9IH9: KEAP1 complexed to linear peptide 6

KEAP1 complexed to linear peptide 6. Determined by X-ray diffraction at 1.7 Å resolution. Released 4 Mar 2026.

Method: X-ray diffraction
Resolution: 1.7 Å
Organisms: Homo sapiens, synthetic construct
Chains: 6
Atoms: 7,446
Mol. weight: 97.92 kDa
Ligands: DHL, MG
Released: 4 Mar 2026

Explore 9IH9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9IH9 contains 17 α-helices and 122 β-strands across 3 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 6 helices, 40 β-strands

Element	Residues	Length	Sheet
β-strand	328-331	4	24
β-strand	334	1	25
β-strand	338	1	25
β-strand	342-346	5	24
β-strand	351-354	4	24
α-helix	356-358	3
β-strand	363	1	26
β-strand	366-370	5	27
β-strand	373-377	5	27
β-strand	380-383	4	26
β-strand	386-389	4	26
β-strand	393-397	5	27
β-strand	402-405	4	27
α-helix	407-409	3
β-strand	414	1	28
β-strand	417-421	5	29
β-strand	424-428	5	29
β-strand	431-432	2	28
β-strand	435-436	2	28
β-strand	440-444	5	29
α-helix	445-447	3
β-strand	449-453	5	29
α-helix	454-456	3
β-strand	461	1	30
β-strand	464-468	5	30
β-strand	471-478	8	30
β-strand	483-491	9	30
β-strand	496-500	5	30
α-helix	501-503	3
β-strand	508	1	31
β-strand	511-515	5	32
β-strand	518-522	5	32
β-strand	525	1	31
β-strand	530	1	31
β-strand	534-538	5	32
β-strand	543-546	4	32
α-helix	548-550	3
β-strand	555	1	33
β-strand	558-562	5	34
β-strand	565-569	5	34
β-strand	572	1	33
β-strand	577	1	33
β-strand	580-585	6	34
β-strand	590-596	7	34
β-strand	602	1	25
β-strand	605-608	4	24

Chain B: 5 helices, 40 β-strands

Element	Residues	Length	Sheet
β-strand	328-331	4	13
β-strand	334	1	14
β-strand	338	1	14
β-strand	342-346	5	13
β-strand	351-354	4	13
α-helix	356-358	3
β-strand	363	1	15
β-strand	366-370	5	16
β-strand	373-377	5	16
β-strand	380-383	4	15
β-strand	386-389	4	15
β-strand	393-397	5	16
β-strand	402-405	4	16
α-helix	407-409	3
β-strand	414	1	17
β-strand	417-421	5	18
β-strand	424-428	5	18
β-strand	431-432	2	17
β-strand	435-436	2	17
β-strand	440-444	5	18
β-strand	449-453	5	18
α-helix	454-456	3
β-strand	461	1	19
β-strand	464-468	5	19
β-strand	471-478	8	19
β-strand	483-491	9	19
β-strand	496-499	4	19
α-helix	501-503	3
β-strand	508	1	20
β-strand	511-515	5	21
β-strand	518-522	5	21
β-strand	525	1	20
β-strand	530	1	20
β-strand	534-538	5	21
β-strand	543-546	4	21
α-helix	548-550	3
β-strand	555	1	22
β-strand	558-562	5	23
β-strand	565-569	5	23
β-strand	572	1	22
β-strand	577	1	22
β-strand	580-585	6	23
β-strand	590-596	7	23
β-strand	602	1	14
β-strand	605-608	4	13

Chain C: 6 helices, 42 β-strands

Element	Residues	Length	Sheet
β-strand	328-331	4	1
β-strand	334	1	2
β-strand	338	1	2
β-strand	342-346	5	1
β-strand	351-354	4	1
α-helix	356-358	3
β-strand	363	1	3
β-strand	366-370	5	4
β-strand	373-377	5	4
β-strand	380-383	4	3
β-strand	386-389	4	3
β-strand	393-397	5	4
β-strand	402-405	4	4
α-helix	407-409	3
β-strand	414	1	5
β-strand	417-421	5	6
β-strand	424-428	5	6
β-strand	431-432	2	5
β-strand	435-436	2	5
β-strand	440-444	5	6
α-helix	445-447	3
β-strand	449-453	5	6
α-helix	454-456	3
β-strand	461	1	7
β-strand	464-468	5	8
β-strand	471-475	5	8
β-strand	478	1	7
β-strand	483	1	7
β-strand	487-491	5	8
β-strand	496-499	4	8
α-helix	501-503	3
β-strand	508	1	9
β-strand	511-515	5	10
β-strand	518-522	5	10
β-strand	525	1	9
β-strand	530	1	9
β-strand	534-538	5	10
β-strand	543-546	4	10
α-helix	548-550	3
β-strand	555	1	11
β-strand	558-562	5	12
β-strand	565-569	5	12
β-strand	572	1	11
β-strand	577	1	11
β-strand	580-585	6	12
β-strand	590-596	7	12
β-strand	602	1	2
β-strand	605-608	4	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Kelch-like ECH-associated protein 1	C	protein	290	Homo sapiens	Q14145 (AlphaFold model)
Kelch-like ECH-associated protein 1	B	protein	290	Homo sapiens	Q14145 (AlphaFold model)
Kelch-like ECH-associated protein 1	A	protein	290	Homo sapiens	Q14145 (AlphaFold model)
Designed peptide	X, Y, Z	protein	4	synthetic construct

