Macromolecule Content

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

8OO5

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.220
R-Value Work: 0.181
R-Value Observed: 0.183

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9Y4B6
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
VUF (Subject of Investigation/LOI) Query on VUF Download Ideal Coordinates CCD File SDF format, chain B [auth P] SDF format, chain C [auth P] MOL2 format, chain B [auth P] MOL2 format, chain C [auth P]	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		Ligand Interaction
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain D [auth P] SDF format, chain E [auth P] SDF format, chain F [auth P] SDF format, chain G [auth P] MOL2 format, chain D [auth P] MOL2 format, chain E [auth P] MOL2 format, chain F [auth P] MOL2 format, chain G [auth P]	D [auth P], E [auth P], F [auth P], G [auth P]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.220
R-Value Work: 0.181
R-Value Observed: 0.183
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

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-05-24

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2023-05-24
Type: Initial release

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.