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- PDB-3r2b: MK2 kinase bound to Compound 5b -

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Basic information

Entry
Database: PDB / ID: 3r2b
TitleMK2 kinase bound to Compound 5b
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 / intracellular signal transduction / protein kinase activity / 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-05B / MAP kinase-activated protein kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsOubrie, A. / van Zeeland, M. / Versteegh, J.
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 14, 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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
B: MAP kinase-activated protein kinase 2
C: MAP kinase-activated protein kinase 2
D: MAP kinase-activated protein kinase 2
E: MAP kinase-activated protein kinase 2
F: MAP kinase-activated protein kinase 2
G: MAP kinase-activated protein kinase 2
H: MAP kinase-activated protein kinase 2
I: MAP kinase-activated protein kinase 2
J: MAP kinase-activated protein kinase 2
K: MAP kinase-activated protein kinase 2
L: MAP kinase-activated protein kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)441,75314
Polymers440,94612
Non-polymers8072
Water0
1
A: MAP kinase-activated protein kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1492
Polymers36,7451
Non-polymers4031
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: MAP kinase-activated protein kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1492
Polymers36,7451
Non-polymers4031
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: MAP kinase-activated protein kinase 2


Theoretical massNumber of molelcules
Total (without water)36,7451
Polymers36,7451
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: MAP kinase-activated protein kinase 2


Theoretical massNumber of molelcules
Total (without water)36,7451
Polymers36,7451
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: MAP kinase-activated protein kinase 2


Theoretical massNumber of molelcules
Total (without water)36,7451
Polymers36,7451
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: MAP kinase-activated protein kinase 2


Theoretical massNumber of molelcules
Total (without water)36,7451
Polymers36,7451
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: MAP kinase-activated protein kinase 2


Theoretical massNumber of molelcules
Total (without water)36,7451
Polymers36,7451
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: MAP kinase-activated protein kinase 2


Theoretical massNumber of molelcules
Total (without water)36,7451
Polymers36,7451
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: MAP kinase-activated protein kinase 2


Theoretical massNumber of molelcules
Total (without water)36,7451
Polymers36,7451
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
J: MAP kinase-activated protein kinase 2


Theoretical massNumber of molelcules
Total (without water)36,7451
Polymers36,7451
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
K: MAP kinase-activated protein kinase 2


Theoretical massNumber of molelcules
Total (without water)36,7451
Polymers36,7451
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
12
L: MAP kinase-activated protein kinase 2


Theoretical massNumber of molelcules
Total (without water)36,7451
Polymers36,7451
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)139.803, 180.249, 217.109
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J
111K
121L

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: 4 / Auth seq-ID: 47 - 345 / Label seq-ID: 1 - 299

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF
7GG
8HH
9II
10JJ
11KK
12LL

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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: 36745.484 Da / Num. of mol.: 12 / Fragment: UNP residues 47-364
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-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.: 2 / Source method: obtained synthetically / Formula: C22H21N5O3

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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: 3.1 Å3/Da / Density % sol: 60.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100 mM Tris, 2.3 M AmSO4, pH 8.5, 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: Sep 9, 2008 / 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: 2.9→51.97 Å / Num. obs: 74678 / % possible obs: 61.3 % / Redundancy: 3.22 % / Rmerge(I) obs: 0.156 / Χ2: 1.02 / Net I/σ(I): 5 / Scaling rejects: 1817
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
2.9-33.140.5411.92452277980.8164.6
3-3.123.160.4932.12456577620.8864.4
3.12-3.273.180.4452.42449776950.9163.9
3.27-3.443.180.3942.72443176700.9763.5
3.44-3.653.160.3672.92428176101.1462.9
3.65-3.943.110.28142379975321.2661.9
3.94-4.333.230.25.32399573941.1561
4.33-4.963.270.15472416873441.0859.9
4.96-6.243.370.13382402570891.0157.8
6.24-51.973.440.07414.12395467840.9653.4

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Processing

Software
NameVersionClassificationNB
d*TREK9.5Ldata scaling
REFMAC5.4.0078refinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
d*TREKdata reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→51.97 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.894 / Occupancy max: 1 / Occupancy min: 1 / SU B: 52.857 / SU ML: 0.429 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.669 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.3157 3743 5 %RANDOM
Rwork0.2766 ---
obs0.2785 74643 61.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 167.37 Å2 / Biso mean: 100.5853 Å2 / Biso min: 75.78 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å20 Å20 Å2
2--0.41 Å20 Å2
3----0.26 Å2
Refinement stepCycle: LAST / Resolution: 2.9→51.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26321 0 60 0 26381
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02226943
X-RAY DIFFRACTIONr_bond_other_d0.0010.0218788
X-RAY DIFFRACTIONr_angle_refined_deg0.8391.97236355
X-RAY DIFFRACTIONr_angle_other_deg0.777345805
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6153204
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.9923.7481190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.715154977
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.14815180
X-RAY DIFFRACTIONr_chiral_restr0.0470.24038
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02128998
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025312
X-RAY DIFFRACTIONr_mcbond_it0.0531.516284
X-RAY DIFFRACTIONr_mcbond_other0.0171.56504
X-RAY DIFFRACTIONr_mcangle_it0.106226401
X-RAY DIFFRACTIONr_scbond_it0.172310659
X-RAY DIFFRACTIONr_scangle_it0.2794.59954
Refine LS restraints NCS

