3FMK: P38 kinase crystal structure

P38 kinase crystal structure in complex with 6-(2,4-Difluoro-phenoxy)-8-methyl-2-((S)-1-methyl-2-tetrazol-2-yl-ethylamino)-8H-pyrido[2,3-d]pyrimidin-7-one. Determined by X-ray diffraction at 1.7 Å resolution. Released 22 Dec 2009.

Method: X-ray diffraction
Resolution: 1.7 Å
Organism: Homo sapiens
Chains: 1
Atoms: 3,195
Mol. weight: 43.16 kDa
Ligands: FMK
Released: 22 Dec 2009

Explore 3FMK in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3FMK contains 24 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: 24 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	5-7	3
β-strand	8-12	5	1
β-strand	17-21	5	1
β-strand	24-33	10	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
β-strand	103-107	5	2
α-helix	108-109	2
β-strand	111-112	2	3
α-helix	113-117	5
α-helix	121-123	3
α-helix	124-143	20
α-helix	153-155	3
β-strand	156-158	3	3
β-strand	164-166	3	3
α-helix	184-187	4
α-helix	191-194	4
α-helix	204-218	15
α-helix	228-239	12
α-helix	244-249	6
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	293-295	3
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

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Mitogen-activated protein kinase 14	A	protein	372	Homo sapiens	Q16539 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3FMK_1 Mitogen-activated protein kinase 14 (chains A)
MRGSHHHHHHGSMSQERPTFYRQELNKTIWEVPERYQNLSPVGSGAYGSVCAAFDTKTGL
RVAVKKLSRPFQSIIHAKRTYRELRLLKHMKHENVIGLLDVFTPARSLEEFNDVYLVTHL
MGADLNNIVKCQKLTDDHVQFLIYQILRGLKYIHSADIIHRDLKPSNLAVNEDCELKILD
FGLARHTDDEMTGYVATRWYRAPEIMLNWMHYNQTVDIWSVGCIMAELLTGRTLFPGTDH
IDQLKLILRLVGTPGAELLKKISSESARNYIQSLTQMPKMNFANVFIGANPLAVDLLEKM
LVLDSDKRITAAQALAHAYFAQYHDPDDEPVADPYDQSFESRDLLIDEWKSLTYDEVISF
VPPPLDQEEMES

Ligands and cofactors

ID	Name	Formula	Copies
FMK	6-(2,4-difluorophenoxy)-8-methyl-2-{[(1S)-1-methyl-2-(2H-tetrazol-2-yl)ethyl]am…	C18 H16 F2 N8 O2	1

Primary citation

The Discovery of Pamapimod and R1487 as Orally Bioavailable and Highly Selective Inhibitors of p38 Map Kinase. Soth, M., Kuglstatter, A., Goldstein, D. 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
8YD9 1.66 Å, Crystal structure of p38alpha with an allosteric inhibitor 3
2FSL 1.7 Å, mitogen activated protein kinase p38alpha (D176A+F327S) activating mutant form-A

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