8PKX: Kelch domain of KEAP1

Kelch domain of KEAP1 in complex with a ortho-dimethylbenzene linked cyclic peptide 11 (ortho-WRCNPETaEC). Determined by X-ray diffraction at 1.79 Å resolution. Released 15 Nov 2023.

Method: X-ray diffraction
Resolution: 1.79 Å
Organism: Homo sapiens
Chains: 3
Atoms: 4,913
Mol. weight: 71.6 kDa
Ligands: ZK2
Released: 15 Nov 2023

Explore 8PKX in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8PKX contains 13 α-helices and 84 β-strands across 2 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, 42 β-strands

Element	Residues	Length	Sheet
β-strand	326-331	6	1
β-strand	334-335	2	2
β-strand	337-338	2	2
β-strand	342-345	4	1
β-strand	352-354	3	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
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	543-547	5	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	605-610	6	1
α-helix	611-613	3

Chain B: 7 helices, 42 β-strands

Element	Residues	Length	Sheet
β-strand	327-331	5	13
β-strand	334-335	2	14
β-strand	337-338	2	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
α-helix	437	1
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	20
β-strand	471-475	5	20
β-strand	478	1	19
β-strand	483	1	19
β-strand	487-491	5	20
α-helix	492-494	3
β-strand	496-499	4	20
α-helix	501-503	3
β-strand	508	1	21
β-strand	511-515	5	22
β-strand	518-522	5	22
β-strand	525	1	21
β-strand	530	1	21
β-strand	534-538	5	22
β-strand	543-546	4	22
α-helix	548-550	3
β-strand	555	1	23
β-strand	558-562	5	24
β-strand	565-569	5	24
β-strand	572	1	23
β-strand	577	1	23
β-strand	580-585	6	24
β-strand	590-596	7	24
β-strand	602	1	14
β-strand	605-609	5	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Kelch-like ECH-associated protein 1	A, B	protein	316	Homo sapiens	Q14145 (AlphaFold model)
CP11	P	protein	12	Homo sapiens

Sequence of entity 1 (A, B), FASTA

>8PKX_1 Kelch-like ECH-associated protein 1 (chains A, B)
GHMKPTQVMPSRAPKVGRLIYTAGGYFRQSLSYLEAYNPSDGTWLRLADLQVPRSGLAGC
VVGGLLYAVGGRNNSPDGNTDSSALDCYNPMTNQWSPCAPMSVPRNRIGVGVIDGHIYAV
GGSHGCIHHNSVERYEPERDEWHLVAPMLTRRIGVGVAVLNRLLYAVGGFDGTNRLNSAE
CYYPERNEWRMITAMNTIRSGAGVCVLHNCIYAAGGYDGQDQLNSVERYDVATATWTFVA
PMKHRRSALGITVHQGRIYVLGGYDGHTFLDSVECYDPDTDTWSEVTRMTSGRSGVGVAV
TMEPSRKQIDQQNSTS

Sequence of entity 2 (P), FASTA

>8PKX_2 CP11 (chains P)
XWRCNPETAECX

Ligands and cofactors

ID	Name	Formula	Copies
ZK2	(2-methylphenyl)methanol	C8 H10 O	1

Water and common crystallization additives (SO4, NA, GOL, EDO, CL) are not listed.

Primary citation

Computational Prediction of Cyclic Peptide Structural Ensembles and Application to the Design of Keap1 Binders. Fonseca Lopez, F., Miao, J., Damjanovic, J. et al. J Chem Inf Model (2023) 63:6925-6937. DOI 10.1021/acs.jcim.3c01337 · 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

Browse structure collections

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