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新型コロナウイルスの構造情報

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コロナウイルス
コロナウイルス, 2020. David S. Goodsell@RCSB PDB による原画を修正

最近、新型コロナウイルス感染症(Novel Coronavirus disease 2019: COVID-19)の拡大が世界中で深刻な問題となっています。早急にこの新型ウイルス(Severe Acute Respiratory Syndrome Coronavirus 2: SARS-CoV-2)を理解し有効な薬を開発するため,関連するタンパク質の構造研究は既に始まっています。そして,解明された構造はPDBに登録されていっています。PDBjでは利用者の利便を図るため,新型コロナウイルス特集ページを作成しました。新たなエントリーが毎週水曜日の週次更新で公開されると、同時にこのページにも追加されます。

またこのウイルスのタンパク質に関する解説記事を以下の「今月の分子」ページに掲載しています。

「全エントリー」のタブでは,同じ著者によるグループ登録のエントリーも全て区別し,すべてのPDB IDを省略せず表示しています。 「代表構造」タブには最も分解能の高い代表構造のみを表示しており,アミノ酸配列が100%同じPDBエントリーはリガンドが異なるものも含め除外してあります。 「最新のエントリー」のタブは,今週公開された最も新しいエントリーです。


作成日: 2020-09-03 (最終更新日: more than 1 year ago)2022-09-02
9C80
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BU of 9c80 by Molmil
Co-structure of SARS-CoV-2 (COVID-19 with covalent inhibitor
分子名称: (5R,7S,8R)-7-(2-fluorophenyl)-3-[(2-fluorophenyl)carbamoyl]-4,5,6,7-tetrahydropyrazolo[1,5-a]pyrimidine-5-carboxylic acid, 3C-like proteinase nsp5
著者Ornelas, E, Knapp, M.S.
登録日2024-06-11
公開日2024-10-16
最終更新日2024-10-23
実験手法X-RAY DIFFRACTION (1.77 Å)
主引用文献Identification of Potent, Broad-Spectrum Coronavirus Main Protease Inhibitors for Pandemic Preparedness.
J.Med.Chem., 67, 2024
9C8Q
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Co-structure of Main Protease of SARS-CoV-2 (COVID-19) with covalent inhibitor
分子名称: (7P,8S)-3-cyclohexyl-7-(3-methylpyridin-2-yl)pyrazolo[1,5-a]pyrimidine, 3C-like proteinase nsp5
著者Knapp, M.S, Ornelas, E.
登録日2024-06-12
公開日2024-10-16
最終更新日2024-10-23
実験手法X-RAY DIFFRACTION (1.692 Å)
主引用文献Identification of Potent, Broad-Spectrum Coronavirus Main Protease Inhibitors for Pandemic Preparedness.
J.Med.Chem., 67, 2024
9CMJ
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Room-temperature X-ray structure of SARS-CoV-2 main protease drug resistant mutant (L50F, E166V)
分子名称: 3C-like proteinase nsp5
著者Kovalevsky, A, Coates, L, Gerlits, O.
登録日2024-07-15
公開日2024-10-16
最終更新日2024-11-06
実験手法X-RAY DIFFRACTION (2.1 Å)
主引用文献Effects of SARS-CoV-2 Main Protease Mutations at Positions L50, E166, and L167 Rendering Resistance to Covalent and Noncovalent Inhibitors.
J.Med.Chem., 67, 2024
9CMN
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Room-temperature X-ray structure of SARS-CoV-2 main protease drug resistant mutant (E166A, L167F)
分子名称: 3C-like proteinase nsp5
著者Kovalevsky, A, Coates, L, Gerlits, O.
登録日2024-07-15
公開日2024-10-16
最終更新日2024-11-06
実験手法X-RAY DIFFRACTION (2 Å)
主引用文献Effects of SARS-CoV-2 Main Protease Mutations at Positions L50, E166, and L167 Rendering Resistance to Covalent and Noncovalent Inhibitors.
J.Med.Chem., 67, 2024
9CMS
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BU of 9cms by Molmil
Room-temperature X-ray structure of SARS-CoV-2 main protease drug resistant mutant (E166V) in complex with ensitrelvir (ESV)
分子名称: 3C-like proteinase nsp5, 6-[(6-chloranyl-2-methyl-indazol-5-yl)amino]-3-[(1-methyl-1,2,4-triazol-3-yl)methyl]-1-[[2,4,5-tris(fluoranyl)phenyl]methyl]-1,3,5-triazine-2,4-dione
著者Kovalevsky, A, Coates, L, Gerlits, O.
登録日2024-07-15
公開日2024-10-16
最終更新日2024-11-06
実験手法X-RAY DIFFRACTION (2 Å)
主引用文献Effects of SARS-CoV-2 Main Protease Mutations at Positions L50, E166, and L167 Rendering Resistance to Covalent and Noncovalent Inhibitors.
J.Med.Chem., 67, 2024
9CMU
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BU of 9cmu by Molmil
Room-temperature X-ray structure of SARS-CoV-2 main protease drug resistant mutant (L50F, E166V) in complex with ensitrelvir (ESV)
