4IN4 | pdb_00004in4

Crystal structure of cpd 15 bound to Keap1 Kelch domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 
    0.250 (Depositor), 0.254 (DCC) 
  • R-Value Work: 
    0.191 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 
    0.194 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

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

  • 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.

Macromolecule Content 

  • Total Structure Weight: 101.78 kDa 
  • Atom Count: 7,007 
  • Modeled Residue Count: 861 
  • Deposited Residue Count: 897 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Kelch-like ECH-associated protein 1
A, B, C
299Homo sapiensMutation(s): 0 
Gene Names: INRF2KEAP1KIAA0132KLHL19
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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ14145
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
4ID

Query on 4ID



Download:Ideal Coordinates CCD File
H [auth A]
I [auth A]
M [auth B]
N [auth B]
P [auth C]
H [auth A],
I [auth A],
M [auth B],
N [auth B],
P [auth C],
Q [auth C]
2-({5-[(2,4-dimethylphenyl)sulfonyl]-6-oxo-1,6-dihydropyrimidin-2-yl}sulfanyl)-N-[2-(trifluoromethyl)phenyl]acetamide
C21 H18 F3 N3 O4 S2
XHKKCXMZBGDTIT-UHFFFAOYSA-N
PO4

Query on PO4



Download:Ideal Coordinates CCD File
D [auth A]
E [auth A]
F [auth A]
G [auth A]
J [auth B]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
J [auth B],
K [auth B],
L [auth B],
O [auth C]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Binding Affinity Annotations 
IDSourceBinding Affinity
4ID BindingDB:  4IN4 Ki: 2800 (nM) from 1 assay(s)
Kd: 5.10e+4 (nM) from 1 assay(s)
IC50: 1.18e+5 (nM) from 1 assay(s)
EC50: 1.10e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free:  0.250 (Depositor), 0.254 (DCC) 
  • R-Value Work:  0.191 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 0.194 (Depositor) 
Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.604α = 90
b = 96.509β = 90
c = 142.462γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
XDSdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description