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- PDB-5ccl: Crystal structure of SMYD3 with SAM and oxindole compound -

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Basic information

Entry
Database: PDB / ID: 5ccl
TitleCrystal structure of SMYD3 with SAM and oxindole compound
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 / metal ion binding / nucleus / 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-4ZW / S-ADENOSYLMETHIONINE / Histone-lysine N-methyltransferase SMYD3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.5 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)50,8498
Polymers49,6741
Non-polymers1,1757
Water8,089449
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.594, 65.232, 105.966
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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 Histone-lysine N-methyltransferase SMYD3 / SET and MYND domain-containing protein 3 / Zinc finger MYND domain-containing protein 1


Mass: 49673.633 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

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Non-polymers , 5 types, 456 molecules

#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 / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#4: Chemical ChemComp-4ZW / 2-oxidanylidene-N-piperidin-4-yl-1,3-dihydroindole-5-carboxamide


Mass: 259.304 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H17N3O2
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 449 / 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: 2.07 Å3/Da / Density % sol: 40.72 %
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. Crystals of SMYD3-SAM were produced and compound was soaked into the pre-formed crystals

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97907 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97907 Å / Relative weight: 1
ReflectionResolution: 1.5→55.55 Å / Num. obs: 62186 / % possible obs: 94.4 % / Redundancy: 5 % / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.033 / Rrim(I) all: 0.077 / Χ2: 1.05 / Net I/av σ(I): 17.437 / Net I/σ(I): 14.6 / Num. measured all: 312049
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.5-1.554.90.22663990.9480.1110.2530.98398.6
1.55-1.624.90.17363960.9690.0850.1931.04698.3
1.62-1.694.90.14563470.9770.0710.1621.08697.8
1.69-1.7850.11163680.9860.0540.1241.12197.2
1.78-1.8950.09363050.9890.0450.1031.0496.6
1.89-2.045.10.07562760.9930.0360.0841.02195.9
2.04-2.245.10.06562310.9940.0310.0731.09594.8
2.24-2.565.20.07161790.9910.0340.0790.9693.5
2.56-3.235.20.08261180.9890.0390.0911.12691.7
3.23-5050.04855670.9960.0230.0531.01880.2

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Processing

Software
NameVersionClassification
HKL-2000data reduction
SCALEPACKdata scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
RefinementResolution: 1.5→55.55 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.113 / SU ML: 0.037 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.078 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1643 3081 5 %RANDOM
Rwork0.1134 ---
obs0.1159 59053 94.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 120.69 Å2 / Biso mean: 22.997 Å2 / Biso min: 8.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.61 Å20 Å2-0 Å2
2---0.56 Å20 Å2
3----0.05 Å2
Refinement stepCycle: final / Resolution: 1.5→55.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3400 0 73 449 3922
Biso mean--23.46 30.48 -
Num. residues----425
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0193816
X-RAY DIFFRACTIONr_bond_other_d0.0010.023680
X-RAY DIFFRACTIONr_angle_refined_deg1.7322.0015146
X-RAY DIFFRACTIONr_angle_other_deg0.9133.0018506
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.115468
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.61423.873173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.19615719
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8651532
X-RAY DIFFRACTIONr_chiral_restr0.1240.2555
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214280
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02859
X-RAY DIFFRACTIONr_mcbond_it3.3671.951839
X-RAY DIFFRACTIONr_mcbond_other3.3671.951839
X-RAY DIFFRACTIONr_mcangle_it3.7872.9252318
X-RAY DIFFRACTIONr_rigid_bond_restr3.32337496
X-RAY DIFFRACTIONr_sphericity_free23.573590
X-RAY DIFFRACTIONr_sphericity_bonded11.64657760
LS refinement shellResolution: 1.499→1.538 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.183 215 -
Rwork0.115 4464 -
all-4679 -
obs--97.28 %

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