9PLY | pdb_00009ply

Crystal structure of the human DCAF1 WDR domain in complex with OICR-40156

PDB DOI: https://doi.org/10.2210/pdb9PLY/pdb

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

Deposited: 2025-07-16 Released: 2025-07-30
Deposition Author(s): Kimani, S., Dong, A., Li, Y., Seitova, A., Krausser, C., Wilson, B., Al-awar, R., Ackloo, S., Arrowsmith, C.H., Edwards, A.M., Halabelian, L., Structural Genomics Consortium (SGC)
Funding Organization(s): Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free:
0.174 (Depositor), 0.183 (DCC)
R-Value Work:
0.146 (Depositor), 0.163 (DCC)
R-Value Observed:
0.147 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 9PLY

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

Literature

Crystal structure of the human DCAF1 WDR domain in complex with OICR-40156

Kimani, S., Dong, A., Li, Y., Seitova, A., Krausser, C., Wilson, B., Al-awar, R., Ackloo, S., Arrowsmith, C.H., Edwards, A.M., Halabelian, L., Structural Genomics Consortium (SGC)

To be published.

Macromolecule Content

Total Structure Weight: 72.47 kDa
Atom Count: 5,403
Modeled Residue Count: 592
Deposited Residue Count: 630
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9Y4B6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1CI0 Query on A1CI0 Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain C [auth A] MOL2 format, chain F [auth B] MOL2 format, chain C [auth A] mmCIF format, chain F [auth B] mmCIF format, chain C [auth A]	C [auth A], F [auth B]	(4P)-N-[(1S)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-4-(4-chloro-2-fluorophenyl)-5-{(1E)-3-[(3-methoxypropyl)amino]-3-oxoprop-1-en-1-yl}-1H-pyrrole-3-carboxamide C₂₇ H₂₆ Cl₂ F₂ N₄ O₄ LYOVEJQNXMPQIE-MNQSQUENSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain D [auth A] MOL2 format, chain G [auth B] MOL2 format, chain D [auth A] mmCIF format, chain G [auth B] mmCIF format, chain D [auth A]	D [auth A], G [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]
UNX (Subject of Investigation/LOI) Query on UNX Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A]	E [auth A], H [auth B]	UNKNOWN ATOM OR ION X		Interactions Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.174 (Depositor), 0.183 (DCC)
R-Value Work: 0.146 (Depositor), 0.163 (DCC)
R-Value Observed: 0.147 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.35	α = 90
b = 88.6	β = 98.01
c = 73.409	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-07-30

Deposition Author(s):

Arrowsmith, C.H.

Structural Genomics Consortium (SGC)

Funding Organization	Location	Grant Number
Other private		--

Revision History (Full details and data files)

Version 1.0: 2025-07-30
Type: Initial release

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.