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- PDB-8sc7: Structure of EGFR in complex with MTX-531 -

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基本情報

登録情報
データベース: PDB / ID: 8sc7
タイトルStructure of EGFR in complex with MTX-531
要素Epidermal growth factor receptor
キーワードTRANSFERASE/INHIBITOR / EGFR / dual EGFR/PI3K inhibitor / TRANSFERASE / TRANSFERASE-INHIBITOR complex
機能・相同性
機能・相同性情報


positive regulation of protein kinase C activity / multivesicular body, internal vesicle lumen / positive regulation of prolactin secretion / negative regulation of cardiocyte differentiation / response to hydroxyisoflavone / diterpenoid metabolic process / Shc-EGFR complex / Inhibition of Signaling by Overexpressed EGFR / ovulation cycle / EGFR interacts with phospholipase C-gamma ...positive regulation of protein kinase C activity / multivesicular body, internal vesicle lumen / positive regulation of prolactin secretion / negative regulation of cardiocyte differentiation / response to hydroxyisoflavone / diterpenoid metabolic process / Shc-EGFR complex / Inhibition of Signaling by Overexpressed EGFR / ovulation cycle / EGFR interacts with phospholipase C-gamma / positive regulation of mucus secretion / epidermal growth factor binding / regulation of peptidyl-tyrosine phosphorylation / response to UV-A / tongue development / PLCG1 events in ERBB2 signaling / midgut development / ERBB2-EGFR signaling pathway / digestive tract morphogenesis / hydrogen peroxide metabolic process / morphogenesis of an epithelial fold / PTK6 promotes HIF1A stabilization / ERBB2 Activates PTK6 Signaling / Signaling by EGFR / intracellular vesicle / response to cobalamin / negative regulation of epidermal growth factor receptor signaling pathway / eyelid development in camera-type eye / cerebral cortex cell migration / protein insertion into membrane / ERBB2 Regulates Cell Motility / protein tyrosine kinase activator activity / Signaling by ERBB4 / Respiratory syncytial virus (RSV) attachment and entry / PI3K events in ERBB2 signaling / negative regulation of mitotic cell cycle / MAP kinase kinase kinase activity / hair follicle development / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / positive regulation of G1/S transition of mitotic cell cycle / GAB1 signalosome / positive regulation of bone resorption / embryonic placenta development / positive regulation of phosphorylation / salivary gland morphogenesis / peptidyl-tyrosine autophosphorylation / positive regulation of peptidyl-serine phosphorylation / positive regulation of glial cell proliferation / positive regulation of vasoconstriction / Signaling by ERBB2 / transmembrane receptor protein tyrosine kinase activity / GRB2 events in EGFR signaling / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / SHC1 events in EGFR signaling / EGFR Transactivation by Gastrin / GRB2 events in ERBB2 signaling / cellular response to epidermal growth factor stimulus / SHC1 events in ERBB2 signaling / cellular response to dexamethasone stimulus / positive regulation of synaptic transmission, glutamatergic / ossification / positive regulation of DNA repair / neuron projection morphogenesis / positive regulation of superoxide anion generation / positive regulation of epithelial cell proliferation / epithelial cell proliferation / liver regeneration / basal plasma membrane / Signal transduction by L1 / positive regulation of DNA replication / positive regulation of protein localization to plasma membrane / astrocyte activation / phosphatidylinositol 3-kinase/protein kinase B signal transduction / NOTCH3 Activation and Transmission of Signal to the Nucleus / cellular response to amino acid stimulus / positive regulation of smooth muscle cell proliferation / cellular response to estradiol stimulus / lung development / EGFR downregulation / synaptic membrane / clathrin-coated endocytic vesicle membrane / Signaling by ERBB2 TMD/JMD mutants / placental growth factor receptor activity / insulin receptor activity / vascular endothelial growth factor receptor activity / Constitutive Signaling by EGFRvIII / hepatocyte growth factor receptor activity / macrophage colony-stimulating factor receptor activity / platelet-derived growth factor alpha-receptor activity / platelet-derived growth factor beta-receptor activity / stem cell factor receptor activity / boss receptor activity / protein tyrosine kinase collagen receptor activity / brain-derived neurotrophic factor receptor activity / transmembrane-ephrin receptor activity / GPI-linked ephrin receptor activity / epidermal growth factor receptor activity / fibroblast growth factor receptor activity / insulin-like growth factor receptor activity / Signaling by ERBB2 ECD mutants
類似検索 - 分子機能
: / Epidermal growth factor receptor transmembrane-juxtamembrane segment / Tyrosine protein kinase, EGF/ERB/XmrK receptor / Growth factor receptor domain 4 / Growth factor receptor domain IV / Receptor L-domain / Furin-like cysteine-rich domain / Receptor L-domain superfamily / Furin-like cysteine rich region / Receptor L domain ...: / Epidermal growth factor receptor transmembrane-juxtamembrane segment / Tyrosine protein kinase, EGF/ERB/XmrK receptor / Growth factor receptor domain 4 / Growth factor receptor domain IV / Receptor L-domain / Furin-like cysteine-rich domain / Receptor L-domain superfamily / Furin-like cysteine rich region / Receptor L domain / Furin-like repeat / Furin-like repeats / Growth factor receptor cysteine-rich domain superfamily / : / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
類似検索 - ドメイン・相同性
: / Epidermal growth factor receptor
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / フーリエ合成 / 解像度: 1.984 Å
データ登録者Whitehead, C.E. / Leopold, J.
資金援助1件
組織認可番号国
Not funded
引用ジャーナル: Nat Cancer / 年: 2024
タイトル: A first-in-class selective inhibitor of EGFR and PI3K offers a single-molecule approach to targeting adaptive resistance.
著者: Whitehead, C.E. / Ziemke, E.K. / Frankowski-McGregor, C.L. / Mumby, R.A. / Chung, J. / Li, J. / Osher, N. / Coker, O. / Baladandayuthapani, V. / Kopetz, S. / Sebolt-Leopold, J.S.
履歴
登録2023年4月5日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02024年6月12日Provider: repository / タイプ: Initial release
改定 1.12024年12月25日Group: Database references / Structure summary
カテゴリ: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

