9NA6 | pdb_00009na6

IRAK4 in Complex with Compound 34

PDB DOI: https://doi.org/10.2210/pdb9NA6/pdb

Classification: IMMUNE SYSTEM,TRANSFERASE/INHIBITOR
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2025-02-11 Released: 2025-05-28
Deposition Author(s): Ferrao, R., Lansdon, E.B.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.14 Å
R-Value Free:
0.246 (Depositor), 0.245 (DCC)
R-Value Work:
0.214 (Depositor), 0.214 (DCC)
R-Value Observed:
0.215 (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 Edecesertib (GS-5718): A Potent, Selective Inhibitor of IRAK4.

Ammann, S.E., Cottell, J.J., Wright, N.E., Warr, M.R., Snyder, C.A., Bacon, E.M., Brizgys, G., Chin, E., Chou, C., Conway, A., Dick, R.A., Ferrao, R.D., Garrison, K.L., Hammond, A., Lansdon, E.B., Link, J.O., Mukherjee, P.K., Murray, B.P., Mwangi, J., Ndukwe, M.S., Park, G.Y., Serone, A.P., Suekawa-Pirrone, K., Yang, Z.Y., Zipfel, S.M., Taylor, J.G.

(2025) J Med Chem 68: 10619-10630

PubMed: 40375634 Search on PubMed
DOI: https://doi.org/10.1021/acs.jmedchem.5c00463
Primary Citation Related Structures:
9NA2, 9NA3, 9NA4, 9NA5, 9NA6

PubMed Abstract:
Interleukin-1 receptor-associated kinase 4 (IRAK4) activity mediates pro-inflammatory signaling and cytokine production downstream of toll-like and interleukin-1 receptors (TLR, IL-1R). Selective IRAK4 inhibitors have generated interest as potential treatments for inflammatory diseases. Herein, we report the discovery of GS-5718 (edecesertib), a potent, selective, orally bioavailable IRAK4 inhibitor. Key to this endeavor were efforts undertaken to improve the chemical series' profile after a significant hERG liability was encountered for an early compound. GS-5718 was safe and well-tolerated in IND-enabling preclinical animal toxicity studies, demonstrated efficacy in a mouse NZB lupus model, and additionally demonstrated human pharmacokinetic properties suitable for once-daily administration. Edecesertib is currently under clinical evaluation for the treatment of lupus.

Organizational Affiliation

Gilead Sciences Inc., 333 Lakeside Drive, Foster City, California 94404, United States.

Macromolecule Content

Total Structure Weight: 139.28 kDa
Atom Count: 9,528
Modeled Residue Count: 1,124
Deposited Residue Count: 1,216
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-1 receptor-associated kinase 4	A, B, C, D	304	Homo sapiens	Mutation(s): 0 Gene Names: IRAK4 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NWZ3 (Homo sapiens) Explore Q9NWZ3 Go to UniProtKB: Q9NWZ3
PHAROS: Q9NWZ3 GTEx: ENSG00000198001
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9NWZ3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1BWZ (Subject of Investigation/LOI) Query on A1BWZ Download:Ideal Coordinates CCD File SDF format, chain L [auth D] SDF format, chain J [auth C] SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain L [auth D] MOL2 format, chain J [auth C] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain L [auth D] mmCIF format, chain J [auth C] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	E [auth A], G [auth B], J [auth C], L [auth D]	(6P)-4-{[(1S)-1-cyanoethyl]amino}-6-[(8S)-3-cyanopyrrolo[1,2-b]pyridazin-7-yl]-N-[(2S)-2-fluoro-3-hydroxy-3-methylbutyl]pyridine-3-carboxamide C₂₂ H₂₂ F N₇ O₂ HORBHQPSWJRDSV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain J [auth C] Focus chain L [auth D]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain M [auth D] SDF format, chain N [auth D] SDF format, chain O [auth D] SDF format, chain K [auth C] SDF format, chain I [auth B] SDF format, chain H [auth B] MOL2 format, chain F [auth A] MOL2 format, chain M [auth D] MOL2 format, chain N [auth D] MOL2 format, chain O [auth D] MOL2 format, chain K [auth C] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] mmCIF format, chain F [auth A] mmCIF format, chain M [auth D] mmCIF format, chain N [auth D] mmCIF format, chain O [auth D] mmCIF format, chain K [auth C] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B]	F [auth A] H [auth B] I [auth B] K [auth C] M [auth D] F [auth A], H [auth B], I [auth B], K [auth C], M [auth D], N [auth D], O [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain N [auth D] Focus chain O [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain N [auth D] Focus chain O [auth D]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP Query on SEP	A, B, C, D	L-PEPTIDE LINKING	C₃ H₈ N O₆ P		SER
TPO Query on TPO	A, B, C, D	L-PEPTIDE LINKING	C₄ H₁₀ N O₆ P		THR