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- PDB-5arg: SMYD2 in complex with SGC probe BAY-598 -

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Basic information

Entry
Database: PDB / ID: 5arg
TitleSMYD2 in complex with SGC probe BAY-598
ComponentsN-LYSINE METHYLTRANSFERASE SMYD2
KeywordsTRANSFERASE / OXIDOREDUCTASE / METHYLTRANSFERASE / SET DOMAIN / SMALL MOLECULE INHIBITOR / SGC PROBE / DRUG TARGET
Function / homology
Function and homology information


lysine N-methyltransferase activity / [histone H3]-lysine4 N-trimethyltransferase / peptidyl-lysine monomethylation / peptidyl-lysine dimethylation / histone H3K36 methyltransferase activity / histone H3K4 trimethyltransferase activity / protein-lysine N-methyltransferase activity / histone H3 methyltransferase activity / regulation of DNA damage response, signal transduction by p53 class mediator / RNA polymerase II complex binding ...lysine N-methyltransferase activity / [histone H3]-lysine4 N-trimethyltransferase / peptidyl-lysine monomethylation / peptidyl-lysine dimethylation / histone H3K36 methyltransferase activity / histone H3K4 trimethyltransferase activity / protein-lysine N-methyltransferase activity / histone H3 methyltransferase activity / regulation of DNA damage response, signal transduction by p53 class mediator / RNA polymerase II complex binding / Transferases; Transferring one-carbon groups; Methyltransferases / regulation of signal transduction by p53 class mediator / Regulation of TP53 Activity through Methylation / PKMTs methylate histone lysines / p53 binding / heart development / negative regulation of cell population proliferation / negative regulation of transcription by RNA polymerase II / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
SMYD2, SET domain / MYND finger / Zinc finger, MYND-type / Zinc finger MYND-type signature. / Zinc finger MYND-type profile. / Beta-clip-like / SET domain / Tetratricopeptide repeat domain / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily ...SMYD2, SET domain / MYND finger / Zinc finger, MYND-type / Zinc finger MYND-type signature. / Zinc finger MYND-type profile. / Beta-clip-like / SET domain / Tetratricopeptide repeat domain / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily / SET domain / SET domain profile. / SET domain / Beta Complex / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Chem-H41 / S-ADENOSYLMETHIONINE / N-lysine methyltransferase SMYD2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsHillig, R.C. / Badock, V. / Barak, N. / Stellfeld, T. / Eggert, E. / ter Laak, A. / Weiske, J. / Christ, C.D. / Koehr, S. / Stoeckigt, D. ...Hillig, R.C. / Badock, V. / Barak, N. / Stellfeld, T. / Eggert, E. / ter Laak, A. / Weiske, J. / Christ, C.D. / Koehr, S. / Stoeckigt, D. / Mowat, J. / Mueller, T. / Fernandez-Montalvan, A.E. / Hartung, I.V. / Stresemann, C. / Brumby, T. / Weinmann, H.
CitationJournal: J.Med.Chem. / Year: 2016
Title: Discovery and Characterization of a Highly Potent and Selective Aminopyrazoline-Based in Vivo Probe (Bay-598) for the Protein Lysine Methyltransferase Smyd2.
Authors: Eggert, E. / Hillig, R.C. / Kohr, S. / Stockigt, D. / Weiske, J. / Barak, N. / Mowat, J. / Brumby, T. / Christ, C.D. / Ter Laak, A. / Lang, T. / Fernandez-Montalvan, A.E. / Badock, V. / ...Authors: Eggert, E. / Hillig, R.C. / Kohr, S. / Stockigt, D. / Weiske, J. / Barak, N. / Mowat, J. / Brumby, T. / Christ, C.D. / Ter Laak, A. / Lang, T. / Fernandez-Montalvan, A.E. / Badock, V. / Weinmann, H. / Hartung, I.V. / Barsyte-Lovejoy, D. / Szewczyk, M. / Kennedy, S. / Li, F. / Vedadi, M. / Brown, P.J. / Santhakumar, V. / Arrowsmith, C.H. / Stellfeld, T. / Stresemann, C.
History
DepositionSep 24, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2016Group: Database references
Revision 1.2Sep 13, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.3Apr 3, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: N-LYSINE METHYLTRANSFERASE SMYD2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8987
Polymers49,6861
Non-polymers1,2126
Water2,468137
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.343, 69.600, 131.115
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein N-LYSINE METHYLTRANSFERASE SMYD2 / HSKM-B / HISTONE METHYLTRANSFERASE SMYD2 / LYSINE N-METHYLTRANSFERASE 3C / SET AND MYND DOMAIN- ...HSKM-B / HISTONE METHYLTRANSFERASE SMYD2 / LYSINE N-METHYLTRANSFERASE 3C / SET AND MYND DOMAIN-CONTAINING PROTEIN 2


