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- PDB-5yjo: Crystal structure of SmyD3 in complex with covalent inhibitor 4 -

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Basic information

Entry
Database: PDB / ID: 5yjo
TitleCrystal structure of SmyD3 in complex with covalent inhibitor 4
ComponentsHistone-lysine N-methyltransferase SMYD3
KeywordsTRANSFERASE/INHIBITOR / covalent inhibitor / methyltransferase / methyltransferase inhibitor / 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. ...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 / SET domain superfamily / 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-8W0 / S-ADENOSYLMETHIONINE / Histone-lysine N-methyltransferase SMYD3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.135 Å
AuthorsBaburajendran, N. / Anna E, J.
CitationJournal: Acs Med.Chem.Lett. / Year: 2019
Title: Discovery of Irreversible Inhibitors Targeting Histone Methyltransferase, SMYD3.
Authors: Huang, C. / Liew, S.S. / Lin, G.R. / Poulsen, A. / Ang, M.J.Y. / Chia, B.C.S. / Chew, S.Y. / Kwek, Z.P. / Wee, J.L.K. / Ong, E.H. / Retna, P. / Baburajendran, N. / Li, R. / Yu, W. / Koh- ...Authors: Huang, C. / Liew, S.S. / Lin, G.R. / Poulsen, A. / Ang, M.J.Y. / Chia, B.C.S. / Chew, S.Y. / Kwek, Z.P. / Wee, J.L.K. / Ong, E.H. / Retna, P. / Baburajendran, N. / Li, R. / Yu, W. / Koh-Stenta, X. / Ngo, A. / Manesh, S. / Fulwood, J. / Ke, Z. / Chung, H.H. / Sepramaniam, S. / Chew, X.H. / Dinie, N. / Lee, M.A. / Chew, Y.S. / Low, C.B. / Pendharkar, V. / Manoharan, V. / Vuddagiri, S. / Sangthongpitag, K. / Joy, J. / Matter, A. / Hill, J. / Keller, T.H. / Foo, K.
History
DepositionOct 11, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)49,6226
Polymers48,6021
Non-polymers1,0195
Water2,846158
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area19420 Å2
Unit cell
Length a, b, c (Å)61.428, 66.181, 107.648
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: 48602.457 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-8W0 / propyl (3~{S})-4-[[(6~{R})-6-(aminomethyl)-5,6,7,8-tetrahydroacridin-3-yl]carbonyl]-3-methyl-piperazine-1-carboxylate


Mass: 424.536 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H32N4O3
#4: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


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


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.25 Å3/Da / Density % sol: 45.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.2M Magnesium acetate, 17% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5419 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Feb 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5419 Å / Relative weight: 1
ReflectionResolution: 2.135→50 Å / Num. obs: 24856 / % possible obs: 99.3 % / Redundancy: 4.8 % / Biso Wilson estimate: 21.85 Å2 / Rmerge(I) obs: 0.165 / Χ2: 1.337 / Net I/σ(I): 11.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.14-2.184.40.3112031.413197.9
2.18-2.224.80.30112251.454198.4
2.22-2.264.80.2712121.459198.7
2.26-2.314.80.26712071.468198.8
2.31-2.364.80.25412051.489198.9
2.36-2.414.80.22912161.417199.1
2.41-2.474.80.22112391.375199.4
2.47-2.544.80.22312171.441199.3
2.54-2.614.80.20812141.403199.4
2.61-2.74.80.20812501.404199.3
2.7-2.794.80.19212371.384199.7
2.79-2.94.80.18812231.413199.8
2.9-3.044.80.17412571.325199.7
3.04-3.24.80.17212431.311199.8
3.2-3.44.80.15912561.211199.9
3.4-3.664.80.14712571.1611100
3.66-4.034.70.14512571.154199.6
4.03-4.614.60.14612721.118199.9
4.61-5.814.70.14812991.043199.8
5.81-504.40.12113671.328198.2

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.135→31.63 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.3
RfactorNum. reflection% reflection
Rfree0.2317 2027 8.17 %
Rwork0.1901 --
obs0.1935 24817 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 63.67 Å2 / Biso mean: 24.2532 Å2 / Biso min: 12.41 Å2
Refinement stepCycle: final / Resolution: 2.135→31.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3339 0 61 158 3558
Biso mean--21.54 22.6 -
Num. residues----423
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023467
X-RAY DIFFRACTIONf_angle_d0.5254681
X-RAY DIFFRACTIONf_chiral_restr0.038516
X-RAY DIFFRACTIONf_plane_restr0.003601
X-RAY DIFFRACTIONf_dihedral_angle_d6.2792154
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1354-2.18880.26471370.21611537167495
2.1888-2.24790.25971550.20841568172399
2.2479-2.31410.27341330.2021598173199
2.3141-2.38870.24091380.20341622176099
2.3887-2.47410.2511480.20861597174599
2.4741-2.57310.28011360.21291623175999
2.5731-2.69010.27711420.216216141756100
2.6901-2.83190.28491420.206616261768100
2.8319-3.00920.25881470.223116311778100
3.0092-3.24130.24671500.213116361786100
3.2413-3.56710.22471400.192116431783100
3.5671-4.08230.22441530.16516561809100
4.0823-5.13980.18231490.149816881837100
5.1398-31.63330.16741570.16591751190899

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