新型コロナウイルスの構造情報

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)

全エントリー (4406)代表構造 (1944)最新のエントリー (19)

7T2T

SARS-CoV2 Mpro native form
分子名称:	3C-like proteinase
著者	Mathews, I.I, Hameedi, M.A, Wakatsuki, S.
登録日	2021-12-06
公開日	2022-09-14
最終更新日	2023-10-18
実験手法	X-RAY DIFFRACTION (1.45 Å)
主引用文献	Structural and functional characterization of NEMO cleavage by SARS-CoV-2 3CLpro. Nat Commun, 13, 2022

7T2U

SARS-CoV2 3C-Like protease complexed with Nemo peptide
分子名称:	3C-Like Protease, NEMO peptide
著者	Wakatsuki, S, Mathews, I.I, Hameedi, M.A.
登録日	2021-12-06
公開日	2022-09-14
最終更新日	2024-04-03
実験手法	X-RAY DIFFRACTION (2.1 Å)
主引用文献	Structural and functional characterization of NEMO cleavage by SARS-CoV-2 3CLpro. Nat Commun, 13, 2022

7T2V

SARS CoV2 Mpro C145S mutant
分子名称:	3C-Like Protease
著者	Mathews, I.I, Hameedi, M.A, Wakatsuki, S.
登録日	2021-12-06
公開日	2022-09-14
最終更新日	2024-04-03
実験手法	X-RAY DIFFRACTION (2.47 Å)
主引用文献	Structural and functional characterization of NEMO cleavage by SARS-CoV-2 3CLpro. Nat Commun, 13, 2022

7XXL

RBD in complex with Fab14
分子名称:	2-acetamido-2-deoxy-beta-D-glucopyranose, Fab14 heavy chain, Fab14 light chain, ...
著者	Lin, J.Q, Tan, Y.J.E, Wu, B, Lescar, J.
登録日	2022-05-30
公開日	2022-09-14
最終更新日	2022-10-05
実験手法	ELECTRON MICROSCOPY (7.3 Å)
主引用文献	Engineering SARS-CoV-2 specific cocktail antibodies into a bispecific format improves neutralizing potency and breadth. Nat Commun, 13, 2022

8E64

Crystal structure of SARS-CoV-2 3CL protease in complex with a benzimidazole dimethyl sulfane inhibitor
分子名称:	(1S,2S)-2-{[N-({2-[(1H-benzimidazol-2-yl)sulfanyl]-2-methylpropoxy}carbonyl)-L-leucyl]amino}-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid, (1~{R},2~{S})-2-[[(2~{S})-2-[[2-(1~{H}-benzimidazol-2-ylsulfanyl)-2-methyl-propoxy]carbonylamino]-4-methyl-pentanoyl]amino]-1-oxidanyl-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propane-1-sulfonic acid;molecular oxygen, 3C-like proteinase
著者	Lovell, S, Liu, L, Battaile, K.P, Madden, T.K, Groutas, W.C.
登録日	2022-08-22
公開日	2022-09-14
最終更新日	2024-05-01
実験手法	X-RAY DIFFRACTION (1.75 Å)
主引用文献	Structure-guided design of direct-acting antivirals that exploit the gem-dimethyl effect and potently inhibit 3CL proteases of severe acute respiratory syndrome Coronavirus-2 (SARS-CoV-2) and middle east respiratory syndrome coronavirus (MERS-CoV). Eur.J.Med.Chem., 254, 2023

8E65

Crystal structure of SARS-CoV-2 3CL protease in complex with a p-chlorodimethyl oxybenzene inhibitor
分子名称:	(1S,2S)-2-[(N-{[2-(4-chlorophenoxy)-2-methylpropoxy]carbonyl}-L-leucyl)amino]-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid, 3C-like proteinase
著者	Lovell, S, Liu, L, Battaile, K.P, Miller, M.J, Groutas, W.C.
登録日	2022-08-22
公開日	2022-09-14
最終更新日	2024-05-01
実験手法	X-RAY DIFFRACTION (1.8 Å)
主引用文献	Structure-guided design of direct-acting antivirals that exploit the gem-dimethyl effect and potently inhibit 3CL proteases of severe acute respiratory syndrome Coronavirus-2 (SARS-CoV-2) and middle east respiratory syndrome coronavirus (MERS-CoV). Eur.J.Med.Chem., 254, 2023

