8F8E

Crystal structure of the WDR domain of human DCAF1 in complex with OICR-8268 compound

• PDB DOI: https://doi.org/10.2210/pdb8F8E/pdb

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


• Deposited: 2022-11-21 Released: 2023-03-01 
• Deposition Author(s): Kimani, S., Li, A., Dong, A., Li, Y., Hutchinson, A., Seitova, A., Wilson, B., Al-Awar, R., Vedadi, M., Brown, P., 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: 1.55 Å
• R-Value Free: 0.209 
• R-Value Work: 0.181 
• R-Value Observed: 0.182 

Starting Model: experimental

Literature

Crystal structure of the WDR domain of human DCAF1 in complex with OICR-8268 compound

Kimani, S., Li, A., Dong, A., Li, Y., Hutchinson, A., Seitova, A., Wilson, B., Al-Awar, R., Vedadi, M., Brown, P., Arrowsmith, C.H., Edwards, A.M., Halabelian, L.

To be published.

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: 72.26 kDa 
• Atom Count: 5,137 
• Modelled Residue Count: 593 
• 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): 2  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
XJI (Subject of Investigation/LOI)	C [auth A], D [auth B]	(3P)-N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-3-(4-chloro-2-fluorophenyl)-1H-pyrazole-4-carboxamide C19 H14 Cl2 F2 N4 O2 IPDMIUDPUBUHSU-INIZCTEOSA-N
CIT	E [auth B]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.209 
• R-Value Work: 0.181 
• R-Value Observed: 0.182 
• Space Group: P 1 2₁ 1
• Diffraction Data: https://doi.org/10.18430/M38F8E

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.865	α = 90
b = 88.084	β = 97.56
c = 73.562	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-03-01 
Deposition Author(s): Kimani, S., Li, A., Dong, A., Li, Y., Hutchinson, A., Seitova, A., Wilson, B., Al-Awar, R., Vedadi, M., Brown, P., 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: 2023-03-01
  Type: Initial release
  
• Version 1.1: 2024-05-22
  Changes: Data collection