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- PDB-3fi3: Crystal structure of JNK3 with indazole inhibitor, SR-3737 -

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Basic information

Entry
Database: PDB / ID: 3fi3
TitleCrystal structure of JNK3 with indazole inhibitor, SR-3737
ComponentsMitogen-activated protein kinase 10
KeywordsTRANSFERASE / JNK3 / protein-inhibitor complex / Alternative splicing / ATP-binding / Chromosomal rearrangement / Cytoplasm / Epilepsy / Kinase / Nucleotide-binding / Phosphoprotein / Serine/threonine-protein kinase
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 ...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 / rhythmic process / cellular senescence / Oxidative Stress Induced Senescence / protein phosphorylation / protein serine kinase activity / signal transduction / mitochondrion / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Mitogen-activated protein (MAP) kinase, JNK / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain ...Mitogen-activated protein (MAP) kinase, JNK / Mitogen-activated protein (MAP) kinase, conserved site / MAP kinase signature. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-JK2 / Mitogen-activated protein kinase 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsHabel, J.E. / Duckett, D. / LoGrasso, P.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Structure-activity relationships and X-ray structures describing the selectivity of aminopyrazole inhibitors for c-Jun N-terminal kinase 3 (JNK3) over p38.
Authors: Kamenecka, T. / Habel, J. / Duckett, D. / Chen, W. / Ling, Y.Y. / Frackowiak, B. / Jiang, R. / Shin, Y. / Song, X. / LoGrasso, P.
History
DepositionDec 10, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mitogen-activated protein kinase 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8734
Polymers42,2361
Non-polymers6373
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.862, 124.105, 69.519
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-412-

HOH

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Components

#1: Protein Mitogen-activated protein kinase 10 / Stress-activated protein kinase JNK3 / c-Jun N-terminal kinase 3 / MAP kinase p49 3F12


Mass: 42235.887 Da / Num. of mol.: 1 / Fragment: UNP residues 39-402
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: JNK3, JNK3A, MAPK10, PRKM10 / Plasmid: pDEST14 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P53779, mitogen-activated protein kinase
#2: Chemical ChemComp-JK2 / 3-{5-[(2-fluorophenyl)amino]-1H-indazol-1-yl}-N-(3,4,5-trimethoxyphenyl)benzamide


Mass: 512.532 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H25FN4O4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 41.87 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 5.5
Details: 10mg/mL JNK3 mixed with 1mM AMP-PCP, 2mM MgCl2, 0.4mM Zwittergent 3-14, 10% ethylene. Crystals grown in 0.2M NaCl, 0.1M Bis-Tris, 28-31% PEG 3350, pH 5.5, Microbatch, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 11, 2007
RadiationMonochromator: Side-scattering cuberoot I-beam bent single crystal, asymetric cut 12.2 deg
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 17506 / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Biso Wilson estimate: 38.66 Å2 / Rsym value: 0.049
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3.1 % / Rsym value: 0.367

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(AutoMR)model building
PHENIX(phenix.refine)refinement
HKL-2000data reduction
SCALAdata scaling
PHENIX(AutoMR)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1JNK

1jnk


Resolution: 2.2→48.94 Å / SU ML: 0.33 / σ(F): 0.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2488 1751 10 %random 10%
Rwork0.1803 ---
obs0.187 17506 93.79 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.499 Å2 / ksol: 0.326 e/Å3
Displacement parametersBiso mean: 50.41 Å2
Refinement stepCycle: LAST / Resolution: 2.2→48.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2731 0 46 148 2925
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.007
X-RAY DIFFRACTIONf_angle_d1.134
X-RAY DIFFRACTIONf_dihedral_angle_d17.959
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.25580.2674910.2384836X-RAY DIFFRACTION65
2.2558-2.32220.34811160.23281025X-RAY DIFFRACTION81
2.3222-2.39720.30531290.21981140X-RAY DIFFRACTION90
2.3972-2.48280.29321310.2051187X-RAY DIFFRACTION93
2.4828-2.58220.31231340.21421235X-RAY DIFFRACTION96
2.5822-2.69980.31651380.20341241X-RAY DIFFRACTION98
2.6998-2.84210.30871410.21391252X-RAY DIFFRACTION98
2.8421-3.02010.32011410.21491271X-RAY DIFFRACTION99
3.0201-3.25330.28761420.18871276X-RAY DIFFRACTION99
3.2533-3.58060.21711440.15881292X-RAY DIFFRACTION99
3.5806-4.09840.20251440.13781296X-RAY DIFFRACTION100
4.0984-5.16270.19261460.1411322X-RAY DIFFRACTION100
5.1627-48.95390.20591540.16341382X-RAY DIFFRACTION100
Refinement TLS params.

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

IDL11 (°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)
12.1371-0.40661.25721.90761.16641.4407-0.11130.281-0.1907-0.1555-0.00910.27140.004-0.00320.1180.1645-0.00280.02890.1784-0.00480.1942-31.0968-47.2855-13.406
2-4.92064.24562.34034.23840.80776.24840.38830.0125-0.887-0.06590.2012-1.4153-0.6391.1701-0.42820.18020.0821-0.00370.4326-0.14190.563-14.5753-40.2276-3.8431
30.10040.8727-0.00753.01591.37541.118-0.03520.00710.04710.17350.06970.3235-0.00520.0713-0.02770.1610.03960.02180.2027-0.01410.2006-27.2301-31.245-4.646
40.6502-0.11230.3016-0.0282-0.16430.168-0.1792-0.0331-0.44550.283-0.0438-0.05210.1117-0.03780.20070.29710.2298-0.2250.5924-0.1460.6017-10.367-26.0978-8.7302
50.52430.96070.34820.74321.00983.8318-0.06020.1935-0.0668-0.04640.2294-0.0989-0.21851.1329-0.1270.1653-0.08440.01330.4474-0.0330.1664-17.8373-16.523-7.7919
62.241.3408-1.79151.61531.85236.2398-0.09990.0389-0.5146-0.50570.5566-0.4057-0.63651.8952-0.44760.2859-0.26350.11670.9359-0.18920.3211-5.8521-10.2253-10.739
71.44440.5691-0.32731.89471.08411.6829-0.269-0.1190.3634-0.11280.09260.2887-0.50550.21040.12030.269-0.0828-0.02090.16790.00090.2103-25.2287-6.5958-3.8951
81.96030.4801-0.74114.38233.02062.22280.2882-0.4185-0.12310.98070.1527-0.70010.6070.4545-0.39850.33790.1438-0.11080.2971-0.02150.453-12.3947-42.6932.4926
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 46:96)
2X-RAY DIFFRACTION2chain A and resid 97:119)
3X-RAY DIFFRACTION3chain A and resid 120:209)
4X-RAY DIFFRACTION4chain A and resid 210:227)
5X-RAY DIFFRACTION5chain A and resid 228:265)
6X-RAY DIFFRACTION6chain A and resid 266:298)
7X-RAY DIFFRACTION7chain A and resid 299:362)
8X-RAY DIFFRACTION8chain A and resid 363:401)

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