9Y76 | pdb_00009y76

Crystal structure of the human DCAF1 WDR domain in complex with OICR-40120

• PDB DOI: https://doi.org/10.2210/pdb9Y76/pdb

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


• Deposited: 2025-09-09 Released: 2025-10-15 
• 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: 1.56 Å
• R-Value Free: 
  0.208 (Depositor), 0.222 (DCC) 
• R-Value Work: 
  0.167 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.169 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the human DCAF1 WDR domain in complex with OICR-40120

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)

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: 72.44 kDa 
• Atom Count: 5,236 
• Modeled Residue Count: 596 
• 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
A1CSX (Subject of Investigation/LOI)	C [auth A], E [auth B]	(4P,5M)-N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-4-(4-chloro-2-fluorophenyl)-5-{1-[2-(morpholin-4-yl)ethyl]-1H-pyrazol-4-yl}-1H-pyrrole-3-carboxamide C29 H28 Cl2 F2 N6 O3 YZJAUYCZRMQXSE-VWLOTQADSA-N
UNX	D [auth A]	UNKNOWN ATOM OR ION X

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.56 Å
• R-Value Free:  0.208 (Depositor), 0.222 (DCC) 
• R-Value Work:  0.167 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.169 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.954	α = 90
b = 88.41	β = 97.86
c = 73.556	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-10-15 
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		--

Revision History  

• Version 1.0: 2025-10-15
  Type: Initial release