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- PDB-7xuc: Structure of G9a in complex with compound 11a -

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Basic information

Entry
Database: PDB / ID: 7xuc
TitleStructure of G9a in complex with compound 11a
ComponentsHistone-lysine N-methyltransferase EHMT2
KeywordsTRANSFERASE / histone lysine methyltransferase / inhibitor / protein-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 / histone H3K27 methyltransferase activity / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity ...regulation of protein modification process / histone H3K56 methyltransferase activity / : / phenotypic switching / neuron fate specification / : / [histone H3]-lysine9 N-methyltransferase / histone H3K27 methyltransferase activity / histone H3K9 methyltransferase activity / histone H3K9me2 methyltransferase activity / peptidyl-lysine dimethylation / synaptonemal complex assembly / negative regulation of autophagosome assembly / oocyte development / protein-lysine N-methyltransferase activity / C2H2 zinc finger domain binding / fertilization / : / cellular response to cocaine / : / organ growth / Transcriptional Regulation by E2F6 / spermatid development / behavioral response to cocaine / regulation of DNA replication / RNA Polymerase I Transcription Initiation / Transcriptional Regulation by VENTX / long-term memory / response to fungicide / Transferases; Transferring one-carbon groups; Methyltransferases / cellular response to starvation / transcription corepressor binding / 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 / cellular response to xenobiotic stimulus / p53 binding / 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 domain / Pre-SET motif / Pre-SET domain profile. / N-terminal to some SET domains / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily ...Histone-lysine N-methyltransferase EHMT2 / Histone-lysine N-methyltransferase EHMT1/EHMT2 / : / Histone-lysine N-methyltransferase EHMT1/EHMT2, Cys-rich region / Pre-SET domain / Pre-SET motif / Pre-SET domain profile. / N-terminal to some SET domains / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain superfamily / SET domain / 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-I6S / SINEFUNGIN / Histone-lysine N-methyltransferase EHMT2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.67 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

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)67,53718
Polymers65,2102
Non-polymers2,32716
Water12,214678
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3120 Å2
ΔGint-3 kcal/mol
Surface area25430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.572, 77.620, 66.573
Angle α, β, γ (deg.)90.000, 90.645, 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 , 6 types, 694 molecules

#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-I6S / 3,6,6-trimethyl-4-oxidanylidene-~{N}-[(2~{S})-1-oxidanylidene-1-phenylazanyl-hexan-2-yl]-5,7-dihydro-1~{H}-indole-2-carboxamide


Mass: 409.521 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H31N3O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 678 / 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: 45.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M Bis-Tris propane (pH7.5), 0.2M Sodium Fluoride, 10% Ethylene Glycol, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.5418 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Dec 24, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.67→50 Å / Num. obs: 65265 / % possible obs: 97.9 % / Redundancy: 2.7 % / Biso Wilson estimate: 13.69 Å2 / Rpim(I) all: 0.038 / Rrim(I) all: 0.07 / Rsym value: 0.058 / Net I/σ(I): 14.5
Reflection shellResolution: 1.67→1.7 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 2 / Num. unique obs: 3021 / CC1/2: 0.754 / Rpim(I) all: 0.311 / Rrim(I) all: 0.472 / Rsym value: 0.353 / % possible all: 91.6