Mass: 49685.957 Da / Num. of mol.: 1 / Fragment: SET DOMAIN, UNP RESIDUES 2-433
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm)
References: UniProt: Q9NRG4, Transferases; Transferring one-carbon groups; Methyltransferases, histone-lysine N-methyltransferase

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Non-polymers , 5 types, 143 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-H41 / N-[1-(N'-CYANO-N-[3-(DIFLUOROMETHOXY)PHENYL]CARBAMIMIDOYL)-3-(3,4-DICHLOROPHENYL)-4,5-DIHYDRO-1H-PYRAZOL-4-YL]-N-ETHYL-2-HYDROXYACETAMIDE


Mass: 525.335 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H20Cl2F2N6O3
#4: 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
#5: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 2.45 Å3/Da / Density % sol: 49.9 % / Description: NONE
Crystal growTemperature: 277 K / pH: 7
Details: 22% PEG 3350, 100 MMOL HEPES PH 7.0. CRYO BUFFER CONTAINS AN ADDTIONAL 20% GLYCEROL AND 1 MMOL LIGAND. OTHER CRYSTALISATION REMARKS:4 MILLIMOLAR COFACTOR SAM ADDED AND MIXTURE INCUBATED FOR ...Details: 22% PEG 3350, 100 MMOL HEPES PH 7.0. CRYO BUFFER CONTAINS AN ADDTIONAL 20% GLYCEROL AND 1 MMOL LIGAND. OTHER CRYSTALISATION REMARKS:4 MILLIMOLAR COFACTOR SAM ADDED AND MIXTURE INCUBATED FOR 2 HOURS AT 4 DEGREE CELSIUS PRIOR TO CRYSTALLIZATION. CO- COMPLEX WITH BAY-598 FORMED BY SOAKING SMYD2-SAM CRYSTALS WITH 5 MILLIMOLAR LIGAND FOR 4 DAYS.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 1.99→48.61 Å / Num. obs: 33656 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 6.58 % / Biso Wilson estimate: 35.09 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 14.39
Reflection shellResolution: 1.99→2.11 Å / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 2.41 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3TG5

3tg5


Resolution: 1.99→47.72 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.925 / SU B: 13.313 / SU ML: 0.198 / Cross valid method: THROUGHOUT / ESU R: 0.215 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. B FACTORS WITH TLS ADDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.27318 1683 5 %RANDOM
Rwork0.23001 ---
obs0.2322 31972 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.525 Å2
Baniso -1Baniso -2Baniso -3
1--2.24 Å20 Å20 Å2
2--0.05 Å20 Å2
3---2.18 Å2
Refinement stepCycle: LAST / Resolution: 1.99→47.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3428 0 71 137 3636
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0193641
X-RAY DIFFRACTIONr_bond_other_d0.0020.023445
X-RAY DIFFRACTIONr_angle_refined_deg2.0331.9884919
X-RAY DIFFRACTIONr_angle_other_deg0.93.0037940
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6045441
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.54124170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.92915658
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4221523
X-RAY DIFFRACTIONr_chiral_restr0.0990.2522
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214060
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02826
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_it3.5331.4061725
X-RAY DIFFRACTIONr_mcbond_other3.5191.4061725
X-RAY DIFFRACTIONr_mcangle_it4.5763.142158
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.0151.8441916
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: 1.989→2.04 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 120 -
Rwork0.332 2294 -
obs--98.97 %
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)
10.9032-0.6868-0.15797.9542-4.05744.51220.40170.0466-0.03370.34780.03180.7051-0.72530.2019-0.43350.3683-0.00950.10580.0454-0.00760.0964-13.0837.735-19.721
21.1383-0.6555-0.22667.3592-3.2554.43770.0923-0.2470.15931.453-0.423-0.579-0.78080.81560.33070.48-0.1371-0.07160.19790.03240.0665-3.506-8.293-1.763
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A18 - 271
2X-RAY DIFFRACTION2A272 - 430

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