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- PDB-8bzp: JNK3 (Mitogen-activated protein kinase 10) in Complex with Compou... -

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Basic information

Entry
Database: PDB / ID: 8bzp
TitleJNK3 (Mitogen-activated protein kinase 10) in Complex with Compound 23 bearing a C(sp3)F2Br moiety
ComponentsMitogen-activated protein kinase 10
KeywordsTRANSFERASE / Fragment / CF2X / CF2Br / Halogen Bond
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. / 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
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / Chem-C15 / DI(HYDROXYETHYL)ETHER / Chem-SWM / Mitogen-activated protein kinase 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsStahlecker, J. / Vaas, S. / Stehle, T. / Boeckler, F.M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2023
Title: Principles and Applications of CF 2 X Moieties as Unconventional Halogen Bond Donors in Medicinal Chemistry, Chemical Biology, and Drug Discovery.
Authors: Vaas, S. / Zimmermann, M.O. / Schollmeyer, D. / Stahlecker, J. / Engelhardt, M.U. / Rheinganz, J. / Drotleff, B. / Olfert, M. / Lammerhofer, M. / Kramer, M. / Stehle, T. / Boeckler, F.M.
History
DepositionDec 15, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 2, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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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)87,23425
Polymers84,1192
Non-polymers3,11523
Water5,170287
1
A: Mitogen-activated protein kinase 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,54613
Polymers42,0601
Non-polymers1,48712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mitogen-activated protein kinase 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,68812
Polymers42,0601
Non-polymers1,62811
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)109.797, 155.376, 43.960
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Mitogen-activated protein kinase 10 / MAP kinase 10 / MAPK 10 / MAP kinase p49 3F12 / Stress-activated protein kinase 1b / SAPK1b / ...MAP kinase 10 / MAPK 10 / MAP kinase p49 3F12 / Stress-activated protein kinase 1b / SAPK1b / Stress-activated protein kinase JNK3 / c-Jun N-terminal kinase 3


Mass: 42059.676 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAPK10, JNK3, JNK3A, PRKM10, SAPK1B / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P53779, mitogen-activated protein kinase

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Non-polymers , 8 types, 310 molecules

#2: Chemical ChemComp-SWM / 2-bromanyl-2,2-bis(fluoranyl)-~{N}-(5-pyridin-4-yl-1,3,4-thiadiazol-2-yl)ethanamide


Mass: 335.128 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H5BrF2N4OS / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-C15 / N-DODECYL-N,N-DIMETHYL-3-AMMONIO-1-PROPANESULFONATE


Mass: 336.554 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C17H38NO3S
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 287 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.23 Å3/Da / Density % sol: 44.81 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6
Details: Protein was concentrated to 7-9 mg/ml and incubated with (final conc.): 1mM AMP-PCP, 0.4 mM Zwittergent and 10% EG. Protein was mixed 2+2 ul with mother liquor containing: 100 mM BisTris ...Details: Protein was concentrated to 7-9 mg/ml and incubated with (final conc.): 1mM AMP-PCP, 0.4 mM Zwittergent and 10% EG. Protein was mixed 2+2 ul with mother liquor containing: 100 mM BisTris pH=6, PEG3350 27% and NaCl 200 mM

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9188 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 29, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9188 Å / Relative weight: 1
ReflectionResolution: 1.86→50 Å / Num. obs: 63868 / % possible obs: 99.4 % / Redundancy: 13.4 % / Biso Wilson estimate: 45.7 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.114 / Net I/σ(I): 13.95
Reflection shellResolution: 1.86→1.97 Å / Redundancy: 13.6 % / Mean I/σ(I) obs: 1.05 / Num. unique obs: 10233 / CC1/2: 0.54 / Rrim(I) all: 2.5 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4x21

