9IH9 | pdb_00009ih9

KEAP1 complexed to linear peptide 6

PDB DOI: https://doi.org/10.2210/pdb9IH9/pdb

Classification: STRUCTURAL PROTEIN
Organism(s): Homo sapiens, synthetic construct
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2025-02-20 Released: 2026-03-04
Deposition Author(s): Ji, X., Lau, K.
Funding Organization(s): Swiss National Science Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.203 (Depositor), 0.203 (DCC)
R-Value Work:
0.161 (Depositor), 0.160 (DCC)
R-Value Observed:
0.163 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

De novo generation of a membrane-permeable cyclic peptides that target an intracellular protein-protein interaction

Xinjian, J., Kelvin, L.

To be published.

Macromolecule Content

Total Structure Weight: 97.92 kDa
Atom Count: 7,446
Modeled Residue Count: 867
Deposited Residue Count: 882
Unique protein chains: 4

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Kelch-like ECH-associated protein 1	A [auth C]	290	Homo sapiens	Mutation(s): 2 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q14145
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Kelch-like ECH-associated protein 1	B	290	Homo sapiens	Mutation(s): 2 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q14145
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Kelch-like ECH-associated protein 1	C [auth A]	290	Homo sapiens	Mutation(s): 2 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q14145
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Designed peptide	D [auth X], E [auth Y], F [auth Z]	4	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain Q [auth A] SDF format, chain L [auth B] SDF format, chain H [auth C] MOL2 format, chain Q [auth A] MOL2 format, chain L [auth B] MOL2 format, chain H [auth C] mmCIF format, chain Q [auth A] mmCIF format, chain L [auth B] mmCIF format, chain H [auth C]	H [auth C], L [auth B], Q [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain H [auth C] Focus chain L [auth B] Focus chain Q [auth A] Interactions & Density Focus chain H [auth C] Focus chain L [auth B] Focus chain Q [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain P [auth A] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain G [auth C] MOL2 format, chain K [auth B] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain G [auth C] mmCIF format, chain K [auth B] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain G [auth C]	G [auth C], K [auth B], N [auth A], O [auth A], P [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth C] Focus chain K [auth B] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Interactions & Density Focus chain G [auth C] Focus chain K [auth B] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A]
DHL (Subject of Investigation/LOI) Query on DHL Download:Ideal Coordinates CCD File SDF format, chain U [auth X] SDF format, chain Z SDF format, chain W [auth Y] MOL2 format, chain U [auth X] MOL2 format, chain Z MOL2 format, chain W [auth Y] mmCIF format, chain U [auth X] mmCIF format, chain Z mmCIF format, chain W [auth Y]	U [auth X], W [auth Y], Z	2-AMINO-ETHANETHIOL C₂ H₇ N S UFULAYFCSOUIOV-UHFFFAOYSA-N		Interactions Focus chain U [auth X] Focus chain W [auth Y] Focus chain Z Interactions & Density Focus chain U [auth X] Focus chain W [auth Y] Focus chain Z
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain X [auth Z] SDF format, chain J [auth B] MOL2 format, chain X [auth Z] MOL2 format, chain J [auth B] mmCIF format, chain X [auth Z] mmCIF format, chain J [auth B]	J [auth B], X [auth Z]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Focus chain X [auth Z] Interactions & Density Focus chain J [auth B] Focus chain X [auth Z]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain Y [auth Z] SDF format, chain V [auth Y] SDF format, chain T [auth X] MOL2 format, chain Y [auth Z] MOL2 format, chain V [auth Y] MOL2 format, chain T [auth X] mmCIF format, chain Y [auth Z] mmCIF format, chain V [auth Y] mmCIF format, chain T [auth X]	T [auth X], V [auth Y], Y [auth Z]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain T [auth X] Focus chain V [auth Y] Focus chain Y [auth Z] Interactions & Density Focus chain T [auth X] Focus chain V [auth Y] Focus chain Y [auth Z]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain M [auth B] SDF format, chain I [auth C] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain M [auth B] MOL2 format, chain I [auth C] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain M [auth B] mmCIF format, chain I [auth C]	I [auth C], M [auth B], R [auth A], S [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain I [auth C] Focus chain M [auth B] Focus chain R [auth A] Focus chain S [auth A] Interactions & Density Focus chain I [auth C] Focus chain M [auth B] Focus chain R [auth A] Focus chain S [auth A]

Modified Residues 3 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO Query on CSO	A [auth C]	L-PEPTIDE LINKING	C₃ H₇ N O₃ S		CYS
CME Query on CME	C [auth A]	L-PEPTIDE LINKING	C₅ H₁₁ N O₃ S₂		CYS
A1JAL Query on A1JAL	D [auth X], E [auth Y], F [auth Z]	L-PEPTIDE LINKING	C₁₂ H₂₀ N₂ O₃		--
ABA Query on ABA	D [auth X], E [auth Y], F [auth Z]	L-PEPTIDE LINKING	C₄ H₉ N O₂		ALA