6Q36 | pdb_00006q36

TEAD4(216-434) complexed with optimized peptide 9 and myristoate (covalently bound) at 2.01A resolution: Structure-based design of potent linear peptide inhibitors of the YAP-TEAD protein-protein interaction derived from the YAP omega-loop sequence

• PDB DOI: https://doi.org/10.2210/pdb6Q36/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2018-12-03 Released: 2019-07-03 
• Deposition Author(s): Kallen, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 
  0.244 (Depositor), 0.256 (DCC) 
• R-Value Work: 
  0.217 (Depositor) 
• R-Value Observed: 
  0.218 (Depositor) 

Starting Model: experimental

Literature

Structure-based design of potent linear peptide inhibitors of the YAP-TEAD protein-protein interaction derived from the YAP omega-loop sequence.

Furet, P., Salem, B., Mesrouze, Y., Schmelzle, T., Lewis, I., Kallen, J., Chene, P.

(2019) Bioorg Med Chem Lett 29: 2316-2319

• PubMed: 31235263 
• DOI: https://doi.org/10.1016/j.bmcl.2019.06.022
• Primary Citation Related Structures: 
  6Q2X, 6Q36


• PubMed Abstract: 
  

  The YAP-TEAD protein-protein interaction is a potential therapeutic target to treat cancers in which the Hippo signaling pathway is deregulated. However, the extremely large surface of interaction between the two proteins presents a formidable challenge for a small molecule interaction disrupter approach. We have accomplished progress towards showing the feasibility of this approach by the identification of a 15-mer peptide able to potently (nanomolar range) disrupt the YAP-TEAD interaction by targeting only one of the two important sites of interaction. This peptide, incorporating non-natural amino acids selected by structure-based design, is derived from the Ω-loop sequence 85-99 of YAP.

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Organizational Affiliation: 
• Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland. Electronic address: [e-mail].
Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 56.15 kDa 
• Atom Count: 4,164 
• Modeled Residue Count: 463 
• Deposited Residue Count: 474 
• Unique protein chains: 2

Macromolecules

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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ACE-PRO-6CW-ARG-LEU-ARG-LYS-2JH-HYP-ASP-SER-PHE-ALN-LYS-GLU-PRO-NH2	C, D	17	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MYR	E [auth A], H [auth B]	MYRISTIC ACID C14 H28 O2 TUNFSRHWOTWDNC-UHFFFAOYSA-N
PO4	F [auth A], G [auth A], I [auth B], J [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Modified Residues  3 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
2JH	C, D	L-PEPTIDE LINKING	C7 H13 N O2		--
6CW	C, D	L-PEPTIDE LINKING	C11 H11 Cl N2 O2		TRP
ALN	C, D	L-PEPTIDE LINKING	C13 H13 N O2		ALA
HYP	C, D	L-PEPTIDE LINKING	C5 H9 N O3		PRO

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free:  0.244 (Depositor), 0.256 (DCC) 
• R-Value Work:  0.217 (Depositor) 
• R-Value Observed: 0.218 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 172.868	α = 90
b = 40.438	β = 93.44
c = 98.034	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-07-03 
Deposition Author(s): Kallen, J.

Revision History  

• Version 1.0: 2019-07-03
  Type: Initial release
  
• Version 1.1: 2019-08-21
  Changes: Data collection, Database references
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Database references, Derived calculations
• Version 2.1: 2024-01-24
  Changes: Refinement description