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- PDB-7qk4: EED in complex with PRC2 allosteric inhibitor compound 22 (MAK683) -

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基本情報

登録情報
データベース: PDB / ID: 7qk4
タイトルEED in complex with PRC2 allosteric inhibitor compound 22 (MAK683)
要素
  • Histone-lysine N-methyltransferase EZH2
  • Polycomb protein EED
キーワードTRANSFERASE / Inhibitor / Complex
機能・相同性
機能・相同性情報


hepatocyte homeostasis / cellular response to trichostatin A / regulation of gliogenesis / negative regulation of striated muscle cell differentiation / regulation of kidney development / [histone H3]-lysine27 N-trimethyltransferase / negative regulation of keratinocyte differentiation / histone H3K27 trimethyltransferase activity / negative regulation of retinoic acid receptor signaling pathway / cerebellar cortex development ...hepatocyte homeostasis / cellular response to trichostatin A / regulation of gliogenesis / negative regulation of striated muscle cell differentiation / regulation of kidney development / [histone H3]-lysine27 N-trimethyltransferase / negative regulation of keratinocyte differentiation / histone H3K27 trimethyltransferase activity / negative regulation of retinoic acid receptor signaling pathway / cerebellar cortex development / response to tetrachloromethane / primary miRNA binding / regulatory ncRNA-mediated heterochromatin formation / skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration / histone H3K27 methyltransferase activity / facultative heterochromatin formation / positive regulation of cell cycle G1/S phase transition / ESC/E(Z) complex / negative regulation of stem cell differentiation / pronucleus / chromatin silencing complex / protein-lysine N-methyltransferase activity / cardiac muscle hypertrophy in response to stress / G1 to G0 transition / positive regulation of dendrite development / histone H3 methyltransferase activity / synaptic transmission, GABAergic / DNA methylation-dependent constitutive heterochromatin formation / lncRNA binding / histone methyltransferase activity / negative regulation of G1/S transition of mitotic cell cycle / spinal cord development / negative regulation of gene expression, epigenetic / Transcriptional Regulation by E2F6 / negative regulation of transcription elongation by RNA polymerase II / positive regulation of protein serine/threonine kinase activity / subtelomeric heterochromatin formation / ribonucleoprotein complex binding / pericentric heterochromatin / positive regulation of epithelial to mesenchymal transition / RNA polymerase II core promoter sequence-specific DNA binding / nucleosome binding / keratinocyte differentiation / protein localization to chromatin / negative regulation of cytokine production involved in inflammatory response / positive regulation of GTPase activity / positive regulation of MAP kinase activity / B cell differentiation / enzyme activator activity / hippocampus development / liver regeneration / Regulation of PTEN gene transcription / PRC2 methylates histones and DNA / transcription corepressor binding / Defective pyroptosis / stem cell differentiation / promoter-specific chromatin binding / regulation of circadian rhythm / protein modification process / PKMTs methylate histone lysines / chromatin DNA binding / cellular response to hydrogen peroxide / Activation of anterior HOX genes in hindbrain development during early embryogenesis / G1/S transition of mitotic cell cycle / HCMV Early Events / transcription corepressor activity / rhythmic process / heterochromatin formation / response to estradiol / chromatin organization / chromosome / Oxidative Stress Induced Senescence / methylation / histone binding / chromosome, telomeric region / positive regulation of cell migration / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / synapse / chromatin binding / regulation of DNA-templated transcription / chromatin / negative regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / identical protein binding / nucleus / cytosol
類似検索 - 分子機能
EZH2, SET domain / Histone-lysine N-methyltransferase EZH1/EZH2 / Polycomb repressive complex 2 subunit EZH1/EZH2, tri-helical domain / Pre-SET CXC domain / : / WD repeat binding protein EZH2 / Polycomb repressive complex 2 tri-helical domain / CXC domain / Ezh2, MCSS domain / Tesmin/TSO1-like CXC domain ...EZH2, SET domain / Histone-lysine N-methyltransferase EZH1/EZH2 / Polycomb repressive complex 2 subunit EZH1/EZH2, tri-helical domain / Pre-SET CXC domain / : / WD repeat binding protein EZH2 / Polycomb repressive complex 2 tri-helical domain / CXC domain / Ezh2, MCSS domain / Tesmin/TSO1-like CXC domain / Tesmin/TSO1-like CXC domain / CXC domain / Histone-lysine N-methyltransferase EZH1/2-like / CXC domain profile. / : / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain superfamily / SET domain profile. / SET domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
類似検索 - ドメイン・相同性
Chem-EJR / Polycomb protein EED / Histone-lysine N-methyltransferase EZH2
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 1.602 Å
データ登録者Zhao, K. / Zhao, M. / Luo, X. / Zhang, H. / Scheufler, C.
資金援助1件
組織認可番号国
Not funded
引用ジャーナル: J.Med.Chem. / 年: 2022
タイトル: Discovery of the Clinical Candidate MAK683: An EED-Directed, Allosteric, and Selective PRC2 Inhibitor for the Treatment of Advanced Malignancies.
著者: Huang, Y. / Sendzik, M. / Zhang, J. / Gao, Z. / Sun, Y. / Wang, L. / Gu, J. / Zhao, K. / Yu, Z. / Zhang, L. / Zhang, Q. / Blanz, J. / Chen, Z. / Dubost, V. / Fang, D. / Feng, L. / Fu, X. / ...著者: Huang, Y. / Sendzik, M. / Zhang, J. / Gao, Z. / Sun, Y. / Wang, L. / Gu, J. / Zhao, K. / Yu, Z. / Zhang, L. / Zhang, Q. / Blanz, J. / Chen, Z. / Dubost, V. / Fang, D. / Feng, L. / Fu, X. / Kiffe, M. / Li, L. / Luo, F. / Luo, X. / Mi, Y. / Mistry, P. / Pearson, D. / Piaia, A. / Scheufler, C. / Terranova, R. / Weiss, A. / Zeng, J. / Zhang, H. / Zhang, J. / Zhao, M. / Dillon, M.P. / Jeay, S. / Qi, W. / Moggs, J. / Pissot-Soldermann, C. / Li, E. / Atadja, P. / Lingel, A. / Oyang, C.
履歴
登録2021年12月17日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02022年4月13日Provider: repository / タイプ: Initial release
改定 1.12022年4月27日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
改定 1.22024年1月31日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
A: Polycomb protein EED
B: Histone-lysine N-methyltransferase EZH2
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)46,3326
ポリマ－45,8492
非ポリマー4834
水5,224290
1