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集合体

登録構造単位
A: Epidermal growth factor receptor
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)38,1454
ポリマ－37,5631
非ポリマー5813
水3,909217
1


  • 登録構造と同一
  • 登録者が定義した集合体
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)145.517, 145.517, 145.517
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDモデル要素
11A-1370-

HOH

21A-1414-

HOH

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要素

#1: タンパク質 Epidermal growth factor receptor / Proto-oncogene c-ErbB-1 / Receptor tyrosine-protein kinase erbB-1


分子量: 37563.457 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: EGFR, ERBB, ERBB1, HER1
発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ)
参照: UniProt: P00533, receptor protein-tyrosine kinase
#2: 化合物 ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / グリセロ-ル


分子量: 92.094 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C3H8O3
#3: 化合物 ChemComp-CL / CHLORIDE ION / クロリド


分子量: 35.453 Da / 分子数: 1 / 由来タイプ: 合成 / 式: Cl
#4: 化合物 ChemComp-D0D / N-[(5P)-2-chloro-5-(4-{[(1R)-1-phenylethyl]amino}quinazolin-6-yl)pyridin-3-yl]methanesulfonamide


分子量: 453.945 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C22H20ClN5O2S / タイプ: SUBJECT OF INVESTIGATION
#5: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 217 / 由来タイプ: 天然 / 式: H2O
研究の焦点であるリガンドがあるかY
Has protein modificationN

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実験情報

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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: 3.42 Å3/Da / 溶媒含有率: 64.01 %
結晶化温度: 285 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 7.5
詳細: 1.05 M Sodium Succinate pH 7.0, 0.1 M HEPES-NaOH pH 6.7

