8E1O

Crystal structure of hTEAD2 bound to a methoxypyridine lipid pocket binder

PDB DOI: https://doi.org/10.2210/pdb8E1O/pdb

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

Deposited: 2022-08-10 Released: 2023-08-16
Deposition Author(s): Noland, C.L., Dey, A., Zbieg, J., Crawford, J.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.247
R-Value Work: 0.200
R-Value Observed: 0.203

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Targeting the Hippo pathway in cancers via ubiquitination dependent TEAD degradation

Pham, T., Pahuja, K., Hagenbeek, T., Zbieg, Z., Noland, C.L., Pham, V.C., Yao, X., Rose, C., Browder, K., Lee, H.J., Yu, M., Chu, M.L., Martin, S., Verschueren, E., Li, J., Kubala, M., Fong, R., Lorenzo, M., Beroza, P., Hsu, P., Paul, S., Villemure, E., Lee, W., Cheung, T., Clausen, S., Lacap, J., Liang, Y., Schmidt, S., Modrusan, Z., Cohen, M., Crawford, J., Jasper, H., Ashworth, A., Lill, J.R., Malek, S., Rudolph, J., Wertz, I., Chang, M., Ye, X., Dey, A.

(2024) Biorxiv

DOI: https://doi.org/10.1101/2023.10.03.560675

Macromolecule Content

Total Structure Weight: 58.13 kDa
Atom Count: 3,275
Modelled Residue Count: 399
Deposited Residue Count: 500
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional enhancer factor TEF-4	A, B	250	Homo sapiens	Mutation(s): 0 Gene Names: TEAD2, TEF4
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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q15562
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
Y2S (Subject of Investigation/LOI) Query on Y2S Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth B]	D [auth A], E [auth B]	5-methoxy-N-({3-[2-(methylamino)-2-oxoethyl]phenyl}methyl)-4-{(E)-2-[trans-4-(trifluoromethyl)cyclohexyl]ethenyl}pyridine-2-carboxamide C₂₆ H₃₀ F₃ N₃ O₃ YBEYBRFOUHYJAL-ZDXIVYMOSA-N		Interactions Focus chain D [auth A] Focus chain E [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth B]
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.247
R-Value Work: 0.200
R-Value Observed: 0.203
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 122.15	α = 90
b = 62.069	β = 117.41
c = 79.856	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
PHASER	phasing
PDB_EXTRACT	data extraction
STARANISO	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2023-08-16

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2023-08-16
Type: Initial release
Version 1.1: 2024-02-28
Changes: Database references

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.