- PDB-2ydk: Discovery of Checkpoint Kinase Inhibitor AZD7762 by Structure Bas... -
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基本情報
登録情報
データベース: PDB / ID: 2ydk
タイトル
Discovery of Checkpoint Kinase Inhibitor AZD7762 by Structure Based Design and Optimization of Thiophene Carboxamide Ureas
要素
SERINE/THREONINE-PROTEIN KINASE CHK1
キーワード
TRANSFERASE
機能・相同性
機能・相同性情報
negative regulation of G0 to G1 transition / apoptotic process involved in development / histone H3T11 kinase activity / negative regulation of DNA biosynthetic process / mitotic G2/M transition checkpoint / negative regulation of mitotic nuclear division / regulation of mitotic centrosome separation / Activation of ATR in response to replication stress / inner cell mass cell proliferation / regulation of double-strand break repair via homologous recombination ...negative regulation of G0 to G1 transition / apoptotic process involved in development / histone H3T11 kinase activity / negative regulation of DNA biosynthetic process / mitotic G2/M transition checkpoint / negative regulation of mitotic nuclear division / regulation of mitotic centrosome separation / Activation of ATR in response to replication stress / inner cell mass cell proliferation / regulation of double-strand break repair via homologous recombination / negative regulation of gene expression, epigenetic / nucleus organization / cellular response to caffeine / Transcriptional Regulation by E2F6 / mitotic G2 DNA damage checkpoint signaling / Presynaptic phase of homologous DNA pairing and strand exchange / condensed nuclear chromosome / replicative senescence / signal transduction in response to DNA damage / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / positive regulation of cell cycle / regulation of signal transduction by p53 class mediator / DNA damage checkpoint signaling / replication fork / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / TP53 Regulates Transcription of DNA Repair Genes / peptidyl-threonine phosphorylation / G2/M DNA damage checkpoint / cellular response to mechanical stimulus / Signaling by SCF-KIT / G2/M transition of mitotic cell cycle / Processing of DNA double-strand break ends / regulation of cell population proliferation / DNA replication / Regulation of TP53 Activity through Phosphorylation / chromatin remodeling / non-specific serine/threonine protein kinase / protein kinase activity / protein domain specific binding / protein phosphorylation / intracellular membrane-bounded organelle / DNA repair / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / DNA damage response / chromatin / apoptotic process / protein-containing complex / extracellular space / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol 類似検索 - 分子機能
Checkpoint kinase 1, catalytic domain / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain / Protein kinase, ATP binding site ...Checkpoint kinase 1, catalytic domain / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta 類似検索 - ドメイン・相同性
モノクロメーター: SI111 / 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: 1.0052 Å / 相対比: 1
反射
解像度: 1.9→23.9 Å / Num. obs: 23512 / % possible obs: 94.9 % / Observed criterion σ(I): 2 / 冗長度: 2.39 % / Biso Wilson estimate: 13.696 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 5.9
反射 シェル
解像度: 1.9→2 Å / 冗長度: 2.1 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2 / % possible all: 83.8
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解析
ソフトウェア
名称
バージョン
分類
REFMAC
5.5.0110
精密化
MOSFLM
データ削減
SCALA
データスケーリング
AMoRE
位相決定
精密化
構造決定の手法: 分子置換 / 解像度: 1.9→23.01 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.931 / SU B: 7.715 / SU ML: 0.106 / 交差検証法: THROUGHOUT / ESU R: 0.159 / ESU R Free: 0.148 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD / 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
Rfactor
反射数
%反射
Selection details
Rfree
0.22612
1196
5.1 %
RANDOM
Rwork
0.18057
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obs
0.18303
22316
94.32 %
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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: 1.4 Å / 溶媒モデル: BABINET MODEL WITH MASK