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データ収集

回折平均測定温度: 100 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: ESRF / ビームライン: MASSIF-1 / 波長: 0.965459 Å
検出器タイプ: DECTRIS PILATUS3 2M / 検出器: PIXEL / 日付: 2022年10月29日
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: 0.965459 Å / 相対比: 1
反射解像度: 1.984→34.299 Å / Num. obs: 34279 / % possible obs: 96.6 % / 冗長度: 39.82 %
詳細: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last ...詳細: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last updated 2020-04-13: http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Index/) and the actual quantities provided by MRFANA (https://github.com/githubgphl/MRFANA) from the autoPROC package (https://www.globalphasing.com/autoproc/). In general, the mmCIF categories here should provide items that are currently used in the PDB archive. If there are alternatives, the one recommended by the PDB developers has been selected. The distinction between *_all and *_obs quantities is not always clear: often only one version is actively used within the PDB archive (or is the one recommended by PDB developers). The intention of distinguishing between classes of reflections before and after some kind of observation criterion was applied, can in principle be useful - but such criteria change in various ways throughout the data processing steps (rejection of overloaded or too partial reflections, outlier/misfit rejections during scaling etc) and there is no retrospect computation of data scaling/merging statistics for the reflections used in the final refinement (where another observation criterion might have been applied). Typical data processing will usually only provide one version of statistics at various stages and these are given in the recommended item here, irrespective of the "_all" and "_obs" connotation, see e.g. the use of _reflns.pdbx_Rmerge_I_obs, _reflns.pdbx_Rrim_I_all and _reflns.pdbx_Rpim_I_all. Please note that all statistics related to "merged intensities" (or "merging") are based on inverse-variance weighting of the individual measurements making up a symmetry-unique reflection. This is standard for several decades now, even if some of the dictionary definitions seem to suggest that a simple "mean" or "average" intensity is being used instead. R-values are always given for all symmetry-equivalent reflections following Friedel's law, i.e. Bijvoet pairs are not treated separately (since we want to describe the overall mean intensity and not the mean I(+) and I(-) here). The Rrim metric is identical to the Rmeas R-value and only differs in name. _reflns.pdbx_number_measured_all is the number of measured intensities just before the final merging step (at which point no additional rejection takes place). _reflns.number_obs is the number of symmetry-unique observations, i.e. the result of merging those measurements via inverse-variance weighting. _reflns.pdbx_netI_over_sigmaI is based on the merged intensities (_reflns.number_obs) as expected. _reflns.pdbx_redundancy is synonymous with "multiplicity". The per-shell item _reflns_shell.number_measured_all corresponds to the overall value _reflns.pdbx_number_measured_all. The per-shell item _reflns_shell.number_unique_all corresponds to the overall value _reflns.number_obs. The per-shell item _reflns_shell.percent_possible_all corresponds to the overall value _reflns.percent_possible_obs. The per-shell item _reflns_shell.meanI_over_sigI_obs corresponds to the overall value given as _reflns.pdbx_netI_over_sigmaI. But be aware of the incorrect definition of the former in the current dictionary!
CC1/2: 1 / CC1/2 anomalous: -0.372 / Rmerge(I) obs: 0.0874 / Rpim(I) all: 0.0141 / Rrim(I) all: 0.0886 / AbsDiff over sigma anomalous: 0.748 / Aniso diffraction limit 1: 1.984 Å / Aniso diffraction limit 2: 1.984 Å / Aniso diffraction limit 3: 1.984 Å / Aniso diffraction limit axis 1 ortho1: 1 / Aniso diffraction limit axis 1 ortho2: 0 / Aniso diffraction limit axis 1 ortho3: 0 / Aniso diffraction limit axis 2 ortho1: 0 / Aniso diffraction limit axis 2 ortho2: 1 / Aniso diffraction limit axis 2 ortho3: 0 / Aniso diffraction limit axis 3 ortho1: 0 / Aniso diffraction limit axis 3 ortho2: 0 / Aniso diffraction limit axis 3 ortho3: 1 / Net I/σ(I): 29.54 / Num. measured all: 1364986 / Observed signal threshold: 1.2 / Orthogonalization convention: pdb / % possible anomalous: 96.6 / % possible ellipsoidal: 96.6 / % possible ellipsoidal anomalous: 96.6 / % possible spherical: 96.6 / % possible spherical anomalous: 96.6 / Redundancy anomalous: 20.54 / Signal type: local
反射 シェル
解像度 (Å)冗長度 (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. measured obsNum. unique allNum. unique obsCC1/2CC1/2 anomalousRpim(I) allRrim(I) allAbsDiff over sigma anomalous% possible anomalous% possible ellipsoidal% possible ellipsoidal anomalous% possible spherical% possible spherical anomalousRedundancy anomalous% possible all
4.376-34.29935.430.039194.16121027121027341634160.999-0.3960.00650.03960.77910010010010010018.97100
3.459-4.37638.120.04880.41131526131526345034500.999-0.4640.00780.04870.7410010010010010019.81100
3.015-3.45941.190.083451.87141112141112342634260.998-0.4020.01320.08440.75410010010010010021.3100
2.733-3.01536.960.158628.5126102126102341234120.997-0.1250.02630.16080.75710010010010010019.05100
2.537-2.73339.440.305816.6135679135679344034400.992-0.0490.04920.30980.75910010010010010020.26100
2.385-2.53741.190.54619.47141174141174342734270.98-0.0220.08590.55290.7410010010010010021.11100
2.264-2.38541.840.836.17143332143332342634260.953-0.0610.12950.84010.72610010010010010021.42100
2.165-2.26441.931.2384.16143689143689342734270.901-0.0570.19311.25310.7310010010010010021.45100
2.08-2.16542.51.96342.53145978145978343534350.802-0.0070.30411.9870.72810010010010010021.71100
1.984-2.0839.583.32561.45135367135367342034200.588-0.010.53393.36840.76774.574.174.574.174.520.1574.1

