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- PDB-2r9s: c-Jun N-terminal Kinase 3 with 3,5-Disubstituted Quinoline inhibitor -

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Basic information

Entry
Database: PDB / ID: 2r9s
Titlec-Jun N-terminal Kinase 3 with 3,5-Disubstituted Quinoline inhibitor
ComponentsMitogen-activated protein kinase 10
KeywordsSIGNALING PROTEIN / TRANSFERASE / jnk3
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 / 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-255 / trifluoroacetic acid / Mitogen-activated protein kinase 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsHabel, J.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2007
Title: 3,5-Disubstituted quinolines as novel c-Jun N-terminal kinase inhibitors.
Authors: Jiang, R. / Duckett, D. / Chen, W. / Habel, J. / Ling, Y.Y. / LoGrasso, P. / Kamenecka, T.M.
History
DepositionSep 13, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Aug 30, 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_ncs_dom_lim / struct_ref_seq_dif / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details / _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
B: Mitogen-activated protein kinase 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,03539
Polymers82,5702
Non-polymers1,46637
Water3,279182
1
A: Mitogen-activated protein kinase 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,08024
Polymers41,2851
Non-polymers79523
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Mitogen-activated protein kinase 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,95515
Polymers41,2851
Non-polymers67114
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.318, 81.344, 123.760
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 4 / Auth seq-ID: 46 - 401 / Label seq-ID: 1 - 356

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsThe biological unit is a monomer. There are two biological units in the assymetric unit (chains A & B).

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Mitogen-activated protein kinase 10 / E.C.2.7.11.24 / Stress-activated protein kinase JNK3 / c-Jun N-terminal kinase 3 / MAP kinase p49 3F12


Mass: 41284.789 Da / Num. of mol.: 2 / Fragment: residues 39-402
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAPK10, JNK3, JNK3A, PRKM10 / Plasmid: pdest14 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P53779, mitogen-activated protein kinase

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Non-polymers , 5 types, 219 molecules

#2: Chemical ChemComp-255 / N-(tert-butyl)-4-[5-(pyridin-2-ylamino)quinolin-3-yl]benzenesulfonamide


Mass: 432.538 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H24N4O2S
#3: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 27 / Source method: obtained synthetically
#4: Chemical ChemComp-TFA / trifluoroacetic acid / Trifluoroacetic acid


Mass: 114.023 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2HF3O2
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 2.08 Å3/Da / Density % sol: 40.9 %
Crystal growTemperature: 298 K / Method: microbatch / pH: 5.5
Details: 25-32% PEG 3350, 100mM NaCl, 1mM AMP-PCP, 2mM MgCl2, 0.4mM Zwittergent 314, 10%(v/v) ethylene glycol, pH 5.5, microbatch, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.997 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 10, 2007
RadiationMonochromator: Silicon (111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.997 Å / Relative weight: 1
ReflectionResolution: 2.27→50 Å / Num. obs: 32372 / % possible obs: 99.2 % / Redundancy: 6.9 % / Biso Wilson estimate: 41.67 Å2 / Rmerge(I) obs: 0.056 / Χ2: 1.174 / Net I/σ(I): 15.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.27-2.354.70.50730051.415193.9
2.35-2.456.10.42331681.375198.9
2.45-2.566.90.32232081.326199.8
2.56-2.697.30.24132251.3281100
2.69-2.867.40.16632211.2191100
2.86-3.087.40.10832401.1551100
3.08-3.397.40.06632561.1911100
3.39-3.887.40.04132781.0551100
3.88-4.897.30.03133090.9261100
4.89-506.90.02634620.918199.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3data extraction
HKL-2000data collection
HKL-2000data reduction
PHASERphasing
RefinementStarting model: PDB Entry 1JNK

