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新型コロナウイルスの構造情報

このページの他言語版もあります: English简体中文繁體中文한국어
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
全エントリー (5197)代表構造 (2266)最新のエントリー (44)
8YLS
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BU of 8yls by Molmil
Structure of SARS-CoV-2 Mpro in complex with its degrader
分子名称: (4-methoxyphenyl)methyl ~{N}-[(2~{S})-4-methyl-1-oxidanylidene-1-[[(2~{S})-1-oxidanylidene-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]pentan-2-yl]carbamate, 3C-like proteinase nsp5
著者Feng, Y, Li, W, Cheng, S.H, Li, X.B.
登録日2024-03-06
公開日2024-09-04
最終更新日2025-03-19
実験手法X-RAY DIFFRACTION (1.93 Å)
主引用文献Development of novel antivrial agents that induce the degradation of the main protease of human-infecting coronaviruses.
Eur.J.Med.Chem., 275, 2024
8ZER
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BU of 8zer by Molmil
Crystal structure of the complex of Wuhan SARS-CoV-2 RBD (319-541) with P2C5 nanobody
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Nanobody P2C5, Spike protein S1, ...
著者Sluchanko, N.N, Varfolomeeva, L.A, Shcheblyakov, D.V, Logunov, D.Y, Gintsburg, A.L, Popov, V.O, Boyko, K.M.
登録日2024-05-06
公開日2024-09-04
最終更新日2024-11-06
実験手法X-RAY DIFFRACTION (3.1 Å)
主引用文献Structural Basis for Evasion of New SARS-CoV-2 Variants from the Potent Virus-Neutralizing Nanobody Targeting the S-Protein Receptor-Binding Domain.
Biochemistry Mosc., 89, 2024
8ZES
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BU of 8zes by Molmil
Crystal structure of the Wuhan SARS-CoV-2 RBD (333-541) complexed with P2C5 nanobody
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, Nanobody P2C5, ...
著者Sluchanko, N.N, Varfolomeeva, L.A, Shcheblyakov, D.V, Logunov, D.Y, Gintsburg, A.L, Popov, V.O, Boyko, K.M.
登録日2024-05-06
公開日2024-09-04
最終更新日2024-10-16
実験手法X-RAY DIFFRACTION (3.7 Å)
主引用文献Structural Basis for Evasion of New SARS-CoV-2 Variants from the Potent Virus-Neutralizing Nanobody Targeting the S-Protein Receptor-Binding Domain.
Biochemistry Mosc., 89, 2024
9EO6
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BU of 9eo6 by Molmil
SARS-CoV2 major protease in complex with a covalent inhibitor SLL11.
分子名称: 3C-like proteinase nsp5, Inhibitor SLL11, POTASSIUM ION
著者Moche, M, Lennerstrand, J, Nyman, T, Strandback, E, Akaberi, D.
登録日2024-03-14
公開日2024-09-04
最終更新日2024-10-16
実験手法X-RAY DIFFRACTION (2.11 Å)
主引用文献Identification of novel and potent inhibitors of SARS-CoV-2 main protease from DNA-encoded chemical libraries.
Antimicrob.Agents Chemother., 68, 2024
9EOR
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BU of 9eor by Molmil
SARS-CoV2 major protease in complex with a covalent inhibitor SLL12.
分子名称: 3C-like proteinase nsp5, Inhibitor SLL12, POTASSIUM ION
著者Moche, M, Lennerstrand, J, Nyman, T, Strandback, E, Akaberi, D.
登録日2024-03-15
公開日2024-09-04
最終更新日2024-10-16
実験手法X-RAY DIFFRACTION (2.25 Å)
主引用文献Identification of novel and potent inhibitors of SARS-CoV-2 main protease from DNA-encoded chemical libraries.
Antimicrob.Agents Chemother., 68, 2024
9EOX
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BU of 9eox by Molmil
SARS-CoV2 major protease in covalent complex with a soluble inhibitor.
