9DU7 | pdb_00009du7

KEAP1 BTB domain in complex with the covalent activator VVD-065

PDB DOI: https://doi.org/10.2210/pdb9DU7/pdb

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

Deposited: 2024-10-02 Released: 2024-10-23
Deposition Author(s): Bernard, S.M.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.87 Å
R-Value Free:
0.231 (Depositor), 0.239 (DCC)
R-Value Work:
0.192 (Depositor), 0.199 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Suppression of NRF2-dependent cancer growth by a covalent allosteric molecular glue

Roy, N., Wyseure, T., Lo, I.C., Metzger, J., Eissler, C.L., Bernard, S.M., Bok, I., Snead, A.N., Parker, A., Green, J.C., Inloes, J., Jacinto, S.R., Kuenzi, B., Horning, B.D., Ibrahim, N., Grabow, S., Panda, H., Bhatt, D.P., Saeidi, S., Zolkind, P., Rush, Z., Negri, K., Williams, H.N., Walton, E., Pastuszka, M.K., Sigler, J.J., Tran, E., Hee, K., McLaughlin, J., Ambrus-Aikelin, G., Pollock, J., Abraham, R.T., Kinsella, T.M., Simon, G.M., Major, M.B., Weinstein, D.S., Patricelli, M.P.

(2024) bioRxiv

DOI: https://doi.org/10.1101/2024.10.04.616592

Macromolecule Content

Total Structure Weight: 31.28 kDa
Atom Count: 2,138
Modeled Residue Count: 254
Deposited Residue Count: 274
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, B	137	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 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
A1BCT (Subject of Investigation/LOI) Query on A1BCT Download Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	1-{(3S)-3-[3-(4-amino-1,3,5-triazin-2-yl)-5-chlorophenyl]morpholin-4-yl}propan-1-one C₁₆ H₁₈ Cl N₅ O₂ HFRULTGTUQPJLO-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.87 Å
R-Value Free: 0.231 (Depositor), 0.239 (DCC)
R-Value Work: 0.192 (Depositor), 0.199 (DCC)

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.737	α = 90
b = 72.737	β = 90
c = 64.209	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-10-23

Deposition Author(s):

Funding Organization	Location	Grant Number
Other private	United States	--

Revision History (Full details and data files)

Version 1.0: 2024-10-23
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.