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- PDB-2p3g: Crystal structure of a pyrrolopyridine inhibitor bound to MAPKAP ... -

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Basic information

Entry
Database: PDB / ID: 2p3g
TitleCrystal structure of a pyrrolopyridine inhibitor bound to MAPKAP Kinase-2
ComponentsMAP kinase-activated protein kinase 2
KeywordsTRANSFERASE / kinase domain / ATP-binding / serine/threonine kinase / MAP kinases / MK-2 / MK2
Function / homology
Function and homology information


macropinocytosis / CREB phosphorylation / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / leukotriene metabolic process / calcium-dependent protein serine/threonine kinase activity / Synthesis of Leukotrienes (LT) and Eoxins (EX) / regulation of tumor necrosis factor production / regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of macrophage cytokine production ...macropinocytosis / CREB phosphorylation / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / leukotriene metabolic process / calcium-dependent protein serine/threonine kinase activity / Synthesis of Leukotrienes (LT) and Eoxins (EX) / regulation of tumor necrosis factor production / regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of macrophage cytokine production / mitogen-activated protein kinase binding / regulation of interleukin-6 production / calmodulin-dependent protein kinase activity / 3'-UTR-mediated mRNA stabilization / toll-like receptor signaling pathway / p38MAPK cascade / inner ear development / Regulation of HSF1-mediated heat shock response / cellular response to vascular endothelial growth factor stimulus / vascular endothelial growth factor receptor signaling pathway / regulation of cellular response to heat / p38MAPK events / regulation of mRNA stability / response to cytokine / activated TAK1 mediates p38 MAPK activation / Regulation of TNFR1 signaling / VEGFA-VEGFR2 Pathway / positive regulation of tumor necrosis factor production / MAPK cascade / peptidyl-serine phosphorylation / Oxidative Stress Induced Senescence / response to lipopolysaccharide / calmodulin binding / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / inflammatory response / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / DNA damage response / extracellular exosome / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
MAP kinase activated protein kinase, C-terminal / 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, ATP binding site ...MAP kinase activated protein kinase, C-terminal / 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, 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-F10 / MAP kinase-activated protein kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.8 Å
AuthorsKurumbail, R.G. / Caspers, N.
CitationJournal: J.Med.Chem. / Year: 2007
Title: Pyrrolopyridine Inhibitors of Mitogen-Activated Protein Kinase-Activated Protein Kinase 2 (MK-2).
Authors: Anderson, D.R. / Meyers, M.J. / Vernier, W.F. / Mahoney, M.W. / Kurumbail, R.G. / Caspers, N. / Poda, G.I. / Schindler, J.F. / Reitz, D.B. / Mourey, R.J.
History
DepositionMar 8, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2007Provider: repository / Type: Initial release
Revision 1.1Mar 5, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 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 1.4Feb 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
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: MAP kinase-activated protein kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2052
Polymers37,8981
Non-polymers3071
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)253.941, 253.941, 253.941
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number210
Space group name H-MF4132

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Components

#1: Protein MAP kinase-activated protein kinase 2 / MAPK-activated protein kinase 2 / MAPKAP kinase 2 / MAPKAPK-2 / MK2


Mass: 37897.750 Da / Num. of mol.: 1 / Fragment: N- and C-terminally truncated
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAPKAPK2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3
References: UniProt: P49137, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-F10 / 2-[2-(2-FLUOROPHENYL)PYRIDIN-4-YL]-1,5,6,7-TETRAHYDRO-4H-PYRROLO[3,2-C]PYRIDIN-4-ONE


Mass: 307.322 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H14FN3O

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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: 4.5 Å3/Da / Density % sol: 72.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: Protein solution (5 mg/ml) euqilibrated against 1.6 - 2.0 M sodium malonate at pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 1, 2005
RadiationMonochromator: Si(111)double-crystal system / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.7→20 Å / Num. all: 7892 / Num. obs: 7853 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -1 / Redundancy: 7.4 % / Biso Wilson estimate: 105 Å2 / Rmerge(I) obs: 0.051 / Rsym value: 0.051 / Χ2: 1.015 / Net I/σ(I): 11.6
Reflection shellResolution: 3.7→3.83 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.407 / Mean I/σ(I) obs: 3.8 / Num. unique all: 752 / Rsym value: 0.407 / Χ2: 1.073 / % possible all: 99.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
HKL-2000data reduction
X-PLORphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: Structure of MAPKAP Kinase-2/AMP-PNP complex solved using ERK-2 as a starting model for molecular replacement

Resolution: 3.8→20 Å / Cor.coef. Fo:Fc: 0.896 / Cor.coef. Fo:Fc free: 0.836 / SU B: 55.356 / SU ML: 0.821 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.839 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.374 335 4.6 %RANDOM
Rwork0.3 ---
obs0.303 7247 99.52 %-
all-8020 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 135.676 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.83 Å0.97 Å
Refinement stepCycle: LAST / Resolution: 3.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2298 0 23 0 2321
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222370
X-RAY DIFFRACTIONr_angle_refined_deg1.4431.9753194
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.155279
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.324.128109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.3615451
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8321516
X-RAY DIFFRACTIONr_chiral_restr0.0920.2347
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021793
X-RAY DIFFRACTIONr_nbd_refined0.2640.21414
X-RAY DIFFRACTIONr_nbtor_refined0.3320.21590
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1980.2136
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2040.225
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1590.23
X-RAY DIFFRACTIONr_mcbond_it0.7391.51449
X-RAY DIFFRACTIONr_mcangle_it1.33122283
X-RAY DIFFRACTIONr_scbond_it0.90731054
X-RAY DIFFRACTIONr_scangle_it1.6324.5911
LS refinement shellResolution: 3.8→3.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.418 22 -
Rwork0.338 495 -
obs-517 100 %

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