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- PDB-9klc: G9a in complex with the S-isomer of RK-131902 (racemic compound r... -

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Basic information

Entry
Database: PDB / ID: 9klc
TitleG9a in complex with the S-isomer of RK-131902 (racemic compound rac-10a)
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: 2.15 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)67,52914
Polymers65,2102
Non-polymers2,31912
Water3,945219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-10 kcal/mol
Surface area25500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.714, 78.066, 70.583
Angle α, β, γ (deg.)90.00, 91.30, 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-A1L58 / ~{N}-[(2~{S})-1-[[6-(1-methylpiperidin-4-yl)oxypyridin-3-yl]amino]-1-oxidanylidene-hexan-2-yl]-3-(pyridin-4-ylamino)benzamide


Mass: 516.635 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H36N6O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / 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: 2.4 Å3/Da / Density % sol: 48.65 %
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: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 31362 / % possible obs: 93.6 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.075 / Rrim(I) all: 0.145 / Net I/σ(I): 7.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.15-2.192.90.42210770.7410.9230.2830.510.95863.8
2.19-2.232.90.39811130.7960.9410.2650.480.94167.9
2.23-2.272.90.32312530.9230.980.2130.3891.04475.5
2.27-2.3230.39113610.8320.9530.2560.4690.97582.6
2.32-2.373.10.34415060.9070.9750.2220.4110.9989.1
2.37-2.423.20.39315770.8720.9650.2520.4681.00695
2.42-2.483.40.36416480.910.9760.2290.4311.02698.8
2.48-2.553.50.37316730.8970.9720.230.4391.07699.9
2.55-2.623.60.30216550.940.9840.1830.3541.06599.9
2.62-2.713.70.26516800.950.9870.160.311.14399.9
2.71-2.813.70.23416530.9540.9880.1410.2731.04499.9
2.81-2.923.70.19316810.9660.9910.1160.2251.107100
2.92-3.053.80.17516650.9690.9920.1050.2041.157100
3.05-3.213.80.14316850.9760.9940.0860.1671.051100
3.21-3.413.80.12716620.9770.9940.0760.1481.077100
3.41-3.683.80.11616760.980.9950.0690.1351.105100
3.68-4.053.80.11116890.9820.9950.0660.131.096100
4.05-4.633.80.09316850.9830.9960.0550.1081.111100
4.63-5.833.80.06716910.9930.9980.040.0781.074100
5.83-503.70.05917320.9950.9990.0360.0691.20199.5

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→38.79 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 29.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2534 1588 5.07 %
Rwork0.2074 --
obs0.2098 31332 93.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.15→38.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4326 0 138 219 4683
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_d0.917
X-RAY DIFFRACTIONf_dihedral_angle_d17.6251700
X-RAY DIFFRACTIONf_chiral_restr0.053650
X-RAY DIFFRACTIONf_plane_restr0.007804
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.220.35881060.26491833X-RAY DIFFRACTION65
2.22-2.30.28651080.26442209X-RAY DIFFRACTION76
2.3-2.390.31111380.25932538X-RAY DIFFRACTION89
2.39-2.50.33081550.25952817X-RAY DIFFRACTION98
2.5-2.630.27161670.24172869X-RAY DIFFRACTION100
2.63-2.80.29541580.23142898X-RAY DIFFRACTION100
2.8-3.010.29321280.23072927X-RAY DIFFRACTION100
3.01-3.320.26111480.22282890X-RAY DIFFRACTION100
3.32-3.80.24731690.18612876X-RAY DIFFRACTION100
3.8-4.780.21861520.16562932X-RAY DIFFRACTION100
4.78-38.790.20181590.18282955X-RAY DIFFRACTION100
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)
11.96920.7508-0.3510.3-0.21331.2158-0.0002-0.2207-0.2745-0.0825-0.01630.48930.109-0.18870.0410.21150.01720.01540.31220.07240.8698-14.6413-4.6532106.6217
20.64050.6439-0.12240.8142-0.81912.74880.24270.1512-0.05160.1459-0.1210.085-0.16880.4367-0.06290.17510.0257-00.3592-0.06370.623612.902810.9849105.8394
32.1060.4027-0.8622.9552-0.83553.69180.0591-0.391-0.13870.3502-0.0554-0.0860.05190.30920.01230.23790.0373-0.02130.4019-0.01790.470713.76613.5905116.7952
43.47761.91160.20392.0145-0.881.52160.1278-0.2158-0.3659-0.03390.12510.35910.0222-0.1387-0.18120.16810.0314-0.02470.24950.0230.5821-4.4109-3.8779113.6628
51.3339-1.39490.94661.8993-1.53981.8662-0.0838-0.42780.18970.71680.42190.4228-0.4918-0.1406-0.23190.28030.01290.09890.2447-0.07350.7872-5.777910.3232114.0799
61.5504-0.50880.51431.135-0.29290.46930.0701-0.26040.15790.25730.1430.3267-0.133-0.047-0.24650.2580.02290.07840.2779-0.06250.6319-3.14288.9807113.8556
74.39520.5847-0.52192.0450.62182.44160.428-0.3181-0.47620.3499-0.13920.3231-0.1021-0.0774-0.26850.25310.02220.04820.30570.05760.4709-3.6338-0.7621121.6812
82.0650.39661.12821.40810.4894.2955-0.1333-1.6750.70220.4944-0.0360.7294-0.5899-0.94710.17760.67010.07940.3970.9352-0.17841.1724-16.318310.7374132.2613
94.33511.3045-0.69551.4005-1.24673.7415-0.4387-0.2328-0.83970.16460.0893-0.60230.18260.80670.37980.24820.0915-0.06560.3384-0.0210.564823.2753-6.839392.9057
104.29150.2136-0.51760.67680.12240.54410.06440.42580.0877-0.07180.028-0.099-0.0680.0052-0.0820.20410.0218-0.00540.3017-0.00190.51096.56971.968485.4816
111.89430.185-0.5133.50862.00295.36130.11250.61710.9633-0.3732-0.0390.0988-0.45530.2155-0.08880.1651-0.02570.0010.45320.02690.675117.09710.549281.7105
122.4582-1.01-1.10871.34580.95482.26180.180.57720.0902-0.31430.0001-0.278-0.24650.286-0.18660.2423-0.02590.05010.5236-0.02630.655916.47755.492473.5507
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 918:954 )
2X-RAY DIFFRACTION2chain 'A' and (resseq 955:985 )
3X-RAY DIFFRACTION3chain 'A' and (resseq 986:1025 )
4X-RAY DIFFRACTION4chain 'A' and (resseq 1026:1054 )
5X-RAY DIFFRACTION5chain 'A' and (resseq 1055:1096 )
6X-RAY DIFFRACTION6chain 'A' and (resseq 1097:1134 )
7X-RAY DIFFRACTION7chain 'A' and (resseq 1135:1155 )
8X-RAY DIFFRACTION8chain 'A' and (resseq 1156:1189 )
9X-RAY DIFFRACTION9chain 'B' and (resseq 917:935 )
10X-RAY DIFFRACTION10chain 'B' and (resseq 936:1079 )
11X-RAY DIFFRACTION11chain 'B' and (resseq 1080:1118 )
12X-RAY DIFFRACTION12chain 'B' and (resseq 1119:1187 )

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