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- PDB-4l7f: Co-crystal Structure of JNK1 and AX13587 -

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Basic information

Entry
Database: PDB / ID: 4l7f
TitleCo-crystal Structure of JNK1 and AX13587
ComponentsMitogen-activated protein kinase 8
KeywordsTransferase/Transferase Inhibitor / protein kinase fold / protein kinase / jun-c / phosphorylation / Transferase-Transferase Inhibitor complex
Function / homology
Function and homology information


JUN phosphorylation / positive regulation of cell killing / Interleukin-38 signaling / Activation of BMF and translocation to mitochondria / basal dendrite / Activation of BIM and translocation to mitochondria / positive regulation of establishment of protein localization to mitochondrion / JUN kinase activity / WNT5:FZD7-mediated leishmania damping / positive regulation of cyclase activity ...JUN phosphorylation / positive regulation of cell killing / Interleukin-38 signaling / Activation of BMF and translocation to mitochondria / basal dendrite / Activation of BIM and translocation to mitochondria / positive regulation of establishment of protein localization to mitochondrion / JUN kinase activity / WNT5:FZD7-mediated leishmania damping / positive regulation of cyclase activity / histone deacetylase regulator activity / NRAGE signals death through JNK / positive regulation of NLRP3 inflammasome complex assembly / Activation of the AP-1 family of transcription factors / Fc-epsilon receptor signaling pathway / mitogen-activated protein kinase / regulation of macroautophagy / response to mechanical stimulus / response to UV / protein serine/threonine kinase binding / stress-activated MAPK cascade / energy homeostasis / JNK cascade / positive regulation of protein metabolic process / cellular response to cadmium ion / cellular response to amino acid starvation / NRIF signals cell death from the nucleus / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / negative regulation of protein binding / peptidyl-threonine phosphorylation / FCERI mediated MAPK activation / regulation of circadian rhythm / histone deacetylase binding / cellular response to mechanical stimulus / cellular response to reactive oxygen species / cellular senescence / rhythmic process / Signaling by ALK fusions and activated point mutants / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / regulation of protein localization / cellular response to oxidative stress / peptidyl-serine phosphorylation / cellular response to lipopolysaccharide / protein phosphatase binding / Oxidative Stress Induced Senescence / response to oxidative stress / positive regulation of apoptotic process / protein phosphorylation / axon / protein serine kinase activity / protein serine/threonine kinase activity / synapse / positive regulation of gene expression / negative regulation of apoptotic process / enzyme binding / nucleoplasm / ATP binding / nucleus / 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. ...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-1V5 / Mitogen-activated protein kinase 8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsWalter, R.L. / Ranieri, G.M. / Riggs, A.M. / Weissig, H. / Li, B. / Shreder, K.R.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2013
Title: Hit-to-lead optimization and kinase selectivity of imidazo[1,2-a]quinoxalin-4-amine derived JNK1 inhibitors.
Authors: Li, B. / Cociorva, O.M. / Nomanbhoy, T. / Weissig, H. / Li, Q. / Nakamura, K. / Liyanage, M. / Zhang, M.C. / Shih, A.Y. / Aban, A. / Hu, Y. / Cajica, J. / Pham, L. / Kozarich, J.W. / Shreder, K.R.
History
DepositionJun 13, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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

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Assembly

Deposited unit
A: Mitogen-activated protein kinase 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8372
Polymers42,3771
Non-polymers4601
Water8,089449
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)135.802, 135.802, 94.208
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Mitogen-activated protein kinase 8 / MAP kinase 8 / MAPK 8 / JNK-46 / Stress-activated protein kinase 1c / SAPK1c / Stress-activated ...MAP kinase 8 / MAPK 8 / JNK-46 / Stress-activated protein kinase 1c / SAPK1c / Stress-activated protein kinase JNK1 / c-Jun N-terminal kinase 1


Mass: 42377.102 Da / Num. of mol.: 1 / Fragment: UNP residues 7-362
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAPK8, JNK1, PRKM8, SAPK1, SAPK1C
References: UniProt: P45983, mitogen-activated protein kinase
#2: Chemical ChemComp-1V5 / N-[1-(4-fluorophenyl)cyclopropyl]-4-[(trans-4-hydroxycyclohexyl)amino]imidazo[1,2-a]quinoxaline-8-carboxamide


Mass: 459.515 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H26FN5O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 449 / 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: 3.95 Å3/Da / Density % sol: 68.82 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM
DetectorDate: Feb 17, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 47064

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→50 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.945 / Occupancy max: 1 / Occupancy min: 0.38 / SU B: 2.581 / SU ML: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.109 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1977 2380 5.1 %RANDOM
Rwork0.1605 ---
obs0.1624 47049 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 96.65 Å2 / Biso mean: 27.3579 Å2 / Biso min: 10.07 Å2
Baniso -1Baniso -2Baniso -3
1-0.55 Å20.28 Å20 Å2
2--0.55 Å20 Å2
3----0.83 Å2
Refinement stepCycle: LAST / Resolution: 1.95→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2871 0 34 449 3354
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223211
X-RAY DIFFRACTIONr_bond_other_d0.0030.0226
X-RAY DIFFRACTIONr_angle_refined_deg1.471.9884399
X-RAY DIFFRACTIONr_angle_other_deg3.612359
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7745423
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.23424.43149
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.15215624
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0281520
X-RAY DIFFRACTIONr_chiral_restr0.110.2486
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022434
X-RAY DIFFRACTIONr_gen_planes_other0.0020.0212
X-RAY DIFFRACTIONr_nbd_refined0.2080.21463
X-RAY DIFFRACTIONr_nbd_other0.2740.237
X-RAY DIFFRACTIONr_nbtor_refined0.3050.22195
X-RAY DIFFRACTIONr_nbtor_other0.1270.25
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2140.2357
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2060.276
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2540.230
X-RAY DIFFRACTIONr_mcbond_it1.0681.51965
X-RAY DIFFRACTIONr_mcangle_it1.7123116
X-RAY DIFFRACTIONr_scbond_it2.42831475
X-RAY DIFFRACTIONr_scangle_it3.8654.51245
LS refinement shellResolution: 1.95→2.003 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 172 -
Rwork0.222 3291 -
all-3463 -
obs--98.63 %

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