- PDB-3bm9: Discovery of Benzisoxazoles as Potent Inhibitors of Chaperone Hsp90 -
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基本情報
登録情報
データベース: PDB / ID: 3bm9
タイトル
Discovery of Benzisoxazoles as Potent Inhibitors of Chaperone Hsp90
要素
Heat shock protein HSP 90-alpha
キーワード
CHAPERONE / ATP binding domain / Alternative splicing / ATP-binding / Cytoplasm / Nucleotide-binding / Phosphoprotein / Stress response
機能・相同性
機能・相同性情報
positive regulation of tau-protein kinase activity / sperm mitochondrial sheath / dATP binding / Scavenging by Class F Receptors / sulfonylurea receptor binding / CTP binding / positive regulation of protein polymerization / vRNP Assembly / UTP binding / sperm plasma membrane ...positive regulation of tau-protein kinase activity / sperm mitochondrial sheath / dATP binding / Scavenging by Class F Receptors / sulfonylurea receptor binding / CTP binding / positive regulation of protein polymerization / vRNP Assembly / UTP binding / sperm plasma membrane / chaperone-mediated autophagy / telomerase holoenzyme complex assembly / protein insertion into mitochondrial outer membrane / Respiratory syncytial virus genome replication / Rho GDP-dissociation inhibitor binding / Uptake and function of diphtheria toxin / mitochondrial transport / Drug-mediated inhibition of ERBB2 signaling / Resistance of ERBB2 KD mutants to trastuzumab / Resistance of ERBB2 KD mutants to sapitinib / Resistance of ERBB2 KD mutants to tesevatinib / Resistance of ERBB2 KD mutants to neratinib / Resistance of ERBB2 KD mutants to osimertinib / Resistance of ERBB2 KD mutants to afatinib / Resistance of ERBB2 KD mutants to AEE788 / Resistance of ERBB2 KD mutants to lapatinib / Drug resistance in ERBB2 TMD/JMD mutants / PIWI-interacting RNA (piRNA) biogenesis / TPR domain binding / non-chaperonin molecular chaperone ATPase / Assembly and release of respiratory syncytial virus (RSV) virions / dendritic growth cone / regulation of postsynaptic membrane neurotransmitter receptor levels / Sema3A PAK dependent Axon repulsion / regulation of protein ubiquitination / skeletal muscle contraction / Signaling by ERBB2 / telomere maintenance via telomerase / HSF1-dependent transactivation / positive regulation of cell size / response to unfolded protein / protein unfolding / chaperone-mediated protein complex assembly / HSF1 activation / regulation of protein-containing complex assembly / Attenuation phase / RHOBTB2 GTPase cycle / eNOS activation / axonal growth cone / positive regulation of lamellipodium assembly / DNA polymerase binding / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / positive regulation of defense response to virus by host / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / cardiac muscle cell apoptotic process / endocytic vesicle lumen / Recruitment of NuMA to mitotic centrosomes / response to salt stress / positive regulation of cardiac muscle contraction / Anchoring of the basal body to the plasma membrane / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / activation of innate immune response / nitric-oxide synthase regulator activity / positive regulation of interferon-beta production / response to cold / Constitutive Signaling by Overexpressed ERBB2 / AURKA Activation by TPX2 / lysosomal lumen / ESR-mediated signaling / protein tyrosine kinase binding / Signaling by ERBB2 TMD/JMD mutants / VEGFR2 mediated vascular permeability / Constitutive Signaling by EGFRvIII / response to cocaine / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / brush border membrane / ATP-dependent protein folding chaperone / Downregulation of ERBB2 signaling / neuron migration / DDX58/IFIH1-mediated induction of interferon-alpha/beta / tau protein binding / Regulation of necroptotic cell death / cellular response to virus / Regulation of actin dynamics for phagocytic cup formation / VEGFA-VEGFR2 Pathway / histone deacetylase binding / Aggrephagy / Chaperone Mediated Autophagy / positive regulation of protein import into nucleus / response to estrogen / positive regulation of protein catabolic process / The role of GTSE1 in G2/M progression after G2 checkpoint / regulation of protein localization / disordered domain specific binding / Regulation of PLK1 Activity at G2/M Transition / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / positive regulation of nitric oxide biosynthetic process 類似検索 - 分子機能
Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. / HSP90, C-terminal domain / Heat shock protein Hsp90, N-terminal / Heat shock protein Hsp90 family / Hsp90 protein / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase ...Heat shock protein Hsp90, conserved site / Heat shock hsp90 proteins family signature. / HSP90, C-terminal domain / Heat shock protein Hsp90, N-terminal / Heat shock protein Hsp90 family / Hsp90 protein / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPase, C-terminal domain / Heat Shock Protein 90 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold / 2-Layer Sandwich / Alpha Beta 類似検索 - ドメイン・相同性
Chem-BXZ / Heat shock protein HSP 90-alpha 類似検索 - 構成要素
解像度: 1.6→1.64 Å / 冗長度: 1.6 % / Mean I/σ(I) obs: 3.3 / Num. unique all: 2592 / Rsym value: 0.208 / % possible all: 59.8
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解析
ソフトウェア
名称
バージョン
分類
PHENIX
(phenix.refine)
精密化
StructureStudio
データ収集
HKL-2000
データ削減
HKL-2000
データスケーリング
PHASER
位相決定
精密化
構造決定の手法: 分子置換 / 解像度: 1.6→34.65 Å / SU ML: 0.15 / Isotropic thermal model: isotropic / 交差検証法: THROUGHOUT / σ(F): -3 / 位相誤差: 18 / 立体化学のターゲット値: Engh & Huber 詳細: LIGAND BXZ OCCUPANCY WAS REFINED AS A SINGLE GROUP TO 0.85. FOLLOWING THIS REFINEMENT, THE OCCUPANCY OF THE BROMINE ATOM WAS ADJUSTED TO 0.70 BASED ON RESIDUAL MAPS. RESIDUES 155 to 157 SHOW ...詳細: LIGAND BXZ OCCUPANCY WAS REFINED AS A SINGLE GROUP TO 0.85. FOLLOWING THIS REFINEMENT, THE OCCUPANCY OF THE BROMINE ATOM WAS ADJUSTED TO 0.70 BASED ON RESIDUAL MAPS. RESIDUES 155 to 157 SHOW TWO (MAINCHAIN) CONFORMATIONS, BUT ONLY THE MAJOR CONFORMATION WAS MODELED
Rfactor
反射数
%反射
Selection details
Rfree
0.1861
1744
5.03 %
Random
Rwork
0.1635
-
-
-
all
0.1646
39211
-
-
obs
0.1646
36282
92.4 %
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原子変位パラメータ
Biso mean: 20.11 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-2.2099 Å2
0 Å2
0 Å2
2-
-
1.2539 Å2
0 Å2
3-
-
-
0.9561 Å2
精密化ステップ
サイクル: LAST / 解像度: 1.6→34.65 Å
タンパク質
核酸
リガンド
溶媒
全体
原子数
1662
0
19
355
2036
拘束条件
Refine-ID
タイプ
Dev ideal
X-RAY DIFFRACTION
f_bond_d
0.004
X-RAY DIFFRACTION
f_angle_d
0.924
X-RAY DIFFRACTION
f_dihedral_angle_d
15.044
LS精密化 シェル
Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12