8E68

Crystal structure of SARS-CoV-2 3CL protease in complex with a p-fluorodimethyl oxybenzene inhibitor
分子名称:	(1S,2S)-2-[(N-{[2-(4-fluorophenoxy)-2-methylpropoxy]carbonyl}-L-leucyl)amino]-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid, 3C-like proteinase, N~2~-{[2-(4-fluorophenoxy)-2-methylpropoxy]carbonyl}-N-{(1R,2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]-1-sulfanylpropan-2-yl}-L-leucinamide, ...
著者	Lovell, S, Liu, L, Battaile, K.P, Miller, M.J, Groutas, W.C.
登録日	2022-08-22
公開日	2022-09-14
最終更新日	2024-05-01
実験手法	X-RAY DIFFRACTION (1.6 Å)
主引用文献	Structure-guided design of direct-acting antivirals that exploit the gem-dimethyl effect and potently inhibit 3CL proteases of severe acute respiratory syndrome Coronavirus-2 (SARS-CoV-2) and middle east respiratory syndrome coronavirus (MERS-CoV). Eur.J.Med.Chem., 254, 2023

7SA2

SARS-CoV-2 spike-derived peptide S1060-1068 (VVFLHVTYV) presented by HLA-A*02:01
分子名称:	Beta-2-microglobulin, CADMIUM ION, MHC class I antigen, ...
著者	Szeto, C, Gras, S.
登録日	2021-09-21
公開日	2022-09-21
最終更新日	2023-10-18
実験手法	X-RAY DIFFRACTION (1.85 Å)
主引用文献	*SARS-CoV-2 spike-derived peptide S1060-1068 (VVFLHVTYV) presented by HLA-A02:01** To Be Published

7XCO

Cryo-EM structure of SARS-CoV-2 Omicron spike protein (S-6P-RRAR) in complex with S309 fab
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, S309 Fab heavy chain, ...
著者	Gao, G.F, Qi, J.X, Zhao, Z.N, Liu, S, Xie, Y.F.
登録日	2022-03-24
公開日	2022-09-21
実験手法	ELECTRON MICROSCOPY (2.5 Å)
主引用文献	Omicron SARS-CoV-2 mutations stabilize spike up-RBD conformation and lead to a non-RBM-binding monoclonal antibody escape Nat Commun, 13, 2022

7Y9Z

Cryo-EM structure of SARS-CoV-2 Omicron spike protein (S-6P-RRAR) in complex with human ACE2 ectodomain (one-RBD-up state)
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, Processed angiotensin-converting enzyme 2, ...
著者	Gao, G.F, Qi, J.X, Liu, S, Zhao, Z.N.
登録日	2022-06-26
公開日	2022-09-21
実験手法	ELECTRON MICROSCOPY (2.85 Å)
主引用文献	Omicron SARS-CoV-2 mutations stabilize spike up-RBD conformation and lead to a non-RBM-binding monoclonal antibody escape. Nat Commun, 13, 2022

7YA0

Cryo-EM structure of hACE2-bound SARS-CoV-2 Omicron spike protein with L371S, P373S and F375S mutations (S-6P-RRAR)
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, Processed angiotensin-converting enzyme 2, ...
著者	Zhao, Z.N, Xie, Y.F, Qi, J.X, Gao, G.F.
登録日	2022-06-26
公開日	2022-09-21
最終更新日	2023-08-02
実験手法	ELECTRON MICROSCOPY (3.1 Å)
主引用文献	Omicron SARS-CoV-2 mutations stabilize spike up-RBD conformation and lead to a non-RBM-binding monoclonal antibody escape. Nat Commun, 13, 2022

8DOX

Crystal structure of SARS-CoV-2 main protease in complex with an inhibitor TKB-245
分子名称:	(1R,2S,5S)-N-{(1S,2S)-1-(4-fluoro-1,3-benzothiazol-2-yl)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide, 3C-like proteinase nsp5, DIMETHYL SULFOXIDE
著者	Bulut, H, Hayashi, H, Tsuji, K, Kuwata, N, Das, D, Tamamura, H, Mitsuya, H.
登録日	2022-07-14
公開日	2022-09-21
最終更新日	2023-10-18
実験手法	X-RAY DIFFRACTION (1.46 Å)
主引用文献	Identification of SARS-CoV-2 M pro inhibitors containing P1' 4-fluorobenzothiazole moiety highly active against SARS-CoV-2. Nat Commun, 14, 2023

8DRR

Product structure of SARS-CoV-2 Mpro C145A mutant in complex with nsp4-nsp5 (C4) cut site sequence
分子名称:	3C-like proteinase nsp5, SODIUM ION
著者	Lee, J, Kenward, C, Worrall, L.J, Vuckovic, M, Paetzel, M, Strynadka, N.C.J.
登録日	2022-07-21
公開日	2022-09-21
最終更新日	2023-10-18
実験手法	X-RAY DIFFRACTION (2 Å)
主引用文献	X-ray crystallographic characterization of the SARS-CoV-2 main protease polyprotein cleavage sites essential for viral processing and maturation. Nat Commun, 13, 2022

