+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 6wbz | ||||||
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タイトル | Structure of Human HDAC2 in complex with an ethyl ketone inhibitor containing a spiro-bicyclic group | ||||||
要素 | Histone deacetylase 2 | ||||||
キーワード | HYDROLASE/HYDROLASE Inhibitor / Histone Deacetylase (ヒストン脱アセチル化酵素) / HYDROLASE (加水分解酵素) / HYDROLASE-HYDROLASE Inhibitor complex | ||||||
機能・相同性 | 機能・相同性情報 protein de-2-hydroxyisobutyrylase activity / positive regulation of male mating behavior / negative regulation of peptidyl-lysine acetylation / p75NTR negatively regulates cell cycle via SC1 / epidermal cell differentiation / negative regulation of dendritic spine development / histone decrotonylase activity / fungiform papilla formation / negative regulation of MHC class II biosynthetic process / behavioral response to ethanol ...protein de-2-hydroxyisobutyrylase activity / positive regulation of male mating behavior / negative regulation of peptidyl-lysine acetylation / p75NTR negatively regulates cell cycle via SC1 / epidermal cell differentiation / negative regulation of dendritic spine development / histone decrotonylase activity / fungiform papilla formation / negative regulation of MHC class II biosynthetic process / behavioral response to ethanol / positive regulation of interleukin-1 production / regulation of cell fate specification / NuRD complex / negative regulation of stem cell population maintenance / EGR2 and SOX10-mediated initiation of Schwann cell myelination / negative regulation of transcription by competitive promoter binding / regulation of stem cell differentiation / ESC/E(Z) complex / cellular response to dopamine / STAT3 nuclear events downstream of ALK signaling / ヒストン脱アセチル化酵素 / cardiac muscle hypertrophy / protein lysine deacetylase activity / positive regulation of signaling receptor activity / response to caffeine / 加水分解酵素; ペプチド以外のCN結合加水分解酵素; 鎖状アミドに作用 / histone deacetylase activity / embryonic digit morphogenesis / positive regulation of oligodendrocyte differentiation / positive regulation of stem cell population maintenance / Sin3-type complex / Notch-HLH transcription pathway / dendrite development / eyelid development in camera-type eye / odontogenesis of dentin-containing tooth / positive regulation of proteolysis / RNA Polymerase I Transcription Initiation / response to amyloid-beta / histone deacetylase complex / hair follicle placode formation / Regulation of MECP2 expression and activity / NF-kappaB binding / positive regulation of collagen biosynthetic process / response to hyperoxia / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / heterochromatin formation / positive regulation of epithelial to mesenchymal transition / cellular response to retinoic acid / MECP2 regulates neuronal receptors and channels / positive regulation of tyrosine phosphorylation of STAT protein / Regulation of TP53 Activity through Acetylation / cellular response to transforming growth factor beta stimulus / response to amphetamine / heat shock protein binding / SUMOylation of chromatin organization proteins / negative regulation of cell migration / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / response to cocaine / Regulation of PTEN gene transcription / HDACs deacetylate histones / promoter-specific chromatin binding / negative regulation of transforming growth factor beta receptor signaling pathway / response to nicotine / circadian regulation of gene expression / protein modification process / NoRC negatively regulates rRNA expression / negative regulation of DNA-binding transcription factor activity / NOTCH1 Intracellular Domain Regulates Transcription / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / cellular response to hydrogen peroxide / histone deacetylase binding / positive regulation of tumor necrosis factor production / negative regulation of neuron projection development / cellular response to heat / Factors involved in megakaryocyte development and platelet production / histone binding / RNA polymerase II-specific DNA-binding transcription factor binding / Potential therapeutics for SARS / response to lipopolysaccharide / chromosome, telomeric region / クロマチンリモデリング / response to xenobiotic stimulus / negative regulation of DNA-templated transcription / chromatin binding / クロマチン / positive regulation of cell population proliferation / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / enzyme binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / RNA binding / 核質 / 細胞核 / 細胞質 類似検索 - 分子機能 | ||||||