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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: 1.67→17.55 Å / SU ML: 0.1642 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.3092
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.186 3236 4.96 %
Rwork0.1585 61984 -
obs0.1599 65220 97.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.91 Å2
Refinement stepCycle: LAST / Resolution: 1.67→17.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4337 0 135 678 5150
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00714670
X-RAY DIFFRACTIONf_angle_d0.8416328
X-RAY DIFFRACTIONf_chiral_restr0.0524669
X-RAY DIFFRACTIONf_plane_restr0.0078826
X-RAY DIFFRACTIONf_dihedral_angle_d15.39481756
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.67-1.70.27781140.22052405X-RAY DIFFRACTION88.2
1.7-1.720.23331220.21012577X-RAY DIFFRACTION93.04
1.72-1.750.23141230.20012597X-RAY DIFFRACTION94.74
1.75-1.780.22381170.19722659X-RAY DIFFRACTION95.63
1.78-1.810.23591640.19122623X-RAY DIFFRACTION96.3
1.81-1.850.20871480.18232651X-RAY DIFFRACTION96.88
1.85-1.880.23351340.17562688X-RAY DIFFRACTION97.65
1.88-1.930.20321460.17312678X-RAY DIFFRACTION98.53
1.93-1.970.21081450.16452713X-RAY DIFFRACTION98.65
1.97-2.020.19981280.16432743X-RAY DIFFRACTION98.86
2.02-2.070.20131480.1612681X-RAY DIFFRACTION98.3
2.07-2.140.17631390.15652755X-RAY DIFFRACTION99.38
2.14-2.20.18481550.15432691X-RAY DIFFRACTION99.51
2.2-2.280.17831440.15182777X-RAY DIFFRACTION99.39
2.28-2.370.19311470.15592732X-RAY DIFFRACTION99.62
2.37-2.480.21181620.1612701X-RAY DIFFRACTION99.48
2.48-2.610.17891500.15812729X-RAY DIFFRACTION99.45
2.61-2.770.24081260.16382776X-RAY DIFFRACTION99.55
2.78-2.990.18791220.16322788X-RAY DIFFRACTION99.86
2.99-3.290.17431540.15732739X-RAY DIFFRACTION100
3.29-3.760.15541600.13752771X-RAY DIFFRACTION99.97
3.76-4.720.11981410.12282699X-RAY DIFFRACTION97.29
4.72-17.550.18641470.15942811X-RAY DIFFRACTION99.3
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)
11.729277748870.2806998426540.688536566891.956698101410.5014722784871.53473052304-0.04952774460990.02857129163730.0537440050732-0.01115967031290.0630765849939-0.214348870046-0.008445002002850.187057511723-0.02150032316130.09212267698280.02026701235580.004751073681350.0870954675147-0.02071632234960.10339865540240.300357917311.0123777569100.784058987
21.244397782980.331436645480.479692961580.9013113520850.3231502573611.2250228757-0.0260010626372-0.3222373803780.1219517285750.133832545316-0.0292602251270.146293469776-0.0493679804399-0.3458103926110.03839889928520.1392138619450.01990374779640.02347627215320.1891355597610.004938622869160.11761715924410.8962742687-0.701451155098105.269774639
32.043945524660.8123149201980.3744939672540.4305273507180.3313248374550.398458867440.0338602836806-0.3601514176160.07252066666130.0699511549233-0.06837321210520.0329084479187-0.0211118472818-0.1628004276320.04437094547950.1208820211320.0288158250910.001201575829920.148879305603-0.01938485220930.091792882288221.00266233736.38854521004108.150009388
41.4984209401-0.723554324192-0.02984087563524.522668280581.268838347911.670441248540.0741941878389-0.266127141053-0.180773296610.350330155091-0.06195958317550.06806989053640.341571991931-0.0677818703691-0.01231759222310.154356857243-0.000415665890068-0.01441980948270.1077428662230.005142422537170.086543840737929.5742219297-4.1056244927108.514484468
51.463016125390.4592550498790.5807958007630.690775575110.1942053140020.8950811054680.0347994014967-0.2538133401180.01810675249420.136571068779-0.0238591092211-0.02647819833710.0286541424065-0.0891995954495-0.01134197433950.1190053908570.025915759980.01045839879080.0851397587389-0.01048704755110.07281807076327.90658760111.33386392129110.632185667
63.087021154770.460877077491.058768223021.95938287353-0.3398244076434.130176881360.144807923932-0.664437051407-0.2260406433670.315291124093-0.1010598117580.009350453084730.177349464574-0.0961381402829-0.02935531320640.2583033257760.00280935204783-0.03531031027620.2545565347370.0333505793410.15858207508140.7223554501-3.06790025145126.591268428
