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- PDB-3fi2: Crystal structure of JNK3 with amino-pyrazole inhibitor, SR-3451 -

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Basic information

Entry
Database: PDB / ID: 3fi2
TitleCrystal structure of JNK3 with amino-pyrazole inhibitor, SR-3451
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 / cellular senescence / rhythmic process / Oxidative Stress Induced Senescence / protein phosphorylation / protein serine kinase activity / signal transduction / mitochondrion / nucleoplasm / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol
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-JK1 / Mitogen-activated protein kinase 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsHabel, J.E.
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)41,3153
Polymers40,7651
Non-polymers5502
Water2,792155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.694, 124.525, 69.012
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-22-

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: 40765.348 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-JK1 / 3-{4-[(phenylcarbamoyl)amino]-1H-pyrazol-1-yl}-N-(3,4,5-trimethoxyphenyl)benzamide / 3-(4-(3-phenylureido)-1H-pyrazol-1-yl)-N-(3,4,5-trimethoxyphenyl)benzamide


Mass: 487.507 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H25N5O5
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE STRUCTURE IS DISORDERED IN THE RESIDUE RANGE 364-380. (DPAEVEAPPPQIYDKQL). ONLY SIX RESIDUES ...THE STRUCTURE IS DISORDERED IN THE RESIDUE RANGE 364-380. (DPAEVEAPPPQIYDKQL). ONLY SIX RESIDUES WERE OBSERVED IN THIS REGION AND THEY HAVE BEEN DENOTED AS UNK, SINCE THE AUTHORS COULD NOT DETERMINE WHICH AMINO ACIDS THEY CORRESPOND TO IN THIS REGION. THEY WERE ORIGINALLY MODELED AS ALA.

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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: 2.18 Å3/Da / Density % sol: 43.55 %
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: 2.28→50 Å / Num. obs: 14193 / Observed criterion σ(F): 25.4 / Observed criterion σ(I): 12.5 / Redundancy: 6 % / Biso Wilson estimate: 38.55 Å2 / Rsym value: 0.057
Reflection shellHighest resolution: 2.28 Å

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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: 2.28→46.23 Å / SU ML: 0.38 / σ(F): 0.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2671 1419 10 %random 10%
Rwork0.1805 ---
obs0.1891 14193 85.86 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.068 Å2 / ksol: 0.318 e/Å3
Displacement parametersBiso mean: 48.39 Å2
Refinement stepCycle: LAST / Resolution: 2.28→46.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2686 0 40 155 2881
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_d1.194
X-RAY DIFFRACTIONf_dihedral_angle_d18.901
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.28-2.36650.3037600.2354546X-RAY DIFFRACTION37
2.3665-2.46130.32731030.2244933X-RAY DIFFRACTION64
2.4613-2.57330.29251360.20551215X-RAY DIFFRACTION82
2.5733-2.70890.30081460.21011325X-RAY DIFFRACTION91
2.7089-2.87860.28341580.20471410X-RAY DIFFRACTION95
2.8786-3.10080.32411600.19511438X-RAY DIFFRACTION97
3.1008-3.41280.26771610.16661464X-RAY DIFFRACTION99
3.4128-3.90640.23121550.14451386X-RAY DIFFRACTION93
3.9064-4.92080.20781650.13711489X-RAY DIFFRACTION99
4.9208-46.23820.24811750.1711568X-RAY DIFFRACTION99
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)
11.40480.5432-0.92834.63550.38273.81790.0729-0.02880.19510.21890.06760.5311-0.1654-0.1632-0.04360.1110.0349-0.00940.15740.02870.159810.476147.609513.0478
2-0.88970.0517-1.34553.73191.02453.79270.1606-0.5074-0.08120.36620.0655-0.88130.60750.2398-0.21670.1465-0.0307-0.06890.3347-0.0690.401227.861340.43454.6637
30.4584-1.18450.0063.20030.16922.5713-0.20280.02790.1574-0.38420.09890.2517-0.10050.2527-0.05330.1417-0.0465-0.03350.1782-0.03270.142716.750344.11874.9553
41.11750.1590.15393.91090.60420.88570.0263-0.12380.2964-0.0779-0.0110.6240.05580.0832-0.01270.0953-0.03290.01940.144-0.0660.139113.548723.62094.0683
5-0.916-0.75221.48343.25462.04610.40760.1547-0.09580.13020.25490.2843-0.21060.45480.0644-0.15170.3692-0.2419-0.04940.9636-0.17660.518331.860525.63049.9259
61.76040.4247-0.4841.92790.98332.4711-0.2993-0.4192-0.1966-0.04560.1719-0.04740.2730.8146-0.06140.08840.0735-0.01670.31260.00370.08723.631616.17627.7445
72.533-0.03891.08772.49842.31062.4841-0.1976-0.4984-0.00060.55940.7126-0.25860.41240.8495-0.2390.38850.1841-0.19761.55280.19030.870133.128516.71619.8824
81.77410.22280.19653.06671.17732.642-0.1544-0.1691-0.17150.14240.12490.06560.37310.54780.03930.13910.0958-0.00520.21490.02790.068422.69166.95025.6357
9-3.3131-2.3789-2.55870.580.10452.10150.40770.44320.2252-0.4339-0.1633-0.31550.04110.0688-0.33580.46850.0216-0.04980.5327-0.03010.48224.40832.1253-8.2605
104.444-3.8058-3.28647.76631.75411.26970.21621.61380.7063-2.120.442-0.8484-0.09310.4594-0.60060.5524-0.25260.13950.4285-0.13710.422830.569549.25271.7059
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 45:96)
2X-RAY DIFFRACTION2chain A and resid 97:117)
3X-RAY DIFFRACTION3chain A and resid 118:151)
4X-RAY DIFFRACTION4chain A and resid 152:210)
5X-RAY DIFFRACTION5chain A and resid 211:227)
6X-RAY DIFFRACTION6chain A and resid 228:264)
7X-RAY DIFFRACTION7chain A and resid 265:269)
8X-RAY DIFFRACTION8chain A and resid 270:362)
9X-RAY DIFFRACTION9chain A and resid 363:384)
10X-RAY DIFFRACTION10chain A and resid 385:400)

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