8OO5 | pdb_00008oo5

Crystal structure of human DCAF1 WD40 repeats (Q1250L) in complex with compound 13

• PDB DOI: https://doi.org/10.2210/pdb8OO5/pdb

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


• Deposited: 2023-04-04 Released: 2023-05-24 
• Deposition Author(s): Schroeder, M., Renatus, M.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.220 (Depositor), 0.217 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

Starting Model: experimental

Literature

Reinstating targeted protein degradation with DCAF1 PROTACs in CRBN PROTAC resistant settings

Schroder, M., Renatus, M., Thoma, C.R.

(2023) bioRxiv 

• DOI: https://doi.org/10.1101/2023.04.09.536153

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 37.32 kDa 
• Atom Count: 2,548 
• Modeled Residue Count: 300 
• Deposited Residue Count: 318 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DDB1- and CUL4-associated factor 1	A [auth P]	318	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
VUF (Subject of Investigation/LOI)	B [auth P], C [auth P]	1-[4-[4-(2-azanylethylamino)-2-[1-(4-chlorophenyl)cyclohexyl]quinazolin-7-yl]piperazin-1-yl]ethanone C28 H35 Cl N6 O GGEKTDCCHNVLNE-UHFFFAOYSA-N
EDO	D [auth P], E [auth P], F [auth P], G [auth P]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.220 (Depositor), 0.217 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.577	α = 90
b = 81.577	β = 90
c = 234.132	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: 2023-05-24 
Deposition Author(s): Schroeder, M., Renatus, M.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-05-24
  Type: Initial release
  
• Version 1.1: 2024-06-19
  Changes: Data collection