4IQK | pdb_00004iqk

Crystal structure of cpd 16 bound to Keap1 Kelch domain

• PDB DOI: https://doi.org/10.2210/pdb4IQK/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2013-01-11 Released: 2013-05-15 
• Deposition Author(s): Silvian, L., Marcotte, D.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free: 
  0.179 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.153 (Depositor), 0.157 (DCC) 
• R-Value Observed: 
  0.155 (Depositor) 

Literature

Small molecules inhibit the interaction of Nrf2 and the Keap1 Kelch domain through a non-covalent mechanism.

Marcotte, D., Zeng, W., Hus, J.C., McKenzie, A., Hession, C., Jin, P., Bergeron, C., Lugovskoy, A., Enyedy, I., Cuervo, H., Wang, D., Atmanene, C., Roecklin, D., Vecchi, M., Vivat, V., Kraemer, J., Winkler, D., Hong, V., Chao, J., Lukashev, M., Silvian, L.

(2013) Bioorg Med Chem 21: 4011-4019

• PubMed: 23647822 
• DOI: https://doi.org/10.1016/j.bmc.2013.04.019
• Primary Citation Related Structures: 
  4IN4, 4IQK


• PubMed Abstract: 
  

  Keap1 binds to the Nrf2 transcription factor to promote its degradation, resulting in the loss of gene products that protect against oxidative stress. While cell-active small molecules have been identified that modify cysteines in Keap1 and effect the Nrf2 dependent pathway, few act through a non-covalent mechanism. We have identified and characterized several small molecule compounds that specifically bind to the Keap1 Kelch-DC domain as measured by NMR, native mass spectrometry and X-ray crystallography. One compound upregulates Nrf2 response genes measured by a luciferase cell reporter assay. The non-covalent inhibition strategy presents a reasonable course of action to avoid toxic side-effects due to non-specific cysteine modification.

---

Organizational Affiliation: 
• Biogen Idec, Drug Discovery, 12 Cambridge Center, Cambridge, MA 02142, USA.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 33.06 kDa 
• Atom Count: 2,341 
• Modeled Residue Count: 285 
• Deposited Residue Count: 299 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Kelch-like ECH-associated protein 1	A	299	Homo sapiens	Mutation(s): 2  Gene Names: INRF2, KEAP1, KIAA0132, KLHL19
UniProt & NIH Common Fund Data Resources
Find proteins for Q14145 (Homo sapiens) Explore Q14145  Go to UniProtKB:  Q14145
PHAROS:  Q14145 GTEx:  ENSG00000079999

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IQK	B [auth A]	N,N'-naphthalene-1,4-diylbis(4-methoxybenzenesulfonamide) C24 H22 N2 O6 S2 XLLVCULLOGKYOO-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
IQK	BindingDB:  4IQK	Ki: 250 (nM) from 1 assay(s)
		Kd: min: 370, max: 1700 (nM) from 4 assay(s)
		IC50: min: 940, max: 2700 (nM) from 4 assay(s)
		EC50: min: 1460, max: 5800 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free:  0.179 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.153 (Depositor), 0.157 (DCC) 
• R-Value Observed: 0.155 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.856	α = 90
b = 75.638	β = 106.09
c = 48.341	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-05-15 
Deposition Author(s): Silvian, L., Marcotte, D.

Revision History  

• Version 1.0: 2013-05-15
  Type: Initial release
  
• Version 1.1: 2013-05-22
  Changes: Database references
• Version 1.2: 2013-07-03
  Changes: Database references
• Version 1.3: 2024-11-27
  Changes: Data collection, Database references, Derived calculations, Structure summary