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解析

ソフトウェア
名称バージョン分類
autoPROC1.1.7 20220608data processing
XDSJan 10, 2022データ削減
Aimless0.7.9データスケーリング
STARANISO2.3.87データスケーリング
REFMAC5.8.0352精密化
REFMAC5.8.0352位相決定
精密化構造決定の手法: フーリエ合成 / 解像度: 1.984→34.299 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.956 / SU B: 7.143 / SU ML: 0.099 / 交差検証法: FREE R-VALUE / ESU R: 0.141 / ESU R Free: 0.131 / 詳細: Hydrogens have been added in their riding positions
Rfactor反射数%反射
Rfree0.2156 1439 4.199 %
Rwork0.1859 32835 -
all0.187 --
obs-34274 96.538 %
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: MASK BULK SOLVENT
原子変位パラメータBiso mean: 57.55 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
精密化ステップサイクル: LAST / 解像度: 1.984→34.299 Å
タンパク質核酸リガンド溶媒全体
原子数2606 0 38 217 2861
拘束条件
Refine-IDタイプDev idealDev ideal target数
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0122771
X-RAY DIFFRACTIONr_bond_other_d0.0020.0162593
X-RAY DIFFRACTIONr_ext_dist_refined_b00.013760
X-RAY DIFFRACTIONr_angle_refined_deg1.3151.6723766
X-RAY DIFFRACTIONr_angle_other_deg0.4741.5786049
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5665337
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.941518
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.72210501
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.78110119
X-RAY DIFFRACTIONr_chiral_restr0.0620.2413
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023255
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02533
X-RAY DIFFRACTIONr_nbd_refined0.2090.2493
X-RAY DIFFRACTIONr_symmetry_nbd_other0.180.22496
X-RAY DIFFRACTIONr_nbtor_refined0.1680.21340
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0720.21384
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2141
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0030.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2150.222
X-RAY DIFFRACTIONr_nbd_other0.1490.289
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1870.221
X-RAY DIFFRACTIONr_mcbond_it2.1775.1871331
X-RAY DIFFRACTIONr_mcbond_other2.1765.1871331
X-RAY DIFFRACTIONr_mcangle_it3.7127.7591673
X-RAY DIFFRACTIONr_mcangle_other3.7117.7621674
X-RAY DIFFRACTIONr_scbond_it2.0295.41440
X-RAY DIFFRACTIONr_scbond_other2.0285.3991441
X-RAY DIFFRACTIONr_scangle_it3.4587.9832093
X-RAY DIFFRACTIONr_scangle_other3.4577.9822094
X-RAY DIFFRACTIONr_lrange_it7.07898.9655599
X-RAY DIFFRACTIONr_lrange_other7.06398.3525559
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.984-2.0360.254660.3311384X-RAY DIFFRACTION55.7692
2.036-2.0910.2881060.2872360X-RAY DIFFRACTION97.2781
2.091-2.1520.2481090.2422371X-RAY DIFFRACTION100
2.152-2.2180.2741010.2232275X-RAY DIFFRACTION100
2.218-2.290.264930.222234X-RAY DIFFRACTION100
2.29-2.370.233830.2112155X-RAY DIFFRACTION100
2.37-2.4590.256990.2042069X-RAY DIFFRACTION100
2.459-2.5590.199870.2022005X-RAY DIFFRACTION100
2.559-2.6720.231730.1961936X-RAY DIFFRACTION100
2.672-2.8020.195810.2011831X-RAY DIFFRACTION100
2.802-2.9520.231640.1851766X-RAY DIFFRACTION100
2.952-3.130.244780.1891665X-RAY DIFFRACTION100
3.13-3.3440.194680.1831552X-RAY DIFFRACTION100
3.344-3.6090.214700.1851458X-RAY DIFFRACTION100
3.609-3.9490.206610.1741349X-RAY DIFFRACTION100
3.949-4.4080.204550.1551221X-RAY DIFFRACTION100
4.408-5.0760.17530.1511081X-RAY DIFFRACTION100
5.076-6.1830.257470.204929X-RAY DIFFRACTION100
6.183-8.6050.22260.187747X-RAY DIFFRACTION100
8.605-34.2990.18190.173447X-RAY DIFFRACTION100
精密化 TLS手法: refined / Origin x: 24.8463 Å / Origin y: 7.3736 Å / Origin z: 58.2865 Å
111213212223313233
T0.0655 Å20.0194 Å20.0373 Å2-0.08 Å2-0.0171 Å2--0.0447 Å2
L1.0021 °2-0.9052 °2-0.3673 °2-1.6063 °20.5477 °2--0.3035 °2
S0.1841 Å °0.2407 Å °0.0178 Å °-0.2033 Å °-0.2013 Å °-0.0944 Å °-0.0239 Å °-0.133 Å °0.0172 Å °
精密化 TLSグループSelection: ALL

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  • 万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
  • EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

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