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- PDB-7xud: Structure of G9a in complex with compound 26a -

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Basic information

Entry
Database: PDB / ID: 7xud
TitleStructure of G9a in complex with compound 26a
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
Chem-I6Z / SINEFUNGIN / Histone-lysine N-methyltransferase EHMT2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsNiwa, H. / Shirai, F. / Sato, S. / Nishigaya, Y. / Umehara, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: J.Med.Chem. / Year: 2023
Title: Discovery of Novel Substrate-Competitive Lysine Methyltransferase G9a Inhibitors as Anticancer Agents.
Authors: Nishigaya, Y. / Takase, S. / Sumiya, T. / Kikuzato, K. / Sato, T. / Niwa, H. / Sato, S. / Nakata, A. / Sonoda, T. / Hashimoto, N. / Namie, R. / Honma, T. / Umehara, T. / Shirouzu, M. / ...Authors: Nishigaya, Y. / Takase, S. / Sumiya, T. / Kikuzato, K. / Sato, T. / Niwa, H. / Sato, S. / Nakata, A. / Sonoda, T. / Hashimoto, N. / Namie, R. / Honma, T. / Umehara, T. / Shirouzu, M. / Koyama, H. / Yoshida, M. / Ito, A. / Shirai, F.
History
DepositionMay 18, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)67,68319
Polymers65,2102
Non-polymers2,47317
Water10,395577
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-3 kcal/mol
Surface area25520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.596, 77.451, 66.797
Angle α, β, γ (deg.)90.000, 90.503, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 2 molecules AB

#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) / Description: Cell-free synthesis / Gene: EHMT2, BAT8, C6orf30, G9A, KMT1C, NG36 / Production host: Escherichia coli (E. coli)
References: UniProt: Q96KQ7, Transferases; Transferring one-carbon groups; Methyltransferases

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Non-polymers , 7 types, 594 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-SFG / SINEFUNGIN / ADENOSYL-ORNITHINE


Mass: 381.387 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H23N7O5
#5: Chemical ChemComp-I6Z / ~{N}-[(2~{S})-4-cyclopropyl-1-oxidanylidene-1-phenylazanyl-butan-2-yl]-3,6,6-trimethyl-4-oxidanylidene-5,7-dihydro-1~{H}-indole-2-carboxamide


Mass: 421.532 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H31N3O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 577 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.24 Å3/Da / Density % sol: 45.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M Bis-Tris propane (pH7.5), 0.2M Sodium Fluoride, 10% Ethylene Glycol, 22% 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: RAYONIX MX-225 / Detector: CCD / Date: Nov 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. obs: 101819 / % possible obs: 99.9 % / Redundancy: 3.8 % / Biso Wilson estimate: 14.81 Å2 / Rpim(I) all: 0.038 / Rrim(I) all: 0.076 / Rsym value: 0.065 / Net I/σ(I): 17.1
Reflection shellResolution: 1.45→1.48 Å / Mean I/σ(I) obs: 1.9 / Num. unique obs: 5025 / CC1/2: 0.724 / Rpim(I) all: 0.409 / Rrim(I) all: 0.778 / Rsym value: 0.659

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158+SVNrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7XUA