75.82620839752-0.3123723576672.105753265681.596511533620.2115788028422.83071870942-0.151735474762-0.1907223175570.6235527803050.06648590080420.04305790947340.277572579555-0.181743191189-0.3981778709650.1151396814570.1460423765430.0115495634554-0.002851039775630.1402205103120.0008274615165160.2313359702591.5147520083912.322827220886.2688325934
82.99516889168-0.9965462656781.736553837260.609371507755-0.5095258579681.01485074207-0.0898531804449-0.194671694750.1659266005580.04464029879660.06627386874470.0739953821595-0.0333631964159-0.2304900940620.01316745950550.09276040627620.005425649020420.01636097780710.1432799304520.02232635339840.160624981201-2.91393275675.1700483307683.7455177253
91.665903902420.007489660252370.588719419196-0.00803388698446-0.01845294464850.211887609915-0.0154034904944-0.0498712138994-0.235136796875-0.02251819186920.042261580110.0491124626379-0.00775713247383-0.0192074171557-0.01795911815420.177580056454-0.004684091356-0.003864877143830.09282094773370.01623063513340.14311202016220.9968203183-10.082775044389.1196273053
102.57570094680.1014634833060.4738897632552.42002436738-0.3001128358811.93277037522-0.06759843943940.3868055695810.205351856896-0.2605602182180.02816697667370.0460898310447-0.01911811470950.007754281129490.04549684554760.0968792184663-0.004239539304020.00288010815780.1319646492160.02680409590670.093353302515731.68205787124.8764125962677.9502423619
111.74987914568-0.468852959340.2544053452620.348193332216-0.1301983675421.146633316250.01841096829060.1576325223330.196823254525-0.047075412894-0.02120922098550.04243862762020.0135176929028-0.00766619860236-0.005954219326570.0769525756406-0.0111758296273-0.004243585412740.08092202281220.03234312827180.08999339431398.6024391284.8367906192277.4116756828
122.74736052621-0.2088907989450.1852752905854.36280023240.288295441563.89664517860.1171628450140.339614753915-0.3397509708-0.313133986165-0.02616545659870.09775660791160.502578445833-0.03652213343290.03432287666390.135998934265-0.0190756145294-0.03214248959680.09894846998280.02122993319630.115329477179.20313172443-10.031318892177.8420144298
131.48658011840.1750644172870.2127057112360.810151076758-0.03749287009870.4105830547120.01195036291030.295157885370.0142364759806-0.06162799886910.0435982271708-0.005538193098080.07799689635010.00100705508126-0.04356288457190.104318130824-0.009006860783320.001015699743410.0929136872140.02702670691040.072048228220915.1690409036-0.23255151906175.4932810143
141.60885976180.162657321293-0.5648937918990.9745785647780.4699850747951.01168863464-0.02893583676770.416458897160.477056627644-0.284731707221-0.06917907201720.0417693278224-0.2674322841630.1305062008650.06544898154380.153716719237-0.0222399496939-0.03987969684750.2100164741910.1009332152150.2012713228148.699041695289.578065904568.0269609193
153.73701487199-0.9788662705481.175898026333.21417454346-0.0648163950574.795122531570.02846429798330.524657032482-0.0667686814203-0.33500727788-0.0654030066455-0.04509423524110.287668161020.06436320806830.01984328764680.260375785274-0.0429053638901-0.03837380595260.30027015340.02406844840130.1646778093070.629363632249-4.8464111786359.0899756957
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 954 )AA916 - 9541 - 39
22chain 'A' and (resid 955 through 1001 )AA955 - 100140 - 86
33chain 'A' and (resid 1002 through 1054 )AA1002 - 105487 - 137
44chain 'A' and (resid 1055 through 1096 )AA1055 - 1096138 - 179
55chain 'A' and (resid 1097 through 1155 )AA1097 - 1155180 - 238
66chain 'A' and (resid 1156 through 1189 )AA1156 - 1189239 - 272
77chain 'B' and (resid 917 through 935 )BH917 - 9351 - 19
88chain 'B' and (resid 936 through 954 )BH936 - 95420 - 38
99chain 'B' and (resid 955 through 970 )BH955 - 97039 - 54
1010chain 'B' and (resid 971 through 1030 )BH971 - 103055 - 110
1111chain 'B' and (resid 1031 through 1079 )BH1031 - 1079111 - 159
1212chain 'B' and (resid 1080 through 1106 )BH1080 - 1106160 - 186
1313chain 'B' and (resid 1107 through 1140 )BH1107 - 1140187 - 220
1414chain 'B' and (resid 1141 through 1155 )BH1141 - 1155221 - 235
1515chain 'B' and (resid 1156 through 1189 )BH1156 - 1189236 - 269

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