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- PDB-1oz1: P38 MITOGEN-ACTIVATED KINASE IN COMPLEX WITH 4-AZAINDOLE INHIBITOR -

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Basic information

Entry
Database: PDB / ID: 1oz1
TitleP38 MITOGEN-ACTIVATED KINASE IN COMPLEX WITH 4-AZAINDOLE INHIBITOR
ComponentsMitogen-activated protein kinase 14MAPK14
KeywordsTRANSFERASE / SER/THR PROTEIN KINASE
Function / homology
Function and homology information


positive regulation of cyclase activity / stress-activated protein kinase signaling cascade / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / CD163 mediating an anti-inflammatory response / regulation of synaptic membrane adhesion / stress-induced premature senescence / cell surface receptor protein serine/threonine kinase signaling pathway / 3'-UTR-mediated mRNA stabilization / KSRP (KHSRP) binds and destabilizes mRNA / DSCAM interactions ...positive regulation of cyclase activity / stress-activated protein kinase signaling cascade / Activation of PPARGC1A (PGC-1alpha) by phosphorylation / CD163 mediating an anti-inflammatory response / regulation of synaptic membrane adhesion / stress-induced premature senescence / cell surface receptor protein serine/threonine kinase signaling pathway / 3'-UTR-mediated mRNA stabilization / KSRP (KHSRP) binds and destabilizes mRNA / DSCAM interactions / cartilage condensation / cellular response to UV-B / Platelet sensitization by LDL / mitogen-activated protein kinase p38 binding / positive regulation of myoblast fusion / positive regulation of muscle cell differentiation / negative regulation of hippo signaling / positive regulation of myotube differentiation / NFAT protein binding / Myogenesis / glucose import / Activation of the AP-1 family of transcription factors / ERK/MAPK targets / regulation of cytokine production involved in inflammatory response / p38MAPK cascade / fatty acid oxidation / cellular response to lipoteichoic acid / MAP kinase kinase activity / response to dietary excess / response to muramyl dipeptide / RHO GTPases Activate NADPH Oxidases / MAP kinase activity / regulation of ossification / mitogen-activated protein kinase / cellular response to vascular endothelial growth factor stimulus / positive regulation of myoblast differentiation / signal transduction in response to DNA damage / chondrocyte differentiation / vascular endothelial growth factor receptor signaling pathway / stress-activated MAPK cascade / skeletal muscle tissue development / lipopolysaccharide-mediated signaling pathway / positive regulation of cardiac muscle cell proliferation / negative regulation of inflammatory response to antigenic stimulus / p38MAPK events / striated muscle cell differentiation / response to muscle stretch / positive regulation of brown fat cell differentiation / positive regulation of interleukin-12 production / osteoclast differentiation / positive regulation of erythrocyte differentiation / DNA damage checkpoint signaling / activated TAK1 mediates p38 MAPK activation / cellular response to ionizing radiation / stem cell differentiation / positive regulation of glucose import / placenta development / NOD1/2 Signaling Pathway / response to insulin / bone development / negative regulation of canonical Wnt signaling pathway / cell morphogenesis / platelet activation / cellular response to virus / VEGFA-VEGFR2 Pathway / spindle pole / positive regulation of protein import into nucleus / osteoblast differentiation / ADP signalling through P2Y purinoceptor 1 / glucose metabolic process / positive regulation of reactive oxygen species metabolic process / chemotaxis / cellular senescence / cellular response to tumor necrosis factor / peptidyl-serine phosphorylation / protein phosphatase binding / secretory granule lumen / Oxidative Stress Induced Senescence / angiogenesis / Regulation of TP53 Activity through Phosphorylation / cellular response to lipopolysaccharide / ficolin-1-rich granule lumen / transcription by RNA polymerase II / cell surface receptor signaling pathway / intracellular signal transduction / nuclear speck / protein serine kinase activity / protein serine/threonine kinase activity / glutamatergic synapse / apoptotic process / Neutrophil degranulation / positive regulation of gene expression / regulation of transcription by RNA polymerase II / enzyme binding / signal transduction / positive regulation of transcription by RNA polymerase II / mitochondrion / extracellular region / nucleoplasm / ATP binding
Similarity search - Function
Mitogen-activated protein kinase 14 / Mitogen-activated protein (MAP) kinase p38-like / 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 / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain ...Mitogen-activated protein kinase 14 / Mitogen-activated protein (MAP) kinase p38-like / 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 / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / 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-FPH / Mitogen-activated protein kinase 14
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLovejoy, B. / Villasenor, A. / Browner, M. / Dunten, P.
CitationJournal: J.Med.Chem. / Year: 2003
Title: Design and synthesis of 4-azaindoles as inhibitors of p38 MAP kinase.
Authors: Trejo, A. / Arzeno, H. / Browner, M. / Chanda, S. / Cheng, S. / Comer, D.D. / Dalrymple, S.A. / Dunten, P. / Lafargue, J. / Lovejoy, B. / Freire-Moar, J. / Lim, J. / Mcintosh, J. / Miller, J. ...Authors: Trejo, A. / Arzeno, H. / Browner, M. / Chanda, S. / Cheng, S. / Comer, D.D. / Dalrymple, S.A. / Dunten, P. / Lafargue, J. / Lovejoy, B. / Freire-Moar, J. / Lim, J. / Mcintosh, J. / Miller, J. / Papp, E. / Reuter, D. / Roberts, R. / Sanpablo, F. / Saunders, J. / Song, K. / Villasenor, A. / Warren, S.D. / Welch, M. / Weller, P. / Whiteley, P.E. / Zeng, L. / Goldstein, D.M.
History
DepositionApr 7, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0542
Polymers42,7491
Non-polymers3051
Water3,621201
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.405, 85.454, 125.841
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Mitogen-activated protein kinase 14 / MAPK14 / Mitogen-activated protein kinase p38alpha / MAP kinase p38alpha / Cytokine suppressive anti- ...Mitogen-activated protein kinase p38alpha / MAP kinase p38alpha / Cytokine suppressive anti-inflammatory drug binding protein / CSAID binding protein / CSBP / MAX-interacting protein 2 / MAP kinase MXI2 / SAPK2A


