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- PDB-7cbx: Crystal structure of MAP2K7 complexed with a covalent inhibitor 12 -

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Basic information

Entry
Database: PDB / ID: 7cbx
TitleCrystal structure of MAP2K7 complexed with a covalent inhibitor 12
ComponentsDual specificity mitogen-activated protein kinase kinase 7
KeywordsTRANSFERASE / Protein kinase / inhibitor
Function / homology
Function and homology information


JUN kinase kinase activity / regulation of motor neuron apoptotic process / mitogen-activated protein kinase kinase / response to osmotic stress / Fc-epsilon receptor signaling pathway / positive regulation of telomere capping / MAP kinase kinase activity / Uptake and function of anthrax toxins / MAP kinase activity / cellular response to interleukin-1 ...JUN kinase kinase activity / regulation of motor neuron apoptotic process / mitogen-activated protein kinase kinase / response to osmotic stress / Fc-epsilon receptor signaling pathway / positive regulation of telomere capping / MAP kinase kinase activity / Uptake and function of anthrax toxins / MAP kinase activity / cellular response to interleukin-1 / response to tumor necrosis factor / stress-activated MAPK cascade / response to UV / positive regulation of JUN kinase activity / JNK cascade / positive regulation of telomerase activity / positive regulation of telomere maintenance via telomerase / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / molecular function activator activity / FCERI mediated MAPK activation / positive regulation of JNK cascade / response to wounding / cellular senescence / response to heat / protein phosphatase binding / protein tyrosine kinase activity / Oxidative Stress Induced Senescence / cellular response to lipopolysaccharide / positive regulation of ERK1 and ERK2 cascade / phosphorylation / protein serine kinase activity / apoptotic process / protein kinase binding / positive regulation of DNA-templated transcription / enzyme binding / magnesium ion binding / signal transduction / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Chem-FU6 / Dual specificity mitogen-activated protein kinase kinase 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.061 Å
AuthorsKinoshita, T. / Murakawa, Y.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2020
Title: Structural basis for producing selective MAP2K7 inhibitors.
Authors: Murakawa, Y. / Valter, S. / Barr, H. / London, N. / Kinoshita, T.
History
DepositionJun 15, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dual specificity mitogen-activated protein kinase kinase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2883
Polymers36,8521
Non-polymers4362
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-0 kcal/mol
Surface area14040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.965, 70.517, 84.346
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Dual specificity mitogen-activated protein kinase kinase 7 / MAPKK 7 / JNK-activating kinase 2 / MAPK/ERK kinase 7 / MEK 7 / Stress-activated protein kinase ...MAPKK 7 / JNK-activating kinase 2 / MAPK/ERK kinase 7 / MEK 7 / Stress-activated protein kinase kinase 4 / SAPKK4 / c-Jun N-terminal kinase kinase 2 / JNKK 2


Mass: 36851.641 Da / Num. of mol.: 1 / Mutation: C218S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAP2K7, JNKK2, MEK7, MKK7, PRKMK7, SKK4 / Production host: Escherichia coli (E. coli)
References: UniProt: O14733, mitogen-activated protein kinase kinase
#2: Chemical ChemComp-FU6 / 3-(1H-indazol-3-yl)-5-(prop-2-enoylamino)-N-prop-2-ynyl-benzamide


Mass: 344.367 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H16N4O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.46 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: PEG3350

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.06→50 Å / Num. obs: 23058 / % possible obs: 99.8 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 17.4
Reflection shellResolution: 2.06→2.19 Å / Rmerge(I) obs: 0.47 / Num. unique obs: 3634

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5y90

5y90


Resolution: 2.061→46.162 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.94 / SU B: 4.226 / SU ML: 0.113 / Cross valid method: FREE R-VALUE / ESU R: 0.169 / ESU R Free: 0.156
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2236 1245 5.399 %
Rwork0.1816 21813 -
all0.184 --
obs-23058 99.801 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 40.38 Å2
Baniso -1Baniso -2Baniso -3
1-1.176 Å20 Å2-0 Å2
2---1.318 Å20 Å2
3---0.142 Å2
Refinement stepCycle: LAST / Resolution: 2.061→46.162 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2244 0 32 104 2380
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0132336
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172245
X-RAY DIFFRACTIONr_angle_refined_deg1.6961.6573142
X-RAY DIFFRACTIONr_angle_other_deg1.361.595213
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9485284
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.1921.88117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.0215443
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.2421516
X-RAY DIFFRACTIONr_chiral_restr0.080.2296
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022551
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02490
X-RAY DIFFRACTIONr_nbd_refined0.2260.2472
X-RAY DIFFRACTIONr_symmetry_nbd_other0.190.22021
X-RAY DIFFRACTIONr_nbtor_refined0.1690.21131
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.21146
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.2117
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0360.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2590.27
X-RAY DIFFRACTIONr_nbd_other0.1920.243
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1460.29
X-RAY DIFFRACTIONr_mcbond_it3.8573.9131127
X-RAY DIFFRACTIONr_mcbond_other3.8563.911126
X-RAY DIFFRACTIONr_mcangle_it5.6465.8381405
X-RAY DIFFRACTIONr_mcangle_other5.6455.8431406
X-RAY DIFFRACTIONr_scbond_it5.1954.5631209
X-RAY DIFFRACTIONr_scbond_other5.1954.5631210
X-RAY DIFFRACTIONr_scangle_it7.7696.5731734
X-RAY DIFFRACTIONr_scangle_other7.7676.5741735
X-RAY DIFFRACTIONr_lrange_it10.34374.2449476
X-RAY DIFFRACTIONr_lrange_other10.34274.2439476
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.061-2.1140.297840.2581578X-RAY DIFFRACTION98.285
2.114-2.1720.239840.221547X-RAY DIFFRACTION100
2.172-2.2350.265760.2031495X-RAY DIFFRACTION99.9364
2.235-2.3030.249980.1971449X-RAY DIFFRACTION100
2.303-2.3790.234700.1911432X-RAY DIFFRACTION100
2.379-2.4620.263830.1891380X-RAY DIFFRACTION100
2.462-2.5550.236780.1891338X-RAY DIFFRACTION100
2.555-2.6590.274600.1871288X-RAY DIFFRACTION100
2.659-2.7770.236700.2031226X-RAY DIFFRACTION100
2.777-2.9120.252820.1941181X-RAY DIFFRACTION100
2.912-3.0690.266660.2051121X-RAY DIFFRACTION100
3.069-3.2550.237590.2031067X-RAY DIFFRACTION100
3.255-3.4780.228650.1931001X-RAY DIFFRACTION100
3.478-3.7560.221530.177941X-RAY DIFFRACTION99.7992
3.756-4.1120.2530.164868X-RAY DIFFRACTION99.7833
4.112-4.5940.156410.145798X-RAY DIFFRACTION99.881
4.594-5.2990.208520.151706X-RAY DIFFRACTION100
5.299-6.4740.163290.18618X-RAY DIFFRACTION100
6.474-9.0910.231250.154488X-RAY DIFFRACTION99.8055
9.091-46.1620.203170.178291X-RAY DIFFRACTION96.8553

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