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- PDB-3fv8: JNK3 bound to piperazine amide inhibitor, SR2774. -

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Basic information

Entry
Database: PDB / ID: 3fv8
TitleJNK3 bound to piperazine amide inhibitor, SR2774.
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-JK3 / 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: Bioorg.Med.Chem.Lett. / Year: 2009
Title: Synthesis and SAR of piperazine amides as novel c-jun N-terminal kinase (JNK) inhibitors.
Authors: Shin, Y. / Chen, W. / Habel, J. / Duckett, D. / Ling, Y.Y. / Koenig, M. / He, Y. / Vojkovsky, T. / LoGrasso, P. / Kamenecka, T.M.
History
DepositionJan 15, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 16, 2017Group: Data collection / Source and taxonomy / Category: diffrn_detector / entity_src_gen / Item: _diffrn_detector.detector
Revision 2.0Sep 6, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _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)41,7417
Polymers41,0081
Non-polymers7336
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.565, 125.315, 69.253
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-815-

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: 41007.574 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: SD-D-Topo pENTR coupled with pDEST14 / Source: (gene. exp.) Homo sapiens (human) / Gene: JNK3, JNK3A, MAPK10, PRKM10 / Plasmid: pDEST 14 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P53779, mitogen-activated protein kinase
#2: Chemical ChemComp-JK3 / 5-bromo-N-(3-chloro-2-(4-(prop-2-ynyl)piperazin-1-yl)phenyl)furan-2-carboxamide


Mass: 422.703 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H17BrClN3O2
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 121 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHERE IS A BREAK IN ELECTRON DENSITY BETWEEN AMINO ACIDS 366 AND 381. PORTIONS OF THE ELECTRON ...THERE IS A BREAK IN ELECTRON DENSITY BETWEEN AMINO ACIDS 366 AND 381. PORTIONS OF THE ELECTRON DENSITY WITHIN THE BREAK WERE FITTED WITH THE FIVE UNK AMINO ACIDS. THE AUTHORS WERE UNABLE TO IDENTIFY THESE AMINO ACIDS AND THEIR POSITION IN THE SEQUENCE BASED ON THE ELECTRON DENSITY

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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: 2.16 Å3/Da / Density % sol: 42.99 %
Crystal growTemperature: 293 K / pH: 5.5
Details: 10MG/ML JNK3 MIXED WITH 1MM AMP-PCP, 2MM MGCL2, 0.4MM ZWITTERGENT 3-14, AND 10% ETHYLENE GLYCOL. CRYSTALS GROWN IN 0.2M NACL, 0.1M BIS-TRIS, 28-31% PEG 3350, PH 5.5, micobatch, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jul 7, 2005
RadiationMonochromator: monochromator / 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. all: 14625 / Num. obs: 14111 / % possible obs: 85.2 % / Observed criterion σ(I): 1 / Redundancy: 5.3 % / Biso Wilson estimate: 53.2 Å2 / Rsym value: 0.055
Reflection shellResolution: 2.27→2.35 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 2.44 / Rsym value: 0.245

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Processing

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

1jnk


Resolution: 2.28→40.783 Å / SU ML: 0.38 / σ(F): 0.08 / Phase error: 31.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2844 1403 9.94 %
Rwork0.1949 --
obs0.2037 14109 85.19 %
all-14111 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.064 Å2 / ksol: 0.32 e/Å3
Displacement parametersBiso mean: 36.9 Å2
Refine analyzeLuzzati coordinate error obs: 0.37 Å
Refinement stepCycle: LAST / Resolution: 2.28→40.783 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2725 0 45 121 2891
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062827
X-RAY DIFFRACTIONf_angle_d1.053811
X-RAY DIFFRACTIONf_dihedral_angle_d16.661081
X-RAY DIFFRACTIONf_chiral_restr0.067413
X-RAY DIFFRACTIONf_plane_restr0.009487
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2802-2.36170.3732560.2458482X-RAY DIFFRACTION33
2.3617-2.45620.328870.264885X-RAY DIFFRACTION60
2.4562-2.5680.38871300.26191170X-RAY DIFFRACTION79
2.568-2.70340.36551480.25561341X-RAY DIFFRACTION91
2.7034-2.87270.33731570.23811401X-RAY DIFFRACTION95
2.8727-3.09440.33221630.23031456X-RAY DIFFRACTION99
3.0944-3.40570.28961640.20371467X-RAY DIFFRACTION98
3.4057-3.89820.25261630.16561464X-RAY DIFFRACTION98
3.8982-4.910.23161630.14191492X-RAY DIFFRACTION98
4.91-40.7890.23821720.16971548X-RAY DIFFRACTION98
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)
10.2034-0.01210.24760.24-0.35790.63130.1560.14910.04310.3484-0.2822-0.3489-0.14940.3908-00.2154-0.0545-0.02730.3170.08410.2645-10.537-46.490114.1164
20.03570.002-0.03840.01880.00060.0213-0.0477-0.61030.01830.0147-0.03720.2805-0.25120.1431-0.00010.3604-0.01650.08640.69290.2470.6262-30.5156-42.073110.1855
30.5675-0.62840.36220.6222-0.69760.0302-0.0362-0.0979-0.0387-0.25580.076-0.11420.0875-0.0598-00.2214-0.08160.04120.14490.03260.198-14.1528-32.2554.3339
40.7423-0.081-0.4482.8572-2.21612.1015-0.2261-0.24320.16680.27390.55380.1006-0.356-0.86370.42910.17340.10210.02850.3787-0.00110.0963-22.8974-11.13336.9375
50.0211-0.05150.03350.0428-0.0454-0.02460.34430.0691-0.338-0.37040.21590.3955-0.03590.13550.00031.57150.19250.13680.9681-0.10740.9074-14.4566-28.1335-10.9093
60.0051-0.0378-0.03040.0489-0.10190.0099-0.19750.50920.0899-0.51610.680.26520.3728-0.4439-0.00010.3158-0.0321-0.06270.33310.13990.3835-30.2342-48.62531.3146
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 46:95
2X-RAY DIFFRACTION2chain A and resid 96:107
3X-RAY DIFFRACTION3chain A and resid 108:209
4X-RAY DIFFRACTION4chain A and resid 210:362
5X-RAY DIFFRACTION5chain A and resid 363:382
6X-RAY DIFFRACTION6chain A and resid 383:400

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