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- PDB-6cjh: Co-crystal structure of MNK2 in complex with an inhibitor -

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Basic information

Entry
Database: PDB / ID: 6cjh
TitleCo-crystal structure of MNK2 in complex with an inhibitor
ComponentsMAP kinase-interacting serine/threonine-protein kinase 2
KeywordsTRANSFERASE/TRANSFERASE Inhibitor / mnk2 inhibitor / TRANSFERASE / TRANSFERASE-TRANSFERASE Inhibitor complex
Function / homology
Function and homology information


calcium-dependent protein serine/threonine kinase activity / cellular response to arsenic-containing substance / calcium/calmodulin-dependent protein kinase activity / hemopoiesis / extrinsic apoptotic signaling pathway in absence of ligand / PML body / regulation of translation / cell surface receptor signaling pathway / nuclear body / non-specific serine/threonine protein kinase ...calcium-dependent protein serine/threonine kinase activity / cellular response to arsenic-containing substance / calcium/calmodulin-dependent protein kinase activity / hemopoiesis / extrinsic apoptotic signaling pathway in absence of ligand / PML body / regulation of translation / cell surface receptor signaling pathway / nuclear body / non-specific serine/threonine protein kinase / calmodulin binding / intracellular signal transduction / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / nucleoplasm / ATP binding / nucleus / metal ion binding / cytoplasm
Similarity search - Function
: / 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 ...: / 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
3-phenyl-5-(pyridin-4-yl)-1H-indazole / MAP kinase-interacting serine/threonine-protein kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsHan, Q.
CitationJournal: J. Med. Chem. / Year: 2018
Title: Structure-based Design of Pyridone-Aminal eFT508 Targeting Dysregulated Translation by Selective Mitogen-activated Protein Kinase Interacting Kinases 1 and 2 (MNK1/2) Inhibition.
Authors: Reich, S.H. / Sprengeler, P.A. / Chiang, G.G. / Appleman, J.R. / Chen, J. / Clarine, J. / Eam, B. / Ernst, J.T. / Han, Q. / Goel, V.K. / Han, E.Z.R. / Huang, V. / Hung, I.N.J. / Jemison, A. ...Authors: Reich, S.H. / Sprengeler, P.A. / Chiang, G.G. / Appleman, J.R. / Chen, J. / Clarine, J. / Eam, B. / Ernst, J.T. / Han, Q. / Goel, V.K. / Han, E.Z.R. / Huang, V. / Hung, I.N.J. / Jemison, A. / Jessen, K.A. / Molter, J. / Murphy, D. / Neal, M. / Parker, G.S. / Shaghafi, M. / Sperry, S. / Staunton, J. / Stumpf, C.R. / Thompson, P.A. / Tran, C. / Webber, S.E. / Wegerski, C.J. / Zheng, H. / Webster, K.R.
History
DepositionFeb 26, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MAP kinase-interacting serine/threonine-protein kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9413
Polymers35,6041
Non-polymers3372
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)105.850, 105.850, 72.690
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein MAP kinase-interacting serine/threonine-protein kinase 2 / MAP kinase signal-integrating kinase 2 / Mnk2


Mass: 35604.461 Da / Num. of mol.: 1 / Mutation: D228G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MKNK2, GPRK7, MNK2 / Production host: Escherichia coli (E. coli) / Strain (production host): K-12
References: UniProt: Q9HBH9, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ET8 / 3-phenyl-5-(pyridin-4-yl)-1H-indazole


Mass: 271.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H13N3
Has protein modificationY

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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: 3.3 Å3/Da / Density % sol: 62.75 %
Crystal growTemperature: 300.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20-30% (w/v) polyacrylic acid 5100, 1-5% PEG 400, and 50 mM Hepes (pH 7.5)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.9→60 Å / Num. obs: 11166 / % possible obs: 89 % / Redundancy: 12 % / Net I/σ(I): 4
Reflection shellResolution: 2.9→3.1 Å

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.6→57 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.893 / SU B: 29.571 / SU ML: 0.434 / Cross valid method: THROUGHOUT / ESU R Free: 0.604 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.26074 259 4.6 %RANDOM
Rwork0.18337 ---
obs0.18682 5430 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 81.653 Å2
Baniso -1Baniso -2Baniso -3
1--1.97 Å2-0.98 Å20 Å2
2---1.97 Å20 Å2
3---2.95 Å2
Refinement stepCycle: 1 / Resolution: 3.6→57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2154 0 22 0 2176
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0192224
X-RAY DIFFRACTIONr_bond_other_d0.0030.0213
X-RAY DIFFRACTIONr_angle_refined_deg1.681.962999
X-RAY DIFFRACTIONr_angle_other_deg2.131326
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6515267
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.39724.054111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.24215380
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.051515
X-RAY DIFFRACTIONr_chiral_restr0.1150.2318
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211704
X-RAY DIFFRACTIONr_gen_planes_other0.0030.0213
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.6→3.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.189 10 -
Rwork0.242 354 -
obs--100 %

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