+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 4a4l | ||||||
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タイトル | CRYSTAL STRUCTURE OF POLO-LIKE KINASE 1 IN COMPLEX WITH A 5-(2-AMINO- PYRIMIDIN-4-YL)-1H-PYRROLE INHIBITOR | ||||||
要素 | SERINE/THREONINE-PROTEIN KINASE PLK1 | ||||||
キーワード | TRANSFERASE (転移酵素) | ||||||
機能・相同性 | 機能・相同性情報 Mitotic Telophase/Cytokinesis / regulation of protein localization to cell cortex / Mitotic Metaphase/Anaphase Transition / Golgi inheritance / synaptonemal complex disassembly / Activation of NIMA Kinases NEK9, NEK6, NEK7 / homologous chromosome segregation / polo kinase / nuclear membrane disassembly / mitotic nuclear membrane disassembly ...Mitotic Telophase/Cytokinesis / regulation of protein localization to cell cortex / Mitotic Metaphase/Anaphase Transition / Golgi inheritance / synaptonemal complex disassembly / Activation of NIMA Kinases NEK9, NEK6, NEK7 / homologous chromosome segregation / polo kinase / nuclear membrane disassembly / mitotic nuclear membrane disassembly / protein localization to nuclear envelope / Phosphorylation of Emi1 / metaphase/anaphase transition of mitotic cell cycle / synaptonemal complex / female meiosis chromosome segregation / Phosphorylation of the APC/C / regulation of protein binding / anaphase-promoting complex binding / outer kinetochore / negative regulation of cyclin-dependent protein serine/threonine kinase activity / positive regulation of ubiquitin protein ligase activity / regulation of mitotic spindle assembly / microtubule bundle formation / Polo-like kinase mediated events / Golgi Cisternae Pericentriolar Stack Reorganization / mitotic chromosome condensation / regulation of mitotic metaphase/anaphase transition / sister chromatid cohesion / positive regulation of ubiquitin-protein transferase activity / centrosome cycle / double-strand break repair via alternative nonhomologous end joining / regulation of mitotic cell cycle phase transition / mitotic spindle assembly checkpoint signaling / mitotic spindle pole / regulation of anaphase-promoting complex-dependent catabolic process / mitotic G2 DNA damage checkpoint signaling / mitotic sister chromatid segregation / establishment of mitotic spindle orientation / positive regulation of proteolysis / mitotic cytokinesis / centriolar satellite / spindle midzone / negative regulation of double-strand break repair via homologous recombination / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Cyclin A/B1/B2 associated events during G2/M transition / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / protein localization to chromatin / Resolution of Sister Chromatid Cohesion / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / regulation of mitotic cell cycle / 中心小体 / AURKA Activation by TPX2 / Condensation of Prophase Chromosomes / mitotic spindle organization / positive regulation of peptidyl-threonine phosphorylation / regulation of cytokinesis / RHO GTPases Activate Formins / protein destabilization / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / establishment of protein localization / 動原体 / 紡錘体 / spindle / positive regulation of protein localization to nucleus / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / G2/M transition of mitotic cell cycle / microtubule cytoskeleton / Regulation of PLK1 Activity at G2/M Transition / double-strand break repair / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / mitotic cell cycle / midbody / microtubule binding / peptidyl-serine phosphorylation / protein ubiquitination / regulation of cell cycle / protein kinase activity / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / 中心体 / クロマチン / negative regulation of apoptotic process / protein kinase binding / negative regulation of transcription by RNA polymerase II / magnesium ion binding / 核質 / ATP binding / identical protein binding / 細胞核 / 細胞質基質 / 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 / 分子置換 / 解像度: 2.35 Å | ||||||
データ登録者 | Bertrand, J.A. / Bossi, R.T. | ||||||
引用 | ジャーナル: Bioorg.Med.Chem.Lett. / 年: 2012 タイトル: 5-(2-Amino-Pyrimidin-4-Yl)-1H-Pyrrole and 2-(2-Amino-Pyrimidin-4-Yl)-1,5,6,7-Tetrahydro-Pyrrolo[3,2-C]Pyridin-4-One Derivatives as New Classes of Selective and Orally Available Polo- ...タイトル: 5-(2-Amino-Pyrimidin-4-Yl)-1H-Pyrrole and 2-(2-Amino-Pyrimidin-4-Yl)-1,5,6,7-Tetrahydro-Pyrrolo[3,2-C]Pyridin-4-One Derivatives as New Classes of Selective and Orally Available Polo-Like Kinase 1 Inhibitors. 著者: Caruso, M. / Valsasina, B. / Ballinari, D. / Bertrand, J.A. / Brasca, M.G. / Caldarelli, M. / Cappella, P. / Fiorentini, F. / Gianellini, L.M. / Scolaro, A. / Beria, I. | ||||||
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 | 4a4l.cif.gz | 76.1 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb4a4l.ent.gz | 55.6 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 4a4l.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/a4/4a4l ftp://data.pdbj.org/pub/pdb/validation_reports/a4/4a4l | 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: 35646.531 Da / 分子数: 1 / 断片: KINASE DOMAIN, RESIDUES 36-345 / 由来タイプ: 組換発現 / 由来: (組換発現) HOMO SAPIENS (ヒト) / 細胞株 (発現宿主): High Five 発現宿主: SPODOPTERA FRUGIPERDA (ツマジロクサヨトウ) 参照: UniProt: P53350, polo kinase |
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#2: 化合物 | ChemComp-ZN / |
#3: 化合物 | ChemComp-TLA / |
#4: 化合物 | ChemComp-939 / |
#5: 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: 2.8 Å3/Da / 溶媒含有率: 56.1 % / 解説: NONE |
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結晶化 | 温度: 277 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 6 詳細: 1.2 M NA/K TARTRATE, 25 MM ZN ACETATE, 0.10 M MES PH 6.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277 K |
-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: ESRF / ビームライン: ID14-3 / 波長: 0.931 |
検出器 | タイプ: ADSC CCD / 検出器: CCD / 日付: 2007年5月5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: 0.931 Å / 相対比: 1 |
反射 | 解像度: 2.35→57.35 Å / Num. obs: 16356 / % possible obs: 95.9 % / Observed criterion σ(I): 0 / 冗長度: 2.3 % / Biso Wilson estimate: 26.9 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.4 |
反射 シェル | 解像度: 2.35→2.48 Å / 冗長度: 2.1 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2 / % possible all: 78.9 |
-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 開始モデル: INTERNAL STRUCTURE WITH AMP-PNP 解像度: 2.35→28.84 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1698701.39 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / 交差検証法: THROUGHOUT / σ(F): 0
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溶媒の処理 | 溶媒モデル: FLAT MODEL / Bsol: 47.7489 Å2 / ksol: 0.390391 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 42.4 Å2
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Refine analyze |
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精密化ステップ | サイクル: LAST / 解像度: 2.35→28.84 Å
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拘束条件 |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS精密化 シェル | 解像度: 2.35→2.5 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
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Xplor file |
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