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- PDB-5ccm: Crystal structure of SMYD3 with SAM and EPZ030456 -

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Basic information

Entry
Database: PDB / ID: 5ccm
TitleCrystal structure of SMYD3 with SAM and EPZ030456
ComponentsHistone-lysine N-methyltransferase SMYD3
KeywordsTRANSFERASE/TRANSFERASE Inhibitor / protein-inhibitor complex / methyltransferase / epigenetics / drug discovery / TRANSFERASE-TRANSFERASE Inhibitor complex
Function / homology
Function and homology information


histone H3K36 dimethyltransferase activity / histone H4 methyltransferase activity / [histone H3]-lysine4 N-trimethyltransferase / myotube cell development / histone H3K4 trimethyltransferase activity / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / RNA polymerase II complex binding / cellular response to dexamethasone stimulus / establishment of protein localization / PKMTs methylate histone lysines ...histone H3K36 dimethyltransferase activity / histone H4 methyltransferase activity / [histone H3]-lysine4 N-trimethyltransferase / myotube cell development / histone H3K4 trimethyltransferase activity / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / RNA polymerase II complex binding / cellular response to dexamethasone stimulus / establishment of protein localization / PKMTs methylate histone lysines / nucleosome assembly / positive regulation of peptidyl-serine phosphorylation / methylation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / metal ion binding / cytosol
Similarity search - Function
Annexin V; domain 1 - #160 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #970 / Helix Hairpins - #2220 / Histone-lysine N-methyltransferase Smyd3 / SMYD3, SET domain / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / MYND finger / Zinc finger, MYND-type / Zinc finger MYND-type signature. / Zinc finger MYND-type profile. ...Annexin V; domain 1 - #160 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #970 / Helix Hairpins - #2220 / Histone-lysine N-methyltransferase Smyd3 / SMYD3, SET domain / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / MYND finger / Zinc finger, MYND-type / Zinc finger MYND-type signature. / Zinc finger MYND-type profile. / Annexin V; domain 1 / Beta-clip-like / SET domain / Tetratricopeptide repeat domain / Helix Hairpins / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily / SET domain / SET domain profile. / SET domain / Beta Complex / Helix non-globular / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Special / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Chem-4ZX / S-ADENOSYLMETHIONINE / Histone-lysine N-methyltransferase SMYD3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsBoriack-Sjodin, P.A.
CitationJournal: Acs Med.Chem.Lett. / Year: 2016
Title: Novel Oxindole Sulfonamides and Sulfamides: EPZ031686, the First Orally Bioavailable Small Molecule SMYD3 Inhibitor.
Authors: Mitchell, L.H. / Boriack-Sjodin, P.A. / Smith, S. / Thomenius, M. / Rioux, N. / Munchhof, M. / Mills, J.E. / Klaus, C. / Totman, J. / Riera, T.V. / Raimondi, A. / Jacques, S.L. / West, K. / ...Authors: Mitchell, L.H. / Boriack-Sjodin, P.A. / Smith, S. / Thomenius, M. / Rioux, N. / Munchhof, M. / Mills, J.E. / Klaus, C. / Totman, J. / Riera, T.V. / Raimondi, A. / Jacques, S.L. / West, K. / Foley, M. / Waters, N.J. / Kuntz, K.W. / Wigle, T.J. / Scott, M.P. / Copeland, R.A. / Smith, J.J. / Chesworth, R.
History
DepositionJul 2, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2016Group: Database references
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone-lysine N-methyltransferase SMYD3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3176
Polymers49,1501
Non-polymers1,1675
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.484, 65.852, 107.358
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 Histone-lysine N-methyltransferase SMYD3 / SET and MYND domain-containing protein 3 / Zinc finger MYND domain-containing protein 1


Mass: 49150.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMYD3, ZMYND1, ZNFN3A1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9H7B4, histone-lysine N-methyltransferase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#4: Chemical ChemComp-4ZX / 6-chloranyl-2-oxidanylidene-N-[(1S,5R)-8-[4-[(phenylmethyl)amino]piperidin-1-yl]sulfonyl-8-azabicyclo[3.2.1]octan-3-yl]-1,3-dihydroindole-5-carboxamide


Mass: 572.119 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H34ClN5O4S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.2 Å3/Da / Density % sol: 44.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.10 M Magnesium formate, 0.1M Tris 8.0, 14% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300HS / Detector: CCD / Date: Feb 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 19568 / % possible obs: 98.4 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.146 / Rpim(I) all: 0.069 / Rrim(I) all: 0.162 / Χ2: 1.407 / Net I/av σ(I): 13.212 / Net I/σ(I): 6 / Num. measured all: 98933
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.382.50.4817500.8160.2880.5660.83190.2
2.38-2.483.50.45418760.8680.2470.5210.85197
2.48-2.594.50.46219410.8990.2290.5180.89299.3
2.59-2.735.40.42119480.9480.1960.4660.9299.5
2.73-2.95.70.3319690.9590.150.3631.03699.5
2.9-3.125.90.2319570.9780.1040.2531.23399.4
3.12-3.445.80.15719670.9870.0710.1731.48599.5
3.44-3.935.80.1120030.9920.050.1211.841100
3.93-4.955.70.07820140.9950.0360.0862.03799.8
4.95-505.40.06621430.9960.0310.0742.04999.5

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Processing

Software
NameVersionClassification
HKL-2000data reduction
SCALEPACKdata scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
RefinementResolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.908 / SU B: 8.939 / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.432 / ESU R Free: 0.263 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2551 948 4.9 %RANDOM
Rwork0.2005 ---
obs0.2033 18577 98.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 104.03 Å2 / Biso mean: 34.062 Å2 / Biso min: 15.82 Å2
Baniso -1Baniso -2Baniso -3
1-6.2 Å2-0 Å20 Å2
2---1.46 Å2-0 Å2
3----4.74 Å2
Refinement stepCycle: final / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3384 0 69 123 3576
Biso mean--31.69 30.21 -
Num. residues----423
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0193540
X-RAY DIFFRACTIONr_bond_other_d0.0010.023419
X-RAY DIFFRACTIONr_angle_refined_deg1.2112.0014769
X-RAY DIFFRACTIONr_angle_other_deg0.7723.0037883
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7815424
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.53824.074162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.37615658
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9381527
X-RAY DIFFRACTIONr_chiral_restr0.0660.2519
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213903
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02794
X-RAY DIFFRACTIONr_mcbond_it1.4423.2791696
X-RAY DIFFRACTIONr_mcbond_other1.4423.2791696
X-RAY DIFFRACTIONr_mcangle_it2.4544.912117
LS refinement shellResolution: 2.292→2.351 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 50 -
Rwork0.297 1182 -
all-1232 -
obs--86.82 %

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