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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 (4406)代表構造 (1944)最新のエントリー (19)
8HVY
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Crystal structure of SARS-Cov-2 main protease K90R mutant in complex with PF07304814
分子名称: 3C-like proteinase nsp5, [(3~{S})-3-[[(2~{S})-2-[(4-methoxy-1~{H}-indol-2-yl)carbonylamino]-4-methyl-pentanoyl]amino]-2-oxidanylidene-4-[(3~{R})-2-oxidanylidene-3,4-dihydropyrrol-3-yl]butyl] dihydrogen phosphate
著者Wang, J, Zhang, J, Li, J.
登録日2022-12-28
公開日2024-01-17
最終更新日2024-02-07
実験手法X-RAY DIFFRACTION (1.97 Å)
主引用文献Crystal structures of main protease (M pro ) mutants of SARS-CoV-2 variants bound to PF-07304814.
Mol Biomed, 4, 2023
8HVZ
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Crystal structure of SARS-Cov-2 main protease V186F mutant in complex with PF07304814
分子名称: 3C-like proteinase nsp5, [(3~{S})-3-[[(2~{S})-2-[(4-methoxy-1~{H}-indol-2-yl)carbonylamino]-4-methyl-pentanoyl]amino]-2-oxidanylidene-4-[(3~{R})-2-oxidanylidene-3,4-dihydropyrrol-3-yl]butyl] dihydrogen phosphate
著者Zou, X.F, Zhang, J, Li, J.
登録日2022-12-28
公開日2024-01-17
最終更新日2024-02-07
実験手法X-RAY DIFFRACTION (1.7 Å)
主引用文献Crystal structures of main protease (M pro ) mutants of SARS-CoV-2 variants bound to PF-07304814.
Mol Biomed, 4, 2023
8HZR
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Crystal structure of SARS-Cov-2 main protease S46F mutant in complex with PF07321332
分子名称: (1R,2S,5S)-N-{(1E,2S)-1-imino-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
著者Zeng, X.Y, Zhang, J, Li, J.
登録日2023-01-09
公開日2024-01-17
実験手法X-RAY DIFFRACTION (1.92 Å)
主引用文献Crystal structure of SARS-Cov-2 main protease S46F mutant in complex with PF07321332
To Be Published
8OKB
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SARS-CoV2 NSP5 in complex with a peptidomimetic ligand
分子名称: 3C-like proteinase nsp5, methyl (4~{S})-4-[[(2~{S})-4-methyl-2-(phenylmethoxycarbonylamino)pentanoyl]amino]-5-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]pentanoate
著者Calderone, V.
登録日2023-03-28
公開日2024-01-17
最終更新日2024-02-28
実験手法X-RAY DIFFRACTION (2.31 Å)
主引用文献Development of a GC-376 Based Peptidomimetic PROTAC as a Degrader of 3-Chymotrypsin-like Protease of SARS-CoV-2.
Acs Med.Chem.Lett., 15, 2024
8OKC
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SARS-CoV2 NSP5 in complex with a GC-376 based peptidomimetic PROTAC
分子名称: (phenylmethyl) ~{N}-[(2~{R})-1-[[(~{Z},2~{S})-5-[4-[[1-[2-[(3~{R})-2,6-bis(oxidanylidene)piperidin-3-yl]-6-fluoranyl-1,3-bis(oxidanylidene)isoindol-5-yl]piperidin-4-yl]methyl]piperazin-1-yl]-5-oxidanylidene-1-[(3~{R})-2-oxidanylidenepyrrolidin-3-yl]pent-3-en-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]carbamate, 3C-like proteinase nsp5
著者Calderone, V.
登録日2023-03-28
公開日2024-01-17
最終更新日2024-02-28
実験手法X-RAY DIFFRACTION (2 Å)
主引用文献Development of a GC-376 Based Peptidomimetic PROTAC as a Degrader of 3-Chymotrypsin-like Protease of SARS-CoV-2.
