PDB-6emh: Crystal structure of JNK3 in complex with a pyridinylimidazole in...

ID or keywords:

Entry

Database: PDB / ID: 6emh

Title

Crystal structure of JNK3 in complex with a pyridinylimidazole inhibitor

Components

Mitogen-activated protein kinase 10

Keywords

TRANSFERASE / Protein Kinase Activity Map Kinase Activity ATP Binding Protein Phosphorylation

Function / homology

Function and homology information

JUN kinase activity / Activation of the AP-1 family of transcription factors / Fc-epsilon receptor signaling pathway /

MAP kinase kinase activity / response to light stimulus /

mitogen-activated protein kinase / JNK cascade / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / FCERI mediated MAPK activation /

regulation of circadian rhythm ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.76 Å

Authors

Macedo, J.T. / Stehle, T. / Blaum, B.S.

Citation

Journal: ACS Omega / Year: 2018
Title: Structural Optimization of a Pyridinylimidazole Scaffold: Shifting the Selectivity from p38 alpha Mitogen-Activated Protein Kinase to c-Jun N-Terminal Kinase 3.
Authors: Ansideri, F. / Macedo, J.T. / Eitel, M. / El-Gokha, A. / Zinad, D.S. / Scarpellini, C. / Kudolo, M. / Schollmeyer, D. / Boeckler, F.M. / Blaum, B.S. / Laufer, S.A. / Koch, P.

History

Deposition	Oct 2, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 8, 2018	Provider: repository / Type: Initial release
Revision 1.1	Aug 22, 2018	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	Oct 16, 2019	Group: Data collection / Category: reflns_shell
Revision 1.3	Jan 17, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6emh.cif.gz	586.2 KB	Display	PDBx/mmCIF format
PDB format	pdb6emh.ent.gz	483.2 KB	Display	PDB format
PDBx/mmJSON format	6emh.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/em/6emh ftp://data.pdbj.org/pub/pdb/validation_reports/em/6emh	HTTPS FTP

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Related structure data

Related structure data	6ekdC 6eq9C 4x21S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	7ksi-d 1pmn-d 3fi3-d 3pze-d 2ok1-d 2zdt-d 1pmv-d 2exc-d 3fc1-d 4xne-d 3v6r-1 3ptg-d 2r9s-1 4xrj-d 3cgf-d 4x21-1 2zdu-d 2f49-1 4w4v-d 3da6-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

6ekdC

6eq9C

4x21S

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#52 - Apr 2004 Growth Hormone similarity (1) #60 - Dec 2004 Ubiquitin similarity (1) #122 - Feb 2010 Enhanceosome similarity (1) #234 - Jun 2019 MDM2 and Cancer similarity (2) #252 - Dec 2020 Hepatitis C Virus Protease/Helicase similarity (1) #9 - Sep 2000 Lysozyme similarity (1)

Deposited unit

A: Mitogen-activated protein kinase 10

B: Mitogen-activated protein kinase 10

C: Mitogen-activated protein kinase 10

D: Mitogen-activated protein kinase 10

hetero molecules

172 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Mitogen-activated protein kinase 10

hetero molecules

defined by author
Evidence: gel filtration
43.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Mitogen-activated protein kinase 10

hetero molecules

defined by author
43.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Mitogen-activated protein kinase 10

hetero molecules

defined by author
42.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: Mitogen-activated protein kinase 10

hetero molecules

defined by author
43 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	88.560, 114.260, 157.800
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Protein , 1 types, 4 molecules ABCD

#1: Protein	Mitogen-activated protein kinase 10 / MAPK 10 / MAP kinase p49 3F12 / Stress-activated protein kinase 1b / SAPK1b / Stress-activated ...MAPK 10 / MAP kinase p49 3F12 / Stress-activated protein kinase 1b / SAPK1b / Stress-activated protein kinase JNK3 / c-Jun N-terminal kinase 3 Mass: 42260.855 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MAPK10, JNK3, JNK3A, PRKM10, SAPK1B / Production host: Escherichia coli (E. coli) References: UniProt: P53779, mitogen-activated protein kinase

#1: Protein

Mitogen-activated protein kinase 10 / MAPK 10 / MAP kinase p49 3F12 / Stress-activated protein kinase 1b / SAPK1b / Stress-activated ...

