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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
7FR0
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BU of 7fr0 by Molmil
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z2890182452
分子名称: 2-hydroxy-N-(pentan-3-yl)-3H-imidazo[4,5-b]pyridine-7-carboxamide, Non-structural protein 3
著者Correy, G.J, Fraser, J.S.
登録日2022-10-20
公開日2022-11-09
最終更新日2024-05-22
実験手法X-RAY DIFFRACTION (1.15 Å)
主引用文献Ligand screen against SARS-CoV-2 NSP3 macrodomain
To be published
7FR1
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BU of 7fr1 by Molmil
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z1423250928
分子名称: 1-methyl-N'-(7H-purin-6-yl)cyclopropane-1-carbohydrazide, Non-structural protein 3
著者Correy, G.J, Fraser, J.S.
登録日2022-10-20
公開日2022-11-09
最終更新日2024-05-22
実験手法X-RAY DIFFRACTION (1.15 Å)
主引用文献Ligand screen against SARS-CoV-2 NSP3 macrodomain
To be published
7FR2
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BU of 7fr2 by Molmil
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z5551425673 - (S) isomer
分子名称: 3-cyclohexyl-N-{(2S)-1-[(9H-purin-6-yl)amino]butan-2-yl}propanamide, Non-structural protein 3
著者Correy, G.J, Fraser, J.S.
登録日2022-10-20
公開日2022-11-09
最終更新日2024-05-22
実験手法X-RAY DIFFRACTION (1.15 Å)
主引用文献Ligand screen against SARS-CoV-2 NSP3 macrodomain
To be published
7FR3
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BU of 7fr3 by Molmil
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with PTERA_A01A - (S) isomer
分子名称: 3-cyclohexyl-N-{(2S)-1-[(9H-purin-6-yl)amino]butan-2-yl}propanamide, Non-structural protein 3
著者Correy, G.J, Fraser, J.S.
登録日2022-10-20
公開日2022-11-09
最終更新日2024-05-22
実験手法X-RAY DIFFRACTION (1 Å)
主引用文献Ligand screen against SARS-CoV-2 NSP3 macrodomain
To be published
7FR4
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BU of 7fr4 by Molmil
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with PTERA_A26A - (S) isomer
分子名称: 2-cyclohexyl-N-{(2S)-1-[(7H-purin-6-yl)amino]butan-2-yl}acetamide, DIMETHYL SULFOXIDE, Non-structural protein 3
著者Correy, G.J, Fraser, J.S.
登録日2022-10-20
公開日2022-11-09
最終更新日2024-05-22
実験手法X-RAY DIFFRACTION (1 Å)
主引用文献Ligand screen against SARS-CoV-2 NSP3 macrodomain
To be published
7FR5
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BU of 7fr5 by Molmil
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z2890189003
分子名称: 2-hydroxy-N-propyl-3H-imidazo[4,5-b]pyridine-7-carboxamide, Non-structural protein 3
著者Correy, G.J, Fraser, J.S.
登録日2022-10-20
公開日2022-11-09
最終更新日2024-05-22
実験手法X-RAY DIFFRACTION (1 Å)
主引用文献Ligand screen against SARS-CoV-2 NSP3 macrodomain
To be published
7FR6
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BU of 7fr6 by Molmil
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z2890147894
分子名称: (azepan-1-yl)(2-hydroxy-3H-imidazo[4,5-b]pyridin-7-yl)methanone, Non-structural protein 3
著者Correy, G.J, Fraser, J.S.
登録日2022-10-20
公開日2022-11-09
最終更新日2024-05-22
実験手法X-RAY DIFFRACTION (1 Å)
主引用文献Ligand screen against SARS-CoV-2 NSP3 macrodomain
To be published
7FR7
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BU of 7fr7 by Molmil
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z431872694
分子名称: 6-(azepane-1-carbonyl)pyrido[2,3-d]pyrimidine-2,4(1H,3H)-dione, Non-structural protein 3
著者Correy, G.J, Fraser, J.S.
登録日2022-10-20
公開日2022-11-09
最終更新日2024-05-22
実験手法X-RAY DIFFRACTION (1 Å)
主引用文献Ligand screen against SARS-CoV-2 NSP3 macrodomain
To be published
7FR8
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BU of 7fr8 by Molmil
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z2890408258 - (R) isomer
分子名称: (2-hydroxy-3H-imidazo[4,5-b]pyridin-7-yl)[(2R)-2-methylmorpholin-4-yl]methanone, Non-structural protein 3
著者Correy, G.J, Fraser, J.S.
登録日2022-10-20
公開日2022-11-09
最終更新日2024-05-22
実験手法X-RAY DIFFRACTION (1 Å)
主引用文献Ligand screen against SARS-CoV-2 NSP3 macrodomain
To be published
7FR9
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BU of 7fr9 by Molmil
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z1367095370
分子名称: N-(1-methylcyclopropyl)-2,4-dioxo-1,2,3,4-tetrahydropyrido[2,3-d]pyrimidine-6-sulfonamide, Non-structural protein 3
著者Correy, G.J, Fraser, J.S.
