5DAD

Crystal Structure of Human KEAP1 BTB Domain in Complex with Small Molecule TX64014

• PDB DOI:  https://doi.org/10.2210/pdb5DAD/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-08-19 Released: 2016-08-10 
• Deposition Author(s): Huerta, C., Jiang, X., Trevino, I., Bender, C.F., Swinger, K.K., Stoll, V.S., Ferguson, D.A., Thomas, P.J., Probst, B., Dulubova, I., Visnick, M., Wigley, W.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.61 Å
• R-Value Free: 0.245 
• R-Value Work: 0.204 
• R-Value Observed: 0.206 

Literature

Characterization of novel small-molecule NRF2 activators: Structural and biochemical validation of stereospecific KEAP1 binding.

Huerta, C., Jiang, X., Trevino, I., Bender, C.F., Ferguson, D.A., Probst, B., Swinger, K.K., Stoll, V.S., Thomas, P.J., Dulubova, I., Visnick, M., Wigley, W.C.

(2016) Biochim Biophys Acta 1860: 2537-2552

• PubMed: 27474998 
• DOI: https://doi.org/10.1016/j.bbagen.2016.07.026
• Primary Citation of Related Structures:  
  5DAD, 5DAF


• PubMed Abstract: 
  

  Semi-synthetic oleanane triterpenoid antioxidant inflammation modulators (tpAIMs) are small molecules that interact with KEAP1 cysteine residue 151 (C151) and activate NRF2. Exploration of the structure-activity relationship between the tpAIMs and KEAP1 is limited by the predominantly hydrocarbon nature of the oleanane triterpenoid pentacyclic ring structure. Therefore, we used novel, chemically-tractable, synthetic antioxidant inflammation modulators (sAIMs) to probe the stereoselectivity of the ligand-protein interaction.

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Organizational Affiliation: 

Department of Research, Reata Pharmaceuticals, Inc., Irving, TX 75063, United States.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 15.89 kDa 
• Atom Count: 990 
• Modelled Residue Count: 123 
• Deposited Residue Count: 140 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Kelch-like ECH-associated protein 1	A	140	Homo sapiens	Mutation(s): 0  Gene Names: KEAP1, INRF2, KIAA0132, KLHL19
UniProt & NIH Common Fund Data Resources
Find proteins for Q14145 (Homo sapiens) Explore Q14145  Go to UniProtKB:  Q14145
PHAROS:  Q14145

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TX6	B [auth A]	(6aS,7S,10aS)-8-hydroxy-4-methoxy-2,7,10a-trimethyl-5,6,6a,7,10,10a-hexahydrobenzo[h]quinazoline-9-carbonitrile C17 H21 N3 O2 LBBXSDQROZEAQX-YHYSRRTLSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.61 Å
• R-Value Free: 0.245 
• R-Value Work: 0.204 
• R-Value Observed: 0.206 
• Space Group: P 3₁ 1 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.22	α = 90
b = 43.22	β = 90
c = 135.171	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-08-10 
Deposition Author(s): Huerta, C., Jiang, X., Trevino, I., Bender, C.F., Swinger, K.K., Stoll, V.S., Ferguson, D.A., Thomas, P.J., Probst, B., Dulubova, I., Visnick, M., Wigley, W.C.

Revision History  

• Version 1.0: 2016-08-10
  Type: Initial release
  
• Version 1.1: 2016-09-14
  Changes: Database references
• Version 1.2: 2017-11-22
  Changes: Database references, Derived calculations, Refinement description
• Version 1.3: 2023-09-27
  Changes: Data collection, Database references, Refinement description