Mass: 42260.855 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Gene: MAPK10, JNK3, JNK3A, PRKM10, SAPK1B / Production host:

Escherichia coli (E. coli)
References: UniProt: P53779,

mitogen-activated protein kinase

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Non-polymers , 8 types, 883 molecules

#2: Chemical	ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₆OS
#3: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-BGE / 4-(4-methyl-1~{H}-imidazol-5-yl)-~{N}-(4-morpholin-4-ylphenyl)pyridin-2-amine Mass: 335.403 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₉H₂₁N₅O / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₂H₆O₂
#6: Chemical	ChemComp-C15 / N-DODECYL-N,N-DIMETHYL-3-AMMONIO-1-PROPANESULFONATE Mass: 336.554 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₇H₃₈NO₃S
#7: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#8: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
#9: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 861 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.36 Å³/Da / Density % sol: 47.91 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 100 mM Bis-Tris pH5.5, 200 mM NaCl, 29% PEG 3350, 1mM AMP-PCP, 0.4 mM Zwittergent 3-14, 10% Ethylene glycol

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.9 Å
Detector	Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 22, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.9 Å / Relative weight: 1
Reflection	Resolution: 1.76→50 Å / Num. obs: 157963 / % possible obs: 99.9 % / Redundancy: 26.4 % / R_rim(I) all: 0.089 / Net I/σ(I): 22.98

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0158	refinement
XDS		data reduction
XSCALE		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4X21

4x21

Resolution: 1.76→48.01 Å / Cor.coef. F_o:F_c: 0.96 / Cor.coef. F_o:F_c free: 0.94 / Cross valid method: FREE R-VALUE / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS /

	Num. reflection	% reflection
obs	156383	99.9 %

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.48 Å²	-0 Å²	0 Å²
2-	-	0.88 Å²	-0 Å²
3-	-	-	-0.41 Å²

Refinement step

Cycle: 1 / Resolution: 1.76→48.01 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10762	0	211	861	11834

