9D4E | pdb_00009d4e

Crystal structure of the human DCAF1 WDR domain in complex with OICR-41103

• PDB DOI: https://doi.org/10.2210/pdb9D4E/pdb

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


• Deposited: 2024-08-12 Released: 2024-12-18 
• Deposition Author(s): Kimani, S., Dong, A., Li, Y., Seitova, A., Al-awar, R., Mamai, A., 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: 1.70 Å
• R-Value Free: 
  0.206 (Depositor), 0.214 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.187 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the human DCAF1 WDR domain in complex with OICR-1103

Kimani, S., Dong, A., Li, Y., Seitova, A., Al-awar, R., Mamai, A., 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: 72.53 kDa 
• Atom Count: 5,149 
• Modeled Residue Count: 597 
• 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
A1A1Q (Subject of Investigation/LOI)	C [auth A], E [auth B]	(4P)-N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-4-(4-chloro-2-fluorophenyl)-5-[(1E)-3-oxo-3-(piperidin-1-yl)prop-1-en-1-yl]-1H-pyrrole-3-carboxamide C28 H26 Cl2 F2 N4 O3 WQUCFJCZXPDBNP-KDLSMAQYSA-N
CIT	D [auth A]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.206 (Depositor), 0.214 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.187 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.574	α = 90
b = 87.975	β = 96.94
c = 73.136	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-12-18 
Deposition Author(s): Kimani, S., Dong, A., Li, Y., Seitova, A., Al-awar, R., Mamai, A., 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: 2024-12-18
  Type: Initial release