8OG7

Crystal structure of human DCAF1 WD40 repeats (Q1250L) in complex with compound 2

• PDB DOI: https://doi.org/10.2210/pdb8OG7/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2023-03-19 Released: 2023-06-14 
• Deposition Author(s): Schroeder, M., Vulpetti, A., Renatus, M.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.64 Å
• R-Value Free: 0.206 
• R-Value Work: 0.158 
• R-Value Observed: 0.160 

Starting Model: experimental

Literature

Discovery of New Binders for DCAF1, an Emerging Ligase Target in the Targeted Protein Degradation Field.

Vulpetti, A., Holzer, P., Schmiedeberg, N., Imbach-Weese, P., Pissot-Soldermann, C., Hollingworth, G.J., Radimerski, T., Thoma, C.R., Stachyra, T.M., Wojtynek, M., Maschlej, M., Chau, S., Schuffenhauer, A., Fernandez, C., Schroder, M., Renatus, M.

(2023) ACS Med Chem Lett 14: 949-954

• PubMed: 37465299 
• DOI: https://doi.org/10.1021/acsmedchemlett.3c00104
• Primary Citation of Related Structures:  
  8OG5, 8OG6, 8OG7, 8OG8, 8OG9, 8OGA, 8OGB, 8OGC


• PubMed Abstract: 
  

  In this study, we describe the rapid identification of potent binders for the WD40 repeat domain (WDR) of DCAF1. This was achieved by two rounds of iterative focused screening of a small set of compounds selected on the basis of internal WDR domain knowledge followed by hit expansion. Subsequent structure-based design led to nanomolar potency binders with a clear exit vector enabling DCAF1-based bifunctional degrader exploration.

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Organizational Affiliation: 

Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Basel 4002, Switzerland.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 42.17 kDa 
• Atom Count: 2,602 
• Modelled Residue Count: 300 
• Deposited Residue Count: 367 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DDB1- and CUL4-associated factor 1	A	367	Homo sapiens	Mutation(s): 1  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
VMR (Subject of Investigation/LOI)	D [auth A]	(4~{R})-4-[3-(4-chloranylphenoxy)phenyl]pyrrolidin-2-imine C16 H15 Cl N2 O YHXWMEXRFSXVKK-LBPRGKRZSA-N
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT	B [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.64 Å
• R-Value Free: 0.206 
• R-Value Work: 0.158 
• R-Value Observed: 0.160 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.75	α = 90
b = 81.75	β = 90
c = 235.633	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-06-14 
Deposition Author(s): Schroeder, M., Vulpetti, A., Renatus, M.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-06-14
  Type: Initial release
  
• Version 1.1: 2023-08-02
  Changes: Database references
• Version 1.2: 2024-06-19
  Changes: Data collection