分子名称: 3C-like proteinase nsp5, POTASSIUM ION, Soluble inhibitor
著者Moche, M, Lennerstrand, J, Nyman, T, Strandback, E, Akaberi, D.
登録日2024-03-15
公開日2024-09-04
最終更新日2024-10-16
実験手法X-RAY DIFFRACTION (2.54 Å)
主引用文献Identification of novel and potent inhibitors of SARS-CoV-2 main protease from DNA-encoded chemical libraries.
Antimicrob.Agents Chemother., 68, 2024
8AJ1
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BU of 8aj1 by Molmil
SARS-CoV-2 Mpro in Complex with RK-107
分子名称: (2R,3S)-3-[[(2S)-3-cyclopropyl-2-[2-oxidanylidene-3-(phenylcarbamoylamino)pyridin-1-yl]propanoyl]amino]-N-methyl-2-oxidanyl-4-[(3S)-2-oxidanylidenepyrrolidin-3-yl]butanamide, 3C-like proteinase nsp5
著者El Kilani, H, Hilgenfeld, R.
登録日2022-07-27
公開日2024-09-11
最終更新日2025-01-29
実験手法X-RAY DIFFRACTION (2.6 Å)
主引用文献Structure-Based Optimization of Pyridone alpha-Ketoamides as Inhibitors of the SARS-CoV-2 Main Protease.
J.Med.Chem., 2025
8Y4A
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BU of 8y4a by Molmil
BA.2.86 S-trimer in complex with Nab XG2v046
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, Spike glycoprotein, ...
著者Zhu, Q, Liu, P.
登録日2024-01-30
公開日2024-09-11
最終更新日2024-10-09
実験手法ELECTRON MICROSCOPY (3.4 Å)
主引用文献Enhancing RBD exposure and S1 shedding by an extremely conserved SARS-CoV-2 NTD epitope.
Signal Transduct Target Ther, 9, 2024
8U3O
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BU of 8u3o by Molmil
SARS-CoV-2 Main Protease A173V in complex with CDD-1819
分子名称: (2P)-2-(isoquinolin-4-yl)-1-[(1s,3R)-3-(methylcarbamoyl)cyclobutyl]-N-[(1S)-1-(naphthalen-2-yl)ethyl]-1H-benzimidazole-7-carboxamide, ORF1a polyprotein
著者Nnabuife, C, Palzkill, T.
登録日2023-09-08
公開日2024-09-18
実験手法X-RAY DIFFRACTION (1.88 Å)
主引用文献SARS-CoV-2 Main Protease A173V in complex with CDD-1819
To Be Published
8ZBQ
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BU of 8zbq by Molmil
Local map of Omicron Subvariant JN.1 RBD with ACE2
分子名称: Angiotensin-converting enzyme 2, Spike protein S2'
著者Yan, R.H, Yang, H.N.
登録日2024-04-27
公開日2024-09-18
最終更新日2024-11-20
実験手法ELECTRON MICROSCOPY (3.03 Å)
主引用文献Structural basis for the evolution and antibody evasion of SARS-CoV-2 BA.2.86 and JN.1 subvariants.
Nat Commun, 15, 2024
9ATO
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BU of 9ato by Molmil
XBB.1.5 spike/Nanosota-3C complex
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, Nanosota-3C, ...
著者Ye, G, Bu, F, Liu, B, Li, F.
登録日2024-02-27
公開日2024-09-18
最終更新日2025-04-02
実験手法ELECTRON MICROSCOPY (3.2 Å)
主引用文献Structure-guided in vitro evolution of nanobodies targeting new viral variants.
Plos Pathog., 20, 2024
9ATP
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BU of 9atp by Molmil
local refinement of XBB.1.5 spike/Nanosota-3C complex
分子名称: Nanosota-3C, Spike glycoprotein
著者Ye, G, Bu, F, Liu, B, Li, F.
