5DAF

Crystal Structure of Human KEAP1 BTB Domain in Complex with Small Molecule TX64063

PDB DOI: https://doi.org/10.2210/pdb5DAF/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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.37 Å
R-Value Free: 0.233
R-Value Work: 0.202
R-Value Observed: 0.203

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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 Search on PubMed
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.

Organizational Affiliation

Department of Research, Reata Pharmaceuticals, Inc., Irving, TX 75063, United States; Department of Physiology, UT Southwestern Medical Center, Dallas, TX 75390, United States.

Macromolecule Content

Total Structure Weight: 15.93 kDa
Atom Count: 989
Modelled Residue Count: 121
Deposited Residue Count: 140
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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 GTEx: ENSG00000079999
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q14145
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
58E Query on 58E Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	(5aS,6S,9aS)-7-hydroxy-2,6,9a-trimethyl-3-(pyridin-3-yl)-4,5,5a,6,9,9a-hexahydro-2H-benzo[g]indazole-8-carbonitrile C₂₀ H₂₂ N₄ O IQRJTLOGKWCNQB-APXLUKDGSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.37 Å
R-Value Free: 0.233
R-Value Work: 0.202
R-Value Observed: 0.203
Space Group: P 3₁ 1 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.449	α = 90
b = 42.449	β = 90
c = 134.044	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2016-08-10

Deposition Author(s):

Revision History (Full details and data files)

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