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- PDB-7buc: Crystal structure of EHMT2 SET domain in complex with compound 13 -

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Basic information

Entry
Database: PDB / ID: 7buc
TitleCrystal structure of EHMT2 SET domain in complex with compound 13
ComponentsHistone-lysine N-methyltransferase EHMT2
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / PROTEIN-SMALL MOLECULE INHIBITOR COMPLEX / TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX
Function / homology
Function and homology information


regulation of protein modification process / histone H3K56 methyltransferase activity / phenotypic switching / neuron fate specification / [histone H3]-lysine9 N-methyltransferase / peptidyl-lysine dimethylation / histone H3K27 methyltransferase activity / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / synaptonemal complex assembly ...regulation of protein modification process / histone H3K56 methyltransferase activity / phenotypic switching / neuron fate specification / [histone H3]-lysine9 N-methyltransferase / peptidyl-lysine dimethylation / histone H3K27 methyltransferase activity / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / synaptonemal complex assembly / negative regulation of autophagosome assembly / oocyte development / protein-lysine N-methyltransferase activity / C2H2 zinc finger domain binding / fertilization / DNA methylation-dependent constitutive heterochromatin formation / cellular response to cocaine / organ growth / negative regulation of gene expression via chromosomal CpG island methylation / regulation of DNA replication / Transcriptional Regulation by E2F6 / RNA Polymerase I Transcription Initiation / behavioral response to cocaine / Transcriptional Regulation by VENTX / spermatid development / long-term memory / response to fungicide / cellular response to starvation / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / transcription corepressor binding / Transferases; Transferring one-carbon groups; Methyltransferases / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / promoter-specific chromatin binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Regulation of TP53 Activity through Methylation / PKMTs methylate histone lysines / p53 binding / cellular response to xenobiotic stimulus / Senescence-Associated Secretory Phenotype (SASP) / response to ethanol / nuclear speck / chromatin / negative regulation of transcription by RNA polymerase II / enzyme binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
Histone-lysine N-methyltransferase EHMT2 / Histone-lysine N-methyltransferase EHMT1/EHMT2 / : / Histone-lysine N-methyltransferase EHMT1/EHMT2, Cys-rich region / Pre-SET motif / Pre-SET domain / Pre-SET domain profile. / N-terminal to some SET domains / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain ...Histone-lysine N-methyltransferase EHMT2 / Histone-lysine N-methyltransferase EHMT1/EHMT2 / : / Histone-lysine N-methyltransferase EHMT1/EHMT2, Cys-rich region / Pre-SET motif / Pre-SET domain / Pre-SET domain profile. / N-terminal to some SET domains / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain superfamily / SET domain profile. / SET domain / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily
Similarity search - Domain/homology
Chem-F80 / S-ADENOSYLMETHIONINE / Histone-lysine N-methyltransferase EHMT2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSuzuki, M. / Mizuno, M. / Katayama, K.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2020
Title: Discovery of novel histone lysine methyltransferase G9a/GLP (EHMT2/1) inhibitors: Design, synthesis, and structure-activity relationships of 2,4-diamino-6-methylpyrimidines.
Authors: Katayama, K. / Ishii, K. / Tsuda, E. / Yotsumoto, K. / Hiramoto, K. / Suzuki, M. / Yasumatsu, I. / Igarashi, W. / Torihata, M. / Ishiyama, T. / Katagiri, T.
History
DepositionApr 6, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 11, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 16, 2021Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.pdbx_collection_date
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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: Histone-lysine N-methyltransferase EHMT2
B: Histone-lysine N-methyltransferase EHMT2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,20914
Polymers65,2102
Non-polymers1,99912
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA v1.52 [20/10/2014] REMARK 350 TOTAL BURIED SURFACE AREA: 2470 ANGSTROM**2 REMARK 350 SURFACE AREA ...Evidence: REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA v1.52 [20/10/2014] REMARK 350 TOTAL BURIED SURFACE AREA: 2470 ANGSTROM**2 REMARK 350 SURFACE AREA FOR THE COMPLEX: 25180 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -86 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-7 kcal/mol
Surface area24280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.500, 78.430, 72.990
Angle α, β, γ (deg.)90.000, 91.620, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Histone-lysine N-methyltransferase EHMT2 / Euchromatic histone-lysine N-methyltransferase 2 / HLA-B-associated transcript 8 / Histone H3-K9 ...Euchromatic histone-lysine N-methyltransferase 2 / HLA-B-associated transcript 8 / Histone H3-K9 methyltransferase 3 / H3-K9-HMTase 3 / Lysine N-methyltransferase 1C / Protein G9a


Mass: 32604.924 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EHMT2, BAT8, C6orf30, G9A, KMT1C, NG36 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q96KQ7, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#4: Chemical ChemComp-F80 / N2-[4-methoxy-3-(2,3,4,7-tetrahydro-1H-azepin-5-yl)phenyl]-N4,6-dimethyl-pyrimidine-2,4-diamine


Mass: 339.435 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H25N5O / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.48 Å3/Da / Density % sol: 50.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M magnesium acetate, 20% polyethyleneglycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→78.43 Å / Num. obs: 19580 / % possible obs: 99.3 % / Redundancy: 3.1 % / CC1/2: 0.992 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.078 / Rrim(I) all: 0.141 / Net I/σ(I): 6.8 / Num. measured all: 60135 / Scaling rejects: 21
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.6-2.723.20.678748423670.6480.4480.8161.799.5
9.01-78.432.90.04514604990.9910.0320.05618.799

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimless0.7.2data scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VSE

5vse


Resolution: 2.6→25 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.903 / SU B: 17.319 / SU ML: 0.327 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.042 / ESU R Free: 0.335 / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2618 913 4.7 %RANDOM
Rwork0.2095 ---
obs0.2118 18627 99.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 111.49 Å2 / Biso mean: 48.87 Å2 / Biso min: 24.32 Å2
Baniso -1Baniso -2Baniso -3
1--4.63 Å20 Å22.27 Å2
2--0.94 Å2-0 Å2
3---3.55 Å2
Refinement stepCycle: final / Resolution: 2.6→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4212 0 112 24 4348
Biso mean--48.98 33.62 -
Num. residues----542
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0124417
X-RAY DIFFRACTIONr_angle_refined_deg0.7771.6516000
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8245539
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.74421.888249
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.97315669
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7421534
X-RAY DIFFRACTIONr_chiral_restr0.0570.2585
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023492
LS refinement shellResolution: 2.6→2.69 Å / Rfactor Rfree error: 0 / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.352 106 -
Rwork0.37 1779 -
all-1885 -
obs--99.42 %

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