_00009ba2

Crystal structure of the binary complex of DCAF1 and WDR5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.97 Å
  • R-Value Free: 
    0.266 (Depositor), 0.219 (DCC) 
  • R-Value Work: 
    0.230 (Depositor) 
  • R-Value Observed: 
    0.231 (Depositor) 

Starting Models: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Crystal structures of DCAF1-PROTAC-WDR5 ternary complexes provide insight into DCAF1 substrate specificity.

Mabanglo, M.F.Wilson, B.Noureldin, M.Kimani, S.W.Mamai, A.Krausser, C.Gonzalez-Alvarez, H.Srivastava, S.Mohammed, M.Hoffer, L.Chan, M.Avrumutsoae, J.Li, A.S.M.Hajian, T.Tucker, S.Green, S.Szewczyk, M.Barsyte-Lovejoy, D.Santhakumar, V.Ackloo, S.Loppnau, P.Li, Y.Seitova, A.Kiyota, T.Wang, J.G.Prive, G.G.Kuntz, D.A.Patel, B.Rathod, V.Vala, A.Rout, B.Aman, A.Poda, G.Uehling, D.Ramnauth, J.Halabelian, L.Marcellus, R.Al-Awar, R.Vedadi, M.

(2024) Nat Commun 15: 10165-10165

  • DOI: https://doi.org/10.1038/s41467-024-54500-x
  • Primary Citation Related Structures: 
    9B9H, 9B9T, 9B9W, 9BA2, 9DLW

  • PubMed Abstract: 

    Proteolysis-targeting chimeras (PROTACs) have been explored for the degradation of drug targets for more than two decades. However, only a handful of E3 ligase substrate receptors have been efficiently used. Downregulation and mutation of these receptors would reduce the effectiveness of such PROTACs. We recently developed potent ligands for DCAF1, a substrate receptor of EDVP and CUL4 E3 ligases. Here, we focus on DCAF1 toward the development of PROTACs for WDR5, a drug target in various cancers. We report four DCAF1-based PROTACs with endogenous and exogenous WDR5 degradation effects and high-resolution crystal structures of the ternary complexes of DCAF1-PROTAC-WDR5. The structures reveal detailed insights into the interaction of DCAF1 with various WDR5-PROTACs, indicating a significant role of DCAF1 loops in providing needed surface plasticity, and reflecting the mechanism by which DCAF1 functions as a substrate receptor for E3 ligases with diverse sets of substrates.


  • Organizational Affiliation
    • Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, ON, Canada.

Macromolecule Content 

  • Total Structure Weight: 74.8 kDa 
  • Atom Count: 4,887 
  • Modeled Residue Count: 611 
  • Deposited Residue Count: 667 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DDB1- and CUL4-associated factor 1338Homo sapiensMutation(s): 0 
Gene Names: DCAF1KIAA0800RIPVPRBP
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y4B6 (Homo sapiens)
Explore Q9Y4B6 
Go to UniProtKB:  Q9Y4B6
PHAROS:  Q9Y4B6
GTEx:  ENSG00000145041 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y4B6
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
WD repeat-containing protein 5329Homo 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 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IMD
(Subject of Investigation/LOI)

Query on IMD



Download:Ideal Coordinates CCD File
C [auth A]IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.97 Å
  • R-Value Free:  0.266 (Depositor), 0.219 (DCC) 
  • R-Value Work:  0.230 (Depositor) 
  • R-Value Observed: 0.231 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.597α = 90
b = 83.185β = 90
c = 158.152γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
pointlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ontario Institute for Cancer ResearchCanada--

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-06
    Type: Initial release
  • Version 1.1: 2024-12-04
    Changes: Database references