  • 登録構造と同一
  • 登録者が定義した集合体
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)50.456, 91.202, 179.016
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Space group name H-MC2221

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要素

#1: タンパク質 Polycomb protein EED / hEED / Embryonic ectoderm development protein / WD protein associating with integrin cytoplasmic ...hEED / Embryonic ectoderm development protein / WD protein associating with integrin cytoplasmic tails 1 / WAIT-1


分子量: 42227.070 Da / 分子数: 1 / 由来タイプ: 組換発現 / 詳細: N-terminal glycine left after TEV cleavage / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: EED / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: O75530
#2: タンパク質・ペプチド Histone-lysine N-methyltransferase EZH2 / ENX-1 / Enhancer of zeste homolog 2 / Lysine N-methyltransferase 6


分子量: 3622.164 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) Homo sapiens (ヒト)
参照: UniProt: Q15910, [histone H3]-lysine27 N-trimethyltransferase
#3: 化合物 ChemComp-CL / CHLORIDE ION / クロリド


分子量: 35.453 Da / 分子数: 3 / 由来タイプ: 合成 / 式: Cl
#4: 化合物 ChemComp-EJR / N-[(5-fluoranyl-2,3-dihydro-1-benzofuran-4-yl)methyl]-8-(2-methylpyridin-3-yl)-[1,2,4]triazolo[4,3-c]pyrimidin-5-amine


分子量: 376.387 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C20H17FN6O / タイプ: SUBJECT OF INVESTIGATION
#5: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 290 / 由来タイプ: 天然 / 式: H2O
研究の焦点であるリガンドがあるかY

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 2.25 Å3/Da / 溶媒含有率: 45.23 %
結晶化温度: 293 K / 手法: 蒸気拡散法, シッティングドロップ法 / 詳細: 0.1 M Bis-Tris pH 6.0, 0.2 M MgCl2, 20% PEG 3350