1jnk


Resolution: 2.4→38.63 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.905 / SU B: 18.952 / SU ML: 0.23 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.624 / ESU R Free: 0.329 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29 1390 5 %RANDOM
Rwork0.205 ---
obs0.209 27603 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.866 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20 Å20 Å2
2---0.26 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 2.4→38.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5362 0 125 182 5669
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0225572
X-RAY DIFFRACTIONr_angle_refined_deg1.9441.9887514
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.835650
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.24124.341258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.469151012
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6061532
X-RAY DIFFRACTIONr_chiral_restr0.1390.2830
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024066
X-RAY DIFFRACTIONr_nbd_refined0.2350.22626
X-RAY DIFFRACTIONr_nbtor_refined0.3120.23722
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.2259
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2370.289
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3770.212
X-RAY DIFFRACTIONr_mcbond_it1.0481.53397
X-RAY DIFFRACTIONr_mcangle_it1.6225324
X-RAY DIFFRACTIONr_scbond_it2.51932500
X-RAY DIFFRACTIONr_scangle_it3.7154.52190
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2681 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.290.5
MEDIUM THERMAL0.882
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 99 -
Rwork0.23 1887 -
all-1986 -
obs--99.15 %
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)
17.578-2.21470.85126.88271.32714.2906-0.1345-0.02060.1635-0.16770.1753-0.4231-0.11870.3411-0.0408-0.2494-0.00590.1144-0.19130.0492-0.271213.482410.033615.6033
226.6664-12.8859-4.365714.5452.11399.58480.4455-0.8795-0.95410.32150.0426-0.79170.71170.6107-0.48810.03060.003-0.0231-0.14640.0232-0.12967.5002-8.388721.1891
32.6277-0.063-1.04152.60030.51734.88340.08560.0021-0.0133-0.131-0.0813-0.25560.0754-0.1886-0.0043-0.20750.00370.0639-0.21580.0558-0.29776.13586.100522.7913
43.7310.94280.37074.7578-1.40144.23430.02330.2126-0.33910.1435-0.0302-0.6947-0.12390.19630.0069-0.30450.021-0.0254-0.2118-0.0123-0.28695.41512.747640.3882
56.04715.08811.096315.86773.82943.8339-0.049-0.0683-0.8480.3484-0.0326-1.01850.02830.58010.0816-0.0769-0.0363-0.2568-0.03240.1172-0.030410.8223-8.497954.4928
62.00710.1995-1.47092.0016-0.39354.51460.11360.0412-0.16320.0331-0.2168-0.0453-0.1071-0.67080.1032-0.28290.0423-0.0896-0.21250.0725-0.309-0.92171.321938.5178
712.80471.6784-0.15336.43630.88357.0598-0.12550.0895-1.20340.02070.11170.14980.17210.19940.0138-0.27960.0083-0.04-0.2380.0186-0.119447.8014-9.754845.5792
815.77239.8238-4.756438.430811.25997.69450.81340.64860.9307-0.4052-0.0378-1.2505-0.68280.0928-0.77560.06090.0380.05170.0530.0781-0.005344.055510.241640.8701
93.0027-0.27911.32782.57210.94096.39110.07540.0506-0.29710.0523-0.12930.0552-0.0388-0.17930.0538-0.2114-0.0102-0.0451-0.1838-0.0146-0.121440.0648-4.914238.5852
105.8055-1.7092-0.63652.8207-0.9734.58430.0926-0.39771.25940.02990.1363-0.9370.04950.1767-0.2289-0.303-0.0155-0.0013-0.2112-0.13710.185539.3765-2.421420.7378
115.9450.91620.489815.56211.71344.25630.01110.24561.7802-0.7033-0.1399-0.6035-0.27060.39230.1288-0.0670.06250.30550.03490.22420.737144.60158.11476.464
121.437-0.31191.61482.41640.33075.25170.1105-0.03630.2907-0.0957-0.2569-0.08580.0261-0.66470.1464-0.3287-0.0370.1099-0.15190.0722-0.083532.9419-0.870923.1787
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA46 - 961 - 51
2X-RAY DIFFRACTION2AA97 - 11152 - 66
3X-RAY DIFFRACTION3AA112 - 16167 - 116
4X-RAY DIFFRACTION4AA162 - 267117 - 222
5X-RAY DIFFRACTION5AA268 - 321223 - 276
6X-RAY DIFFRACTION6AA322 - 400277 - 355
7X-RAY DIFFRACTION7BB46 - 961 - 51
8X-RAY DIFFRACTION8BB97 - 10752 - 62
9X-RAY DIFFRACTION9BB108 - 16163 - 116
10X-RAY DIFFRACTION10BB162 - 267117 - 222
11X-RAY DIFFRACTION11BB268 - 322223 - 277
12X-RAY DIFFRACTION12BB323 - 400278 - 355

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