8BZP: JNK3

JNK3 (Mitogen-activated protein kinase 10) in Complex with Compound 23 bearing a C(sp3)F2Br moiety. Determined by X-ray diffraction at 1.86 Å resolution. Released 2 Aug 2023.

Method: X-ray diffraction
Resolution: 1.86 Å
Organism: Homo sapiens
Chains: 2
Atoms: 5,834
Mol. weight: 87.23 kDa
Ligands: SWM, C15
Released: 2 Aug 2023

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

Secondary structure: helices and β-sheets

8BZP contains 42 α-helices and 22 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: 23 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	48-53	6	1
β-strand	56-61	6	1
β-strand	64-72	9	2
β-strand	76-83	8	2
β-strand	88-95	8	2
α-helix	102-117	16
β-strand	123	1	3
β-strand	126-130	5	2
β-strand	143-147	5	2
α-helix	148-149	2
β-strand	151-152	2	3
α-helix	153-157	5
α-helix	160-161	2
α-helix	163-182	20
α-helix	192-194	3
β-strand	195-197	3	3
β-strand	203-205	3	3
α-helix	232-235	4
α-helix	244-258	15
α-helix	268-279	12
α-helix	281-283	3
α-helix	284-289	6
α-helix	294-299	6
α-helix	302-303	2
α-helix	309-312	4
α-helix	315-317	3
α-helix	323-339	17
α-helix	344-346	3
α-helix	348-349	2
α-helix	350-355	6
α-helix	357-360	4
α-helix	365-368	4
α-helix	370-373	4
α-helix	387-399	13

Chain B: 19 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	48-52	5	4
β-strand	57-61	5	4
β-strand	64-69	6	5
β-strand	77-83	7	5
β-strand	88-96	9	5
α-helix	102-117	16
β-strand	123	1	6
β-strand	126-130	5	5
β-strand	141-147	7	5
β-strand	151-152	2	6
α-helix	153-158	6
α-helix	163-182	20
α-helix	192-194	3
β-strand	195-197	3	6
β-strand	203-205	3	6
α-helix	232-235	4
α-helix	244-258	15
α-helix	268-279	12
α-helix	281-283	3
α-helix	284-288	5
α-helix	292-300	9
α-helix	309-312	4
α-helix	315-317	3
α-helix	323-339	17
α-helix	348-349	2
α-helix	350-354	5
α-helix	360-362	3
α-helix	365-368	4
α-helix	370-373	4
α-helix	387-399	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Mitogen-activated protein kinase 10	A, B	protein	364	Homo sapiens	P53779 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8BZP_1 Mitogen-activated protein kinase 10 (chains A, B)
MSKSKVDNQFYSVEVGDSTFTVLKRYQNLKPIGSGAQGIVCAAYDAVLDRNVAIKKLSRP
FQNQTHAKRAYRELVLMKCVNHKNIISLLNVFTPQKTLEEFQDVYLVMELMDANLCQVIQ
MELDHERMSYLLYQMLCGIKHLHSAGIIHRDLKPSNIVVKSDCTLKILDFGLARTAGTSF
MMTPYVVTRYYRAPEVILGMGYKENVDIWSVGCIMGEMVRHKILFPGRDYIDQWNKVIEQ
LGTPCPEFMKKLQPTVRNYVENRPKYAGLTFPKLFPDSLFPADSEHNKLKASQARDLLSK
MLVIDPAKRISVDDALQHPYINVWYDPAEVEAPPPQIYDKQLDEREHTIEEWKELIYKEV
MNSE

Ligands and cofactors

ID	Name	Formula	Copies
SWM	2-bromanyl-2,2-bis(fluoranyl)-~{N}-(5-pyridin-4-yl-1,3,4-thiadiazol-2-yl)ethana…	C9 H5 Br F2 N4 O S	2
C15	N-dodecyl-n,n-dimethyl-3-ammonio-1-propanesulfonate	C17 H38 N O3 S	3

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

Primary citation

Principles and Applications of CF 2 X Moieties as Unconventional Halogen Bond Donors in Medicinal Chemistry, Chemical Biology, and Drug Discovery. Vaas, S., Zimmermann, M.O., Schollmeyer, D. et al. J Med Chem (2023) 66:10202-10225. DOI 10.1021/acs.jmedchem.3c00634 · PubMed

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.
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
4H39 1.99 Å, Crystal Structure of JNK3 in Complex with JIP1 Peptide

Browse structure collections

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