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- PDB-3r2y: MK2 kinase bound to Compound 1 -

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Basic information

Entry
Database: PDB / ID: 3r2y
TitleMK2 kinase bound to Compound 1
ComponentsMAP kinase-activated protein kinase 2
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Kinase domain / Phosphotransferase / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


macropinocytosis / CREB phosphorylation / calcium-dependent protein serine/threonine kinase activity / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / leukotriene metabolic process / Synthesis of Leukotrienes (LT) and Eoxins (EX) / regulation of tumor necrosis factor-mediated signaling pathway / regulation of tumor necrosis factor production / calmodulin-dependent protein kinase activity ...macropinocytosis / CREB phosphorylation / calcium-dependent protein serine/threonine kinase activity / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / leukotriene metabolic process / Synthesis of Leukotrienes (LT) and Eoxins (EX) / regulation of tumor necrosis factor-mediated signaling pathway / regulation of tumor necrosis factor production / calmodulin-dependent protein kinase activity / positive regulation of macrophage cytokine production / mitogen-activated protein kinase binding / regulation of interleukin-6 production / 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 / MAPK cascade / positive regulation of tumor necrosis factor production / 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
MALONATE ION / Chem-P4O / MAP kinase-activated protein kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å
AuthorsOubrie, A. / Leonard, P.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2011
Title: Structure-based lead identification of ATP-competitive MK2 inhibitors.
Authors: Barf, T. / Kaptein, A. / Wilde, S. / Heijden, R. / Someren, R. / Demont, D. / Schultz-Fademrecht, C. / Versteegh, J. / Zeeland, M. / Seegers, N. / Kazemier, B. / Kar, B. / Hoek, M. / Roos, J. ...Authors: Barf, T. / Kaptein, A. / Wilde, S. / Heijden, R. / Someren, R. / Demont, D. / Schultz-Fademrecht, C. / Versteegh, J. / Zeeland, M. / Seegers, N. / Kazemier, B. / Kar, B. / Hoek, M. / Roos, J. / Klop, H. / Smeets, R. / Hofstra, C. / Hornberg, J. / Oubrie, A.
History
DepositionMar 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 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: MAP kinase-activated protein kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4374
Polymers36,8931
Non-polymers5443
Water543
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)253.258, 253.258, 253.258
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: 36892.656 Da / Num. of mol.: 1 / Fragment: Kinase domain, UNP residues 46-364
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAPKAPK2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: P49137, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#3: Chemical ChemComp-P4O / 2-(2-QUINOLIN-3-YLPYRIDIN-4-YL)-1,5,6,7-TETRAHYDRO-4H-PYRROLO[3,2-C]PYRIDIN-4-ONE


Mass: 340.378 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H16N4O
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 4.59 Å3/Da / Density % sol: 73.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 1.6 M Sodium Malonate, pH 5.0, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 24, 2006 / Details: mirrors
RadiationMonochromator: VariMax-HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 3→19.84 Å / Num. all: 14420 / Num. obs: 14405 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 5.45 % / Net I/σ(I): 7
Reflection shellResolution: 3→3.11 Å / Rmerge(I) obs: 0.613 / Mean I/σ(I) obs: 1.8 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→19.84 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.864 / Occupancy max: 1 / Occupancy min: 0.33 / SU B: 17.439 / SU ML: 0.328 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.419 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3337 1442 10 %RANDOM
Rwork0.2894 ---
obs0.2939 14369 99.85 %-
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 max: 112.37 Å2 / Biso mean: 75.8717 Å2 / Biso min: 20 Å2
Refinement stepCycle: LAST / Resolution: 3→19.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2057 0 40 3 2100
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222144
X-RAY DIFFRACTIONr_bond_other_d0.0010.021467
X-RAY DIFFRACTIONr_angle_refined_deg1.6081.9852894
X-RAY DIFFRACTIONr_angle_other_deg0.94833586
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4135256
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.70124.09188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.14815390
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8591512
X-RAY DIFFRACTIONr_chiral_restr0.0890.2323
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212312
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02413
X-RAY DIFFRACTIONr_mcbond_it0.6981.51296
X-RAY DIFFRACTIONr_mcbond_other0.0921.5519
X-RAY DIFFRACTIONr_mcangle_it1.36122097
X-RAY DIFFRACTIONr_scbond_it1.8063848
X-RAY DIFFRACTIONr_scangle_it3.2514.5797
LS refinement shellResolution: 3.001→3.077 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.417 101 -
Rwork0.341 919 -
all-1020 -
obs--100 %

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