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データ収集

回折平均測定温度: 100 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: SSRF / ビームライン: BL17U1 / 波長: 0.979 Å
検出器タイプ: ADSC QUANTUM 315r / 検出器: CCD / 日付: 2014年9月19日
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 0.979 Å / 相対比: 1
反射解像度: 1.602→19.96 Å / Num. obs: 43547 / % possible obs: 84.5 % / 冗長度: 6.69 %
詳細: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last ...詳細: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last updated 2020-04-13: http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Index/) and the actual quantities provided by MRFANA (https://github.com/githubgphl/MRFANA) from the autoPROC package (https://www.globalphasing.com/autoproc/). In general, the mmCIF categories here should provide items that are currently used in the PDB archive. If there are alternatives, the one recommended by the PDB developers has been selected. The distinction between *_all and *_obs quantities is not always clear: often only one version is actively used within the PDB archive (or is the one recommended by PDB developers). The intention of distinguishing between classes of reflections before and after some kind of observation criterion was applied, can in principle be useful - but such criteria change in various ways throughout the data processing steps (rejection of overloaded or too partial reflections, outlier/misfit rejections during scaling etc) and there is no retrospect computation of data scaling/merging statistics for the reflections used in the final refinement (where another observation criterion might have been applied). Typical data processing will usually only provide one version of statistics at various stages and these are given in the recommended item here, irrespective of the "_all" and "_obs" connotation, see e.g. the use of _reflns.pdbx_Rmerge_I_obs, _reflns.pdbx_Rrim_I_all and _reflns.pdbx_Rpim_I_all. Please note that all statistics related to "merged intensities" (or "merging") are based on inverse-variance weighting of the individual measurements making up a symmetry-unique reflection. This is standard for several decades now, even if some of the dictionary definitions seem to suggest that a simple "mean" or "average" intensity is being used instead. R-values are always given for all symmetry-equivalent reflections following Friedel's law, i.e. Bijvoet pairs are not treated separately (since we want to describe the overall mean intensity and not the mean I(+) and I(-) here). The Rrim metric is identical to the Rmeas R-value and only differs in name. _reflns.pdbx_number_measured_all is the number of measured intensities just before the final merging step (at which point no additional rejection takes place). _reflns.number_obs is the number of symmetry-unique observations, i.e. the result of merging those measurements via inverse-variance weighting. _reflns.pdbx_netI_over_sigmaI is based on the merged intensities (_reflns.number_obs) as expected. _reflns.pdbx_redundancy is synonymous with "multiplicity". The per-shell item _reflns_shell.number_measured_all corresponds to the overall value _reflns.pdbx_number_measured_all. The per-shell item _reflns_shell.number_unique_all corresponds to the overall value _reflns.number_obs. The per-shell item _reflns_shell.percent_possible_all corresponds to the overall value _reflns.percent_possible_obs. The per-shell item _reflns_shell.meanI_over_sigI_obs corresponds to the overall value given as _reflns.pdbx_netI_over_sigmaI. But be aware of the incorrect definition of the former in the current dictionary!
CC1/2: 0.999 / CC1/2 anomalous: -0.143 / Rmerge(I) obs: 0.0583 / Rpim(I) all: 0.024 / Rrim(I) all: 0.0632 / AbsDiff over sigma anomalous: 0.678 / Baniso tensor eigenvalue 1: 15.2 Å2 / Baniso tensor eigenvalue 2: 29.6 Å2 / Baniso tensor eigenvalue 3: 20.6 Å2 / Baniso tensor eigenvector 1 ortho1: 1 / Baniso tensor eigenvector 1 ortho2: 0 / Baniso tensor eigenvector 1 ortho3: 0 / Baniso tensor eigenvector 2 ortho1: 0 / Baniso tensor eigenvector 2 ortho2: 1 / Baniso tensor eigenvector 2 ortho3: 0 / Baniso tensor eigenvector 3 ortho1: 0 / Baniso tensor eigenvector 3 ortho2: 0 / Baniso tensor eigenvector 3 ortho3: 1 / Aniso diffraction limit 1: 1.522 Å / Aniso diffraction limit 2: 1.753 Å / Aniso diffraction limit 3: 1.622 Å / Aniso diffraction limit axis 1 ortho1: 1 / Aniso diffraction limit axis 1 ortho2: 0 / Aniso diffraction limit axis 1 ortho3: 0 / Aniso diffraction limit axis 2 ortho1: 0 / Aniso diffraction limit axis 2 ortho2: 1 / Aniso diffraction limit axis 2 ortho3: 0 / Aniso diffraction limit axis 3 ortho1: 0 / Aniso diffraction limit axis 3 ortho2: 0 / Aniso diffraction limit axis 3 ortho3: 1 / Net I/σ(I): 17.13 / Num. measured all: 291362 / Observed signal threshold: 1.2 / Orthogonalization convention: pdb / % possible anomalous: 84 / % possible ellipsoidal: 84.5 / % possible ellipsoidal anomalous: 84 / % possible spherical: 79.6 / % possible spherical anomalous: 79.1 / Redundancy anomalous: 3.51 / Signal type: local
反射 シェル
解像度 (Å)冗長度 (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. measured obsNum. unique allNum. unique obsCC1/2CC1/2 anomalousRpim(I) allRrim(I) allAbsDiff over sigma anomalous% possible anomalous% possible ellipsoidal% possible ellipsoidal anomalous% possible spherical% possible spherical anomalousRedundancy anomalous% possible all
4.693-19.966.320.037437.641375413754217621760.998-0.0840.0160.04080.6393.694.493.694.493.63.5894.4
3.724-4.6936.570.040438.271430814308217921790.998-0.1650.01690.04390.67496.997.596.997.596.93.5697.5
3.231-3.7246.770.043636.31473114731217721770.998-0.1870.01790.04720.69491.992.191.992.191.93.6192.1
2.944-3.2316.960.046132.961514815148217721770.998-0.1840.01870.04980.70799.910099.910099.93.68100
2.735-2.9447.060.051629.571536915369217721770.998-0.1440.02080.05570.73299.999.999.999.999.93.7199.9
2.559-2.7357.130.061425.871553115531217821780.998-0.1660.02460.06620.70788.488.588.488.588.43.7488.5
2.434-2.5597.180.068223.051563315633217721770.997-0.1660.02730.07350.721001001001001003.76100
2.33-2.4347.220.076420.891571915719217721770.997-0.1450.03050.08240.71510099.910099.91003.7799.9
2.209-2.337.20.08718.61567715677217821780.996-0.150.03480.09380.70270.470.770.470.770.43.7670.7
2.137-2.2097.270.099316.661583015830217821780.996-0.1470.03950.1070.6861001001001001003.78100
2.018-2.1377.210.119813.971568415684217621760.995-0.0590.04780.12920.71250.550.750.550.750.53.7650.7
1.967-2.0187.320.158511.141593115931217721770.992-0.0320.06280.17070.6981001001001001003.79100
1.871-1.9676.980.21968.191521915219217921790.988-0.0250.08830.23710.68944.946.244.946.244.93.746.2
1.833-1.8717.320.30486.581592315923217521750.979-0.030.12020.3280.6681001001001001003.78100
1.797-1.8337.310.37555.511593915939218021800.964-0.0080.14790.40390.65999.699.599.699.599.63.7899.5
1.763-1.7977.140.42814.881553615536217621760.9610.0080.1710.46160.64794.194.294.194.294.13.6994.2
1.728-1.7636.050.44934.081317113171217821780.945-0.0240.19520.49110.63489.58989.58686.93.189
1.69-1.7285.470.48843.411190811908217621760.918-0.0230.22360.53890.62786.586.386.574.574.92.886.3
1.649-1.695.020.53192.91094210942217921790.885-0.0060.25790.59370.63885.185.585.161.361.52.5785.5
1.602-1.6494.320.61292.1994099409217721770.833-0.0360.3230.6970.62172.974.972.948.947.12.2774.9

