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- PDB-3r1n: MK3 kinase bound to Compound 5b -

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Basic information

Entry
Database: PDB / ID: 3r1n
TitleMK3 kinase bound to Compound 5b
ComponentsMAP kinase-activated protein kinase 3
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Kinase domain with bound inhibitor / Kinase domain / phosphotransferase / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


macropinocytosis / calcium-dependent protein serine/threonine kinase activity / calmodulin-dependent protein kinase activity / mitogen-activated protein kinase binding / toll-like receptor signaling pathway / MAP kinase kinase activity / vascular endothelial growth factor receptor signaling pathway / p38MAPK events / response to cytokine / activated TAK1 mediates p38 MAPK activation ...macropinocytosis / calcium-dependent protein serine/threonine kinase activity / calmodulin-dependent protein kinase activity / mitogen-activated protein kinase binding / toll-like receptor signaling pathway / MAP kinase kinase activity / vascular endothelial growth factor receptor signaling pathway / p38MAPK events / response to cytokine / activated TAK1 mediates p38 MAPK activation / VEGFA-VEGFR2 Pathway / peptidyl-serine phosphorylation / Oxidative Stress Induced Senescence / response to lipopolysaccharide / calmodulin binding / non-specific serine/threonine protein kinase / intracellular signal transduction / protein serine kinase activity / protein serine/threonine kinase activity / signal transduction / 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-05B / MAP kinase-activated protein kinase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsOubrie, A. / Kazemier, B.
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 11, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3Feb 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 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8322
Polymers36,4291
Non-polymers4031
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.130, 75.790, 61.340
Angle α, β, γ (deg.)90.000, 108.010, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein MAP kinase-activated protein kinase 3 / MAPK-activated protein kinase 3 / MAPKAP kinase 3 / MAPKAPK-3 / Chromosome 3p kinase / 3pK


Mass: 36428.602 Da / Num. of mol.: 1 / Fragment: Kinase domain (UNP residues 33-349)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAPKAPK3 / Plasmid: pTrilJ-POPIN / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q16644, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-05B / 2'-[2-(1,3-benzodioxol-5-yl)pyrimidin-4-yl]-5',6'-dihydrospiro[piperidine-4,7'-pyrrolo[3,2-c]pyridin]-4'(1'H)-one


Mass: 403.434 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H21N5O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.55 Å3/Da / Density % sol: 51.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1 M citrate/Bis-tris propane, 12 % PEG3350, 10 mM DTT, 1 mM Compound 5b, 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: Mar 15, 2010 / 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: 2.09→45.098 Å / Num. all: 21617 / Num. obs: 21617 / % possible obs: 99.8 % / Redundancy: 3.2 % / Rsym value: 0.057 / Net I/σ(I): 12
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.09-2.213.10.5151.3949430810.51598.5
2.21-2.343.10.3542935929740.354100
2.34-2.53.20.2392.9893328170.239100
2.5-2.73.20.1644.1838526210.164100
2.7-2.963.20.0966.9770124000.096100
2.96-3.313.20.0610.7706121850.06100
3.31-3.823.30.03916.1626419260.039100
3.82-4.683.30.03316.9533416380.033100
4.68-6.623.30.03516.2412712650.03599.9
6.62-45.0983.20.02322.322817100.02399.2

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Processing

Software
NameVersionClassificationNB
SCALA3.3.15data scaling
REFMAC5.5.0102refinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.09→39.11 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.921 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 11.953 / SU ML: 0.156 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2576 1119 5.2 %RANDOM
Rwork0.2142 ---
obs0.2165 21614 99.74 %-
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: 147.49 Å2 / Biso mean: 63.2263 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å20 Å2
2---0.07 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.09→39.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2218 0 30 73 2321
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0222328
X-RAY DIFFRACTIONr_bond_other_d0.0010.021602
X-RAY DIFFRACTIONr_angle_refined_deg21.9723154
X-RAY DIFFRACTIONr_angle_other_deg1.13933909
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2145278
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.14524.234111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.45615418
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.5031514
X-RAY DIFFRACTIONr_chiral_restr0.1220.2340
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212543
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02463
X-RAY DIFFRACTIONr_mcbond_it1.1871.51376
X-RAY DIFFRACTIONr_mcbond_other0.3011.5553
X-RAY DIFFRACTIONr_mcangle_it2.04422230
X-RAY DIFFRACTIONr_scbond_it2.893952
X-RAY DIFFRACTIONr_scangle_it4.2254.5920
LS refinement shellResolution: 2.093→2.147 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 83 -
Rwork0.255 1426 -
all-1509 -
obs--96.98 %
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)
12.1276-0.0939-0.08176.1663-3.50086.1492-0.09580.16460.25110.295-0.0488-0.7037-0.24040.39470.14460.0424-0.003-0.01790.25010.00220.336410.96712.4345.907
24.9907-0.0877-1.52028.23740.39115.28860.1613-0.4983-0.14720.5115-0.09670.35560.2161-0.1689-0.06470.0518-0.03450.02730.18910.07880.15027.786-0.79817.42
34.17711.82316.33126.0401-2.881515.76190.63170.0013-0.57630.9854-0.3255-0.73430.25580.4884-0.30620.25410.0508-0.05970.35060.10680.315716.306-8.58821.283
43.21271.3767-0.96774.8395-0.6074.44190.2905-0.8612-0.37761.2607-0.1114-0.17780.4930.2133-0.17920.5425-0.0226-0.1240.44840.16880.363214.473-8.8227.175
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A33 - 133
2X-RAY DIFFRACTION2A138 - 195
3X-RAY DIFFRACTION3A219 - 242
4X-RAY DIFFRACTION4A263 - 343

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