登録日2022-10-20
公開日2022-11-09
最終更新日2024-05-22
実験手法X-RAY DIFFRACTION (1 Å)
主引用文献Ligand screen against SARS-CoV-2 NSP3 macrodomain
To be published
7FRA
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BU of 7fra by Molmil
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z1343520564
分子名称: 6-(azepane-1-sulfonyl)pyrido[2,3-d]pyrimidine-2,4(1H,3H)-dione, Non-structural protein 3
著者Correy, G.J, Fraser, J.S.
登録日2022-10-20
公開日2022-11-09
最終更新日2024-05-22
実験手法X-RAY DIFFRACTION (1 Å)
主引用文献Ligand screen against SARS-CoV-2 NSP3 macrodomain
To be published
7FRB
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BU of 7frb by Molmil
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z5551426009 - (S) isomer
分子名称: 1-methyl-N-{(2S)-3-methyl-2-[(9H-purin-6-yl)amino]butyl}cyclobutane-1-carboxamide, Non-structural protein 3
著者Correy, G.J, Fraser, J.S.
登録日2022-10-20
公開日2022-11-09
最終更新日2024-05-22
実験手法X-RAY DIFFRACTION (1 Å)
主引用文献Ligand screen against SARS-CoV-2 NSP3 macrodomain
To be published
7FRC
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BU of 7frc by Molmil
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with PTERA_A05 - (R) isomer
分子名称: 3-cyclohexyl-N-{(2R)-2-[(1H-pyrazolo[3,4-d]pyrimidin-4-yl)amino]butyl}propanamide, Non-structural protein 3
著者Correy, G.J, Fraser, J.S.
登録日2022-10-20
公開日2022-11-09
最終更新日2024-05-22
実験手法X-RAY DIFFRACTION (1 Å)
主引用文献Ligand screen against SARS-CoV-2 NSP3 macrodomain
To be published
7FRD
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BU of 7frd by Molmil
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with PTERA_A25A - (S) isomer
分子名称: 3-phenyl-N-{(2S)-1-[(7H-purin-6-yl)amino]butan-2-yl}propanamide, Non-structural protein 3
著者Correy, G.J, Fraser, J.S.
登録日2022-10-20
公開日2022-11-09
最終更新日2024-05-22
実験手法X-RAY DIFFRACTION (1 Å)
主引用文献Ligand screen against SARS-CoV-2 NSP3 macrodomain
To be published
7SD9
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BU of 7sd9 by Molmil
Structure of the SARS-CoV-2 main protease in complex with inhibitor MPI48
分子名称: 3C-like proteinase, N-[(2S)-1-({(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}amino)-4,4-dimethyl-1-oxopentan-2-yl]-1H-indole-2-carboxamide
著者Yang, K.S, Liu, W.R.
登録日2021-09-29
公開日2022-11-09
最終更新日2024-03-20
実験手法X-RAY DIFFRACTION (1.85 Å)
主引用文献A Systematic Survey of Reversibly Covalent Dipeptidyl Inhibitors of the SARS-CoV-2 Main Protease.
J.Med.Chem., 66, 2023
7SDA
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BU of 7sda by Molmil
Structure of the SARS-CoV-2 main protease in complex with inhibitor MPI49
分子名称: 3C-like proteinase, N-[(2S)-1-({(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}amino)-4,4-dimethyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide
著者Yang, K.S, Liu, W.R.
登録日2021-09-29
公開日2022-11-09
最終更新日2024-03-20
実験手法X-RAY DIFFRACTION (1.85 Å)
主引用文献A Systematic Survey of Reversibly Covalent Dipeptidyl Inhibitors of the SARS-CoV-2 Main Protease.
J.Med.Chem., 66, 2023
7SDC
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BU of 7sdc by Molmil
Structure of the SARS-CoV-2 main protease in complex with inhibitor MI-09
分子名称: (1R,2S,5S)-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-{[4-(trifluoromethoxy)phenoxy]acetyl}-3-azabicyclo[3.1.0]hexane-2-carboxamide, 3C-like proteinase
著者Yang, K.S, Liu, W.R.
登録日2021-09-29
公開日2022-11-09
最終更新日2024-03-20
実験手法X-RAY DIFFRACTION (1.85 Å)
主引用文献A Systematic Survey of Reversibly Covalent Dipeptidyl Inhibitors of the SARS-CoV-2 Main Protease.
J.Med.Chem., 66, 2023
7WSH
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BU of 7wsh by Molmil
Cryo-EM structure of SARS-CoV-2 spike receptor-binding domain in complex with sea lion ACE2
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Angiotensin-converting enzyme, Spike protein S1, ...
著者Li, S, Han, P, Qi, J.
登録日2022-01-29
公開日2022-11-09
実験手法ELECTRON MICROSCOPY (2.89 Å)
主引用文献Cross-species recognition and molecular basis of SARS-CoV-2 and SARS-CoV binding to ACE2s of marine animals.