Acs Med.Chem.Lett., 15, 2024
8TM1
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Antibody N3-1 bound to RBDs in the up and down conformations
分子名称: N3-1 Fab heavy chain, N3-1 Fab light chain, Spike glycoprotein
著者Hsieh, C.-L, McLellan, J.S.
登録日2023-07-27
公開日2024-01-17
実験手法ELECTRON MICROSCOPY (2.79 Å)
主引用文献SARS-COV-2 Omicron variants conformationally escape a rare quaternary antibody binding mode.
Commun Biol, 6, 2023
8TMA
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Antibody N3-1 bound to RBD in the up conformation
分子名称: N3-1 Fab heavy chain, N3-1 Fab light chain, Spike glycoprotein
著者Hsieh, C.-L, McLellan, J.S.
登録日2023-07-29
公開日2024-01-17
実験手法ELECTRON MICROSCOPY (3.2 Å)
主引用文献SARS-COV-2 Omicron variants conformationally escape a rare quaternary antibody binding mode.
Commun Biol, 6, 2023
8VCI
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SARS-CoV-2 Frameshift Stimulatory Element with Upstream Multibranch Loop
分子名称: Frameshift Stimulatory Element with Upstream Multi-branch Loop
著者Peterson, J.M, Becker, S.T, O'Leary, C.A, Juneja, P, Yang, Y, Moss, W.N.
登録日2023-12-14
公開日2024-01-17
最終更新日2024-05-29
実験手法ELECTRON MICROSCOPY (6.1 Å)
主引用文献Structure of the SARS-CoV-2 Frameshift Stimulatory Element with an Upstream Multibranch Loop.
Biochemistry, 63, 2024
8G72
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SARS-CoV-2 spike/Nb2 complex with 1 RBD up (local refinement at 5.6 A)
分子名称: Nanosota-2, Spike glycoprotein
著者Ye, G, Bu, F, Liu, B, Li, F.
登録日2023-02-16
公開日2024-01-24
実験手法ELECTRON MICROSCOPY (5.6 Å)
主引用文献Discovery of Nanosota-2, -3, and -4 as super potent and broad-spectrum therapeutic nanobody candidates against COVID-19.
J.Virol., 97, 2023
8G73
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SARS-CoV-2 spike/Nb3 complex with 2 RBDs up and 3 Nb3 bound at 2.5 A
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-3, ...
著者Ye, G, Bu, F, Liu, B, Li, F.
登録日2023-02-16
公開日2024-01-24
実験手法ELECTRON MICROSCOPY (2.5 Å)
主引用文献Discovery of Nanosota-2, -3, and -4 as super potent and broad-spectrum therapeutic nanobody candidates against COVID-19.
J.Virol., 97, 2023
8G74
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SARS-CoV-2 spike/Nb3 complex with 1 RBD up and 2 Nb3
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-3, ...
著者Ye, G, Bu, F, Liu, B, Li, F.
登録日2023-02-16
公開日2024-01-24
実験手法ELECTRON MICROSCOPY (2.5 Å)
主引用文献Discovery of Nanosota-2, -3, and -4 as super potent and broad-spectrum therapeutic nanobody candidates against COVID-19.
J.Virol., 97, 2023
8G75
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SARS-CoV-2 spike/Nb4 complex with 2 RBDs up and 3 Nb4 bound
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-4, ...
著者Ye, G, Bu, F, Liu, B, Li, F.
登録日2023-02-16
公開日2024-01-24
実験手法ELECTRON MICROSCOPY (3.4 Å)
主引用文献Discovery of Nanosota-2, -3, and -4 as super potent and broad-spectrum therapeutic nanobody candidates against COVID-19.
J.Virol., 97, 2023
8K3K
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The crystal structure of nanobody Nb4 in complex with receptor binding domain (RBD) of BA.1 Spike protein
分子名称: Nanobody Nb4, Spike protein S1
著者Wang, H.Y, Xu, W.Q.
登録日2023-07-16
公開日2024-01-24
実験手法X-RAY DIFFRACTION (2.43 Å)
主引用文献A potent and broad-spectrum neutralizing nanobody for SARS-CoV-2 viruses, including all major Omicron strains.
