8YGQ | pdb_00008ygq

Crystal structure of Human TEAD2 in complex with Cobimetinib


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free: 
    0.257 (Depositor), 0.258 (DCC) 
  • R-Value Work: 
    0.191 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 
    0.198 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Phase separation-based HTS identifies cobimetinib as a YAP-TEAD inhibitor that suppresses hyperactivated YAP-induced cancer progression.

Yang, R.Hu, L.Wang, J.Wang, J.Yuan, L.Wu, M.He, L.Yu, W.Chen, P.Lu, X.Hu, F.Zhang, H.Gao, H.Wang, X.Zhang, H.Sun, Y.Xu, J.Huang, J.Zhou, H.Zhu, J.Wei, F.Jin, Y.Gao, Y.Fu, Q.Qi, X.Yu, J.Li, P.He, X.Zhang, L.

(2026) Sci Transl Med 18: eadu0814-eadu0814

  • DOI: https://doi.org/10.1126/scitranslmed.adu0814
  • Primary Citation Related Structures: 
    8YGQ

  • PubMed Abstract: 

    The Hippo signaling pathway prevents unchecked cell growth, coordinates apoptosis, and preserves proper organ function. Dysregulation of this pathway has been implicated in a myriad of diseases, particularly in cancer. The YAP (Yes-associated protein)-TEAD (TEA domain transcription factor) complex, the key transcriptional downstream effector of the Hippo pathway, hence stands out as an appealing target for therapeutic intervention. In this study, we developed a high-throughput screening (HTS) assay leveraging phase separation principles and found that the US Food and Drug Administration-approved clinical drug cobimetinib is a potent inhibitor of the YAP-TEAD complex. Cocrystallization studies of cobimetinib with TEAD showed that cobimetinib bound to the TEAD lipid pocket and disrupted TEAD palmitoylation. Cobimetinib could overcome resistance to mitogen-activated protein kinase kinase 1/2 inhibitors and to the first-line drug sorafenib in vivo. In addition, cobimetinib suppressed tumor growth and tumorigenesis associated with hyperactivated YAP-TEAD activities in a mouse model of lung cancer. Furthermore, it bolstered the efficacy of the first-line drugs sorafenib and lenvatinib in inhibiting both hepatocellular carcinoma tumor growth and tumorigenesis. These findings establish a strategy for identifying and refining inhibitors of the YAP-TEAD complex in the treatment of cancers driven by aberrant YAP-TEAD activity.


  • Organizational Affiliation
    • Department of Urology, Shanghai Sixth People' s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai Eastern Institute of Urologic Reconstruction, Shanghai Jiao Tong University, Shanghai 200233, China.

Macromolecule Content 

  • Total Structure Weight: 52.25 kDa 
  • Atom Count: 3,297 
  • Modeled Residue Count: 395 
  • Deposited Residue Count: 452 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Transcriptional enhancer factor TEF-4
A, B
226Homo sapiensMutation(s): 0 
Gene Names: TEAD2TEF4
UniProt & NIH Common Fund Data Resources
Find proteins for Q15562 (Homo sapiens)
Explore Q15562 
Go to UniProtKB:  Q15562
PHAROS:  Q15562
GTEx:  ENSG00000074219 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15562
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EUI
(Subject of Investigation/LOI)

Query on EUI



Download:Ideal Coordinates CCD File
D [auth B][3,4-BIS(FLUORANYL)-2-[(2-FLUORANYL-4-IODANYL-PHENYL)AMINO]PHENYL]-[3-OXIDANYL-3-[(2S)-PIPERIDIN-2-YL]AZETIDIN-1-YL]METHANONE
C21 H21 F3 I N3 O2
BSMCAPRUBJMWDF-KRWDZBQOSA-N
PLM

Query on PLM



Download:Ideal Coordinates CCD File
C [auth A]PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free:  0.257 (Depositor), 0.258 (DCC) 
  • R-Value Work:  0.191 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 0.198 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 122.303α = 90
b = 61.774β = 117.7
c = 80.361γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31970672
National Natural Science Foundation of China (NSFC)China32270877

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-05
    Type: Initial release
  • Version 1.1: 2026-04-29
    Changes: Database references