+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 2pog | ||||||
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タイトル | Benzopyrans as Selective Estrogen Receptor b Agonists (SERBAs). Part 2: Structure Activity Relationship Studies on the Benzopyran Scaffold. | ||||||
要素 | Estrogen receptorエストロゲン受容体 | ||||||
キーワード | LIPID BINDING PROTEIN / nuclear receptor (核内受容体) / ligand-binding | ||||||
機能・相同性 | 機能・相同性情報 regulation of epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / regulation of branching involved in prostate gland morphogenesis / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / regulation of toll-like receptor signaling pathway / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / nuclear estrogen receptor activity / epithelial cell proliferation involved in mammary gland duct elongation ...regulation of epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / regulation of branching involved in prostate gland morphogenesis / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / regulation of toll-like receptor signaling pathway / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / nuclear estrogen receptor activity / epithelial cell proliferation involved in mammary gland duct elongation / epithelial cell development / prostate epithelial cord elongation / negative regulation of smooth muscle cell apoptotic process / mammary gland branching involved in pregnancy / uterus development / vagina development / TFIIB-class transcription factor binding / androgen metabolic process / steroid hormone mediated signaling pathway / mammary gland alveolus development / intracellular estrogen receptor signaling pathway / cellular response to estrogen stimulus / estrogen response element binding / : / intracellular steroid hormone receptor signaling pathway / negative regulation of canonical NF-kappaB signal transduction / Nuclear signaling by ERBB4 / RNA polymerase II preinitiation complex assembly / protein localization to chromatin / 14-3-3 protein binding / TBP-class protein binding / steroid binding / nitric-oxide synthase regulator activity / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / ESR-mediated signaling / transcription corepressor binding / negative regulation of miRNA transcription / cellular response to estradiol stimulus / transcription coregulator binding / 細胞分化 / nuclear estrogen receptor binding / positive regulation of nitric-oxide synthase activity / SUMOylation of intracellular receptors / ユークロマチン / negative regulation of DNA-binding transcription factor activity / beta-catenin binding / transcription coactivator binding / positive regulation of DNA-binding transcription factor activity / Nuclear Receptor transcription pathway / response to estrogen / Regulation of RUNX2 expression and activity / Constitutive Signaling by Aberrant PI3K in Cancer / nuclear receptor activity / positive regulation of nitric oxide biosynthetic process / male gonad development / positive regulation of fibroblast proliferation / sequence-specific double-stranded DNA binding / Ovarian tumor domain proteases / PIP3 activates AKT signaling / response to estradiol / phospholipase C-activating G protein-coupled receptor signaling pathway / ATPase binding / positive regulation of cytosolic calcium ion concentration / regulation of inflammatory response / fibroblast proliferation / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / DNA-binding transcription activator activity, RNA polymerase II-specific / Estrogen-dependent gene expression / transcription regulator complex / Extra-nuclear estrogen signaling / calmodulin binding / DNA-binding transcription factor activity, RNA polymerase II-specific / クロマチンリモデリング / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of gene expression / chromatin binding / クロマチン / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / protein kinase binding / positive regulation of DNA-templated transcription / ゴルジ体 / enzyme binding / negative regulation of transcription by RNA polymerase II / シグナル伝達 / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / 核質 / 生体膜 / identical protein binding / 細胞核 / 細胞膜 / 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: 1.84 Å | ||||||
データ登録者 | Richardson, T.I. / Norman, B.H. / Lugar, C.W. / Jones, S.A. / Wang, Y. / Durbin, J.D. / Krishnan, V. / Dodge, J.A. | ||||||
引用 | ジャーナル: Bioorg.Med.Chem.Lett. / 年: 2007 タイトル: Benzopyrans as selective estrogen receptor beta agonists (SERBAs). Part 2: structure-activity relationship studies on the benzopyran scaffold. 著者: Richardson, T.I. / Norman, B.H. / Lugar, C.W. / Jones, S.A. / Wang, Y. / Durbin, J.D. / Krishnan, V. / Dodge, J.A. | ||||||
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 | 2pog.cif.gz | 102.4 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb2pog.ent.gz | 79 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 2pog.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/po/2pog ftp://data.pdbj.org/pub/pdb/validation_reports/po/2pog | HTTPS FTP |
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-関連構造データ
関連構造データ | |
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類似構造データ |
-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: 28297.172 Da / 分子数: 2 / 断片: ligand binding domain (residues 304-551) / 変異: C381S, C417S, C530S / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: ESR1 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P03372 #2: 化合物 | #3: 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: 2.31 Å3/Da / 溶媒含有率: 46.78 % |
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結晶化 | 温度: 289 K / 手法: 蒸気拡散法 / pH: 8 詳細: 0.1 M Tris-HCl, pH 8.0, 0.2 M MgCl2, 20 % PEG 4000 and 10% ethylene glycol., VAPOR DIFFUSION, temperature 289K |
-データ収集
回折 |
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放射光源 | 由来: シンクロトロン / サイト: APS / ビームライン: 31-ID | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
放射 |
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放射波長 | 相対比: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
反射 | 解像度: 1.78→25.203 Å / Num. obs: 50399 / % possible obs: 99.4 % / 冗長度: 6 % / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 7.3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
反射 シェル | Rmerge(I) obs: 0.012
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-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: 1.84→24.98 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2220994.75 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / 交差検証法: THROUGHOUT / σ(F): 0 / 立体化学のターゲット値: Engh & Huber
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溶媒の処理 | 溶媒モデル: FLAT MODEL / Bsol: 45.482 Å2 / ksol: 0.371 e/Å3 | ||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 37.1 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: 1.84→24.98 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 1.84→1.96 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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