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- PDB-3fpm: Crystal Structure of a Squarate Inhibitor bound to MAPKAP Kinase-2 -

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Basic information

Entry
Database: PDB / ID: 3fpm
TitleCrystal Structure of a Squarate Inhibitor bound to MAPKAP Kinase-2
ComponentsMAP kinase-activated protein kinase 2
KeywordsTRANSFERASE / ATP-binding / Alternative splicing / Kinase / Nucleotide-binding / Phosphoprotein / Polymorphism / Serine/threonine-protein kinase
Function / homology
Function and homology information


calcium-dependent protein serine/threonine kinase activity / macropinocytosis / CREB phosphorylation / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / leukotriene metabolic process / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Synthesis of Leukotrienes (LT) and Eoxins (EX) / regulation of tumor necrosis factor production / regulation of tumor necrosis factor-mediated signaling pathway / calcium/calmodulin-dependent protein kinase activity ...calcium-dependent protein serine/threonine kinase activity / macropinocytosis / CREB phosphorylation / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / leukotriene metabolic process / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Synthesis of Leukotrienes (LT) and Eoxins (EX) / regulation of tumor necrosis factor production / regulation of tumor necrosis factor-mediated signaling pathway / calcium/calmodulin-dependent protein kinase activity / regulation of interleukin-6 production / mitogen-activated protein kinase binding / positive regulation of macrophage cytokine production / 3'-UTR-mediated mRNA stabilization / toll-like receptor signaling pathway / p38MAPK cascade / inner ear development / cellular response to vascular endothelial growth factor stimulus / Regulation of HSF1-mediated heat shock response / 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 / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / protein kinase activity / calmodulin binding / intracellular signal transduction / ciliary basal body / protein phosphorylation / inflammatory response / 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 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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-793 / MAP kinase-activated protein kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsParris, K.D.
CitationJournal: Bioorg.Med.Chem. / Year: 2009
Title: Identification and SAR of squarate inhibitors of mitogen activated protein kinase-activated protein kinase 2 (MK-2)
Authors: Lovering, F. / Kirincich, S. / Wang, W. / Combs, K. / Resnick, L. / Sabalski, J.E. / Butera, J. / Liu, J. / Parris, K. / Telliez, J.B.
History
DepositionJan 5, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: MAP kinase-activated protein kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9462
Polymers37,6531
Non-polymers2931
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: MAP kinase-activated protein kinase 2
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)455,35024
Polymers451,83012
Non-polymers3,52012
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_646-z+3/2,x-1/2,-y+11
crystal symmetry operation11_566y+1/2,-z+1,-x+3/21
crystal symmetry operation27_656-x+3/2,y,-z+3/21
crystal symmetry operation29_545z,x-1/2,y+1/21
crystal symmetry operation36_665-y+1,-z+1,x1
crystal symmetry operation50_655-x+3/2,-y+1/2,z1
crystal symmetry operation54_566z,-x+1,-y+11
crystal symmetry operation58_646-y+1,z-1/2,-x+3/21
crystal symmetry operation76_556x,-y+1/2,-z+3/21
crystal symmetry operation79_665-z+3/2,-x+1,y+1/21
crystal symmetry operation81_545y+1/2,z-1/2,x1
Buried area37790 Å2
ΔGint-214 kcal/mol
Surface area147430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)254.658, 254.658, 254.658
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number210
Space group name H-MF4132
DetailsThe asymmetric unit of a crystal structure contains the biological unit

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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: 37652.527 Da / Num. of mol.: 1 / Fragment: Protein kinase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAPKAPK2 / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(de3)
References: UniProt: P49137, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-793 / 3-{[(1R)-1-phenylethyl]amino}-4-(pyridin-4-ylamino)cyclobut-3-ene-1,2-dione


Mass: 293.320 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H15N3O2

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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: 4.57 Å3/Da / Density % sol: 73.08 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 1600 mM Sodium Malonate pH 5, 1 % MPD, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 24, 2003
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.3→30 Å / Num. obs: 10421

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1NY3

1ny3


Resolution: 3.3→30 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.872 / SU B: 25.48 / SU ML: 0.421 / Cross valid method: THROUGHOUT / ESU R: 0.756 / ESU R Free: 0.531 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.33701 519 4.7 %RANDOM
Rwork0.28171 ---
obs0.28419 10421 98.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 127.583 Å2
Refinement stepCycle: LAST / Resolution: 3.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2249 0 22 0 2271
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0222324
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8821.983146
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7065280
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.39224.158101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.01815413
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0331514
X-RAY DIFFRACTIONr_chiral_restr0.0560.2349
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.021740
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1680.2973
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2990.21577
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1170.254
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1430.241
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1060.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.3→3.388 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 31 -
Rwork0.343 779 -
obs--99.51 %

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