9D5Z | pdb_00009d5z

Crystal structure of the human WDR5 in complex with LH168 compound

PDB DOI: https://doi.org/10.2210/pdb9D5Z/pdb

Classification: TRANSCRIPTION
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-08-14 Released: 2025-02-19
Deposition Author(s): Kimani, S., Dong, A., Hoffmann, L., Nemec, V., Ackloo, S., Muller-Knapp, S., Knapp, 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: 1.70 Å
R-Value Free:
0.189 (Depositor), 0.190 (DCC)
R-Value Work:
0.139 (Depositor), 0.151 (DCC)
R-Value Observed:
0.140 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Discovery of an exquisitely selective WDR5 chemical probe accelerated by a high-quality DEL-ML Hit.

Hoffmann, L., Lenz, C., Farges, F., Kimani, S.W., Dopfer, J., Keller, S., Schwalm, M.P., Holzmann, H., Kraemer, A., Dong, A., Li, F., Chau, I., Halabelian, L., Gstaiger, M., Muller, S., Knapp, S., Nemec, V.

(2025) RSC Chem Biol 6: 1585-1594

PubMed: 40927425 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1039/d5cb00109a
Primary Citation Related Structures:
9D5Z

PubMed Abstract:
Herein we present the rapid development of LH168, a potent and highly selective chemical probe for WDR5, streamlined by utilizing a DEL-ML (DNA encoded library-machine learning) hit as the chemical starting point. LH168 was comprehensively characterized in bioassays and demonstrated potent in cellulo target engagement at the WIN-site pocket of WDR5, with an EC ₅₀ of approximately 10 nM, a long residence time, and exceptional proteome-wide selectivity for WDR5. In addition, we present the X-ray co-crystal structure and provide insights into the structure-activity relationships (SAR). In parallel, we developed a matched negative control compound as well as an alkyne analog (compound 16) to facilitate the development of bifunctional molecules. Taken together, we provide the scientific community with a well-characterized chemical probe to enable studies and functional manipulation of WDR5 in a cellular context, as this protein represents a therapeutically relevant target with scaffolding functions that influence multiple cellular processes.

Organizational Affiliation

Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University Max-von-Laue-Str. 9 D-60438 Frankfurt am Main Germany nemec@pharmchem.uni-frankfurt.de knapp@pharmchem.uni-franfurt.de.

Macromolecule Content

Total Structure Weight: 70.06 kDa
Atom Count: 5,271
Modeled Residue Count: 604
Deposited Residue Count: 624
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
WD repeat-containing protein 5	A, B	312	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P61964
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1A16 (Subject of Investigation/LOI) Query on A1A16 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]	(3P)-N-[(2S)-1-(6,7-dihydrothieno[3,2-c]pyridin-5(4H)-yl)-1-oxopentan-2-yl]-3-[1-ethyl-3-(trifluoromethyl)-1H-pyrazol-4-yl]-5-[(1H-imidazol-1-yl)methyl]benzamide C₂₉ H₃₁ F₃ N₆ O₂ S UFKFTBGGMLIIME-DEOSSOPVSA-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 D [auth A] SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain I [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B]	D [auth A], E [auth A], G [auth B], H [auth B], I [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B]