8DRS

Product structure of SARS-CoV-2 Mpro C145A mutant in complex with nsp6-nsp7 (C6) cut site sequence
分子名称:	3C-like proteinase nsp5
著者	Lee, J, Kenward, C, Worrall, L.J, Vuckovic, M, Paetzel, M, Strynadka, N.C.J.
登録日	2022-07-21
公開日	2022-09-21
最終更新日	2023-10-18
実験手法	X-RAY DIFFRACTION (1.8 Å)
主引用文献	X-ray crystallographic characterization of the SARS-CoV-2 main protease polyprotein cleavage sites essential for viral processing and maturation. Nat Commun, 13, 2022

8DRT

Product structure of SARS-CoV-2 Mpro C145A mutant in complex with nsp6-nsp7 (C6) cut site sequence (form 2)
分子名称:	3C-like proteinase nsp5
著者	Lee, J, Kenward, C, Worrall, L.J, Vuckovic, M, Paetzel, M, Strynadka, N.C.J.
登録日	2022-07-21
公開日	2022-09-21
最終更新日	2023-10-18
実験手法	X-RAY DIFFRACTION (1.5 Å)
主引用文献	X-ray crystallographic characterization of the SARS-CoV-2 main protease polyprotein cleavage sites essential for viral processing and maturation. Nat Commun, 13, 2022

8DRU

Product structure of SARS-CoV-2 Mpro C145A mutant in complex with nsp7-nsp8 (C7) cut site sequence
分子名称:	DI(HYDROXYETHYL)ETHER, Fusion protein of 3C-like proteinase nsp5 and nsp7-nsp8 (C7) cut site, PENTAETHYLENE GLYCOL, ...
著者	Lee, J, Kenward, C, Worrall, L.J, Vuckovic, M, Paetzel, M, Strynadka, N.C.J.
登録日	2022-07-21
公開日	2022-09-21
最終更新日	2023-10-18
実験手法	X-RAY DIFFRACTION (2.31 Å)
主引用文献	X-ray crystallographic characterization of the SARS-CoV-2 main protease polyprotein cleavage sites essential for viral processing and maturation. Nat Commun, 13, 2022

8DRV

Product structure of SARS-CoV-2 Mpro C145A mutant in complex with nsp8-nsp9 (C8) cut site sequence
分子名称:	Fusion protein of 3C-like proteinase nsp5 and nsp8-nsp9 (C8) cut site, PENTAETHYLENE GLYCOL
著者	Lee, J, Kenward, C, Worrall, L.J, Vuckovic, M, Paetzel, M, Strynadka, N.C.J.
登録日	2022-07-21
公開日	2022-09-21
最終更新日	2023-10-18
実験手法	X-RAY DIFFRACTION (2.4 Å)
主引用文献	X-ray crystallographic characterization of the SARS-CoV-2 main protease polyprotein cleavage sites essential for viral processing and maturation. Nat Commun, 13, 2022

8DRW

Product structure of SARS-CoV-2 Mpro C145A mutant in complex with nsp9-nsp10 (C9) cut site sequence
分子名称:	DI(HYDROXYETHYL)ETHER, Fusion protein of 3C-like proteinase nsp5 and nsp9-nsp10 (C9) cut site, PENTAETHYLENE GLYCOL, ...
著者	Lee, J, Kenward, C, Worrall, L.J, Vuckovic, M, Paetzel, M, Strynadka, N.C.J.
登録日	2022-07-21
公開日	2022-09-21
最終更新日	2023-10-18
実験手法	X-RAY DIFFRACTION (2.67 Å)
主引用文献	X-ray crystallographic characterization of the SARS-CoV-2 main protease polyprotein cleavage sites essential for viral processing and maturation. Nat Commun, 13, 2022

8DRX

Product structure of SARS-CoV-2 Mpro C145A mutant in complex with nsp10-nsp11 (C10) cut site sequence (form 2)
分子名称:	Fusion protein of 3C-like proteinase nsp5 and nsp10-nsp11 (C10) cut site, SODIUM ION
著者	Lee, J, Kenward, C, Worrall, L.J, Vuckovic, M, Paetzel, M, Strynadka, N.C.J.
登録日	2022-07-21
公開日	2022-09-21
最終更新日	2023-10-18
実験手法	X-RAY DIFFRACTION (1.5 Å)
主引用文献	X-ray crystallographic characterization of the SARS-CoV-2 main protease polyprotein cleavage sites essential for viral processing and maturation. Nat Commun, 13, 2022

8DRY

Product structure of SARS-CoV-2 Mpro C145A mutant in complex with nsp12-nsp13 (C12) cut site sequence
分子名称:	DI(HYDROXYETHYL)ETHER, Fusion protein of 3C-like proteinase nsp5 and nsp12-nsp13 (C12) cut site
著者	Lee, J, Kenward, C, Worrall, L.J, Vuckovic, M, Paetzel, M, Strynadka, N.C.J.
登録日	2022-07-21
公開日	2022-09-21
最終更新日	2023-10-18
実験手法	X-RAY DIFFRACTION (2.49 Å)
主引用文献	X-ray crystallographic characterization of the SARS-CoV-2 main protease polyprotein cleavage sites essential for viral processing and maturation. Nat Commun, 13, 2022

