+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 2v22 | ||||||
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タイトル | REPLACE: A strategy for Iterative Design of Cyclin Binding Groove Inhibitors | ||||||
要素 |
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キーワード | TRANSFERASE (転移酵素) / POLYMORPHISM / CYCLIN GROOVE / CELL DIVISION (細胞分裂) / CDK2 (サイクリン依存性キナーゼ2) / KINASE (キナーゼ) / CYCLIN (サイクリン) / ACTIVE / MITOSIS (有糸分裂) / INHIBITION (酵素阻害剤) / PHOSPHORYLATION (リン酸化) / NUCLEOTIDE-BINDING / SERINE/THREONINE-PROTEIN KINASE / CELL CYCLE (細胞周期) / NONPEPTIDE / ATP-BINDING | ||||||
機能・相同性 | 機能・相同性情報 Phosphorylation of proteins involved in the G2/M transition by Cyclin A:Cdc2 complexes / cyclin A2-CDK1 complex / cell cycle G1/S phase transition / cellular response to luteinizing hormone stimulus / mitotic cell cycle phase transition / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / cellular response to leptin stimulus / male pronucleus / female pronucleus / cellular response to cocaine ...Phosphorylation of proteins involved in the G2/M transition by Cyclin A:Cdc2 complexes / cyclin A2-CDK1 complex / cell cycle G1/S phase transition / cellular response to luteinizing hormone stimulus / mitotic cell cycle phase transition / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / cellular response to leptin stimulus / male pronucleus / female pronucleus / cellular response to cocaine / response to glucagon / cyclin-dependent protein serine/threonine kinase regulator activity / cellular response to insulin-like growth factor stimulus / positive regulation of DNA biosynthetic process / cochlea development / cyclin A1-CDK2 complex / cyclin E2-CDK2 complex / cyclin E1-CDK2 complex / cellular response to platelet-derived growth factor stimulus / 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) / regulation of DNA replication / 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 / cyclin-dependent protein kinase holoenzyme complex / cellular response to nitric oxide / サイクリン依存性キナーゼ / カハール体 / animal organ regeneration / cyclin-dependent protein serine/threonine kinase activity / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / 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 / response to organic substance / male germ cell nucleus / cellular response to estradiol stimulus / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / G1/S transition of mitotic cell cycle / potassium ion transport / DNA Damage/Telomere Stress Induced Senescence / 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 / positive regulation of fibroblast proliferation / 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 / cellular response to hypoxia / Senescence-Associated Secretory Phenotype (SASP) / 遺伝子発現の調節 / peptidyl-serine phosphorylation / Ras protein signal transduction / Regulation of TP53 Activity through Phosphorylation / transcription regulator complex / DNA複製 / chromosome, telomeric region / Ub-specific processing proteases / エンドソーム / クロマチンリモデリング / 細胞分裂 / protein domain specific binding / 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 / protein kinase binding / 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: 2.6 Å | ||||||
データ登録者 | Andrews, M.J. / Kontopidis, G. / McInnes, C. / Plater, A. / Innes, L. / Cowan, A. / Jewsbury, P. / Fischer, P.M. | ||||||
引用 | ジャーナル: Chembiochem / 年: 2006 タイトル: Replace: A Strategy for Iterative Design of Cyclin- Binding Groove Inhibitors 著者: Andrews, M.J. / Kontopidis, G. / Mcinnes, C. / Plater, A. / Innes, L. / Cowan, A. / Jewsbury, P. / Fischer, P.M. #1: ジャーナル: Chem.Biol. / 年: 2006 タイトル: Differential Binding of Inhibitors to Active and Inactive Cdk2 Provides Insights for Drug Design 著者: Kontopidis, G. / Mcinnes, C. / Pandalaneni, S.R. / Mcnae, I. / Gibson, D. / Mezna, M. / Thomas, M. / Wood, G. / Wang, S. / Walkinshaw, M.D. / Fische, P.M. | ||||||
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 | 2v22.cif.gz | 243.4 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb2v22.ent.gz | 197.2 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 2v22.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/v2/2v22 ftp://data.pdbj.org/pub/pdb/validation_reports/v2/2v22 | 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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単位格子 |
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非結晶学的対称性 (NCS) | NCSドメイン:
NCSドメイン領域: Component-ID: 1 / End auth comp-ID: LEU / End label comp-ID: LEU
NCSアンサンブル:
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-要素
#1: タンパク質 | 分子量: 33976.488 Da / 分子数: 2 / 由来タイプ: 組換発現 / 詳細: TRIAZOL-1-METHYL-PYRIMIDIN INHIBITOR / 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, EC: 2.7.1.37 #2: タンパク質 | 分子量: 29753.410 Da / 分子数: 2 / 由来タイプ: 組換発現 / 詳細: CAP-TETRAPEPTIDE INHIBITOR / 由来: (組換発現) HOMO SAPIENS (ヒト) / 発現宿主: ESCHERICHIA COLI (大腸菌) / 参照: UniProt: P20248 #3: 化合物 | #4: 水 | ChemComp-HOH / | |
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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: 2.7 Å3/Da / 溶媒含有率: 54 % / 解説: NONE |
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結晶化 | pH: 7.8 / 詳細: 22% PEG 3350, 0.1M NA3-CIT, pH 7.8 |
-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: ID14-2 / 波長: 0.933 |
検出器 | タイプ: ADSC CCD / 検出器: CCD / 日付: 2003年2月14日 / 詳細: MIRRORS |
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: 0.933 Å / 相対比: 1 |
反射 | 解像度: 2.6→20 Å / Num. obs: 126787 / % possible obs: 95.4 % / Observed criterion σ(I): 2 / 冗長度: 3.4 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 13.2 |
反射 シェル | 解像度: 2.6→2.74 Å / Rmerge(I) obs: 1.06 / % possible all: 98 |
-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: PDB ENTRY 1OL1 解像度: 2.6→16 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.889 / SU B: 12.366 / SU ML: 0.262 / 交差検証法: THROUGHOUT / ESU R: 1.815 / ESU R Free: 0.367 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. CHAIN A AND C RESIDUES 12-17, 37-41, 159-162
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溶媒の処理 | イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.2 Å / 溶媒モデル: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 53.29 Å2
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精密化ステップ | サイクル: LAST / 解像度: 2.6→16 Å
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拘束条件 |
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