7XM2 | pdb_00007xm2

Crystal structure of Keap1 Kelch domain (residues 322-609) in complex with NXPZ-2

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

  • Deposited: 2022-04-24 Released: 2022-07-06 
  • Deposition Author(s): Xu, K.
  • Funding Organization(s): Ministry of Science and Technology (MoST, China), National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.216 (Depositor), 0.212 (DCC) 
  • R-Value Work: 
    0.168 (Depositor) 
  • R-Value Observed: 
    0.172 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


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

Literature

Crystallography-Guided Optimizations of the Keap1-Nrf2 Inhibitors on the Solvent Exposed Region: From Symmetric to Asymmetric Naphthalenesulfonamides.

Liu, G., Hou, R., Xu, L., Zhang, X., Yan, J., Xing, C., Xu, K., Zhuang, C.

(2022) J Med Chem 65: 8289-8302

Macromolecule Content 

  • Total Structure Weight: 33.13 kDa 
  • Atom Count: 2,378 
  • Modeled Residue Count: 280 
  • Deposited Residue Count: 292 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Kelch-like ECH-associated protein 1A [auth X]292Homo sapiensMutation(s): 0 
Gene Names: KEAP1
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 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GFD
(Subject of Investigation/LOI)

Query on GFD


Download:Ideal Coordinates CCD File
B [auth X],
C [auth X]		2-[(4-aminophenyl)sulfonyl-[4-[(2-azanyl-2-oxidanylidene-ethyl)-(4-methoxyphenyl)sulfonyl-amino]naphthalen-1-yl]amino]ethanamide
C27 H27 N5 O7 S2
DFIZGWXPFCOCFG-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
GFD BindingDB:  7XM2 Ki: 95 (nM) from 1 assay(s)
Kd: 230 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.216 (Depositor), 0.212 (DCC) 
  • R-Value Work:  0.168 (Depositor) 
  • R-Value Observed: 0.172 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126.256α = 90
b = 75.619β = 106.386
c = 48.651γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling
Cootmodel building
PHENIXphasing
PHENIXrefinement

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

& Funding Information

Deposition Data

  • Released Date: 2022-07-06 
    • Deposition Author(s): Xu, K.
Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China--
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-06
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-10-30
    Changes: Structure summary