9UJI | pdb_00009uji

Crystal structure of the BTB domain mouse Keap1 in complex with CDDO-Im

PDB DOI: https://doi.org/10.2210/pdb9UJI/pdb

Classification: TRANSCRIPTION
Organism(s): Mus musculus
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2025-04-17 Released: 2025-10-22
Deposition Author(s): Iso, T., Suzuki, T., Takagi, K., Mizushima, T., Yamamoto, M.
Funding Organization(s): Ministry of Education, Culture, Sports, Science and Technology (Japan), Japan Society for the Promotion of Science (JSPS), Japan Agency for Medical Research and Development (AMED)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.44 Å
R-Value Free:
0.256 (Depositor), 0.264 (DCC)
R-Value Work:
0.206 (Depositor), 0.209 (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

Crystal structure of the BTB domain mouse Keap1 in complex with CDDO-Im

Suzuki, T., Takagi, K., Iso, T., Wen, H., Zhang, A., Hatakeyama, T., Mizushima, T., Yamamoto, M.

To be published.

Macromolecule Content

Total Structure Weight: 120.76 kDa
Atom Count: 8,360
Modeled Residue Count: 1,033
Deposited Residue Count: 1,040
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, C, D, E A, B, C, D, E, F, G, H	130	Mus musculus	Mutation(s): 1 Gene Names: Keap1, Inrf2, Kiaa0132
UniProt
Find proteins for Q9Z2X8 (Mus musculus) Explore Q9Z2X8 Go to UniProtKB: Q9Z2X8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9Z2X8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SXJ (Subject of Investigation/LOI) Query on SXJ Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain K [auth B] SDF format, chain L [auth C] SDF format, chain N [auth D] SDF format, chain O [auth E] SDF format, chain P [auth F] SDF format, chain Q [auth G] SDF format, chain R [auth H] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth C] MOL2 format, chain N [auth D] MOL2 format, chain O [auth E] MOL2 format, chain P [auth F] MOL2 format, chain Q [auth G] MOL2 format, chain R [auth H] mmCIF format, chain I [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth C] mmCIF format, chain N [auth D] mmCIF format, chain O [auth E] mmCIF format, chain P [auth F] mmCIF format, chain Q [auth G] mmCIF format, chain R [auth H]	I [auth A] K [auth B] L [auth C] N [auth D] O [auth E] I [auth A], K [auth B], L [auth C], N [auth D], O [auth E], P [auth F], Q [auth G], R [auth H]	(13alpha,18alpha)-2-cyano-3-hydroxy-12-oxooleana-2,9(11)-dien-28-oic acid C₃₁ H₄₃ N O₄ YTXFWWUYCLBPKV-UQMAOPSPSA-N		Interactions Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth C] Focus chain N [auth D] Focus chain O [auth E] Focus chain P [auth F] Focus chain Q [auth G] Focus chain R [auth H] Interactions & Density Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth C] Focus chain N [auth D] Focus chain O [auth E] Focus chain P [auth F] Focus chain Q [auth G] Focus chain R [auth H]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain M [auth C] MOL2 format, chain J [auth A] MOL2 format, chain M [auth C] mmCIF format, chain J [auth A] mmCIF format, chain M [auth C]	J [auth A], M [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain M [auth C] Interactions & Density Focus chain J [auth A] Focus chain M [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.44 Å
R-Value Free: 0.256 (Depositor), 0.264 (DCC)
R-Value Work: 0.206 (Depositor), 0.209 (DCC)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.554	α = 90
b = 79.464	β = 94.602
c = 110.876	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-10-22

Deposition Author(s):

Funding Organization	Location	Grant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	21H05270
Japan Society for the Promotion of Science (JSPS)	Japan	22K06876
Japan Society for the Promotion of Science (JSPS)	Japan	25K02449
Japan Society for the Promotion of Science (JSPS)	Japan	24K01968
Japan Agency for Medical Research and Development (AMED)	Japan	JP23ama121038