+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 4x2f | ||||||
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タイトル | Selection of fragments for kinase inhibitor design: decoration is key | ||||||
要素 | TGF-beta receptor type-1 | ||||||
キーワード | Transferase/Transferase Inhibitor / TRANSFERASE (転移酵素) / PROTEIN KINASE (プロテインキナーゼ) / INHIBITOR COMPLEX (酵素阻害剤) / Transferase-Transferase Inhibitor complex | ||||||
機能・相同性 | 機能・相同性情報 extracellular structure organization / epicardium morphogenesis / parathyroid gland development / transforming growth factor beta ligand-receptor complex / regulation of cardiac muscle cell proliferation / myofibroblast differentiation / positive regulation of tight junction disassembly / positive regulation of epithelial to mesenchymal transition involved in endocardial cushion formation / TGFBR2 Kinase Domain Mutants in Cancer / transforming growth factor beta receptor activity ...extracellular structure organization / epicardium morphogenesis / parathyroid gland development / transforming growth factor beta ligand-receptor complex / regulation of cardiac muscle cell proliferation / myofibroblast differentiation / positive regulation of tight junction disassembly / positive regulation of epithelial to mesenchymal transition involved in endocardial cushion formation / TGFBR2 Kinase Domain Mutants in Cancer / transforming growth factor beta receptor activity / positive regulation of mesenchymal stem cell proliferation / ventricular compact myocardium morphogenesis / SMAD2/3 Phosphorylation Motif Mutants in Cancer / TGFBR1 KD Mutants in Cancer / positive regulation of vasculature development / regulation of epithelial to mesenchymal transition / activin receptor activity, type I / cardiac epithelial to mesenchymal transition / transforming growth factor beta receptor activity, type I / activin receptor complex / mesenchymal cell differentiation / neuron fate commitment / positive regulation of extracellular matrix assembly / type II transforming growth factor beta receptor binding / TGFBR1 LBD Mutants in Cancer / angiogenesis involved in coronary vascular morphogenesis / receptor protein serine/threonine kinase / germ cell migration / transmembrane receptor protein serine/threonine kinase activity / pharyngeal system development / activin binding / coronary artery morphogenesis / activin receptor signaling pathway / ventricular trabecula myocardium morphogenesis / filopodium assembly / transforming growth factor beta binding / embryonic cranial skeleton morphogenesis / response to cholesterol / I-SMAD binding / collagen fibril organization / negative regulation of chondrocyte differentiation / endothelial cell activation / skeletal system morphogenesis / lens development in camera-type eye / endothelial cell proliferation / positive regulation of filopodium assembly / anterior/posterior pattern specification / artery morphogenesis / ventricular septum morphogenesis / roof of mouth development / SMAD binding / TGF-beta receptor signaling activates SMADs / negative regulation of endothelial cell proliferation / positive regulation of SMAD protein signal transduction / blastocyst development / regulation of protein ubiquitination / endothelial cell migration / bicellular tight junction / 上皮間葉転換 / positive regulation of epithelial to mesenchymal transition / positive regulation of stress fiber assembly / cellular response to transforming growth factor beta stimulus / positive regulation of endothelial cell proliferation / Downregulation of TGF-beta receptor signaling / negative regulation of cell migration / transforming growth factor beta receptor signaling pathway / post-embryonic development / thymus development / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / kidney development / skeletal system development / positive regulation of apoptotic signaling pathway / 運動性 / negative regulation of extrinsic apoptotic signaling pathway / wound healing / cellular response to growth factor stimulus / UCH proteinases / male gonad development / nervous system development / heart development / positive regulation of cell growth / 遺伝子発現の調節 / peptidyl-serine phosphorylation / in utero embryonic development / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / regulation of cell cycle / Ub-specific processing proteases / エンドソーム / protein kinase activity / intracellular signal transduction / positive regulation of cell migration / 脂質ラフト / protein serine/threonine kinase activity / apoptotic process / ubiquitin protein ligase binding / positive regulation of cell population proliferation / regulation of DNA-templated transcription / positive regulation of gene expression / positive regulation of DNA-templated transcription 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 / 分子置換 / 解像度: 1.49 Å | ||||||
データ登録者 | Czodrowski, P. / Hoelzemann, G. / Barnickel, G. / Greiner, H. / Musil, D. | ||||||
引用 | ジャーナル: J.Med.Chem. / 年: 2015 タイトル: Selection of fragments for kinase inhibitor design: decoration is key. 著者: Czodrowski, P. / Holzemann, G. / Barnickel, G. / Greiner, H. / Musil, D. | ||||||
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 | 4x2f.cif.gz | 140 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb4x2f.ent.gz | 109.1 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 4x2f.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/x2/4x2f ftp://data.pdbj.org/pub/pdb/validation_reports/x2/4x2f | 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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単位格子 |
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-要素
#1: タンパク質 | 分子量: 34882.148 Da / 分子数: 1 / 断片: UNP residues 200-503 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: TGFBR1, ALK5, SKR4 発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ) 参照: UniProt: P36897, receptor protein serine/threonine kinase |
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#2: 化合物 | ChemComp-3WJ / |
#3: 化合物 | ChemComp-SO4 / |
#4: 水 | ChemComp-HOH / |
-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: 2.11 Å3/Da / 溶媒含有率: 41.69 % |
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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 / pH: 7.5 / 詳細: 0.1 M Tris-HCl, 240 mM Li2SO4, 24% PEG 4000, pH 7.5 / PH範囲: 7.5 |
-データ収集
回折 | 平均測定温度: 100 K |
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放射光源 | 由来: シンクロトロン / サイト: SLS / ビームライン: X06SA / 波長: 1 Å |
検出器 | タイプ: PSI PILATUS 6M / 検出器: PIXEL / 日付: 2007年12月13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: 1.49→17.2 Å / Num. obs: 48030 / % possible obs: 98.5 % / 冗長度: 7 % / Net I/σ(I): 19.8 |
-解析
ソフトウェア |
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精密化 | 構造決定の手法: 分子置換 / 解像度: 1.49→21.82 Å / Cor.coef. Fo:Fc: 0.9581 / Cor.coef. Fo:Fc free: 0.9376 / SU R Cruickshank DPI: 0.067 / 交差検証法: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.07 / SU Rfree Blow DPI: 0.071 / SU Rfree Cruickshank DPI: 0.069
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原子変位パラメータ | Biso max: 86.16 Å2 / Biso mean: 19.2 Å2 / Biso min: 7.16 Å2
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Refine analyze | Luzzati coordinate error obs: 0.158 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: final / 解像度: 1.49→21.82 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 1.49→1.53 Å / Total num. of bins used: 20
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精密化 TLS | 手法: refined / Origin x: 12.0042 Å / Origin y: 76.3805 Å / Origin z: 12.1617 Å
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精密化 TLSグループ | Selection details: { A|* } |