- 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
sperm mitochondrial sheath / sulfonylurea receptor binding / dATP binding / CTP binding / positive regulation of protein polymerization / vRNP Assembly / Scavenging by Class F Receptors / UTP binding / sperm plasma membrane / chaperone-mediated autophagy ...sperm mitochondrial sheath / sulfonylurea receptor binding / dATP binding / CTP binding / positive regulation of protein polymerization / vRNP Assembly / Scavenging by Class F Receptors / UTP binding / sperm plasma membrane / chaperone-mediated autophagy / Rho GDP-dissociation inhibitor binding / Respiratory syncytial virus genome replication / telomerase holoenzyme complex assembly / mitochondrial transport / Uptake and function of diphtheria toxin / protein insertion into mitochondrial outer membrane / 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 / TPR domain binding / Assembly and release of respiratory syncytial virus (RSV) virions / non-chaperonin molecular chaperone ATPase / PIWI-interacting RNA (piRNA) biogenesis / dendritic growth cone / Sema3A PAK dependent Axon repulsion / protein unfolding / positive regulation of cell size / regulation of protein ubiquitination / HSF1-dependent transactivation / response to unfolded protein / enzyme-substrate adaptor activity / skeletal muscle contraction / HSF1 activation / regulation of protein-containing complex assembly / telomere maintenance via telomerase / regulation of postsynaptic membrane neurotransmitter receptor levels / Attenuation phase / chaperone-mediated protein complex assembly / neurofibrillary tangle assembly / axonal growth cone / RHOBTB2 GTPase cycle / positive regulation of lamellipodium assembly / eNOS activation / nitric oxide metabolic process / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / DNA polymerase binding / positive regulation of defense response to virus by host / response to salt stress / Signaling by ERBB2 / positive regulation of telomere maintenance via telomerase / cardiac muscle cell apoptotic process / endocytic vesicle lumen / positive regulation of cardiac muscle contraction / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / nitric-oxide synthase regulator activity / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / activation of innate immune response / Anchoring of the basal body to the plasma membrane / lysosomal lumen / positive regulation of interferon-beta production / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / response to cold / ESR-mediated signaling / Constitutive Signaling by Overexpressed ERBB2 / protein tyrosine kinase binding / AURKA Activation by TPX2 / VEGFR2 mediated vascular permeability / ATP-dependent protein folding chaperone / response to cocaine / Signaling by ERBB2 TMD/JMD mutants / brush border membrane / Constitutive Signaling by EGFRvIII / Signaling by ERBB2 ECD mutants / DDX58/IFIH1-mediated induction of interferon-alpha/beta / Signaling by ERBB2 KD Mutants / cellular response to virus / Regulation of actin dynamics for phagocytic cup formation / Regulation of necroptotic cell death / tau protein binding / VEGFA-VEGFR2 Pathway / histone deacetylase binding / positive regulation of protein import into nucleus / Downregulation of ERBB2 signaling / response to estrogen / Chaperone Mediated Autophagy / positive regulation of protein catabolic process / neuron migration / Aggrephagy / MHC class II protein complex binding / disordered domain specific binding / The role of GTSE1 in G2/M progression after G2 checkpoint 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-like ATPase, C-terminal domain / Heat Shock Protein 90 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / 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-like ATPase, C-terminal domain / Heat Shock Protein 90 / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / 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