登録日2024-02-27
公開日2024-09-18
最終更新日2025-04-02
実験手法ELECTRON MICROSCOPY (3.5 Å)
主引用文献Structure-guided in vitro evolution of nanobodies targeting new viral variants.
Plos Pathog., 20, 2024
8U9H
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BU of 8u9h by Molmil
Structure of the SARS-CoV-2 main protease in complex with inhibitor MPI64
分子名称: (1R,2S,5R)-3-[(cyclohexyloxy)acetyl]-N-{(2R)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2-carboxamide, 3C-like proteinase nsp5
著者Blankenship, L.R, Liu, W.R.
登録日2023-09-19
公開日2024-09-25
最終更新日2024-10-23
実験手法X-RAY DIFFRACTION (1.7 Å)
主引用文献Structure of the SARS-CoV-2 main protease in complex with inhibitors
To Be Published
8U9K
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BU of 8u9k by Molmil
Structure of the SARS-CoV-2 main protease in complex with inhibitor MPI94
分子名称: 3C-like proteinase nsp5, diphenylmethyl (1R,2S,5R)-2-({(2R)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}carbamoyl)-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-3-carboxylate
著者Blankenship, L.R, Liu, W.R.
登録日2023-09-19
公開日2024-09-25
最終更新日2024-10-09
実験手法X-RAY DIFFRACTION (1.85 Å)
主引用文献Structure of the SARS-CoV-2 main protease in complex with inhibitors
To Be Published
8U9M
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BU of 8u9m by Molmil
Structure of the SARS-CoV-2 main protease in complex with inhibitor MPI95
分子名称: 3C-like proteinase nsp5, bis(4-fluorophenyl)methyl (1R,2S,5R)-2-({(2R)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}carbamoyl)-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-3-carboxylate
著者Blankenship, L.R, Liu, W.R.
登録日2023-09-19
公開日2024-09-25
最終更新日2024-10-09
実験手法X-RAY DIFFRACTION (1.85 Å)
主引用文献Structure of the SARS-CoV-2 main protease in complex with inhibitors
To Be Published
8U9N
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BU of 8u9n by Molmil
Structure of the SARS-CoV-2 main protease in complex with inhibitor MPI64
分子名称: (1R,2S,5S)-3-[bis(4-chlorophenyl)acetyl]-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2-carboxamide, 3C-like proteinase nsp5
著者Blankenship, L.R, Liu, W.R.
登録日2023-09-19
公開日2024-09-25
最終更新日2024-11-13
実験手法X-RAY DIFFRACTION (1.7 Å)
主引用文献Structure of the SARS-CoV-2 main protease in complex with inhibitors
To Be Published
8U9T
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BU of 8u9t by Molmil
Structure of the SARS-CoV-2 main protease in complex with inhibitor MPI97
分子名称: (1R,2S,5S)-N~3~,N~3~-bis(4-chlorophenyl)-N~2~-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2,3-dicarboxamide, 3C-like proteinase nsp5
著者Blankenship, L.R, Liu, W.R.
登録日2023-09-20
公開日2024-09-25
最終更新日2024-10-16
実験手法X-RAY DIFFRACTION (1.65 Å)
主引用文献Structure of the SARS-CoV-2 main protease in complex with inhibitors
To Be Published
8U9U
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BU of 8u9u by Molmil
Structure of the SARS-CoV-2 main protease in complex with inhibitor MPI98
分子名称: (1R,2S,5S)-3-[bis(4-chlorophenoxy)acetyl]-N-{(2S)-1-hydroxy-3-[(3R)-2-oxo-3,4-dihydro-2H-pyrrol-3-yl]propan-2-yl}-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2-carboxamide, 3C-like proteinase nsp5
著者Blankenship, L.R, Liu, W.R.
