8R5E: JNK1 covalently

JNK1 covalently bound to RU77 cyclohexenone based inhibitor. Determined by X-ray diffraction at 1.7 Å resolution. Released 27 Nov 2024.

Method: X-ray diffraction
Resolution: 1.7 Å
Organism: Homo sapiens
Chains: 1
Atoms: 3,044
Mol. weight: 42.95 kDa
Ligands: Y6K, ANP, MG
Released: 27 Nov 2024

Explore 8R5E in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8R5E contains 22 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: 22 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	10-15	6	1
β-strand	18-23	6	1
β-strand	26-33	8	2
β-strand	39-45	7	2
β-strand	50-58	9	2
α-helix	64-79	16
β-strand	85	1	3
α-helix	86-87	2
β-strand	88-92	5	2
β-strand	103-109	7	2
β-strand	113-114	2	3
α-helix	115-120	6
α-helix	125-144	20
α-helix	154-156	3
β-strand	157-159	3	3
β-strand	165-167	3	3
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	254-261	8
α-helix	264-266	3
α-helix	271-274	4
α-helix	277-279	3
α-helix	285-301	17
α-helix	306-308	3
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	349-361	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Mitogen-activated protein kinase 8	A	protein	366	Homo sapiens	P45983 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8R5E_1 Mitogen-activated protein kinase 8 (chains A)
GSMSRSKRDNNFYSVEIGDSTFTVLKRYQNLKPIGSGAQGIVCAAYDAILERNVAIKKLS
RPFQNQTHAKRAYRELVLMKCVNHKNIIGLLNVFTPQKSLEEFQDVYIVMELMDANLCQV
IQMELDHERMSYLLYQMLCGIKHLHSAGIIHRDLKPSNIVVKSDCTLKILDFGLARTAGT
SFMMTPYVVTRYYRAPEVILGMGYKENVDIWSVGCIMGEMIKGGVLFPGTDHIDQWNKVI
EQLGTPCPEFMKKLQPTVRTYVENRPKYAGYSFEKLFPDVLFPADSEHNKLKASQARDLL
SKMLVIDASKRISVDEALQHPYINVWYDPSEAEAPPPKIPDKQLDEREHTIEEWKELIYK
EVMDLE

Ligands and cofactors

ID	Name	Formula	Copies
Y6K	~{O}3-~{tert}-butyl ~{O}1-methyl (1~{S},3~{R},5~{R})-6-methylidene-4-oxidanylid…	C16 H22 O5	1
ANP	Phosphoaminophosphonic acid-adenylate ester	C10 H17 N6 O12 P3	1
MG	Magnesium ion	Mg	1

Water and common crystallization additives (GOL) are not listed.

Primary citation

The covalent coordination of cyclohexenone inhibitors in the MAP kinase docking groove. Poti, A., Sok, P., Remenyi, A. To be published.

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…
11ZL 1.55 Å, Crystal Structure of human JNK1 Kinase Domain in complex with inhibitor CCD-3013
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…

Browse structure collections

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