7xua


Resolution: 1.45→28.65 Å / SU ML: 0.1385 / Cross valid method: FREE R-VALUE / σ(F): 1.12 / Phase error: 18.1244
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1769 5090 5.01 %
Rwork0.1607 172209 -
obs0.1615 101753 90.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.43 Å2
Refinement stepCycle: LAST / Resolution: 1.45→28.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4296 0 145 577 5018
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00614643
X-RAY DIFFRACTIONf_angle_d0.86296306
X-RAY DIFFRACTIONf_chiral_restr0.0774666
X-RAY DIFFRACTIONf_plane_restr0.0073824
X-RAY DIFFRACTIONf_dihedral_angle_d15.07071750
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.470.29962880.29315058X-RAY DIFFRACTION80.65
1.47-1.480.28242810.27155527X-RAY DIFFRACTION85.29
1.48-1.50.28382750.25535467X-RAY DIFFRACTION86.01
1.5-1.520.26913010.24055509X-RAY DIFFRACTION86.2
1.52-1.540.2262690.22825514X-RAY DIFFRACTION86.91
1.54-1.560.2152790.2125572X-RAY DIFFRACTION87.15
1.56-1.580.23112920.21415526X-RAY DIFFRACTION87.08
1.58-1.610.21133090.2015565X-RAY DIFFRACTION87.54
1.61-1.630.21633330.19285565X-RAY DIFFRACTION87.82
1.63-1.660.19883050.18545598X-RAY DIFFRACTION88
1.66-1.690.20712770.18585622X-RAY DIFFRACTION88.32
1.69-1.720.19492850.17615736X-RAY DIFFRACTION88.65
1.72-1.750.20282450.16435643X-RAY DIFFRACTION88.98
1.75-1.790.17622830.16435687X-RAY DIFFRACTION89.25
1.79-1.830.19353490.15835699X-RAY DIFFRACTION89.63
1.83-1.870.16573000.1575697X-RAY DIFFRACTION89.8
1.87-1.920.16212850.15345782X-RAY DIFFRACTION90.16
1.92-1.970.17343310.15115775X-RAY DIFFRACTION90.74
1.97-2.030.18592860.15025827X-RAY DIFFRACTION91.06
2.03-2.090.17133520.14995805X-RAY DIFFRACTION91.19
2.09-2.170.17342930.14625795X-RAY DIFFRACTION91.88
2.17-2.250.16353200.14845885X-RAY DIFFRACTION92.17
2.25-2.350.16782970.15465922X-RAY DIFFRACTION92.65
2.35-2.480.18733680.1615878X-RAY DIFFRACTION93.35
2.48-2.630.19453190.16225939X-RAY DIFFRACTION93.77
2.63-2.840.19692860.16436095X-RAY DIFFRACTION94.38
2.84-3.120.16892660.15996097X-RAY DIFFRACTION95.07
3.12-3.570.15393600.14616056X-RAY DIFFRACTION95.96
3.57-4.50.12383400.13066174X-RAY DIFFRACTION97.11
4.5-28.650.18163180.15346194X-RAY DIFFRACTION96.96
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)
17.129262262423.912624696983.232806200834.811911714082.38984704054.29721080728-0.00649356740070.04125438744580.02251289284840.06295603554680.0884394188289-0.320810675826-0.01741089717710.272047143783-0.09740844057390.1313883414170.0362400726096-0.006872567335650.0824163400727-0.01273239925790.1401214481738.574333020816.4647541043100.477479652
21.246526459022.487874976681.536487333774.617170056032.770125531251.83993014043-0.02115227547060.106803383731-0.1537635266660.05000963629970.257195317903-0.4068147379540.1218449043140.317094478398-0.2425525240820.1394783449240.0432445776395-0.008691611393390.148159582296-0.03444793633080.18147123101442.7320517679.67341318099101.980504443
31.221413858750.6695727103970.648413702131.514711722830.2421606518461.67398883452-0.0187390998704-0.380652237254-0.03452924970180.0960952232438-0.002326832629490.151723377642-0.0344863817131-0.3659055847720.02677827823130.1495170435070.009182874925930.008273614846020.1761907425620.008956440245880.091024854729411.9278608298-2.17939490059100.512403385
42.871412894610.6294437889070.6064918961432.22982545431-0.882555918042.22346629881-0.0138247404328-0.6321088495090.3373778320310.646441366707-0.1434286319520.1442302401770.0217223996803-0.4502381183560.1206815097570.3217881167420.03810804350910.07411265154190.385703851001-0.06952962705560.19784255750910.654581266.40120043785113.943880764
54.07475790123-0.1334569634240.5823647123453.970953868730.3457410583013.96181038226-0.146008854998-0.3097528977680.04975170014680.2457751848910.02964549210830.118063274268-0.372395039916-0.3861104104250.1255938109740.1517801212650.03950693958530.02194569758520.204079203237-0.02392626477170.1153099960749.980748368285.20647451843103.180681198
61.493167808790.7954604748360.2206690460481.050948176240.3268599036961.034725144180.0510864489448-0.1614572124590.04507702476090.106430219168-0.0359914789698-0.04938594573650.0546317002547-0.0442320961047-0.004613520399290.1362314337120.027613894938-0.01281619947760.0858199762931-0.01843791668770.093582171191231.40658671577.78381050258108.290279094
71.930312724080.01873792930471.207406539714.528170119580.2177926725783.551080100430.186919046171-0.272074089175-0.3554058325880.472567441827-0.0132712342016-0.1233976321960.514320327140.0846921849808-0.04005941732290.2327926079720.0316016370049-0.04518877271280.1027670965640.009101384230440.1754594113232.7815903365-6.65011105155107.268502986
82.261227776251.223167994841.339949020151.35757568121.00541086631.295793286590.0649123373598-0.2624795169190.03833690842910.173168516735-0.06592204633430.02902877748220.10154185092-0.180450821589-0.00220518133740.1598177345790.02307573808860.008501338047320.101083783895-0.003909383571220.084549338402725.40014540542.18062579683110.54942964
