8YD9: P38alpha with an allosteric inhibitor 3

Crystal structure of p38alpha with an allosteric inhibitor 3. Determined by X-ray diffraction at 1.66 Å resolution. Released 26 Feb 2025.

Method: X-ray diffraction
Resolution: 1.66 Å
Organism: Homo sapiens
Chains: 1
Atoms: 3,488
Mol. weight: 42.29 kDa
Ligands: 6GI
Released: 26 Feb 2025

Explore 8YD9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8YD9 contains 25 α-helices and 12 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: 25 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	5-7	3
β-strand	8-11	4	1
β-strand	18-21	4	1
β-strand	24-32	9	2
β-strand	36-43	8	2
β-strand	48-55	8	2
α-helix	62-77	16
β-strand	80	1	3
β-strand	83	1	3
β-strand	88-90	3	2
α-helix	96-98	3
β-strand	103-107	5	2
α-helix	108-109	2
β-strand	112	1	3
α-helix	114-117	4
α-helix	124-143	20
α-helix	153-155	3
β-strand	156-158	3	3
β-strand	164-166	3	3
α-helix	177-179	3
α-helix	184-187	4
α-helix	191-194	4
α-helix	203-218	16
α-helix	228-239	12
α-helix	244-248	5
α-helix	253-260	8
α-helix	263-264	2
α-helix	266-268	3
α-helix	270-273	4
α-helix	279-288	10
α-helix	297-298	2
α-helix	299-303	5
α-helix	306-308	3
α-helix	320-322	3
α-helix	326-329	4
α-helix	334-346	13
α-helix	350-352	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Mitogen-activated protein kinase 14	A	protein	360	Homo sapiens	Q16539 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8YD9_1 Mitogen-activated protein kinase 14 (chains A)
MSQERPTFYRQELNKTIWEVPERYQNLSPVGSGAYGSVCAAFDTKTGLRVAVKKLSRPFQ
SIIHAKRTYRELRLLKHMKHENVIGLLDVFTPARSLEEFNDVYLVTHLMGADLNNIVKCQ
KLTDDHVQFLIYQILRGLKYIHSADIIHRDLKPSNLAVNEDCELKILDFGLARHTDDEMT
GYVATRWYRAPEIMLNWMHYNQTVDIWSVGCIMAELLTGRTLFPGTDHIDQLKLILRLVG
TPGAELLKKISSESARNYIQSLTQMPKMNFANVFIGANPLAVDLLEKMLVLDSDKRITAA
QALAHAYFAQYHDPDDEPVADPYDQSFESRDLLIDEWKSLTYDEVISFVPPPLDQEEMES

Ligands and cofactors

ID	Name	Formula	Copies
6GI	13-[4-({Imidazo[1,2-a]pyridin-2-yl}methoxy)phenyl]-4,8-dioxa-12,14,16,18-tetraa…	C26 H23 N7 O3	1

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

Primary citation

Identification of a novel target site for ATP-independent p38 alpha inhibitors. Kinoshita, T., Hasegawa, S. To be published.

Other PDB entries of the same protein (UniProt Q16539 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2FST 1.45 Å, mitogen activated protein kinase p38alpha (D176A+F327L) activating mutant
3LFF 1.5 Å, Human p38 MAP Kinase in Complex with RL166
3OEF 1.6 Å, Crystal structure of Y323F inactive mutant of p38alpha MAP kinase
3ZS5 1.6 Å, Structural basis for kinase selectivity of three clinical p38alpha inhibitors
4EHV 1.6 Å, Human p38 MAP kinase in complex with NP-F10 and RL87
5WJJ 1.6 Å, Structure-based Design, Synthesis, and Biological Evaluation of…
6SFI 1.6 Å, Crystal structure of p38 alpha in complex with compound 75 (MCP33)
9MHB 1.65 Å, Crystal Structure of Human P38 alpha MAPK In Complex with MW01-14-064SRM
4GEO 1.66 Å, P38a MAP kinase DEF-pocket penta mutant (M194A, L195A, H228A, I229A, Y258A)
6QYX 1.66 Å, p38(alpha) MAP kinase with the activation loop of ERK2
2FSL 1.7 Å, mitogen activated protein kinase p38alpha (D176A+F327S) activating mutant form-A
2QD9 1.7 Å, P38 Alpha Map Kinase inhibitor based on heterobicyclic scaffolds

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