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解析

ソフトウェア
名称バージョン分類
autoPROC1.1.7 20210420data processing
autoPROCJan 31, 2020data processing
STARANISO0.7.7データスケーリング
autoPROC2.3.73data processing
BUSTER2.11.8精密化
autoPROCデータ削減
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 5H19

5h19


解像度: 1.602→15.97 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.946 / SU R Cruickshank DPI: 0.106 / 交差検証法: THROUGHOUT / SU R Blow DPI: 0.111 / SU Rfree Blow DPI: 0.102 / SU Rfree Cruickshank DPI: 0.1
Rfactor反射数%反射Selection details
Rfree0.2057 2266 -RANDOM
Rwork0.1818 ---
obs0.183 43528 79.6 %-
原子変位パラメータBiso mean: 23.97 Å2
Baniso -1Baniso -2Baniso -3
1--2.0571 Å20 Å20 Å2
2--2.8609 Å20 Å2
3----0.8038 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
精密化ステップサイクル: LAST / 解像度: 1.602→15.97 Å
タンパク質核酸リガンド溶媒全体
原子数3087 0 31 290 3408
拘束条件
Refine-IDタイプDev ideal数Restraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0083225HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.974368HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1133SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes549HARMONIC5
X-RAY DIFFRACTIONt_it3225HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion407SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact2775SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.83
X-RAY DIFFRACTIONt_other_torsion14.79
LS精密化 シェル解像度: 1.602→1.62 Å
Rfactor反射数%反射
Rfree0.3269 48 -
Rwork0.2686 --
obs--43.67 %
精密化 TLS

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)
10.8397-0.07-0.27820.1219-0.06331.5054-0.091-0.03930.0101-0.0393-0.00830.00140.01010.00140.0993-0.05960.0167-0.0063-0.00190.0177-0.020513.178419.482421.2929
22.7201-3.07660.04796.5135-1.11242.0188-0.1190.0632-0.44820.06320.0060.5406-0.44820.54060.113-0.1096-0.031-0.04390.07050.0127-0.047125.308829.206930.0821
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|78-440}A78 - 440
2X-RAY DIFFRACTION1{ A| 504 }A504
3X-RAY DIFFRACTION2{ B|* }B40 - 68

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

  • 万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
  • EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

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