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- PDB-3r30: MK2 kinase bound to Compound 2 -

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Basic information

Entry
Database: PDB / ID: 3r30
TitleMK2 kinase bound to Compound 2
ComponentsMAP kinase-activated protein kinase 2
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Kinase domain with bound 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 production / regulation of tumor necrosis factor-mediated signaling pathway / 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 production / regulation of tumor necrosis factor-mediated signaling pathway / 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
Chem-CD2 / MAP kinase-activated protein kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.2 Å
AuthorsOubrie, A. / Fisher, M.
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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)37,2522
Polymers36,8931
Non-polymers3591
Water0
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

A: MAP kinase-activated protein kinase 2
hetero molecules

A: MAP kinase-activated protein kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,7566
Polymers110,6783
Non-polymers1,0783
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area3670 Å2
ΔGint-24 kcal/mol
Surface area37870 Å2
MethodPISA
3
A: MAP kinase-activated protein kinase 2
hetero molecules

A: MAP kinase-activated protein kinase 2
hetero molecules

A: MAP kinase-activated protein kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,7566
Polymers110,6783
Non-polymers1,0783
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation31_555-z,-x,y1
crystal symmetry operation82_555-y,z,-x1
Buried area3330 Å2
ΔGint-18 kcal/mol
Surface area38210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)253.297, 253.297, 253.297
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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): Tuner (DE3)
References: UniProt: P49137, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-CD2 / 1-(2-aminoethyl)-3-[2-(quinolin-3-yl)pyridin-4-yl]-1H-pyrazole-5-carboxylic acid


Mass: 359.381 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H17N5O2

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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: 73.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 1.8 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 14, 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: 3.2→29.85 Å / Num. all: 21934 / Num. obs: 20639 / % possible obs: 94.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.43 % / Rmerge(I) obs: 0.228
Reflection shellResolution: 3.2→3.31 Å / Rmerge(I) obs: 0.756 / Mean I/σ(I) obs: 2.4 / % possible all: 94.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHASERphasing
REFMAC5.5.0102refinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→29.25 Å / Cor.coef. Fo:Fc: 0.864 / Cor.coef. Fo:Fc free: 0.807 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 43.283 / SU ML: 0.346 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.48 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.332 1176 9.8 %RANDOM
Rwork0.279 ---
obs0.284 11977 100 %-
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: 62.53 Å2
Refinement stepCycle: LAST / Resolution: 3.2→29.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2011 0 27 0 2038
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222107
X-RAY DIFFRACTIONr_bond_other_d0.0010.021356
X-RAY DIFFRACTIONr_angle_refined_deg1.5371.9792867
X-RAY DIFFRACTIONr_angle_other_deg1.04633333
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1985264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.33425.0683
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.52815339
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.493157
X-RAY DIFFRACTIONr_chiral_restr0.2030.2332
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212326
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02398
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4291.51336
X-RAY DIFFRACTIONr_mcbond_other0.0661.5535
X-RAY DIFFRACTIONr_mcangle_it0.85922145
X-RAY DIFFRACTIONr_scbond_it1.4193771
X-RAY DIFFRACTIONr_scangle_it2.5224.5722
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.2→3.28 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 88 -
Rwork0.317 765 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.7853-1.39511.34672.11360.54963.8153-0.1049-0.1833-0.14040.14290.08430.25090.4089-0.39560.02070.1259-0.0908-0.03020.1532-0.020.121213.5321.65439.179
25.7652-1.17982.60615.34870.36385.4796-0.0544-0.6467-0.00850.17-0.02480.29860.0145-0.46620.07910.0597-0.0899-0.03720.2833-0.01160.1898-2.95524.76138.346
36.58870.40680.27315.4595-1.20777.37720.0858-0.78420.02870.45950.14550.4539-0.0481-0.4699-0.23120.1635-0.0863-0.04250.51090.03530.4252-17.16621.9338.152
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A46 - 152
2X-RAY DIFFRACTION2A159 - 215
3X-RAY DIFFRACTION3A232 - 345

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