8E5Z

Crystal structure of SARS-CoV-2 3CL protease in complex with a dimethyl sulfonyl benzene inhibitor
分子名称:	(1R,2S)-2-[(N-{[2-(benzenesulfonyl)-2-methylpropoxy]carbonyl}-L-leucyl)amino]-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid, (1S,2S)-2-[(N-{[2-(benzenesulfonyl)-2-methylpropoxy]carbonyl}-L-leucyl)amino]-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid, 3C-like proteinase
著者	Lovell, S, Liu, L, Battaile, K.P, Miller, M.J, Groutas, W.C.
登録日	2022-08-22
公開日	2022-09-21
最終更新日	2024-05-01
実験手法	X-RAY DIFFRACTION (1.8 Å)
主引用文献	Structure-guided design of direct-acting antivirals that exploit the gem-dimethyl effect and potently inhibit 3CL proteases of severe acute respiratory syndrome Coronavirus-2 (SARS-CoV-2) and middle east respiratory syndrome coronavirus (MERS-CoV). Eur.J.Med.Chem., 254, 2023

8E69

Crystal structure of SARS-CoV-2 3CL protease in complex with a m-fluorodimethyl oxybenzene inhibitor
分子名称:	(1R,2S)-2-[(N-{[2-(3-fluorophenoxy)-2-methylpropoxy]carbonyl}-L-leucyl)amino]-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid, 3C-like proteinase
著者	Lovell, S, Liu, L, Battaile, K.P, Miller, M.J, Groutas, W.C.
登録日	2022-08-22
公開日	2022-09-21
最終更新日	2024-05-01
実験手法	X-RAY DIFFRACTION (2.26 Å)
主引用文献	Structure-guided design of direct-acting antivirals that exploit the gem-dimethyl effect and potently inhibit 3CL proteases of severe acute respiratory syndrome Coronavirus-2 (SARS-CoV-2) and middle east respiratory syndrome coronavirus (MERS-CoV). Eur.J.Med.Chem., 254, 2023

8E6A

Crystal structure of SARS-CoV-2 3CL protease in complex with a p-chlorophenylethanol based inhibitor
分子名称:	(1R,2S)-2-[(N-{[(2S)-2-(3-chlorophenyl)-2-hydroxypropoxy]carbonyl}-L-leucyl)amino]-1-hydroxy-3-[(3R)-2-oxo-3,4-dihydro-2H-pyrrol-3-yl]propane-1-sulfonic acid, (1S,2S)-2-[(N-{[(2R)-2-(3-chlorophenyl)-2-hydroxypropoxy]carbonyl}-L-leucyl)amino]-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid, 3C-like proteinase, ...
著者	Lovell, S, Liu, L, Battaile, K.P, Dampalla, C.S, Groutas, W.C.
登録日	2022-08-22
公開日	2022-09-21
最終更新日	2024-05-01
実験手法	X-RAY DIFFRACTION (2.05 Å)
主引用文献	Structure-guided design of direct-acting antivirals that exploit the gem-dimethyl effect and potently inhibit 3CL proteases of severe acute respiratory syndrome Coronavirus-2 (SARS-CoV-2) and middle east respiratory syndrome coronavirus (MERS-CoV). Eur.J.Med.Chem., 254, 2023

7WRJ

Local CryoEM structure of the SARS-CoV-2 S6P(B.1.1.529) in complex with BD55-4637 Fab
分子名称:	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, BD55-4637H, BD55-4637L, ...
著者	Du, S, Xiao, J.Y.
登録日	2022-01-26
公開日	2022-09-28
最終更新日	2024-05-01
実験手法	ELECTRON MICROSCOPY (4.08 Å)
主引用文献	Rational identification of potent and broad sarbecovirus-neutralizing antibody cocktails from SARS convalescents. Cell Rep, 41, 2022

7XWA

Crystal structure of the receptor binding domain of SARS-CoV-2 Omicron BA.4/5 variant spike protein in complex with its receptor ACE2
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, Processed angiotensin-converting enzyme 2, ...
著者	Suzuki, T, Kimura, K, Hashiguchi, T.
登録日	2022-05-26
公開日	2022-09-28
最終更新日	2023-11-29
実験手法	X-RAY DIFFRACTION (3.36 Å)
主引用文献	Virological characteristics of the SARS-CoV-2 Omicron BA.2 subvariants, including BA.4 and BA.5. Cell, 185, 2022

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全ヒット件数:	4406
表示件数:	25
表示順	公開日の古い順