11ZL: Human JNK1 Kinase Domain

Crystal Structure of human JNK1 Kinase Domain in complex with inhibitor CCD-3013. Determined by X-ray diffraction at 1.55 Å resolution. Released 2 Sept 2026.

Method: X-ray diffraction
Resolution: 1.55 Å
Organism: Homo sapiens
Chains: 1
Atoms: 3,339
Mol. weight: 41.7 kDa
Ligands: A1DA9
Released: 2 Sept 2026

Explore 11ZL in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

11ZL contains 24 α-helices and 11 β-strands across 1 chain. 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: 24 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	10-15	6	1
β-strand	18-23	6	1
β-strand	26-32	7	2
β-strand	39-45	7	2
β-strand	50-58	9	2
α-helix	60-62	3
α-helix	64-79	16
β-strand	85	1	3
α-helix	86-87	2
β-strand	88-92	5	2
β-strand	103-108	6	2
β-strand	113-114	2	3
α-helix	115-118	4
α-helix	125-144	20
α-helix	154-156	3
β-strand	157-159	3	3
β-strand	165-167	3	3
α-helix	185-188	4
α-helix	194-197	4
α-helix	206-220	15
α-helix	230-241	12
α-helix	243-245	3
α-helix	246-249	4
α-helix	254-262	9
α-helix	264-265	2
α-helix	271-274	4
α-helix	277-279	3
α-helix	285-301	17
α-helix	310-311	2
α-helix	312-317	6
α-helix	322-324	3
α-helix	327-330	4
α-helix	332-335	4
α-helix	342-344	3
α-helix	349-360	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Mitogen-activated protein kinase 8	A	protein	357	Homo sapiens	P45983 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>11ZL_1 Mitogen-activated protein kinase 8 (chains A)
DNNFYSVEIGDSTFTVLKRYQNLKPIGSGAQGIVCAAYDAILERNVAIKKLSRPFQNQTH
AKRAYRELVLMKCVNHKNIIGLLNVFTPQKSLEEFQDVYIVMELMDANLCQVIQMELDHE
RMSYLLYQMLCGIKHLHSAGIIHRDLKPSNIVVKSDCTLKILDFGLARTAGTSFMMTPYV
VTRYYRAPEVILGMGYKENVDLWSVGCIMGEMVCHKILFPGRDYIDQWNKVIEQLGTPCP
EFMKKLQPTVRTYVENRPKYAGYSFEKLFPDVLFPADSEHNKLKASQARDLLSKMLVIDA
SKRISVDEALQHPYINVWYDPSEAEAPPPKIPDKQLDEREHTIEEWKELIYKEVMDL

Ligands and cofactors

ID	Name	Formula	Copies
A1DA9	(4M)-N-[4-hydroxy-3-(pyrrolidine-1-carbonyl)phenyl]-4-(1H-pyrrolo[2,3-b]pyridin…	C27 H22 N4 O3 S	1

Primary citation

Identification of potent inhibitors of JUN N-terminal kinases for treatment of endometriosis and associated pain. Madasu, C., Sirupangi, T., Herrera, G.J. et al. Proc Natl Acad Sci U S A (2026) 123:e2607561123-e2607561123. DOI 10.1073/pnas.2607561123 · PubMed

Other PDB entries of the same protein (UniProt P45983 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2XRW 1.33 Å, Linear binding motifs for JNK and for calcineurin antagonistically control the nuclear…
12CV 1.5 Å, Crystal Structure of human JNK1 Kinase Domain in complex with inhibitor CCD-2728
4QTD 1.5 Å, Structure of human JNK1 in complex with SCH772984 and the AMPPNP-hydrolysed triphosphate…
8R5E 1.7 Å, JNK1 covalently bound to RU77 cyclohexenone based inhibitor
3ELJ 1.8 Å, Jnk1 complexed with a bis-anilino-pyrrolopyrimidine inhibitor.
4AWI 1.91 Å, Human Jnk1alpha kinase with 4-phenyl-7-azaindole IKK2 inhibitor.
4L7F 1.95 Å, Co-crystal Structure of JNK1 and AX13587
3PZE 2.0 Å, JNK1 in complex with inhibitor
8X5M 2.0 Å, The Crystal Structure of JNK1 from Biortus.
4HYU 2.15 Å, Crystal structure of JNK1 in complex with JIP1 peptide and…
4E73 2.27 Å, Crystal structure of JNK1beta-JIP in complex with an azaquinolone inhbitor
4IZY 2.3 Å, Crystal structure of JNK1 in complex with JIP1 peptide and…

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