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- PDB-3da6: Crystal Structure of human JNK3 complexed with N-(3-methyl-4-(3-(... -

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Basic information

Entry
Database: PDB / ID: 3da6
TitleCrystal Structure of human JNK3 complexed with N-(3-methyl-4-(3-(2-(methylamino)pyrimidin-4-yl)pyridin-2-yloxy)naphthalen-1-yl)-1H-benzo[d]imidazol-2-amine
ComponentsMitogen-activated protein kinase 10
KeywordsTRANSFERASE / JNK3 / kinase / Alternative splicing / ATP-binding / Chromosomal rearrangement / Cytoplasm / Epilepsy / 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-BZ9 / Mitogen-activated protein kinase 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsCee, V.J. / Cheng, A.C. / Romero, K. / Bellon, S. / Mohr, C. / Whittington, D.A. / Bready, J. / Caenepeel, S. / Coxon, A. / Deak, H.L. ...Cee, V.J. / Cheng, A.C. / Romero, K. / Bellon, S. / Mohr, C. / Whittington, D.A. / Bready, J. / Caenepeel, S. / Coxon, A. / Deak, H.L. / Hodous, B.L. / Kim, J.L. / Lin, J. / Nguyen, H. / Olivieri, P.R. / Patel, V.F. / Wang, L. / Hughes, P. / Geuns-Meyer, S.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2009
Title: Pyridyl-pyrimidine benzimidazole derivatives as potent, selective, and orally bioavailable inhibitors of Tie-2 kinase
Authors: Cee, V.J. / Cheng, A.C. / Romero, K. / Bellon, S. / Mohr, C. / Whittington, D.A. / Bak, A. / Bready, J. / Caenepeel, S. / Coxon, A. / Deak, H.L. / Fretland, J. / Gu, Y. / Hodous, B.L. / ...Authors: Cee, V.J. / Cheng, A.C. / Romero, K. / Bellon, S. / Mohr, C. / Whittington, D.A. / Bak, A. / Bready, J. / Caenepeel, S. / Coxon, A. / Deak, H.L. / Fretland, J. / Gu, Y. / Hodous, B.L. / Huang, X. / Kim, J.L. / Lin, J. / Long, A.M. / Nguyen, H. / Olivieri, P.R. / Patel, V.F. / Wang, L. / Zhou, Y. / Hughes, P. / Geuns-Meyer, S.
History
DepositionMay 28, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 6, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: 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 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)42,5332
Polymers42,0601
Non-polymers4741
Water99155
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.483, 71.283, 106.957
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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: 42059.676 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: MAPK10, JNK3, JNK3A, PRKM10 / Production host: Escherichia coli (E. coli)
References: UniProt: P53779, mitogen-activated protein kinase
#2: Chemical ChemComp-BZ9 / N-[3-methyl-4-({3-[2-(methylamino)pyrimidin-4-yl]pyridin-2-yl}oxy)naphthalen-1-yl]-1H-benzimidazol-2-amine


Mass: 473.529 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H23N7O
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 2.38 Å3/Da / Density % sol: 48.28 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100mM HEPES/HCl, pH7.5 , 20mM 2-Mercaptoethanol , 27% PEG 550MME, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 92 / Detector: CCD / Date: Apr 13, 2005 / Details: Varimax HF
RadiationMonochromator: Osmic Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 27899 / Num. obs: 25873 / % possible obs: 92.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2→2.07 Å / % possible all: 98.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
CrystalCleardata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→22.72 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.886 / SU B: 6.256 / SU ML: 0.175 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.246 / ESU R Free: 0.226 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.31951 1279 5 %RANDOM
Rwork0.256 ---
all0.25931 25448 --
obs0.25931 25448 91.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.667 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 2→22.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2666 0 36 55 2757
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0222764
X-RAY DIFFRACTIONr_angle_refined_deg2.3351.9823737
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2885324
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.24224.048126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.92315503
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.141517
X-RAY DIFFRACTIONr_chiral_restr0.1610.2409
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022061
X-RAY DIFFRACTIONr_nbd_refined0.2410.21295
X-RAY DIFFRACTIONr_nbtor_refined0.3220.21836
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.20.2132
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2010.222
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3310.23
X-RAY DIFFRACTIONr_mcbond_it2.38521716
X-RAY DIFFRACTIONr_mcangle_it3.36132662
X-RAY DIFFRACTIONr_scbond_it5.0194.51272
X-RAY DIFFRACTIONr_scangle_it6.11361075
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 97 -
Rwork0.294 1886 -
all-1983 -
obs--97.93 %

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