8FMU

Crystal structure of human Brachyury G177D variant in complex with SJF-4601

• PDB DOI: https://doi.org/10.2210/pdb8FMU/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2022-12-24 Released: 2024-02-28 
• Deposition Author(s): Bebenek, A., Linhares, B., Jaime-Figueroa, S., Butrin, A., Crews, C.
• Funding Organization(s): The Mark Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Free: 0.266 
• R-Value Work: 0.200 
• R-Value Observed: 0.203 

Literature

Discovery and Development of the First Selective Brachyury Degrader

Chase, D., Bebenek, A., Nie, P., Jaime-Figueroa, S., Butrin, A., Castro, D., Linhares, B., Crews, C.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 44.98 kDa 
• Atom Count: 3,120 
• Modelled Residue Count: 347 
• Deposited Residue Count: 384 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
T-box transcription factor T	A, B	192	Homo sapiens	Mutation(s): 1  Gene Names: TBXT, T
UniProt & NIH Common Fund Data Resources
Find proteins for O15178 (Homo sapiens) Explore O15178  Go to UniProtKB:  O15178
PHAROS:  O15178 GTEx:  ENSG00000164458

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
Y3T	C [auth A], D [auth B]	N-(3-chloro-4-fluorophenyl)-3-[4-(dimethylamino)butanamido]-4-methoxybenzamide C20 H23 Cl F N3 O3 VFCRGORDSAIMRG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Free: 0.266 
• R-Value Work: 0.200 
• R-Value Observed: 0.203 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.892	α = 90
b = 70.294	β = 90
c = 81.874	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-02-28 
Deposition Author(s): Bebenek, A., Linhares, B., Jaime-Figueroa, S., Butrin, A., Crews, C.

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Funding Organization	Location	Grant Number
The Mark Foundation	United States	--

Revision History  

• Version 1.0: 2024-02-28
  Type: Initial release