3K3I: P38alpha

p38alpha bound to novel DGF-out compound PF-00215955. Determined by X-ray diffraction at 1.7 Å resolution. Released 17 Nov 2009.

Method: X-ray diffraction
Resolution: 1.7 Å
Organism: Homo sapiens
Chains: 1
Atoms: 3,094
Mol. weight: 40.92 kDa
Ligands: JZJ, I46
Released: 17 Nov 2009

Explore 3K3I in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3K3I contains 24 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: 24 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	6-7	2
β-strand	8-13	6	1
β-strand	16-21	6	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	83	1	3
β-strand	88-90	3	2
α-helix	96-98	3
β-strand	103-107	5	2
β-strand	111-112	2	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	185-188	4
α-helix	191-194	4
α-helix	203-218	16
α-helix	228-239	12
α-helix	242-243	2
α-helix	244-247	4
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	314-316	3
α-helix	318-322	5
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	350	Homo sapiens	Q16539 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3K3I_1 Mitogen-activated protein kinase 14 (chains A)
GSRPTFYRQELNKTIWEVPERYQNLSPVGSGAYGSVCAAFDTKTGLRVAVKKLSRPFQSI
IHAKRTYRELRLLKHMKHENVIGLLDVFTPARSLEEFNDVYLVTHLMGADLNNIVKCQKL
TDDHVQFLIYQILRGLKYIHSADIIHRDLKPSNLAVNEDCELKILDFGLARHTDDEMTGY
VATRWYRAPEIMLNWMHYNQTVDIWSVGCIMAELLTGRTLFPGTDHIDQLKLILRLVGTP
GAELLKKISSESARNYIQSLTQMPKMNFANVFIGANPLAVDLLEKMLVLDSDKRITAAQA
LAHAYFAQYHDPDDEPVADPYDQSFESRDLLIDEWKSLTYDEVISFVPPP

Ligands and cofactors

ID	Name	Formula	Copies
JZJ	(3S)-3-[4-(4-bromophenyl)-1H-imidazol-2-yl]-1,2,3,4-tetrahydroisoquinoline	C18 H16 Br N3	1
I46	2-fluoro-4-[4-(4-fluorophenyl)-1H-pyrazol-3-yl]pyridine	C14 H9 F2 N3	2

Primary citation

The design, synthesis and potential utility of fluorescence probes that target DFG-out conformation of p38alpha for high throughput screening binding assay. Tecle, H., Feru, F., Liu, H. et al. Chem Biol Drug Des (2009) 74:547-559. DOI 10.1111/j.1747-0285.2009.00884.x · PubMed

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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