生物種 | Homo sapiens (ヒト) | ||||||
手法 | X線回折 / シンクロトロン / フーリエ合成 / 解像度: 1.32 Å | ||||||
データ登録者 | Klein, D.J. / Yu, W. | ||||||
引用 | ジャーナル: Bioorg.Med.Chem.Lett. / 年: 2020 タイトル: Discovery of ethyl ketone-based HDACs 1, 2, and 3 selective inhibitors for HIV latency reactivation. 著者: Yu, W. / Liu, J. / Yu, Y. / Zhang, V. / Clausen, D. / Kelly, J. / Wolkenberg, S. / Beshore, D. / Duffy, J.L. / Chung, C.C. / Myers, R.W. / Klein, D.J. / Fells, J. / Holloway, K. / Wu, J. / ...著者: Yu, W. / Liu, J. / Yu, Y. / Zhang, V. / Clausen, D. / Kelly, J. / Wolkenberg, S. / Beshore, D. / Duffy, J.L. / Chung, C.C. / Myers, R.W. / Klein, D.J. / Fells, J. / Holloway, K. / Wu, J. / Wu, G. / Howell, B.J. / Barnard, R.J.O. / Kozlowski, J. | ||||||
履歴 |
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-構造の表示
構造ビューア | 分子: MolmilJmol/JSmol |
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-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 6wbz.cif.gz | 270.2 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb6wbz.ent.gz | 216.4 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 6wbz.json.gz | ツリー表示 | PDBx/mmJSON形式 | |
その他 | その他のダウンロード |
-検証レポート
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/wb/6wbz ftp://data.pdbj.org/pub/pdb/validation_reports/wb/6wbz | HTTPS FTP |
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-関連構造データ
-リンク
-集合体
登録構造単位 |
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1 |
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2 |
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3 |
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単位格子 |
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-要素
-タンパク質 , 1種, 3分子 ABC
#1: タンパク質 | 分子量: 43061.988 Da / 分子数: 3 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: HDAC2 発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ) 参照: UniProt: Q92769, ヒストン脱アセチル化酵素 |
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-非ポリマー , 6種, 1293分子
#2: 化合物 | #3: 化合物 | ChemComp-SO4 / #4: 化合物 | ChemComp-CA / #5: 化合物 | ChemComp-PEG / #6: 化合物 | #7: 水 | ChemComp-HOH / | |
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-詳細
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
-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: 2.48 Å3/Da / 溶媒含有率: 50.31 % |
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結晶化 | 温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法 詳細: 25% PEG 3350, 0.2 M ammonium sulfate, 0.1 M Hepes pH 7.5 |
-データ収集
回折 | 平均測定温度: 100 K / Serial crystal experiment: N |
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放射光源 | 由来: シンクロトロン / サイト: APS / ビームライン: 17-ID / 波長: 1 Å |
検出器 | タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2015年7月22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: 1 Å / 相対比: 1 |
反射 | 解像度: 1.32→48.56 Å / Num. obs: 298863 / % possible obs: 99.9 % / 冗長度: 6.6 % / CC1/2: 0.999 / Net I/σ(I): 13.1 |
反射 シェル | 解像度: 1.32→1.343 Å / Num. unique obs: 14601 / CC1/2: 0.62 |
-解析
ソフトウェア |
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精密化 | 構造決定の手法: フーリエ合成 / 解像度: 1.32→19.26 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.962 / SU R Cruickshank DPI: 0.046 / 交差検証法: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.048 / SU Rfree Blow DPI: 0.049 / SU Rfree Cruickshank DPI: 0.047
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原子変位パラメータ | Biso max: 189.31 Å2 / Biso mean: 24.48 Å2 / Biso min: 6.11 Å2
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Refine analyze | Luzzati coordinate error obs: 0.17 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: final / 解像度: 1.32→19.26 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 1.32→1.33 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
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