Sequence of entity 1 (C), FASTA

>9IH9_1 Kelch-like ECH-associated protein 1 (chains C)
SAPKVGRLIYTAGGYFRQSLSYLEAYNPSDGTWLRLADLQVPRSGLAGCVVGGLLYAVGG
RNNSPDGNTDSSALDCYNPMTNQWSPCAPMSVPRNRIGVGVIDGHIYAVGGSHGCIHHNS
VERYEPERDEWHLVAPMLTRRIGVGVAVLNRLLYAVGGFDGTNRLNSAECYYPERNEWRM
ITAMNTIRSGAGVCVLHNCIYAAGGYDGQDQLNSVERYDVATATWTFVAPMKHRRSALGI
TVHQGRIYVLGGYDGHTFLDSVECYDPDTDTWSEVTRMTSGRSGVGVAVT

Sequence of entity 2 (B), FASTA

>9IH9_2 Kelch-like ECH-associated protein 1 (chains B)
SAPKVGRLIYTAGGYFRQSLSYLEAYNPSDGTWLRLADLQVPRSGLAGCVVGGLLYAVGG
RNNSPDGNTDSSALDCYNPMTNQWSPCAPMSVPRNRIGVGVIDGHIYAVGGSHGCIHHNS
VERYEPERDEWHLVAPMLTRRIGVGVAVLNRLLYAVGGFDGTNRLNSAECYYPERNEWRM
ITAMNTIRSGAGVCVLHNCIYAAGGYDGQDQLNSVERYDVATATWTFVAPMKHRRSALGI
TVHQGRIYVLGGYDGHTFLDSVECYDPDTDTWSEVTRMTSGRSGVGVAVT

Sequence of entity 3 (A), FASTA

>9IH9_3 Kelch-like ECH-associated protein 1 (chains A)
SAPKVGRLIYTAGGYFRQSLSYLEAYNPSDGTWLRLADLQVPRSGLAGCVVGGLLYAVGG
RNNSPDGNTDSSALDCYNPMTNQWSPCAPMSVPRNRIGVGVIDGHIYAVGGSHGCIHHNS
VERYEPERDEWHLVAPMLTRRIGVGVAVLNRLLYAVGGFDGTNRLNSAECYYPERNEWRM
ITAMNTIRSGAGVCVLHNCIYAAGGYDGQDQLNSVERYDVATATWTFVAPMKHRRSALGI
TVHQGRIYVLGGYDGHTFLDSVECYDPDTDTWSEVTRMTSGRSGVGVAVT

Sequence of entity 4 (X, Y, Z), FASTA

>9IH9_4 Designed peptide (chains X, Y, Z)
XANA

Ligands and cofactors

ID	Name	Formula	Copies
DHL	2-amino-ethanethiol	C2 H7 N S	3
MG	Magnesium ion	Mg	4

Water and common crystallization additives (CL, EDO, PEG, GOL) are not listed.

Primary citation

Generation of membrane-permeable cyclic peptides inhibiting protein-protein interaction. Ji, X., Farrera-Soler, L., Li, J. et al. Nat Chem Biol (2026) 22:1351-1361. DOI 10.1038/s41589-026-02237-7 · PubMed

Other PDB entries of the same protein (UniProt Q14145 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8XGK 1.32 Å, Optimization Efforts for Identification of Novel Highly Potent Keap1-Nrf2…
1ZGK 1.35 Å, 1.35 angstrom structure of the Kelch domain of Keap1
8XGV 1.42 Å, Optimization Efforts for Identification of Novel Highly Potent Keap1-Nrf2…
6TYM 1.42 Å, KEAP1 Kelch domain in complex with Compound 9
9KVW 1.44 Å, Crystal Structures of Keap1-compound complexes
8IXS 1.48 Å, Methyl and Fluorine Effects in Novel Orally Bioavailable Keap1/Nrf2 PPI Inhibitor for…
2FLU 1.5 Å, Crystal Structure of the Kelch-Neh2 Complex
8IVR 1.5 Å, Methyl and Fluorine Effects in Novel Orally Bioavailable Keap1/Nrf2 PPI Inhibitor for…
9R1Z 1.5 Å, Keap1 - inhibitor complex - 3
8PKW 1.54 Å, Kelch domain of KEAP1 in complex with a ortho-dimethylbenzene linked cyclic peptide 5…
8PKV 1.55 Å, Kelch domain of KEAP1 in complex with a ortho-dimethylbenzene linked cyclic peptide 4…
9M24 1.57 Å, Crystal Structure of kelch domain of human KEAP1 in complex with CH7450924

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