9YV4 | pdb_00009yv4

Crystal structure of the human DCAF1 WDR domain in complex with OICR-41109

• PDB DOI: https://doi.org/10.2210/pdb9YV4/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2025-10-23 Released: 2025-11-26 
• Deposition Author(s): Kimani, S., Dong, A., Li, Y., Seitova, A., Mamai, A., Al-awar, R., Ackloo, S., Arrowsmith, C.H., Edwards, A.M., Halabelian, L., Structural Genomics Consortium (SGC)
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.194 (Depositor), 0.203 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.187 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Starting Model: experimental

Literature

OICR-41103 as a chemical probe for the DCAF1 WD40 domain.

Kimani, S.W., Noureldin, M., Wilson, B., Hoffer, L., Green, S.R., Szewczyk, M.M., Gonzalez-Alvarez, H., Mohammed, M., Chan, M., Krausser, C., Li, A.S.M., Hajian, T., Tucker, S., Joshi, D., Saraon, P., Theriault, B., Kim, J.S., Santhakumar, V., Loppnau, P., Li, Y., Seitova, A., Dong, A., Kiyota, T., Hammann, T., Gehrtz, P., Patel, B., Rathod, V., Vala, A., Rout, B., Jagodra, P., Brown, P.J., Aman, A., Ramnauth, J., Poda, G., Uehling, D., Arrowsmith, C.H., Barsyte-Lovejoy, D., Marcellus, R., Ackloo, S., Mamai, A., Al-Awar, R., Halabelian, L.

(2025) Commun Biol 8: 1076-1076

• PubMed: 40683980 
• DOI: https://doi.org/10.1038/s42003-025-08491-0
• Primary Citation of Related Structures:  
  9YV4


• PubMed Abstract: 
  

  Human DCAF1 is a multidomain protein that plays a critical role in protein homeostasis. Its WDR domain functions as a substrate recruitment module for RING-type CRL4 and HECT family EDVP E3 ubiquitin ligases, enabling the ubiquitination and proteasomal degradation of specific substrates. DCAF1's activity has been implicated in cell proliferation and is documented to promote tumorigenesis. Additionally, the DCAF1 WDR domain is hijacked by lentiviral accessory proteins to induce the degradation of host antiviral factors, such as SAMHD1 and UNG2. These diverse roles make DCAF1 an attractive target for therapeutic development in oncology and antiviral strategies. It is also a promising candidate for use in targeted protein degradation. We previously reported a novel ligand, OICR-8268, that targets the DCAF1 WDR domain. In this study, we present the development of OICR-41103, a potent, selective, and cell-active small molecule chemical probe for DCAF1, derived from OICR-8268. The co-crystal structure of the DCAF1-OICR-41103 complex reveals the ligand's binding mode within the WDR central pocket, demonstrating its potential for PROTAC design and development. Notably, OICR-41103 effectively displaces the lentiviral Vpr protein from DCAF1 in both biochemical and cellular settings, highlighting its potential for the development of HIV therapeutics.

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Organizational Affiliation: 
• Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada.
Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, ON, Canada.
Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada.
Medicinal Chemistry, Global Research & Development, Merck Healthcare KGaA, Darmstadt, Germany.
Piramal Discovery Solutions, Pharmaceutical Special Economic Zone, Ahmedabad, Gujarat, India.
Structural Genomics Consortium, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada.
Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.
Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.
Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, ON, Canada. [e-mail].
Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada. [e-mail].
Department of Chemistry, University of Toronto, Toronto, ON, Canada. [e-mail].
Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada. [e-mail].
Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 72.32 kDa 
• Atom Count: 5,469 
• Modeled Residue Count: 599 
• Deposited Residue Count: 630 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DDB1- and CUL4-associated factor 1	A, B	315	Homo sapiens	Mutation(s): 0  Gene Names: DCAF1, KIAA0800, RIP, VPRBP 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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1CY9 (Subject of Investigation/LOI)	C [auth A], F [auth B]	(4P)-4-(4-chloro-2-fluorophenyl)-N-[(1S)-1-(3-chloro-4-fluorophenyl)-2-cyanoethyl]-5-[(1E)-3-oxo-3-(pyrrolidin-1-yl)prop-1-en-1-yl]-1H-pyrrole-3-carboxamide C27 H22 Cl2 F2 N4 O2 UEAYIXMYXYOLSD-MNQSQUENSA-N
NA	D [auth A], G [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N
UNX	E [auth A]	UNKNOWN ATOM OR ION X

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.194 (Depositor), 0.203 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.187 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: P 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.009	α = 90
b = 51.263	β = 90.72
c = 79.97	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-26 
Deposition Author(s): Kimani, S., Dong, A., Li, Y., Seitova, A., Mamai, A., Al-awar, R., Ackloo, S., Arrowsmith, C.H., Edwards, A.M., Halabelian, L., Structural Genomics Consortium (SGC)

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Funding Organization	Location	Grant Number
Other private	Canada	--

Revision History  

• Version 1.0: 2025-11-26
  Type: Initial release
  
• Version 1.1: 2025-12-03
  Changes: Database references