分子名称: 3C-like proteinase nsp5, 6-[(6-chloranyl-2-methyl-indazol-5-yl)amino]-3-[(1-methyl-1,2,4-triazol-3-yl)methyl]-1-[[2,4,5-tris(fluoranyl)phenyl]methyl]-1,3,5-triazine-2,4-dione
著者Kovalevsky, A, Coates, L, Gerlits, O.
登録日2024-07-15
公開日2024-10-16
最終更新日2024-11-06
実験手法X-RAY DIFFRACTION (2 Å)
主引用文献Effects of SARS-CoV-2 Main Protease Mutations at Positions L50, E166, and L167 Rendering Resistance to Covalent and Noncovalent Inhibitors.
J.Med.Chem., 67, 2024
9GS4
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SARS-CoV-2 methyltransferase nsp10-16 in complex with SAM and theophylline derivative LAS 54571130
分子名称: 1,2-ETHANEDIOL, 2'-O-methyltransferase nsp16, 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, ...
著者Kremling, V, Sprenger, J, Oberthuer, D, Kiene, A.
登録日2024-09-13
公開日2024-10-16
実験手法X-RAY DIFFRACTION (2 Å)
主引用文献Crystal structures of SARS-CoV-2 methyltransferase nsp10-16 with Cap0-site binders
To Be Published
8S6M
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SARS-CoV-2 BQ.1.1 RBD bound to the S2V29 and the S2H97 Fab fragments
分子名称: 1,2-ETHANEDIOL, 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose, ...
著者Errico, J.M, Park, Y.J, Rietz, T, Czudnochowski, N, Nix, J.C, Cameroni, E, Corti, D, Snell, G, Marco, A.D, Pinto, D, Seattle Structural Genomics Center for Infectious Disease (SSGCID), Veesler, D.
登録日2024-02-28
公開日2024-10-23
最終更新日2024-12-25
実験手法X-RAY DIFFRACTION (1.67 Å)
主引用文献A potent pan-sarbecovirus neutralizing antibody resilient to epitope diversification.
Cell, 187, 2024
8VIA
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Protective effect of human non-neutralizing cross-reactive spike antibodies elicited by SARS-CoV-2 mRNA vaccination
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, PVI.V5-4 heavy chain, ...
著者Bajic, G.
登録日2024-01-03
公開日2024-10-23
最終更新日2024-11-27
実験手法ELECTRON MICROSCOPY (3.6 Å)
主引用文献Protective effect and molecular mechanisms of human non-neutralizing cross-reactive spike antibodies elicited by SARS-CoV-2 mRNA vaccination.
Cell Rep, 43, 2024
8WS3
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Crystal structure of SARS-CoV-2 Main Protease (Mpro) with covalent inhibitor 5,8-Dihydroxy-1,4-naphthoquinone
分子名称: 3C-like proteinase nsp5, 5,8-bis(oxidanyl)naphthalene-1,4-dione, DI(HYDROXYETHYL)ETHER, ...
著者Yang, Y, Wu, D.
登録日2023-10-16
公開日2024-10-23
実験手法X-RAY DIFFRACTION (2.5 Å)
主引用文献Covalent inhibitors of SARS-CoV-2 main protease
To Be Published
8WSI
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BU of 8wsi by Molmil
Crystal structure of SARS-Cov-2 main protease, pH=6.0
分子名称: 3C-like proteinase nsp5
著者Jiang, H.H, Zhou, X.L, Zhang, J, Li, J.
登録日2023-10-17
公開日2024-10-23
実験手法X-RAY DIFFRACTION (2.46 Å)
主引用文献Crystal structure of SARS-Cov-2 main protease, pH=6.0
To Be Published
8YF2
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BU of 8yf2 by Molmil
Cryo-EM structure of SARS-CoV-2 prototype RBD in complex with raccoon dog ACE2 (local refinement)
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Angiotensin-converting enzyme, ...
著者Li, L.J, Luo, C.L, Qi, J.X, Gao, G.F.
登録日2024-02-23
公開日2024-10-23
最終更新日2025-04-30
実験手法ELECTRON MICROSCOPY (2.64 Å)
主引用文献Receptor binding and structural basis of raccoon dog ACE2 binding to SARS-CoV-2 prototype and its variants.
Plos Pathog., 20, 2024
8YFT
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BU of 8yft by Molmil
Cryo-EM structure of SARS-CoV-2 alpha variant spike protein in complex with raccoon dog ACE2 (local refinement)