Natl Sci Rev, 9, 2022
7X26
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BU of 7x26 by Molmil
S41 neutralizing antibody Fab(MERS-CoV)
分子名称: Spike glycoprotein, antibody S41 heavy chain, antibody S41 light chain
著者Zeng, J.W, Zhang, S.Y, Wang, X.W.
登録日2022-02-25
公開日2022-11-09
最終更新日2022-11-23
実験手法ELECTRON MICROSCOPY (3.685 Å)
主引用文献Cryoelectron microscopy structures of a human neutralizing antibody bound to MERS-CoV spike glycoprotein.
Front Microbiol, 13, 2022
7X29
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BU of 7x29 by Molmil
MERS-CoV spike complex with S41 neutralizing antibody Fab Class2 (1u2d RBD with 2Fab)
分子名称: Spike glycoprotein, antibody S41 heavy chain, antibody S41 light chain
著者Zeng, J.W, Zhang, S.Y, Zhou, H.X, Wang, X.W.
登録日2022-02-25
公開日2022-11-09
最終更新日2022-11-23
実験手法ELECTRON MICROSCOPY (2.49 Å)
主引用文献Cryoelectron microscopy structures of a human neutralizing antibody bound to MERS-CoV spike glycoprotein.
Front Microbiol, 13, 2022
7X2A
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BU of 7x2a by Molmil
MERS-CoV spike complex with S41 neutralizing antibody Fab Class1 (1u2d RBD with 1Fab)
分子名称: MERS-CoV Spike glycoprotein, antibody S41 heavy chain, antibody S41 light chain
著者Zeng, J.W, Zhang, S.Y, Zhou, H.X, Wang, X.W.
登録日2022-02-25
公開日2022-11-09
最終更新日2022-11-23
実験手法ELECTRON MICROSCOPY (2.49 Å)
主引用文献Cryoelectron microscopy structures of a human neutralizing antibody bound to MERS-CoV spike glycoprotein.
Front Microbiol, 13, 2022
7XAR
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BU of 7xar by Molmil
Crystal structure of 3C-like protease from SARS-CoV-2 in complex with covalent inhibitor
分子名称: 3C-like proteinase, 4-fluoranyl-~{N}-[(2~{S})-1-[2-(2-fluoranylethanoyl)-2-[[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]methyl]hydrazinyl]-4-methyl-1-oxidanylidene-pentan-2-yl]-1~{H}-indole-2-carboxamide, CHLORIDE ION, ...
著者Caaveiro, J.M.M, Ochi, J, Takahashi, D, Ueda, T, Ojida, A.
登録日2022-03-18
公開日2022-11-09
最終更新日2023-11-29
実験手法X-RAY DIFFRACTION (1.6 Å)
主引用文献Discovery of Chlorofluoroacetamide-Based Covalent Inhibitors for Severe Acute Respiratory Syndrome Coronavirus 2 3CL Protease.
J.Med.Chem., 65, 2022
7ZR2
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BU of 7zr2 by Molmil
Crystal structure of a chimeric protein mimic of SARS-CoV-2 Spike HR1 in complex with HR2
分子名称: Spike protein S2', Spike protein S2',Chimeric protein mimic of SARS-CoV-2 Spike HR1
著者Camara-Artigas, A, Gavira, J.A, Cano-Munoz, M, Polo-Megias, D, Conejero-Lara, F.
登録日2022-05-03
公開日2022-11-09
最終更新日2024-01-31
実験手法X-RAY DIFFRACTION (1.45 Å)
主引用文献Novel chimeric proteins mimicking SARS-CoV-2 spike epitopes with broad inhibitory activity.
Int.J.Biol.Macromol., 222, 2022
8ERS
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BU of 8ers by Molmil
PanDDA analysis -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z4718398507 - (R,S) isomer
分子名称: (1R,2S)-1-[(4-amino-2-hydroxybenzoyl)oxy]-2,3-dihydro-1H-indene-2-carboxylic acid, Non-structural protein 3
著者Correy, G.J, Fraser, J.S.
登録日2022-10-12
公開日2022-11-09
最終更新日2023-10-18
実験手法X-RAY DIFFRACTION (1.05 Å)
主引用文献Ligand screen against SARS-CoV-2 NSP3 macrodomain
To be published
7Q3Q
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BU of 7q3q by Molmil
Crystal structure of SARS-CoV-2 RBD in complex with the neutralizing nanobody VHH-12
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, CHLORIDE ION, GLYCEROL, ...
著者Fernandez, I, Pederzoli, R, Rey, F.A.
登録日2021-10-28
公開日2022-11-16
最終更新日2024-01-31
実験手法X-RAY DIFFRACTION (2.3 Å)
主引用文献NANOBODIES AGAINST SARS-COV-2 NEUTRALIZE VARIANTS OF CONCERN AND EXPLORE CONFORMATIONAL DIFFERENCES ON THE SPIKE PROTEIN
To Be Published

222415

件を2024-07-10に公開中

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