92.451402097370.919856112442-0.1837846788030.816217317325-0.9366151424622.956152679780.0483836533145-0.3548924103070.3796738523940.297528478245-0.09998043331350.0706339107638-0.216857107366-0.177584138930.02806257763580.1594199643070.0205551145746-0.01567436282180.162315812656-0.06102396491380.13424891344630.662901738212.4478278565117.858387718
103.515983669980.7042310864980.4490593265611.60167361119-0.3313041290165.392811889680.208440732823-0.715472545121-0.4047395521810.143516704933-0.136348231615-0.06095124884170.4347799684760.0132664095233-0.056591168820.3123984700280.00644625619424-0.06647000200540.2715740546090.05619157880010.20138103585341.0850097853-0.548875850361126.636037475
115.44285765412-0.1239068920370.7000261429483.146729121990.2588081293133.7892303538-0.159799382802-0.1961291085750.556871318190.009945937956330.03529115935940.408370174785-0.253341149839-0.5781780776710.105865019970.1850759830520.0320909283787-0.00291805460890.199837367285-0.02567211745960.2623494535211.7036342446414.644635047886.5929782183
125.48292269076-2.942465524573.712002253892.19128558521-1.937322850842.48365130122-0.117397056505-0.2555480809310.1435435812170.05504425109140.1419752424680.159115544795-0.0564552181389-0.280703454391-0.04734397810290.09180427142970.007180784644580.01913847596530.1376287339520.008087218559760.161830465715-2.658465655847.5545097771384.0524421413
137.357859749961.015391227850.8232461769080.576319308101-0.3385970286870.410693055023-0.153516699803-0.155269293455-0.3728371917970.03072886560130.0892471582056-0.0494037850.0233809391556-0.04238556724240.06072907707680.1830907962020.00574773218220.006434132565080.09135448783570.006743662204580.11500131435221.3263055437-7.8629979195689.5038904446
143.157743832630.1069627694820.659083260222.58585039493-0.3458413457663.25745578713-0.1085055449360.4151946840580.231089017663-0.2482172756720.0414910190787-0.0334459193927-0.0690471998880.02062972325740.06089404851980.100347241688-0.006017368646860.0100660866520.1305522810720.02284919435850.10860320406431.89900629756.9920380578.0512944489
152.16361575011-0.5612417049320.3671973592660.616972895052-0.1149412202191.25635840350.007524494835560.1433599092570.22726614875-0.0438741861304-0.002122830615690.05848178103120.0182829437155-0.0311619755879-0.01631890596070.0967876664228-0.01034700099250.001566892736620.09183364663620.02964214691110.1082077342678.914607027586.7173397432777.7195523474
163.54685520479-0.7291693952920.007897519947794.36995211110.172223501413.926068528460.07334611910960.32549003322-0.330051742683-0.240860283397-0.05797514371820.1429692664420.47549861582-0.08178430801190.02972808765450.162343227978-0.018783586272-0.02384323690310.1087887486390.004356919089920.1346599108568.94128365907-7.6903667591278.3849273364
172.75047396796-0.292381792590.7331467022390.987489187842-0.3266343624560.3965761957650.001116273134110.2268995569940.0715390756646-0.06769514517840.00725413020639-0.02592704154430.06262490165640.0151650552388-0.0111422392870.11819652379-0.004661879699690.007072511081940.0945079798080.0152617313230.084870950514615.44670559531.9409425453275.8215021692
181.023947377410.0935138201408-0.5335884264482.53605703496-0.2410455539211.76215425861-0.02943645774060.5970332062230.51363703214-0.262985131239-0.004757671120080.121780307848-0.2765666474410.033652912830.03523516668880.148195646433-0.009750248926-0.03499273654110.2064605064360.1195153467420.2514642291528.9467897184311.782274856668.3496195342
194.28597598528-0.7113044385331.392765064975.770546392480.4787206750426.323352553470.01219968190260.759327774899-0.0106034324599-0.457743212437-0.0597142371587-0.100735172740.2856210270290.1225867771820.03694715263110.25699269716-0.0442470450839-0.04280476766210.3423872056950.02419884369620.153988391490.925626748652-2.6064045039259.2824547972
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 916 through 935 )AA916 - 9351 - 20
22chain 'A' and (resid 936 through 954 )AA936 - 95421 - 39
33chain 'A' and (resid 955 through 985 )AA955 - 98540 - 70
44chain 'A' and (resid 986 through 1010 )AA986 - 101071 - 90
55chain 'A' and (resid 1011 through 1030 )AA1011 - 103091 - 110
66chain 'A' and (resid 1031 through 1079 )AA1031 - 1079111 - 159
77chain 'A' and (resid 1080 through 1106 )AA1080 - 1106160 - 186
88chain 'A' and (resid 1107 through 1140 )AA1107 - 1140187 - 220
99chain 'A' and (resid 1141 through 1155 )AA1141 - 1155221 - 235
1010chain 'A' and (resid 1156 through 1188 )AA1156 - 1188236 - 268
1111chain 'B' and (resid 917 through 935 )BI917 - 9351 - 19
1212chain 'B' and (resid 936 through 954 )BI936 - 95420 - 38
1313chain 'B' and (resid 955 through 970 )BI955 - 97039 - 54
1414chain 'B' and (resid 971 through 1030 )BI971 - 103055 - 111
1515chain 'B' and (resid 1031 through 1079 )BI1031 - 1079112 - 160
1616chain 'B' and (resid 1080 through 1106 )BI1080 - 1106161 - 187
1717chain 'B' and (resid 1107 through 1140 )BI1107 - 1140188 - 221
1818chain 'B' and (resid 1141 through 1155 )BI1141 - 1155222 - 236
1919chain 'B' and (resid 1156 through 1189 )BI1156 - 1189237 - 270

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