9NCV | pdb_00009ncv

Crystal Structure of WDR5 in complex with Triazole-Based Inhibitors

PDB DOI: https://doi.org/10.2210/pdb9NCV/pdb

Classification: STRUCTURAL PROTEIN/INHIBITOR
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-02-17 Released: 2025-08-13
Deposition Author(s): Goins, C.M., Stauffer, S.R.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.58 Å
R-Value Free:
0.287 (Depositor), 0.288 (DCC)
R-Value Work:
0.253 (Depositor), 0.254 (DCC)
R-Value Observed:
0.254 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Development and Characterization of Triazole-Based WDR5 Inhibitors for the Treatment of Glioblastoma

Coker, J.A., Martinez, S.R., Han, S.H., Sloan, A.R., Gupta, A.K., Bukenya, G., Polzer, P., Ramos, J.H., Rico, E., Rico, A., Lindsey, A.A., Navadgi, T., Reitz, N., Romigh, T., Goins, C.M., Hubert, C.G., Wang, N.S., Cheng, F.R., Alvarado, J., Sprowls, S.A., Lathia, J.D., Stauffer, S.R.

(2025) bioRxiv

DOI: https://doi.org/10.1101/2025.07.29.667410

Macromolecule Content

Total Structure Weight: 190.49 kDa
Atom Count: 10,456
Modeled Residue Count: 1,184
Deposited Residue Count: 1,696
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
WD repeat-containing protein 5	A, B, C, D	424	Homo sapiens	Mutation(s): 0 Gene Names: WDR5, BIG3
UniProt & NIH Common Fund Data Resources
Find proteins for P61964 (Homo sapiens) Explore P61964 Go to UniProtKB: P61964
PHAROS: P61964 GTEx: ENSG00000196363
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P61964
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1BW8 (Subject of Investigation/LOI) Query on A1BW8 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain G [auth C] SDF format, chain H [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth C] MOL2 format, chain H [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain G [auth C] mmCIF format, chain H [auth D]	E [auth A], F [auth B], G [auth C], H [auth D]	(6P)-6-[1-ethyl-3-(trifluoromethyl)-1H-pyrazol-4-yl]-3-[(4-fluoro-3-methylphenyl)methyl]-8-[(2-methyl-1H-imidazol-1-yl)methyl]-4,5-dihydro-3H-naphtho[1,2-d][1,2,3]triazole C₂₉ H₂₇ F₄ N₇ XLTBFORPJOMOPM-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.58 Å
R-Value Free: 0.287 (Depositor), 0.288 (DCC)
R-Value Work: 0.253 (Depositor), 0.254 (DCC)
R-Value Observed: 0.254 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.768	α = 89.401
b = 68.834	β = 76.646
c = 94.382	γ = 89.967

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-08-13

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-08-13
Type: Initial release

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.