MedComm (2020), 4, 2023
8TPB
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Synthesis, X-Ray Crystallographic and Biological Activities of Covalent, Non-Peptidic Inhibitors of SARS-CoV-2 Main Protease
分子名称: N-[(1R)-2-(tert-butylamino)-2-oxo-1-(pyridin-3-yl)ethyl]-N-(4-tert-butylphenyl)-2-chloroacetamide, Non-structural protein 7
著者Chua, T.K, Song, Y.
登録日2023-08-04
公開日2024-01-24
最終更新日2024-02-21
実験手法X-RAY DIFFRACTION (1.88 Å)
主引用文献Design, Synthesis, X-ray Crystallography, and Biological Activities of Covalent, Non-Peptidic Inhibitors of SARS-CoV-2 Main Protease.
Acs Infect Dis., 10, 2024
8TPC
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Synthesis, X-Ray Crystallographic and Biological Activities of Covalent, Non-Peptidic Inhibitors of SARS-CoV-2 Main Protease
分子名称: N-[(1R)-2-(benzylamino)-2-oxo-1-(pyridin-3-yl)ethyl]-N-[4-(2-chloroacetamido)phenyl]furan-2-carboxamide, Non-structural protein 7
著者Chua, T.K, Song, Y.
登録日2023-08-04
公開日2024-01-24
最終更新日2024-02-21
実験手法X-RAY DIFFRACTION (1.73 Å)
主引用文献Design, Synthesis, X-ray Crystallography, and Biological Activities of Covalent, Non-Peptidic Inhibitors of SARS-CoV-2 Main Protease.
Acs Infect Dis., 10, 2024
8TPD
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Synthesis, X-Ray Crystallographic and Biological Activities of Covalent, Non-Peptidic Inhibitors of SARS-CoV-2 Main Protease
分子名称: 3C-like proteinase nsp5, N-[(1R)-2-(benzylamino)-2-oxo-1-(pyridin-3-yl)ethyl]-N-[3-(2-chloroacetamido)phenyl]furan-2-carboxamide
著者Chua, T.K, Song, Y.
登録日2023-08-04
公開日2024-01-24
最終更新日2024-02-21
実験手法X-RAY DIFFRACTION (1.68 Å)
主引用文献Design, Synthesis, X-ray Crystallography, and Biological Activities of Covalent, Non-Peptidic Inhibitors of SARS-CoV-2 Main Protease.
Acs Infect Dis., 10, 2024
8TPG
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Synthesis, X-Ray Crystallographic and Biological Activities of Covalent, Non-Peptidic Inhibitors of SARS-CoV-2 Main Protease
分子名称: (3R)-N-(4-tert-butylphenyl)-N-[(1R)-2-(cyclohexylamino)-2-oxo-1-(pyridin-3-yl)ethyl]-3-hydroxybutanamide, Non-structural protein 7
著者Chua, T.K, Song, Y.
登録日2023-08-04
公開日2024-01-24
最終更新日2024-02-21
実験手法X-RAY DIFFRACTION (1.692 Å)
主引用文献Design, Synthesis, X-ray Crystallography, and Biological Activities of Covalent, Non-Peptidic Inhibitors of SARS-CoV-2 Main Protease.
Acs Infect Dis., 10, 2024
8TPH
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Synthesis, X-Ray Crystallographic and Biological Activities of Covalent, Non-Peptidic Inhibitors of SARS-CoV-2 Main Protease
分子名称: (3R)-N-(4-tert-butylphenyl)-N-[(1R)-2-(cyclohexylamino)-2-oxo-1-(pyridin-3-yl)ethyl]-3-hydroxybutanamide, Non-structural protein 7
著者Chua, T.K, Song, Y.
登録日2023-08-04
公開日2024-01-24
最終更新日2024-02-21
実験手法X-RAY DIFFRACTION (1.52 Å)
主引用文献Design, Synthesis, X-ray Crystallography, and Biological Activities of Covalent, Non-Peptidic Inhibitors of SARS-CoV-2 Main Protease.
