8R07 | pdb_00008r07

C-terminal Rel-homology Domain of NFAT1

• PDB DOI: https://doi.org/10.2210/pdb8R07/pdb

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


• Deposited: 2023-10-30 Released: 2024-03-06 
• Deposition Author(s): Zak, K.M., Boettcher, J.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.74 Å
• R-Value Free: 
  0.184 (Depositor), 0.184 (DCC) 
• R-Value Work: 
  0.147 (Depositor), 0.147 (DCC) 
• R-Value Observed: 
  0.149 (Depositor) 

Starting Model: experimental

Literature

Ligandability assessment of the C-terminal Rel-homology domain of NFAT1.

Bottcher, J., Fuchs, J.E., Mayer, M., Kahmann, J., Zak, K.M., Wunberg, T., Woehrle, S., Kessler, D.

(2024) Arch Pharm (Weinheim) 357: e2300649-e2300649

• PubMed: 38396281 
• DOI: https://doi.org/10.1002/ardp.202300649
• Primary Citation Related Structures: 
  8R07, 8R3F


• PubMed Abstract: 
  

  Transcription factors are generally considered challenging, if not "undruggable", targets but they promise new therapeutic options due to their fundamental involvement in many diseases. In this study, we aim to assess the ligandability of the C-terminal Rel-homology domain of nuclear factor of activated T cells 1 (NFAT1), a TF implicated in T-cell regulation. Using a combination of experimental and computational approaches, we demonstrate that small molecule fragments can indeed bind to this protein domain. The newly identified binder is the first small molecule binder to NFAT1 validated with biophysical methods and an elucidated binding mode by X-ray crystallography. The reported eutomer/distomer pair provides a strong basis for potential exploration of higher potency binders on the path toward degrader or glue modalities.

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Organizational Affiliation: 
• Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria.
Evotec SE, Hamburg, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 24.55 kDa 
• Atom Count: 1,993 
• Modeled Residue Count: 205 
• Deposited Residue Count: 210 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear factor of activated T-cells, cytoplasmic 2	A, B	105	Homo sapiens	Mutation(s): 0  Gene Names: NFATC2, NFAT1, NFATP
UniProt & NIH Common Fund Data Resources
Find proteins for Q13469 (Homo sapiens) Explore Q13469  Go to UniProtKB:  Q13469
PHAROS:  Q13469 GTEx:  ENSG00000101096

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.74 Å
• R-Value Free:  0.184 (Depositor), 0.184 (DCC) 
• R-Value Work:  0.147 (Depositor), 0.147 (DCC) 
• R-Value Observed: 0.149 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.456	α = 90
b = 40.32	β = 90.235
c = 54.637	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-03-06 
Deposition Author(s): Zak, K.M., Boettcher, J.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-03-06
  Type: Initial release
  
• Version 1.1: 2024-06-12
  Changes: Database references