+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 2vto | ||||||
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タイトル | Identification of N-(4-piperidinyl)-4-(2,6-dichlorobenzoylamino)-1H- pyrazole-3-carboxamide (AT7519), a Novel Cyclin Dependent Kinase Inhibitor Using Fragment-Based X-Ray Crystallography and Structure Based Drug Design. | ||||||
要素 | CELL DIVISION PROTEIN KINASE 2細胞分裂 | ||||||
キーワード | TRANSFERASE (転移酵素) / MITOSIS (有糸分裂) / CELL CYCLE (細胞周期) / SERINE/THREONINE PROTEIN KINASE | ||||||
機能・相同性 | 機能・相同性情報 cyclin A1-CDK2 complex / cyclin E2-CDK2 complex / cyclin E1-CDK2 complex / cyclin A2-CDK2 complex / positive regulation of DNA-templated DNA replication initiation / G2期 / cyclin-dependent protein kinase activity / Y染色体 / Phosphorylation of proteins involved in G1/S transition by active Cyclin E:Cdk2 complexes / positive regulation of heterochromatin formation ...cyclin A1-CDK2 complex / cyclin E2-CDK2 complex / cyclin E1-CDK2 complex / cyclin A2-CDK2 complex / positive regulation of DNA-templated DNA replication initiation / G2期 / cyclin-dependent protein kinase activity / Y染色体 / Phosphorylation of proteins involved in G1/S transition by active Cyclin E:Cdk2 complexes / positive regulation of heterochromatin formation / p53-Dependent G1 DNA Damage Response / X染色体 / PTK6 Regulates Cell Cycle / regulation of anaphase-promoting complex-dependent catabolic process / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / centriole replication / Regulation of APC/C activators between G1/S and early anaphase / centrosome duplication / Telomere Extension By Telomerase / G0 and Early G1 / Activation of the pre-replicative complex / cellular response to nitric oxide / cyclin-dependent protein kinase holoenzyme complex / サイクリン依存性キナーゼ / cyclin-dependent protein serine/threonine kinase activity / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / カハール体 / Activation of ATR in response to replication stress / Cyclin E associated events during G1/S transition / Cyclin A/B1/B2 associated events during G2/M transition / Cyclin A:Cdk2-associated events at S phase entry / condensed chromosome / mitotic G1 DNA damage checkpoint signaling / regulation of mitotic cell cycle / regulation of G2/M transition of mitotic cell cycle / cyclin binding / post-translational protein modification / : / meiotic cell cycle / positive regulation of DNA replication / male germ cell nucleus / potassium ion transport / DNA Damage/Telomere Stress Induced Senescence / G1/S transition of mitotic cell cycle / CDK-mediated phosphorylation and removal of Cdc6 / SCF(Skp2)-mediated degradation of p27/p21 / 遺伝的組換え / Orc1 removal from chromatin / Transcriptional regulation of granulopoiesis / Cyclin D associated events in G1 / G2/M transition of mitotic cell cycle / 細胞老化 / Regulation of TP53 Degradation / 核膜 / Factors involved in megakaryocyte development and platelet production / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / 遺伝子発現の調節 / peptidyl-serine phosphorylation / Regulation of TP53 Activity through Phosphorylation / DNA複製 / Ras protein signal transduction / transcription regulator complex / chromosome, telomeric region / エンドソーム / クロマチンリモデリング / protein domain specific binding / 細胞分裂 / protein phosphorylation / protein serine kinase activity / DNA修復 / protein serine/threonine kinase activity / 中心体 / DNA-templated transcription / positive regulation of cell population proliferation / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / magnesium ion binding / シグナル伝達 / 核質 / ATP 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 / 分子置換 / 解像度: 2.19 Å | ||||||