登録日2023-09-20
公開日2024-09-25
最終更新日2024-11-06
実験手法X-RAY DIFFRACTION (1.85 Å)
主引用文献Structure of the SARS-CoV-2 main protease in complex with inhibitors
To Be Published
8U9V
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BU of 8u9v by Molmil
Structure of the SARS-CoV-2 main protease in complex with inhibitor MPI101
分子名称: 3C-like proteinase nsp5, DIMETHYL SULFOXIDE, N-{(2R)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-4-methyl-N~2~-{[(pyridin-3-yl)methoxy]carbonyl}-L-leucinamide
著者Blankenship, L.R, Liu, W.R.
登録日2023-09-20
公開日2024-09-25
最終更新日2024-10-09
実験手法X-RAY DIFFRACTION (1.65 Å)
主引用文献Structure of the SARS-CoV-2 main protease in complex with inhibitors
To Be Published
8U9W
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BU of 8u9w by Molmil
Structure of the SARS-CoV-2 main protease in complex with inhibitor MPI105
分子名称: 3C-like proteinase nsp5, N-{(2R)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-4-methyl-N~2~-[(2R)-2-phenylazetidine-1-carbonyl]-L-leucinamide
著者Blankenship, L.R, Liu, W.R.
登録日2023-09-20
公開日2024-09-25
最終更新日2024-10-23
実験手法X-RAY DIFFRACTION (2.1 Å)
主引用文献Structure of the SARS-CoV-2 main protease in complex with inhibitors
To Be Published
8WFH
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BU of 8wfh by Molmil
Crystal structure of Omicron BA.4/5 in complex with a neutralizing antibody scFv D1
分子名称: D1 scFv, Spike protein S1
著者Terekhov, S.S, Mokrushina, Y.A, Zhang, M, Zhang, N, Gabibov, A, Guo, Y.
登録日2023-09-19
公開日2024-09-25
最終更新日2024-11-27
実験手法X-RAY DIFFRACTION (2.72 Å)
主引用文献Crystal structure of Omicron BA.4/5 in complex with a neutralizing antibody scFv D1
To Be Published
8WFM
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BU of 8wfm by Molmil
Crystal structure of Omicron BA.1 in complex with a neutralizing antibody scFv T11
分子名称: Spike protein S1, T11 scFv
著者Terekhov, S.S, Mokrushina, Y.A, Zhang, M, Zhang, N, Gabibov, A, Guo, Y.
登録日2023-09-19
公開日2024-09-25
最終更新日2024-11-27
実験手法X-RAY DIFFRACTION (2.99 Å)
主引用文献Crystal structure of Omicron BA.1 in complex with a neutralizing antibody scFv T11
To Be Published
9DN4
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BU of 9dn4 by Molmil
Crystal structure of a SARS-CoV-2 20-mer RNA in complex with FAB BL3-6S97N
分子名称: CHLORIDE ION, FAB BL3-6S97N HEAVY CHAIN, FAB BL3-6S97N LIGHT CHAIN, ...
著者Lovell, S, Cooper, A, Battaile, K.P, Hegde, S, Wang, J.
登録日2024-09-16
公開日2024-09-25
最終更新日2025-07-02
実験手法X-RAY DIFFRACTION (1.9 Å)
主引用文献Mechanistic studies of small molecule ligands selective to RNA single G bulges.
Nucleic Acids Res., 53, 2025
9GNY
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BU of 9gny by Molmil
SARS-CoV-2 methyltransferase nsp10-16 in complex with SAM and Caffeine
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2024-09-04
公開日2024-09-25
実験手法X-RAY DIFFRACTION (1.8 Å)
主引用文献Crystal structures of SARS-CoV-2 methyltransferase nsp10-16 with Cap0-site binders
to be published
9GRP
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BU of 9grp by Molmil
SARS-CoV-2 methyltransferase nsp10-16 in complex with SAM and beta-chloroethyl theophylline
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2024-09-12
公開日2024-09-25
実験手法X-RAY DIFFRACTION (2.1 Å)
主引用文献Crystal structures of SARS-CoV-2 methyltransferase nsp10-16 with Cap0-site binders
To Be Published

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件を2025-07-09に公開中

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