4x21


Resolution: 1.86→46.84 Å / SU ML: 0.2807 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.6467
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2162 1501 2.35 %
Rwork0.1894 62355 -
obs0.19 63856 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.16 Å2
Refinement stepCycle: LAST / Resolution: 1.86→46.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5259 0 172 287 5718
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00845664
X-RAY DIFFRACTIONf_angle_d0.93567683
X-RAY DIFFRACTIONf_chiral_restr0.0602853
X-RAY DIFFRACTIONf_plane_restr0.0081973
X-RAY DIFFRACTIONf_dihedral_angle_d14.3382096
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.86-1.920.40931360.39735642X-RAY DIFFRACTION99.86
1.92-1.990.31491340.29395580X-RAY DIFFRACTION99.84
1.99-2.070.31491350.23285634X-RAY DIFFRACTION99.78
2.07-2.160.24871350.21415609X-RAY DIFFRACTION99.77
2.16-2.280.24851350.20765575X-RAY DIFFRACTION98.75
2.28-2.420.22791340.18455588X-RAY DIFFRACTION98.6
2.42-2.610.25941370.18455666X-RAY DIFFRACTION99.71
2.61-2.870.21781360.19075668X-RAY DIFFRACTION99.73
2.87-3.280.24281370.19345681X-RAY DIFFRACTION99.08
3.28-4.140.16781380.1675748X-RAY DIFFRACTION99.27
4.14-46.840.19451440.17675964X-RAY DIFFRACTION98.66
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)
10.8410254201160.652596307470.1334028880430.54086462871-0.101055554371.09312261328-0.1688212389960.05079239690650.266431792684-0.09637098943590.0165601372085-0.02351827387540.2441452755460.0771313039860.0001729031562450.4933351233680.01556157332340.01253663679540.496123936558-0.05409549682220.37545252853342.483861209412.8355311192-15.3008697888
21.455446512830.499810751055-1.000429915980.541989726772-0.08773477716481.56139481147-0.04885929048190.1207846558050.0264243152334-0.05172989585090.0445034918298-0.02716493416330.03937445481010.0005956791904330.0001080958043010.3751923472850.00448090326205-0.000703880429720.3596769355410.004921391055550.3286876480737.91190548415.010699510.297767405531
31.994402076480.286728743283-0.4603158989671.798956485160.07589504947931.255096558860.0614121318555-0.07709493992680.30895891654-0.0004259465584960.05680142781780.0301291374775-0.1614333351610.01628657044223.89001661017E-50.312892880918-0.02728766447680.01431956156280.29682921629-0.002305987483550.28643567422623.439853312426.959645246312.3949915355
40.3683240810080.236667644412-0.3454777880560.162139367767-0.2307479735210.3202219797140.161201514937-0.468853827521-0.02161790080810.509888488948-0.116492432567-0.114031292296-0.195833719810.301580035275-0.0004772074195580.4816487803950.0194094668666-0.05642450902020.472572695641-0.05517996623320.49010492037748.926665339717.40149116288.07804921367
50.0290698238867-0.0488713612750.2273215934570.0960481961248-0.443614832842.037350884160.4196652732780.09961225736730.1929328320270.07762362046510.5534195619870.781369552917-0.0365488563251-0.6054109592610.6992904124880.3127778036640.05055790470710.003276137861270.8406242008390.3697762736751.1333787106-36.378213710119.92262002364.39111583114
60.1463253577110.572223659908-0.1904218906642.15895978525-0.6737115229360.8523269299650.1094993159910.05752334375070.1251855532310.3240060494360.1865657136120.738697374257-0.0766122757562-0.307875498414-0.0003239092401490.4002954351830.03507214107210.07494128409010.438111137940.04740617285170.576672880289-19.558686998521.10549250084.39893460783
71.605200185590.276868970191-0.1829440624190.7805991404070.5315983961971.271765090380.1045767626860.0433811675011-0.2948007414260.0445554039642-0.04592469769720.2938930540310.189662797997-0.155934409131-0.0001499161031210.358621600791-0.00287935715206-0.01035144539980.3428652599880.01090252028410.388361776125-7.7320078375719.3870100435-3.66858006419
80.612550930840.0953147745665-0.7140828418471.489400697630.3746015076211.06830423911-0.03031178013580.121407130638-0.3713823133630.135178910138-0.02683814668930.1456555952280.2336539649520.1432336411490.0003061442017960.379957490043-0.0008562848750520.03904894999250.3388922304210.0039221477790.4041520082034.283902892359.58297165297-14.3343586346
91.164300318731.04758844368-0.3773495597562.77133698479-0.450117133550.2110965211970.179357057062-0.1216771102760.1606278546590.198011674337-0.09972009792730.0272577290923-0.234581874382-0.014132007084-0.0004498476557940.4136818351470.029731826319-0.01260030670030.345633817798-0.01747926038940.300448740339-5.0935534903526.285337614-1.44874455314
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 46 through 83 )AA46 - 831 - 38
22chain 'A' and (resid 84 through 183 )AA84 - 18339 - 138
33chain 'A' and (resid 184 through 362 )AA184 - 362139 - 312
44chain 'A' and (resid 363 through 400 )AA363 - 400313 - 350
55chain 'B' and (resid 47 through 87 )BN47 - 871 - 35
66chain 'B' and (resid 88 through 183 )BN88 - 18336 - 131
77chain 'B' and (resid 184 through 258 )BN184 - 258132 - 191
88chain 'B' and (resid 259 through 308 )BN259 - 308192 - 241
99chain 'B' and (resid 309 through 400 )BN309 - 400242 - 326

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