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- PDB-9klb: G9a in complex with RK-133232 (compound 16g) -

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Basic information

Entry
Database: PDB / ID: 9klb
TitleG9a in complex with RK-133232 (compound 16g)
ComponentsHistone-lysine N-methyltransferase EHMT2
KeywordsTRANSFERASE / histone lysine methyltransferase / inhibitor / protein-inhibitor complex
Function / homology
Function and homology information


regulation of protein modification process / phenotypic switching / neuron fate specification / [histone H3]-lysine9 N-methyltransferase / peptidyl-lysine dimethylation / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / histone H3K27 methyltransferase activity / synaptonemal complex assembly / negative regulation of autophagosome assembly ...regulation of protein modification process / phenotypic switching / neuron fate specification / [histone H3]-lysine9 N-methyltransferase / peptidyl-lysine dimethylation / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / histone H3K27 methyltransferase activity / synaptonemal complex assembly / negative regulation of autophagosome assembly / histone H3K56 methyltransferase activity / protein-lysine N-methyltransferase activity / oocyte development / C2H2 zinc finger domain binding / fertilization / cellular response to cocaine / organ growth / DNA methylation-dependent constitutive heterochromatin formation / negative regulation of gene expression via chromosomal CpG island methylation / spermatid development / Transcriptional Regulation by E2F6 / behavioral response to cocaine / regulation of DNA replication / RNA Polymerase I Transcription Initiation / Transcriptional Regulation by VENTX / long-term memory / response to fungicide / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / Transferases; Transferring one-carbon groups; Methyltransferases / epigenetic regulation of gene expression / cellular response to starvation / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / transcription corepressor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / promoter-specific chromatin 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 / 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
: / SINEFUNGIN / Histone-lysine N-methyltransferase EHMT2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsNiwa, H. / Shirai, F. / Sato, S. / Nishigaya, Y. / Ihara, K. / Shirouzu, M. / Umehara, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Eur.J.Med.Chem. / Year: 2025
Title: Discovery of potent substrate-type lysine methyltransferase G9a inhibitors for the treatment of sickle cell disease.
Authors: Nishigaya, Y. / Takase, S. / Sumiya, T. / Kikuzato, K. / Hiroyama, T. / Maemoto, Y. / Aoki, K. / Sato, T. / Niwa, H. / Sato, S. / Ihara, K. / Nakata, A. / Matsuoka, S. / Hashimoto, N. / ...Authors: Nishigaya, Y. / Takase, S. / Sumiya, T. / Kikuzato, K. / Hiroyama, T. / Maemoto, Y. / Aoki, K. / Sato, T. / Niwa, H. / Sato, S. / Ihara, K. / Nakata, A. / Matsuoka, S. / Hashimoto, N. / Namie, R. / Honma, T. / Umehara, T. / Shirouzu, M. / Koyama, H. / Nakamura, Y. / Yoshida, M. / Ito, A. / Shirai, F.
History
DepositionNov 14, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 21, 2025Provider: repository / Type: Initial release
Revision 1.1Jun 4, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)67,41114
Polymers65,2102
Non-polymers2,20112
Water4,197233
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-9 kcal/mol
Surface area24930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.703, 78.341, 70.754
Angle α, β, γ (deg.)90.00, 91.71, 90.00
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) / Production host: Escherichia coli (E. coli)
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-SFG / SINEFUNGIN / ADENOSYL-ORNITHINE


Mass: 381.387 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H23N7O5
#4: Chemical ChemComp-A1L57 / ~{N}-[(~{E},2~{S})-4-cyclopropyl-1-[(6-ethoxypyridin-3-yl)amino]-1-oxidanylidene-but-3-en-2-yl]-4-(pyridin-4-ylamino)benzamide


