8PTA: JNK1 covalently

JNK1 covalently bound to BD837 cyclohexenone based inhibitor. Determined by X-ray diffraction at 2.41 Å resolution. Released 24 Jul 2024.

Method: X-ray diffraction
Resolution: 2.41 Å
Organism: Homo sapiens
Chains: 3
Atoms: 8,442
Mol. weight: 127.97 kDa
Ligands: CIF
Released: 24 Jul 2024

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

Secondary structure: helices and β-sheets

8PTA contains 62 α-helices and 34 β-strands across 3 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: 20 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	10-13	4	1
β-strand	20-23	4	1
β-strand	26-31	6	2
β-strand	40-45	6	2
β-strand	51-57	7	2
α-helix	64-78	15
β-strand	85	1	3
β-strand	88-92	5	2
β-strand	104-109	6	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	246-250	5
α-helix	254-262	9
α-helix	264-265	2
α-helix	271-274	4
α-helix	285-301	17
α-helix	306-308	3
α-helix	310-311	2
α-helix	312-316	5
α-helix	322-324	3
α-helix	327-330	4
α-helix	332-335	4
α-helix	349-361	13

Chain B: 21 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	10-12	3	4
β-strand	21-23	3	4
β-strand	26-31	6	5
β-strand	39-45	7	5
β-strand	50-58	9	5
α-helix	60-62	3
α-helix	64-79	16
β-strand	82	1	6
β-strand	85	1	6
β-strand	88-92	5	5
α-helix	98-100	3
β-strand	103-109	7	5
β-strand	113-114	2	6
α-helix	115-120	6
α-helix	125-144	20
β-strand	157-159	3	6
β-strand	165-167	3	6
α-helix	194-197	4
α-helix	206-220	15
α-helix	230-241	12
α-helix	243-245	3
α-helix	246-250	5
α-helix	254-262	9
α-helix	264-265	2
α-helix	271-274	4
α-helix	285-301	17
α-helix	306-308	3
α-helix	310-311	2
α-helix	312-316	5
α-helix	322-324	3
α-helix	327-330	4
α-helix	332-334	3
α-helix	349-361	13

Chain C: 21 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	10-15	6	7
β-strand	18-23	6	7
β-strand	26-31	6	8
β-strand	39-45	7	8
β-strand	50-56	7	8
α-helix	57	1
α-helix	64-78	15
β-strand	85	1	9
β-strand	88-92	5	8
β-strand	105-109	5	8
β-strand	113-114	2	9
α-helix	115-120	6
α-helix	125-144	20
α-helix	154-156	3
β-strand	157-159	3	9
β-strand	165-167	3	9
α-helix	194-197	4
α-helix	206-220	15
α-helix	232-240	9
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	285-301	17
α-helix	306-308	3
α-helix	310-311	2
α-helix	312-316	5
α-helix	319-322	4
α-helix	327-330	4
α-helix	332-335	4
α-helix	349-359	11

Molecules and chains

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

Sequence of entity 1 (A, B, C), FASTA

>8PTA_1 Mitogen-activated protein kinase 8 (chains A, B, C)
GSMSRSKRDNNFYSVEIGDSTFTVLKRYQNLKPIGSGAQGIVCAAYDAILERNVAIKKLS
RPFQNQTHAKRAYRELVLMKCVNHKNIIGLLNVFTPQKSLEEFQDVYIVMELMDANLCQV
IQMELDHERMSYLLYQMLCGIKHLHSAGIIHRDLKPSNIVVKSDCTLKILDFGLARTAGT
SFMMTPYVVTRYYRAPEVILGMGYKENVDIWSVGCIMGEMIKGGVLFPGTDHIDQWNKVI
EQLGTPCPEFMKKLQPTVRTYVENRPKYAGYSFEKLFPDVLFPADSEHNKLKASQARDLL
SKMLVIDASKRISVDEALQHPYINVWYDPSEAEAPPPKIPDKQLDEREHTIEEWKELIYK
EVMDLE

Ligands and cofactors

ID	Name	Formula	Copies
CIF	methyl (1R,3S)-1-methyl-3-[[3-[[3-methyl-4-[(4-pyridin-3-ylpyrimidin-2-yl)amino…	C33 H32 N6 O5	3

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

Primary citation

Reversible covalent c-Jun N-terminal kinase inhibitors targeting a specific cysteine by precision-guided Michael-acceptor warheads. Balint, D., Poti, A.L., Alexa, A. et al. Nat Commun (2024) 15:8606-8606. DOI 10.1038/s41467-024-52573-2 · 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…
11ZL 1.55 Å, Crystal Structure of human JNK1 Kinase Domain in complex with inhibitor CCD-3013
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

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