9SYI | pdb_00009syi

Crystal structure of TEAD4 in complex with compound 9

PDB DOI: https://doi.org/10.2210/pdb9SYI/pdb

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

Deposited: 2025-10-13 Released: 2026-03-11
Deposition Author(s): Scheufler, C., Izaac, A.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.245 (Depositor), 0.242 (DCC)
R-Value Work:
0.214 (Depositor), 0.208 (DCC)
R-Value Observed:
0.216 (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 Clinical Candidate IAG933, a Potent YAP-TEAD PPI Disrupter.

Vogtle, M., Sellner, H., Chapeau, E., Furet, P., Salem, B., Le Douget, M., Bordas, V., Groell, J.M., Le Goff, A.L., Rouzet, C., Wietlisbach, T., Zimmermann, T., McKenna, J., Brocklehurst, C.E., Chene, P., Wartmann, M., Scheufler, C., Kallen, J., de Kanter, R., Harlfinger, S., Zecri, F., Schmelzle, T., Soldermann, N.

(2026) J Med Chem 69: 7782-7816

PubMed: 41780024 Search on PubMed
DOI: https://doi.org/10.1021/acs.jmedchem.5c03009
Primary Citation Related Structures:
9SYI, 9SYN

PubMed Abstract:
The interaction of transcriptional enhanced associate domain (TEAD) and transcriptional coactivator yes-associated protein (YAP) mediates oncogenic functions downstream of the Hippo pathway. In this report, we outline our efforts to find a potent inhibitor of this protein-protein interaction with suitable properties for clinical evaluation. We detail the medicinal chemistry program that led to the discovery of IAG933, an inhibitor with a balanced ADME profile, enabling its evaluation as a potential treatment option in clinical settings.

Organizational Affiliation

Novartis BioMedical Research, 4002 Basel, Switzerland.

Macromolecule Content

Total Structure Weight: 53.14 kDa
Atom Count: 3,726
Modeled Residue Count: 412
Deposited Residue Count: 440
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional enhancer factor TEF-3	A, B	220	Homo sapiens	Mutation(s): 0 Gene Names: TEAD4, RTEF1, TCF13L1, TEF3
UniProt & NIH Common Fund Data Resources
Find proteins for Q15561 (Homo sapiens) Explore Q15561 Go to UniProtKB: Q15561
PHAROS: Q15561 GTEx: ENSG00000197905
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q15561
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1ICN (Subject of Investigation/LOI) Query on A1ICN Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth B] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] mmCIF format, chain D [auth A] mmCIF format, chain G [auth B]	D [auth A], G [auth B]	2-[(2~{S})-5-chloranyl-2-phenyl-2-[(2~{S})-pyrrolidin-2-yl]-3~{H}-1-benzofuran-4-yl]-3-fluoranyl-4-methoxy-benzamide C₂₆ H₂₄ Cl F N₂ O₃ ICQIMDKJYGSHPF-LVXARBLLSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]
U3O Query on U3O Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B] mmCIF format, chain C [auth A] mmCIF format, chain F [auth B]	C [auth A], F [auth B]	(2~{R})-2-[2-chloranyl-5-[2-chloranyl-4-(trifluoromethyl)phenoxy]phenyl]sulfanylpropanoic acid C₁₆ H₁₁ Cl₂ F₃ O₃ S NFVBERYRRKUMCL-MRVPVSSYSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B]	E [auth A], H [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B]