Mass: 457.524 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H27N5O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.41 Å3/Da / Density % sol: 48.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M Bis-Tris propane (pH~7.5), 0.2M Sodium Formate or Fluoride, 10% Ethylene Glycol, ~25% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 16, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.81→45.92 Å / Num. obs: 56455 / % possible obs: 100 % / Redundancy: 7 % / CC1/2: 0.983 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.048 / Rrim(I) all: 0.128 / Χ2: 1.05 / Net I/σ(I): 9.3
Reflection shellResolution: 1.81→1.85 Å / % possible obs: 100 % / Redundancy: 7.1 % / Rmerge(I) obs: 1.907 / Num. measured all: 23708 / Num. unique obs: 3330 / CC1/2: 0.799 / Rpim(I) all: 0.769 / Rrim(I) all: 2.058 / Χ2: 1.06 / Net I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.81→44.89 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 25.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2209 5594 5.05 %
Rwork0.1828 --
obs0.1847 56355 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.81→44.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4241 0 130 233 4604
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007
X-RAY DIFFRACTIONf_angle_d0.832
X-RAY DIFFRACTIONf_dihedral_angle_d14.0391658
X-RAY DIFFRACTIONf_chiral_restr0.053646
X-RAY DIFFRACTIONf_plane_restr0.007793
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.81-1.830.38041990.33393497X-RAY DIFFRACTION100
1.83-1.850.39082080.32363436X-RAY DIFFRACTION99
1.85-1.870.3341820.32353512X-RAY DIFFRACTION100
1.87-1.90.30181800.28273540X-RAY DIFFRACTION99
1.9-1.920.37711900.27853413X-RAY DIFFRACTION99
1.92-1.950.27381910.27113543X-RAY DIFFRACTION100
1.95-1.980.33941900.25773482X-RAY DIFFRACTION100
1.98-2.010.22981350.23393530X-RAY DIFFRACTION100
2.01-2.040.25391990.23073475X-RAY DIFFRACTION100
2.04-2.070.27241960.21853516X-RAY DIFFRACTION100
2.07-2.110.29881970.20483489X-RAY DIFFRACTION100
2.11-2.150.24991640.21833520X-RAY DIFFRACTION100
2.15-2.190.24021890.21083532X-RAY DIFFRACTION100
2.19-2.230.26081880.2043416X-RAY DIFFRACTION100
2.23-2.280.27281770.20743577X-RAY DIFFRACTION100
2.28-2.330.2021850.18663491X-RAY DIFFRACTION100
2.33-2.390.22242040.18163474X-RAY DIFFRACTION100
2.39-2.460.22661880.18733537X-RAY DIFFRACTION100
2.46-2.530.25192150.19393501X-RAY DIFFRACTION100
2.53-2.610.21311880.18463523X-RAY DIFFRACTION100
2.61-2.70.24452020.18473513X-RAY DIFFRACTION100
2.7-2.810.21411600.18553469X-RAY DIFFRACTION100
2.81-2.940.25361560.18493578X-RAY DIFFRACTION100
2.94-3.090.22391540.18853527X-RAY DIFFRACTION100
3.09-3.290.19631880.17183501X-RAY DIFFRACTION100
3.29-3.540.19352090.16473536X-RAY DIFFRACTION100
3.54-3.90.21062040.14663438X-RAY DIFFRACTION100
3.9-4.460.17991950.13273498X-RAY DIFFRACTION100
4.46-5.620.17021690.14453536X-RAY DIFFRACTION100
5.62-44.890.17291920.16883480X-RAY DIFFRACTION99
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)
10.2945-0.7917-0.48012.83050.45411.9138-0.1186-0.1834-0.07190.10580.12-0.46380.07090.247-0.04670.2427-0.0460.01010.1938-0.0690.396711.3058-3.150334.8479