Acs Infect Dis., 10, 2024
8TPI
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Synthesis, X-Ray Crystallographic and Biological Activities of Covalent, Non-Peptidic Inhibitors of SARS-CoV-2 Main Protease
分子名称: N-(4-tert-butylphenyl)-N-[(1R)-2-(cyclohexylamino)-2-oxo-1-(pyridin-3-yl)ethyl]-2-hydroxy-2-methylpropanamide, Non-structural protein 7
著者Chua, T.K, Song, Y.
登録日2023-08-04
公開日2024-01-24
最終更新日2024-02-21
実験手法X-RAY DIFFRACTION (1.98 Å)
主引用文献Design, Synthesis, X-ray Crystallography, and Biological Activities of Covalent, Non-Peptidic Inhibitors of SARS-CoV-2 Main Protease.
Acs Infect Dis., 10, 2024
8TYJ
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Crystal structure of SARS-CoV-2 nsp10/nsp16 complex with bound SAH
分子名称: 2'-O-methyltransferase, GLYCEROL, Non-structural protein 10, ...
著者Patel, K.P, Bruner, S.D.
登録日2023-08-25
公開日2024-01-24
実験手法X-RAY DIFFRACTION (1.9 Å)
主引用文献Crystal structure of SARS-CoV-2 nsp10/nsp16 complex with bound SAH
To Be Published
8U1G
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Prefusion-stabilized SARS-CoV-2 S2 subunit
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Spike protein S2
著者Hsieh, C.-L, McLellan, J.S.
登録日2023-08-31
公開日2024-01-24
実験手法X-RAY DIFFRACTION (3.2 Å)
主引用文献Structure of prefusion-stabilized SARS-CoV-2 S2-only antigen
To Be Published
8UH8
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Crystal structure of SARS-CoV-2 main protease E166V (Apo structure)
分子名称: ORF1a polyprotein
著者Bulut, H, Hayashi, H, Kuwata, N, Tsuji, K, Das, D, Tamamura, H, Mitsuya, H.
登録日2023-10-07
公開日2024-01-24
実験手法X-RAY DIFFRACTION (1.9 Å)
主引用文献TKB272, an Orally Available SARS-CoV-2-Mpro Inhibitor Containing 5-Fluorobenzothiazole, Potently Blocks SARS-CoV-2 Replication without Ritonavir
To Be Published
8ENS
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Crystal structure of beta'-COPI-WD40 domain in complex with SARS-CoV-2 spike tail hepta-peptide
分子名称: Coatomer subunit beta', spike tail hepta-peptide
著者Dey, D, Hasan, S.S.
登録日2022-09-30
公開日2024-01-31
実験手法X-RAY DIFFRACTION (1.45 Å)
主引用文献A single C-terminal residue controls SARS-CoV-2 spike trafficking and incorporation into VLPs.
Nat Commun, 14, 2023
8ENW
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Crystal structure of beta'-COPI-WD40 domain in complex with SARS-CoV-2 clientized spike tail heptapeptide.
分子名称: 1,2-ETHANEDIOL, Clientized spike tail peptide, Coatomer subunit beta'
著者Dey, D, Hasan, S.S.
登録日2022-09-30
公開日2024-01-31
実験手法X-RAY DIFFRACTION (1.45 Å)
主引用文献A single C-terminal residue controls SARS-CoV-2 spike trafficking and incorporation into VLPs.
Nat Commun, 14, 2023
8ENX
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Crystal structure of beta'-COPI-WD40 domain Y33A mutant in complex with SARS-CoV-2 clientized spike tail heptapeptide.
分子名称: Clientized spike tail heptapeptide, Coatomer subunit beta'
著者Dey, D, Hasan, S.S.
登録日2022-09-30
公開日2024-01-31
実験手法X-RAY DIFFRACTION (1.8 Å)
主引用文献A single C-terminal residue controls SARS-CoV-2 spike trafficking and incorporation into VLPs.
Nat Commun, 14, 2023

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