Mass: 42748.715 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAPK14 OR CSBP1 OR CSBP2 OR CSBP OR MXI2 / Production host: Escherichia coli (E. coli) / Strain (production host): m15[prep4] / References: UniProt: Q16539, EC: 2.7.1.37
#2: Chemical ChemComp-FPH / 3-(4-FLUOROPHENYL)-2-PYRIDIN-4-YL-1H-PYRROLO[3,2-B]PYRIDIN-1-OL / 3-(4-FLUOROPHENYL)-1-HYDROXY-2-(PYRIDIN-4-YL)-1H-PYRROLO[3,2-B]PYRIDINE


Mass: 305.306 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H12FN3O
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 2.86 Å3/Da / Density % sol: 56.92 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: PEG 3350, calcium chloride, Hepes buffer, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal grow
*PLUS
Temperature: 17 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
132 mg/mlprotein1drop
250 mMHEPES1reservoirpH7.6
350 mM1reservoirCaCl2
417 %PEG33501reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 4, 1997
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 25274 / % possible obs: 85.8 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 29.2 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 7.2
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.455 / Num. unique all: 2605 / % possible all: 89.3
Reflection
*PLUS
Highest resolution: 2.1 Å

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.912 / SU B: 4.449 / SU ML: 0.121 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.227 / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25113 1271 5 %RANDOM
Rwork0.20135 ---
obs0.20383 25244 85.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 27.741 Å2
Baniso -1Baniso -2Baniso -3
1--1.17 Å20 Å20 Å2
2--0.15 Å20 Å2
3---1.02 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2779 0 23 201 3003
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0212870
X-RAY DIFFRACTIONr_angle_refined_deg1.3661.9643900
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7955342
X-RAY DIFFRACTIONr_chiral_restr0.0960.2435
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022175
X-RAY DIFFRACTIONr_nbd_refined0.2110.21267
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.2210
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1270.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1050.213
X-RAY DIFFRACTIONr_mcbond_it0.8591.51721
X-RAY DIFFRACTIONr_mcangle_it1.5722793
X-RAY DIFFRACTIONr_scbond_it2.26631149
X-RAY DIFFRACTIONr_scangle_it3.5644.51107
LS refinement shellResolution: 2.1→2.153 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.279 108
Rwork0.222 1828
Refinement
*PLUS
Highest resolution: 2.1 Å / Rfactor Rfree: 0.251 / Rfactor Rwork: 0.201
Solvent computation
*PLUS
Displacement parameters
*PLUS

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