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Angiotensin-converting enzyme, ...
著者Li, L.J, Luo, C.L, Qi, J.X, Gao, G.F.
登録日2024-02-25
公開日2024-10-23
最終更新日2025-04-30
実験手法ELECTRON MICROSCOPY (3.16 Å)
主引用文献Receptor binding and structural basis of raccoon dog ACE2 binding to SARS-CoV-2 prototype and its variants.
Plos Pathog., 20, 2024
9DW6
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BU of 9dw6 by Molmil
Crystal structure of SARS-CoV-2 main protease (Mpro) C145A mutant in complex with peptide from human tRNA methyltransferase TRMT1
分子名称: 3C-like proteinase nsp5, CHLORIDE ION, GLYCEROL, ...
著者D'Oliviera, A, Mugridge, J.S.
登録日2024-10-08
公開日2024-10-23
最終更新日2025-01-22
実験手法X-RAY DIFFRACTION (1.9 Å)
主引用文献Recognition and cleavage of human tRNA methyltransferase TRMT1 by the SARS-CoV-2 main protease.
Elife, 12, 2025
8RRN
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BU of 8rrn by Molmil
Crystal structure of the SARS-CoV-2 S RBD in complex with pT1616 Fab
分子名称: Spike protein S1, pT1616 Fab heavy chain, pT1616 Fab light chain
著者Hansen, G, Krey, T.
登録日2024-01-23
公開日2024-10-30
最終更新日2025-01-01
実験手法X-RAY DIFFRACTION (3.11 Å)
主引用文献A human monoclonal antibody neutralizing SARS-CoV-2 Omicron variants containing the L452R mutation.
J.Virol., 98, 2024
9GDX
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BU of 9gdx by Molmil
SARS-CoV-2 Spike protein Beta Variant at 4C structural flexibility / heterogeneity analyses
分子名称: Spike glycoprotein,Fibritin
著者Herreros, D, Mata, C.P, Noddings, C, Irene, D, Agard, D.A, Tsai, M.-D, Sorzano, C.O.S, Carazo, J.M.
登録日2024-08-06
公開日2024-10-30
最終更新日2025-05-07
実験手法ELECTRON MICROSCOPY (2.8 Å)
主引用文献Real-space heterogeneous reconstruction, refinement, and disentanglement of CryoEM conformational states with HetSIREN.
Nat Commun, 16, 2025
9GDY
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BU of 9gdy by Molmil
SARS-CoV-2 Spike protein Beta Variant at 37C structural flexibility / heterogeneity analyses
分子名称: Spike glycoprotein,Fibritin
著者Herreros, D, Mata, C.P, Noddings, C, Irene, D, Agard, D.A, Tsai, M.-D, Sorzano, C.O.S, Carazo, J.M.
登録日2024-08-06
公開日2024-10-30
最終更新日2025-05-07
実験手法ELECTRON MICROSCOPY (2.8 Å)
主引用文献Real-space heterogeneous reconstruction, refinement, and disentanglement of CryoEM conformational states with HetSIREN.
Nat Commun, 16, 2025
8U25
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Crystal Structure of SARS-CoV-2 Main Protease (Mpro) L50F/E166A/L167F Triple Mutant
分子名称: 3C-like proteinase
著者Kohaal, N, Lewandowski, E.M, Wang, J, Chen, Y.
登録日2023-09-05
公開日2024-11-06
最終更新日2025-02-12
実験手法X-RAY DIFFRACTION (2.23 Å)
主引用文献Distal protein-protein interactions contribute to nirmatrelvir resistance.
Nat Commun, 16, 2025
9CTU
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BU of 9ctu by Molmil
Cryo-EM structure of SARS-CoV-2 M (short conformation)bound to C1P
分子名称: (2S,3R,4E)-2-(hexadecanoylamino)-3-hydroxyoctadec-4-en-1-yl dihydrogen phosphate, Membrane protein, POTASSIUM ION, ...
著者Dolan, K.A, Brohawn, S.G.
登録日2024-07-25
公開日2024-11-06
最終更新日2025-05-28
実験手法ELECTRON MICROSCOPY (3.03 Å)
主引用文献Direct lipid interactions control SARS-CoV-2 M protein conformational dynamics and virus assembly.
Biorxiv, 2024
9CTW
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Cryo-EM structure of SARS-CoV-2 M (long conformation) in the presence of C1P
分子名称: Long conformation Fab heavy chain, Long conformation Fab light chain, Membrane protein
著者Dolan, K.A, Brohawn, S.G.
登録日2024-07-25
公開日2024-11-06
最終更新日2025-05-14
実験手法ELECTRON MICROSCOPY (3.01 Å)