Ens-ID: 1 / Number: 3725 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1AMEDIUM POSITIONAL0.340.5
2BMEDIUM POSITIONAL0.350.5
3CMEDIUM POSITIONAL0.310.5
4DMEDIUM POSITIONAL0.340.5
5EMEDIUM POSITIONAL0.320.5
6FMEDIUM POSITIONAL0.330.5
7GMEDIUM POSITIONAL0.290.5
8HMEDIUM POSITIONAL0.270.5
9IMEDIUM POSITIONAL0.290.5
10JMEDIUM POSITIONAL0.30.5
11KMEDIUM POSITIONAL0.280.5
12LMEDIUM POSITIONAL0.290.5
1AMEDIUM THERMAL0.092
2BMEDIUM THERMAL0.062
3CMEDIUM THERMAL0.072
4DMEDIUM THERMAL0.082
5EMEDIUM THERMAL0.072
6FMEDIUM THERMAL0.092
7GMEDIUM THERMAL0.062
8HMEDIUM THERMAL0.062
9IMEDIUM THERMAL0.062
10JMEDIUM THERMAL0.072
11KMEDIUM THERMAL0.062
12LMEDIUM THERMAL0.062
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.397 297 -
Rwork0.385 5452 -
all-5749 -
obs--64.49 %
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)
13.47361.3219-0.23491.1201-0.01361.12470.01770.1729-0.0608-0.11610.0289-0.1422-0.02310.1019-0.04660.17090.0389-0.01750.10820.01260.0825-13.3014-55.29119.7178
23.93720.016-0.89530.39230.03611.2235-0.01940.0885-0.2328-0.0147-0.02070.14060.0246-0.1030.040.19790.0442-0.01060.2395-0.00170.1791-20.9287-28.0423-13.9909
31.3122-0.1647-0.20713.90140.97762.2573-0.0137-0.20640.13670.33920.0089-0.2025-0.04030.07510.00480.1565-0.029-0.04590.2442-0.02390.1332-27.1503-40.596559.7174
41.1978-0.2750.00612.1535-0.89971.8780.0361-0.05170.20920.06860.00650.0723-0.1766-0.208-0.04260.1225-0.0105-0.0620.1879-0.08560.1492-53.4348-37.566124.3636
53.5017-1.0142-0.51311.6847-0.05360.82020.0636-0.10260.1012-0.0423-0.0789-0.2731-0.04890.17730.01530.3189-0.0117-0.06110.21810.06860.18048.4063-83.78841.1419
61.34130.006-0.14292.479-0.76432.18770.02390.1105-0.1351-0.1114-0.0342-0.11470.15780.00460.01030.0994-0.0014-0.07590.1508-0.05810.0812-50.6912-70.609-2.413
71.60650.34740.43032.49821.10332.8845-0.0038-0.27480.08710.2413-0.08850.18130.0976-0.18440.09230.2232-0.0008-0.03020.28060.05220.2868-20.68-78.378274.1339
81.27540.29440.06684.5941.52792.6438-0.02240.0009-0.28590.1521-0.04610.10920.4527-0.01980.06850.222-0.04340.10160.3926-0.02380.477219.9596-100.2539-4.9873
93.5051-0.0175-0.23441.0588-0.12091.18350.07290.19210.0642-0.0239-0.037-0.11840.0068-0.0815-0.03580.4426-0.0353-0.06570.36870.11950.451327.0551-58.385772.4763
101.41650.26560.26892.69451.19242.67830.0436-0.2094-0.03150.2613-0.03490.01170.1096-0.1788-0.00870.16620.005-0.08350.22360.05080.196215.2308-28.132752.8128
110.749-0.62870.65712.8663-2.0072.4876-0.0257-0.0188-0.02490.03160.1590.3308-0.1049-0.3272-0.13340.34150.04050.02820.5168-0.09740.593-55.75390.153847.5837
121.49390.0520.2083.02631.06452.2391-0.0384-0.03810.1753-0.0744-0.07860.2395-0.3001-0.17240.1170.26440.073-0.00640.38850.06790.2706-7.605714.2196-7.9003
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A47 - 345
2X-RAY DIFFRACTION2B47 - 345
3X-RAY DIFFRACTION3C47 - 345
4X-RAY DIFFRACTION4D47 - 345
5X-RAY DIFFRACTION5E47 - 345
6X-RAY DIFFRACTION6F47 - 345
7X-RAY DIFFRACTION7G47 - 345
8X-RAY DIFFRACTION8H47 - 345
9X-RAY DIFFRACTION9I47 - 345
10X-RAY DIFFRACTION10J47 - 345
11X-RAY DIFFRACTION11K47 - 345
12X-RAY DIFFRACTION12L47 - 345

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