7XM4

Crystal structure of Keap1 Kelch domain (residues 322-609) in complex with 6e

PDB DOI: https://doi.org/10.2210/pdb7XM4/pdb

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: 2.70 Å
R-Value Free: 0.237
R-Value Work: 0.177
R-Value Observed: 0.183

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 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

DOI: https://doi.org/10.1021/acs.jmedchem.2c00170

Macromolecule Content

Total Structure Weight: 32.69 kDa
Atom Count: 2,265
Modelled Residue Count: 280
Deposited Residue Count: 292
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	292	Homo sapiens	Mutation(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 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
GDJ (Subject of Investigation/LOI) Query on GDJ Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	N-[4-[(2-azanyl-2-oxidanylidene-ethyl)-[4-[(2-azanyl-2-oxidanylidene-ethyl)-(4-methoxyphenyl)sulfonyl-amino]naphthalen-1-yl]sulfamoyl]phenyl]-2-(4-ethylpiperazin-1-yl)ethanamide C₃₅ H₄₁ N₇ O₈ S₂ KTGQNHLFJOVZNG-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.237
R-Value Work: 0.177
R-Value Observed: 0.183
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.762	α = 90
b = 76.277	β = 105.24
c = 48.106	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XDS	data scaling
Coot	model building
PHENIX	phasing
PHENIX	refinement

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2022-07-06

Deposition Author(s):

Funding Organization	Location	Grant 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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.