21.7109-1.195-0.96651.32280.06242.0909-0.04250.69790.259-0.07730.05690.0643-0.0567-0.52990.00360.2799-0.00290.02990.370.04940.2392-16.464112.308835.0594
31.0665-0.5342-0.16091.48110.6190.92120.0540.611-0.0807-0.2505-0.10960.04170.0216-0.39850.03850.2841-0.05180.01140.401-0.02820.1969-9.14530.821325.14
42.0059-0.6524-0.23640.55230.61941.32310.07580.34470.5922-0.37560.1464-0.6249-0.516-0.1736-0.11040.3457-0.00390.09880.24150.05280.41653.489616.301428.467
53.4507-0.9264-0.642.30780.18061.78410.04950.59930.0812-0.35380.0035-0.3028-0.026-0.158-0.09450.2417-0.04470.03960.23540.01440.196-0.04216.843224.6091
60.34450.01750.75160.75860.40022.1110.13361.52080.3867-0.4931-0.1011-0.1488-0.0278-0.1011-0.15640.5198-0.02030.28390.7250.08120.5612.30799.845610.4667
71.154-0.47560.32631.72621.03572.2277-0.18960.5823-0.6084-0.30750.16610.25190.1912-0.58860.03040.2392-0.0499-0.01550.366-0.04480.3357-27.3013-5.561748.6276
84.46660.7034-1.10374.0804-1.43752.9895-0.11660.82030.3943-0.15510.34220.3792-0.1274-0.4651-0.24610.1910.0051-0.02020.27270.03090.2329-28.11564.77349.8558
95.2843-1.74640.30983.4817-1.35562.2251-0.1203-0.2230.36110.18270.129-0.2842-0.28130.1447-0.01350.2582-0.05640.00360.191-0.0230.23493.065610.047350.6656
104.0622-0.0751-0.89723.7024-0.64962.9271-0.1368-0.924-0.39660.58750.1683-0.06660.0558-0.10010.01760.24520.0274-0.02560.41320.06760.23880.91391.587359.5233
114.26360.8879-0.58370.9343-0.14571.3738-0.0337-0.133-0.57630.0216-0.0083-0.0450.119-0.0330.04590.19610.00150.00720.18070.04120.257-18.081-3.013357.3649
123.22790.7643-0.96041.54640.02372.97010.1957-0.20430.74710.23120.07020.2017-0.5812-0.1437-0.17210.28110.02650.0360.20790.01430.3272-21.573513.540458.2906
134.09880.4663-0.96511.8357-0.44312.38730.0888-0.5868-0.1360.2351-0.0366-0.0414-0.0314-0.0417-0.04930.18290.0052-0.01880.20330.02170.1535-12.7564.115561.2692
140.8428-0.36621.18922.8166-1.72852.2412-0.0302-0.65460.30630.62660.47920.7718-0.5022-0.6465-0.22070.35080.06140.14390.5189-0.02730.3718-28.300610.142571.7747
150.7502-0.5585-0.0610.8532-0.48340.6407-0.3636-0.95560.68980.62030.33860.3661-0.2656-0.0988-0.78780.45610.04070.18570.8289-0.08180.4933-30.538111.820583.5218
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 918 through 954 )
2X-RAY DIFFRACTION2chain 'A' and (resid 955 through 985 )
3X-RAY DIFFRACTION3chain 'A' and (resid 986 through 1062 )
4X-RAY DIFFRACTION4chain 'A' and (resid 1063 through 1096 )
5X-RAY DIFFRACTION5chain 'A' and (resid 1097 through 1155 )
6X-RAY DIFFRACTION6chain 'A' and (resid 1156 through 1184 )
7X-RAY DIFFRACTION7chain 'B' and (resid 917 through 938 )
8X-RAY DIFFRACTION8chain 'B' and (resid 939 through 958 )
9X-RAY DIFFRACTION9chain 'B' and (resid 959 through 985 )
10X-RAY DIFFRACTION10chain 'B' and (resid 986 through 1027 )
11X-RAY DIFFRACTION11chain 'B' and (resid 1028 through 1069 )
12X-RAY DIFFRACTION12chain 'B' and (resid 1070 through 1118 )
13X-RAY DIFFRACTION13chain 'B' and (resid 1119 through 1155 )
14X-RAY DIFFRACTION14chain 'B' and (resid 1156 through 1175 )
15X-RAY DIFFRACTION15chain 'B' and (resid 1176 through 1191 )

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