主引用文献Direct lipid interactions control SARS-CoV-2 M protein conformational dynamics and virus assembly.
Biorxiv, 2024
9GIJ
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Crystal structure of SARS-CoV-2 Mpro with compound 5
分子名称: (2~{R})-3-(4-chlorophenyl)-2-[2-[(2~{R})-1-isoquinolin-4-ylcarbonylpyrrolidin-2-yl]ethanoyl-methyl-amino]-~{N}-methyl-propanamide, 3C-like proteinase nsp5
著者Prasad, A, Schmitt, A, Preuss, F, Maskos, K, Wang, X, Gotchev, D, Konz Makino, D.L.
登録日2024-08-19
公開日2024-11-06
最終更新日2024-11-27
実験手法X-RAY DIFFRACTION (1.476 Å)
主引用文献Rational Design of Macrocyclic Noncovalent Inhibitors of SARS-CoV-2 M pro from a DNA-Encoded Chemical Library Screening Hit That Demonstrate Potent Inhibition against Pan-Coronavirus Homologues and Nirmatrelvir-Resistant Variants.
J.Med.Chem., 67, 2024
9GIL
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BU of 9gil by Molmil
Crystal structure of SARS-CoV-2 Mpro with compound 12
分子名称: (7~{R},11~{R},19~{E})-11-[(4-chlorophenyl)methyl]-13-oxa-3,10,23-triazatricyclo[19.3.1.0^{3,7}]pentacosa-1(24),19,21(25),22-tetraene-2,9,12-trione, 1,2-ETHANEDIOL, 3C-like proteinase nsp5, ...
著者Schmitt, A, Preuss, F, Prasad, A, Maskos, K, Wang, X, Gotchev, D, Konz Makino, D.L.
登録日2024-08-19
公開日2024-11-06
最終更新日2024-11-27
実験手法X-RAY DIFFRACTION (1.849 Å)
主引用文献Rational Design of Macrocyclic Noncovalent Inhibitors of SARS-CoV-2 M pro from a DNA-Encoded Chemical Library Screening Hit That Demonstrate Potent Inhibition against Pan-Coronavirus Homologues and Nirmatrelvir-Resistant Variants.
J.Med.Chem., 67, 2024
8R1Q
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SARS-CoV-2 Mpro (Omicron, P132H+T169S) in complex with alpha-ketoamide 13b-K
分子名称: 3C-like proteinase nsp5, ~{tert}-butyl ~{N}-[1-[(2~{S})-3-cyclopropyl-1-oxidanylidene-1-[[(2~{S},3~{R})-3-oxidanyl-4-oxidanylidene-1-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]-4-[(phenylmethyl)amino]butan-2-yl]amino]propan-2-yl]-2-oxidanylidene-pyridin-3-yl]carbamate
著者Sun, X, Ibrahim, M, Hilgenfeld, R.
登録日2023-11-02
公開日2024-11-13
最終更新日2025-04-09
実験手法X-RAY DIFFRACTION (1.7 Å)
主引用文献Why is the Omicron main protease of SARS-CoV-2 less stable than its wild-type counterpart? A crystallographic, biophysical, and theoretical study
Hlife, 2, 2024
8R24
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SARS-CoV-2 Mpro (Omicron, P132H+T169S) free enzyme
分子名称: 3C-like proteinase nsp5
著者Sun, X, Ibrahim, M, El Kilani, H, Hilgenfeld, R.
登録日2023-11-02
公開日2024-11-13
最終更新日2025-04-09
実験手法X-RAY DIFFRACTION (1.8 Å)
主引用文献Why is the Omicron main protease of SARS-CoV-2 less stable than its wild-type counterpart? A crystallographic, biophysical, and theoretical study
Hlife, 2, 2024
8R26
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SARS-CoV-2 Mpro (Omicron,P132H) in complex with alpha-ketoamide 13b-K at pH 8.5
分子名称: 3C-like proteinase nsp5, CHLORIDE ION, ~{tert}-butyl ~{N}-[1-[(2~{S})-3-cyclopropyl-1-oxidanylidene-1-[[(2~{S},3~{R})-3-oxidanyl-4-oxidanylidene-1-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]-4-[(phenylmethyl)amino]butan-2-yl]amino]propan-2-yl]-2-oxidanylidene-pyridin-3-yl]carbamate
著者Ibrahim, M, Sun, X, Hilgenfeld, R.
登録日2023-11-03
公開日2024-11-13
最終更新日2025-04-09
実験手法X-RAY DIFFRACTION (2.3 Å)
主引用文献Why is the Omicron main protease of SARS-CoV-2 less stable than its wild-type counterpart? A crystallographic, biophysical, and theoretical study
Hlife, 2, 2024

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件を2025-07-09に公開中

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