8VNX: Mitogen-activated protein kinase 10

A structural study of selectivity mechanisms for JNK3 and p38 alpha with indazole scaffold probing compounds. Determined by X-ray diffraction at 2.0 Å resolution. Released 15 Jan 2025.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,967
Mol. weight: 53.09 kDa
Ligands: WHQ
Released: 15 Jan 2025

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

Secondary structure: helices and β-sheets

8VNX contains 20 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: 20 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	48-53	6	1
β-strand	56-61	6	1
β-strand	64-71	8	2
β-strand	77-83	7	2
β-strand	88-96	9	2
α-helix	98-100	3
α-helix	102-114	13
β-strand	123	1	3
β-strand	128-130	3	2
β-strand	141-147	7	2
β-strand	151-152	2	3
α-helix	153-157	5
α-helix	163-182	20
α-helix	192-194	3
β-strand	195-197	3	3
β-strand	203-205	3	3
α-helix	232-236	5
α-helix	244-258	15
α-helix	268-279	12
α-helix	281-283	3
α-helix	284-287	4
α-helix	292-299	8
α-helix	302-303	2
α-helix	309-312	4
α-helix	315-317	3
α-helix	323-339	17
α-helix	348-349	2
α-helix	350-355	6
α-helix	360-362	3
α-helix	365-368	4
α-helix	387-398	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Mitogen-activated protein kinase 10	A	protein	464	Homo sapiens	P53779 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8VNX_1 Mitogen-activated protein kinase 10 (chains A)
MSLHFLYYCSEPTLDVKIAFCQGFDKQVDVSYIAKHYNMSKSKVDNQFYSVEVGDSTFTV
LKRYQNLKPIGSGAQGIVCAAYDAVLDRNVAIKKLSRPFQNQTHAKRAYRELVLMKCVNH
KNIISLLNVFTPQKTLEEFQDVYLVMELMDANLCQVIQMELDHERMSYLLYQMLCGIKHL
HSAGIIHRDLKPSNIVVKSDCTLKILDFGLARTAGTSFMMTPYVVTRYYRAPEVILGMGY
KENVDIWSVGCIMGEMVRHKILFPGRDYIDQWNKVIEQLGTPCPEFMKKLQPTVRNYVEN
RPKYAGLTFPKLFPDSLFPADSEHNKLKASQARDLLSKMLVIDPAKRISVDDALQHPYIN
VWYDPAEVEAPPPQIYDKQLDEREHTIEEWKELIYKEVMNSEEKTKNGVVKGQPSPSGAA
VNSSESLPPSSSVNDISSMSTDQTLASDTDSSLEASAGPLGCCR

Ligands and cofactors

ID	Name	Formula	Copies
WHQ	(4P)-4-[5-(2-chloro-6-fluoroanilino)-6-(methoxymethyl)-1H-indazol-1-yl]-N-methy…	C21 H18 Cl F N4 O2 S	1

Primary citation

Structural study of selectivity mechanisms for JNK3 and p38 alpha with indazole scaffold probing compounds. Park, H., Feng, Y. J Mol Struct (2025) 1339:142179. DOI 10.1016/j.molstruc.2025.142179

Other PDB entries of the same protein (UniProt P53779 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3OY1 1.7 Å, Highly Selective c-Jun N-Terminal Kinase (JNK) 2 and 3 Inhibitors with In Vitro CNS-like…
7ORF 1.7 Å, Crystal structure of JNK3 in complex with FMU-001-367 (compound 1)
7KSI 1.73 Å, Thiophenyl-Pyrazolourea Derivatives as Potent, Brian Penetrant, Orally Bioavailable, and…
6EMH 1.76 Å, Crystal structure of JNK3 in complex with a pyridinylimidazole inhibitor
4WHZ 1.79 Å, Design and Synthesis of Highly Potent and Isoform Selective JNK3 Inhibitors: SAR Studies…
6EQ9 1.83 Å, Crystal structure of JNK3 in complex with AMP-PCP
7KSK 1.84 Å, Thiophenyl-Pyrazolourea Derivatives as Potent, Brian Penetrant, Orally Bioavailable, and…
8WGF 1.85 Å, The Crystal Structure of JNK3 from Biortus.
8BZP 1.86 Å, JNK3 (Mitogen-activated protein kinase 10) in Complex with Compound 23 bearing a…
2B1P 1.9 Å, inhibitor complex of JNK3
4W4W 1.9 Å, JNK2/3 in complex with N-(2-methylpyridin-4-yl)-3-{4-[(phenylcarbamoyl)amino]-1H-pyrazol-…
4X21 1.95 Å, The MAP kinase JNK3 as target for halogen bonding

Browse structure collections

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