データ登録者 | Wyatt, P.G. / Woodhead, A.J. / Boulstridge, J.A. / Berdini, V. / Carr, M.G. / Cross, D.M. / Danillon, D. / Davis, D.J. / Devine, L.A. / Early, T.R. ...Wyatt, P.G. / Woodhead, A.J. / Boulstridge, J.A. / Berdini, V. / Carr, M.G. / Cross, D.M. / Danillon, D. / Davis, D.J. / Devine, L.A. / Early, T.R. / Feltell, R.E. / Lewis, E.J. / McMenamin, R.L. / Navarro, E.F. / O'Brien, M.A. / O'Reilly, M. / Reule, M. / Saxty, G. / Seavers, L.C.A. / Smith, D. / Squires, M.S. / Trewartha, G. / Walker, M.T. / Woolford, A.J. | ||||||
引用 | ジャーナル: J.Med.Chem. / 年: 2008 タイトル: Identification of N-(4-Piperidinyl)-4-(2,6-Dichlorobenzoylamino)-1H-Pyrazole-3-Carboxamide (at7519), a Novel Cyclin Dependent Kinase Inhibitor Using Fragment-Based X-Ray Crystallography ...タイトル: Identification of N-(4-Piperidinyl)-4-(2,6-Dichlorobenzoylamino)-1H-Pyrazole-3-Carboxamide (at7519), a Novel Cyclin Dependent Kinase Inhibitor Using Fragment-Based X-Ray Crystallography and Structure Based Drug Design. 著者: Wyatt, P.G. / Woodhead, A.J. / Berdini, V. / Boulstridge, J.A. / Carr, M.G. / Cross, D.M. / Davis, D.J. / Devine, L.A. / Early, T.R. / Feltell, R.E. / Lewis, E.J. / McMenamin, R.L. / Navarro, ...著者: Wyatt, P.G. / Woodhead, A.J. / Berdini, V. / Boulstridge, J.A. / Carr, M.G. / Cross, D.M. / Davis, D.J. / Devine, L.A. / Early, T.R. / Feltell, R.E. / Lewis, E.J. / McMenamin, R.L. / Navarro, E.F. / O'Brien, M.A. / O'Reilly, M. / Reule, M. / Saxty, G. / Seavers, L.C.A. / Smith, D. / Squires, M.S. / Trewartha, G. / Walker, M.T. / Woolford, A.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 | 2vto.cif.gz | 77.5 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb2vto.ent.gz | 59.5 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 2vto.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/vt/2vto ftp://data.pdbj.org/pub/pdb/validation_reports/vt/2vto | 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: 33976.488 Da / 分子数: 1 / 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): SF9 発現宿主: SPODOPTERA FRUGIPERDA (ツマジロクサヨトウ) 参照: UniProt: P24941, non-specific serine/threonine protein kinase, サイクリン依存性キナーゼ |
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#2: 化合物 | ChemComp-LZ8 / |
#3: 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: 1.99 Å3/Da / 溶媒含有率: 37.7 % / 解説: NONE |
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結晶化 | pH: 6.7 詳細: 0.1M HEPES/NAOH, 0.0475M AMMONIUM ACETATE, 12% W/V PEG3350, pH 6.7 |
-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: 回転陽極 / タイプ: RIGAKU RU200HR / 波長: 1.5418 |
検出器 | タイプ: RIGAKU CCD / 検出器: CCD / 詳細: OSMIC CONFOCAL PURPLE |
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: 1.5418 Å / 相対比: 1 |
反射 | 解像度: 2.19→37.04 Å / Num. obs: 14546 / % possible obs: 96.2 % / Observed criterion σ(I): 0 / 冗長度: 3.2 % / Biso Wilson estimate: 27.43 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.97 |
反射 シェル | 解像度: 2.19→2.28 Å / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 3 / % possible all: 87.9 |
-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: IN-HOUSE STRUCTURE 解像度: 2.19→37.04 Å / 交差検証法: THROUGHOUT / σ(F): 0
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原子変位パラメータ | Biso mean: 29.17 Å2
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精密化ステップ | サイクル: LAST / 解像度: 2.19→37.04 Å
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LS精密化 シェル | 解像度: 2.19→2.32 Å / Total num. of bins used: 9
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