Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 65.3 kDa 
• Atom Count: 4,643 
• Modelled Residue Count: 570 
• Deposited Residue Count: 586 
• Unique protein chains: 1

 6SP1

KEAP1 IN COMPLEX WITH COMPOUND 6

• PDB DOI: 10.2210/pdb6SP1/pdb

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


• Deposited: 2019-08-30 Released: 2020-06-03 
• Deposition Author(s): Ontoria, J.M., Biancofiore, I., Fezzardi, P., Torrente de Haro, E., Colarusso, S., Bianchi, E., Andreini, M., Patsilinakos, A., Summa, V., Pacifici, R., Munoz-Sanjuan, I., Park, L., Bresciani, A., Dominguez, C., Toledo-Sherman, L., Harper, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.57 Å
• R-Value Free: 0.216 
• R-Value Work: 0.201 
• R-Value Observed: 0.201 

Literature

Combined Peptide and Small-Molecule Approach toward Nonacidic THIQ Inhibitors of the KEAP1/NRF2 Interaction.

Ontoria, J.M., Biancofiore, I., Fezzardi, P., Ferrigno, F., Torrente, E., Colarusso, S., Bianchi, E., Andreini, M., Patsilinakos, A., Kempf, G., Augustin, M., Steinbacher, S., Summa, V., Pacifici, R., Munoz-Sanjuan, I., Park, L., Bresciani, A., Dominguez, C., Sherman, L.T., Harper, S.

(2020) ACS Med Chem Lett 11: 740-746

• PubMed: 32435379 
• DOI: 10.1021/acsmedchemlett.9b00594
• Primary Citation of Related Structures:  
  6SP1, 6SP4


• PubMed Abstract: 
  

The NRF2-ARE pathway is an intrinsic mechanism of defense against oxidative stress. Inhibition of the interaction between NRF2 and its main negative regulator KEAP1 is an attractive strategy toward neuroprotective agents. We report here the identification of nonacidic tetrahydroisoquinolines (THIQs) that inhibit the KEAP1/NRF2 protein-protein interaction. Peptide SAR at one residue is utilized as a tool to probe structural changes within a specific pocket of the KEAP1 binding site. We used structural information from peptide screening at the P2 pocket, noncovalent small-molecules inhibitors, and the outcome from an explorative SAR at position 5 of THIQs to identify a series of neutral THIQ analogs that bind to KEAP1 in the low micromolar range. These analogs establish new H-bond interactions at the P3 and P2 pockets allowing the replacement of the carboxylic acid functionality by a neutral primary carboxamide. X-ray crystallographic studies reveal the novel binding mode of these molecules to KEAP1.

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Organizational Affiliation: 

IRBM S.p.A., Via Pontina km 30.600, 00071 Pomezia, Rome, Italy.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Kelch-like ECH-associated protein 1	A, B	293	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LQ8 (Subject of Investigation/LOI)	C [auth A]	(1~{S},2~{R})-2-[[(1~{S})-1-[[1,3-bis(oxidanylidene)isoindol-2-yl]methyl]-5-(2-hydroxyethyloxy)-3,4-dihydro-1~{H}-isoquinolin-2-yl]carbonyl]cyclohexane-1-carboxylic acid C28 H30 N2 O7 OAFSXLXCZSBCHE-XPWALMASSA-N
ACT	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.57 Å
• R-Value Free: 0.216 
• R-Value Work: 0.201 
• R-Value Observed: 0.201 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.164	α = 90
b = 76.387	β = 90
c = 204.839	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-06-03 
Deposition Author(s): Ontoria, J.M., Biancofiore, I., Fezzardi, P., Torrente de Haro, E., Colarusso, S., Bianchi, E., Andreini, M., Patsilinakos, A., Summa, V., Pacifici, R., Munoz-Sanjuan, I., Park, L., Bresciani, A., Dominguez, C., Toledo-Sherman, L., Harper, S.

Revision History  

• Version 1.0: 2020-06-03
  Type: Initial release