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.019	11523
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	10706
X-RAY DIFFRACTION	r_angle_refined_deg	1.515	1.98	15679
X-RAY DIFFRACTION	r_angle_other_deg	0.937	3	24895
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.559	5	1445
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.127	24.447	515
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.423	15	1998
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.771	15	60
X-RAY DIFFRACTION	r_chiral_restr	0.131	0.2	1748
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.021	12609
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	2255
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.848	1.699	5506
X-RAY DIFFRACTION	r_mcbond_other	0.848	1.699	5505
X-RAY DIFFRACTION	r_mcangle_it	1.393	2.539	6885
X-RAY DIFFRACTION	r_mcangle_other	1.393	2.539	6886
X-RAY DIFFRACTION	r_scbond_it	1.165	1.862	6017
X-RAY DIFFRACTION	r_scbond_other	1.165	1.862	6017
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	1.667	2.728	8741
X-RAY DIFFRACTION	r_long_range_B_refined	6.031	21.584	13287
X-RAY DIFFRACTION	r_long_range_B_other	6.031	21.589	13288
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.762→1.808 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.316	115	-
R_work	0.346	11363	-
obs	-	-	98.93 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	3.1188	1.8817	-0.7119	1.6544	-0.4969	0.87	0.0694	-0.058	0.2287	0.0839	-0.0368	-0.1213	-0.1555	0.2023	-0.0326	0.1325	-0.0157	-0.0108	0.1709	-0.0033	0.1467	2.7045	10.5128	-15.7196
2	1.7414	-0.3528	-0.3069	2.6253	-0.1368	2.2848	-0.0878	0.4078	0.0484	-0.4851	0.0169	0.0513	0.1062	-0.0728	0.0709	0.1391	-0.0588	-0.0113	0.183	0.0069	0.0066	-13.3279	-5.5467	-29.9684
3	2.9501	4.1775	-2.6365	6.7659	-3.9653	2.424	0.2954	0.4936	1.0614	0.5091	0.5582	1.1795	-0.2693	-0.4325	-0.8536	0.5199	0.052	0.0509	0.3492	0.1344	0.543	-7.4548	21.7419	-18.6615
4	7.0239	-0.208	1.4687	4.682	-0.7371	5.2002	0.2608	0.5982	-0.0658	-0.3247	-0.3104	-0.3511	0.0577	0.0588	0.0496	0.0941	0.0553	0.0703	0.2125	0.024	0.1756	15.5455	42.3362	11.5865
5	6.7235	2.8694	-2.2022	3.6537	-1.4249	0.8587	0.1503	-0.2903	-0.1378	0.0135	-0.1233	0.1157	0.0416	0.0684	-0.027	0.2323	0.0301	-0.0285	0.2175	0.018	0.1863	2.0213	39.254	20.871
6	4.3094	-3.1004	0.9994	2.4545	-1.0005	1.1228	0.0066	0.0094	-0.0234	-0.0154	-0.028	-0.1439	0.0179	0.1714	0.0214	0.0764	0.0086	0.0036	0.2196	-0.0116	0.1741	-1.4708	50.294	14.8339
7	3.2589	0.0479	-0.2947	2.7458	1.0484	1.9437	-0.1333	-0.4944	-0.4161	0.4281	0.0409	-0.2169	0.2609	0.1959	0.0925	0.1227	0.0797	-0.0134	0.2771	0.0651	0.0958	-5.4003	51.9062	23.9793
8	1.6269	-0.1325	0.494	2.6177	0.0264	3.2952	-0.1633	-0.4347	0.0764	0.5053	0.095	0.1068	-0.2811	0.1059	0.0683	0.1769	0.085	0.0023	0.258	-0.0155	0.0244	-14.2482	65.5473	29.7158
9	1.858	-2.9393	1.9147	5.0296	-3.1359	2.0125	0.0582	-0.4098	-0.6676	-0.1478	0.5571	0.8083	0.1277	-0.4373	-0.6153	0.3936	-0.0845	0.0045	0.3694	0.1174	0.431	-7.5229	35.5675	19.182
10	1.341	-0.7553	-0.4822	0.8026	0.5864	3.0239	0.0081	0.0106	-0.3531	-0.0223	0.1095	0.0914	1.0054	0.0821	-0.1175	0.4704	0.0364	-0.0455	0.1959	0.0391	0.1684	4.151	5.6518	-58.4031
11	3.4717	-1.0025	2.1407	2.3441	-1.5012	3.1337	0.1459	0.3339	0.0249	-0.3288	-0.1102	0.0451	0.0178	0.0897	-0.0357	0.1841	-0.0102	0.0161	0.1482	0.0295	0.0336	-9.3549	28.1271	-65.0437
12	0.3474	-0.34	0.4917	1.3493	1.2264	4.2499	-0.0352	-0.2463	-0.1064	0.2601	0.4062	-0.0855	0.3372	0.2237	-0.371	0.182	0.0674	0.0081	0.3247	0.0895	0.0967	-1.2974	22.9676	-52.9751
13	6.8014	0.9724	1.7371	3.7178	1.3901	6.2451	-0.0789	0.0046	0.9899	-0.0475	0.0752	0.1977	-0.933	0.1198	0.0036	0.7571	-0.0193	0.0723	0.2953	0.1033	0.573	6.344	65.7568	-98.4096
14	1.8124	0.5804	1.2925	1.2628	-0.1156	6.3536	0.0155	0.1251	0.052	-0.2681	0.2309	0.2786	-0.1799	0.0745	-0.2464	0.4409	-0.1707	0.0005	0.3501	-0.0171	0.163	9.9533	50.8132	-90.0232
15	0.9538	0.4383	0.8129	0.6574	1.2484	4.3036	-0.045	0.1865	0.3213	-0.172	0.1852	-0.0271	-1.1866	0.245	-0.1402	0.4758	-0.0946	0.0436	0.2862	0.1073	0.2055	3.1461	48.4742	-102.5665
16	2.8413	-0.4053	-0.4991	4.7153	-0.7036	2.1444	0.13	-0.3496	0.1412	0.4513	0.0401	-0.0594	-0.5336	0.097	-0.1702	0.2453	-0.0139	-0.0065	0.2433	0.0524	0.0689	-0.8501	38.8473	-96.3251
17	1.3417	-0.1198	-0.7159	0.9564	-0.6848	3.6577	-0.0038	0.0392	-0.0646	0.0388	0.0723	0.0842	0.1737	-0.2914	-0.0685	0.1723	-0.0709	-0.0504	0.1589	0.0565	0.0791	-12.6535	28.997	-99.2612
18	3.8522	2.6323	6.1631	1.9826	4.6872	11.2088	0.1898	1.0368	-0.2174	0.0592	0.8487	-0.391	0.375	1.885	-1.0385	0.6632	-0.2913	-0.0133	0.6854	-0.1659	0.3604	14.3133	43.72	-96.721

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	46 - 205
2	X-RAY DIFFRACTION	2	A	206 - 362
3	X-RAY DIFFRACTION	3	A	363 - 400
4	X-RAY DIFFRACTION	4	B	46 - 87
5	X-RAY DIFFRACTION	5	B	88 - 117
6	X-RAY DIFFRACTION	6	B	118 - 183
7	X-RAY DIFFRACTION	7	B	184 - 231
8	X-RAY DIFFRACTION	8	B	232 - 362
9	X-RAY DIFFRACTION	9	B	363 - 400
10	X-RAY DIFFRACTION	10	C	46 - 202
11	X-RAY DIFFRACTION	11	C	203 - 308
12	X-RAY DIFFRACTION	12	C	309 - 400
13	X-RAY DIFFRACTION	13	D	46 - 88
14	X-RAY DIFFRACTION	14	D	89 - 117
15	X-RAY DIFFRACTION	15	D	118 - 182
16	X-RAY DIFFRACTION	16	D	183 - 241
17	X-RAY DIFFRACTION	17	D	242 - 359
18	X-RAY DIFFRACTION	18	D	360 - 400

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