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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
9CDL
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BU of 9cdl by Molmil
SARS-CoV-2 Mpro E166V/L50F double mutant in complex with small molecule inhibitor Mpro61
分子名称: (5P)-5-[(1P,3M,3'P)-3-{3-chloro-5-[(2-chlorophenyl)methoxy]-4-fluorophenyl}-2-oxo-2H-[1,3'-bipyridin]-5-yl]-1-methylpyrimidine-2,4(1H,3H)-dione, 3C-like proteinase nsp5
著者Tang, S, Kenneson, J.R, Huynh, K, Anderson, K.S.
登録日2024-06-25
公開日2025-02-05
最終更新日2025-03-12
実験手法X-RAY DIFFRACTION (1.52 Å)
主引用文献Exploring Possible Drug-Resistant Variants of SARS-CoV-2 Main Protease (M pro ) with Noncovalent Preclinical Candidate, Mpro61.
Acs Bio Med Chem Au, 5, 2025
9CDM
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BU of 9cdm by Molmil
SARS-CoV-2 Mpro L50F mutant in complex with small molecule inhibitor Mpro61
分子名称: (5P)-5-[(1P,3M,3'P)-3-{3-chloro-5-[(2-chlorophenyl)methoxy]-4-fluorophenyl}-2-oxo-2H-[1,3'-bipyridin]-5-yl]-1-methylpyrimidine-2,4(1H,3H)-dione, 3C-like proteinase nsp5, DIMETHYL SULFOXIDE
著者Tang, S, Kenneson, J.R, Huynh, K, Anderson, K.S.
登録日2024-06-25
公開日2025-02-05
最終更新日2025-03-12
実験手法X-RAY DIFFRACTION (2.05 Å)
主引用文献Exploring Possible Drug-Resistant Variants of SARS-CoV-2 Main Protease (M pro ) with Noncovalent Preclinical Candidate, Mpro61.
Acs Bio Med Chem Au, 5, 2025
9G9C
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BU of 9g9c by Molmil
CryoEM structure of Enterococcus italicus Csm-crRNA-CTR (3.2) complex
分子名称: CRISPR system Cms endoribonuclease Csm3, CRISPR system Cms protein Csm2, CRISPR system Cms protein Csm4, ...
著者Jungfer, K, Jinek, M.
登録日2024-07-25
公開日2025-02-05
実験手法ELECTRON MICROSCOPY (2.72 Å)
主引用文献Mechanistic determinants and dynamics of cA6 synthesis in type III CRISPR-Cas effector complexes.
Nucleic Acids Res., 53, 2025
9G9D
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BU of 9g9d by Molmil
CryoEM structure of Enterococcus italicus Csm-crRNA-CTR (4.3) complex
分子名称: CRISPR system Cms endoribonuclease Csm3, CRISPR system Cms protein Csm2, CRISPR system Cms protein Csm4, ...
著者Jungfer, K, Jinek, M.
登録日2024-07-25
公開日2025-02-05
実験手法ELECTRON MICROSCOPY (2.9 Å)
主引用文献Mechanistic determinants and dynamics of cA6 synthesis in type III CRISPR-Cas effector complexes.
Nucleic Acids Res., 53, 2025
8XSD
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BU of 8xsd by Molmil
BA.5 Spike complex with CR9
分子名称: CR9 heavy chain, CR9 light chain, Spike glycoprotein
著者Feng, L.L.
登録日2024-01-09
公開日2025-02-12
実験手法ELECTRON MICROSCOPY (3.55 Å)
主引用文献A broadly neutralizing antibody against the SARS-CoV-2 Omicron sub-variants BA.1, BA.2, BA.2.12.1, BA.4, and BA.5.
Signal Transduct Target Ther, 10, 2025
8Y42
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BU of 8y42 by Molmil
Crystal structure of SARS-CoV-2 3CL protease (3CLpro) in complex with compound 51
分子名称: 3C-like proteinase nsp5, ~{N}-[(1~{S},2~{R})-2-[[4-cyclopropyl-2-(methylcarbamoyl)-6-nitro-phenyl]amino]cyclohexyl]-2-oxidanylidene-1~{H}-quinoline-4-carboxamide
著者Nie, T.Q, Su, H.X, Li, M.J, Xu, Y.C.
登録日2024-01-30
公開日2025-02-12
最終更新日2025-03-26
実験手法X-RAY DIFFRACTION (2.35 Å)
主引用文献Discovery of Novel Nonpeptidic and Noncovalent Small Molecule 3CL pro Inhibitors as anti-SARS-CoV-2 Drug Candidate.
J.Med.Chem., 67, 2024
8Y44
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BU of 8y44 by Molmil
Crystal structure of SARS-CoV-2 3CL protease (3CLpro) in complex with compound 44
分子名称: 3C-like proteinase nsp5, ~{N}-[(1~{S},2~{R})-2-[(4-bromanyl-2-morpholin-4-ylcarbonyl-6-nitro-phenyl)amino]cyclohexyl]-2-oxidanylidene-1~{H}-quinoline-4-carboxamide
著者Nie, T.Q, Su, H.X, Li, M.J, Xu, Y.C.
登録日2024-01-30
公開日2025-02-12
最終更新日2025-03-26
実験手法X-RAY DIFFRACTION (1.91 Å)
主引用文献Discovery of Novel Nonpeptidic and Noncovalent Small Molecule 3CL pro Inhibitors as anti-SARS-CoV-2 Drug Candidate.
J.Med.Chem., 67, 2024
8Z6Q
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BU of 8z6q by Molmil
SARS-CoV-2 XBB.1.16 Spike in complex with CYFN1006-1(S-CYFN1006-1 dimer trimer).
分子名称: CYFN1006-1 heavy chain, CYFN1006-1 light chain, Spike glycoprotein,Fibritin,Expression Tag
著者Wang, Y.J, Sun, L.
登録日2024-04-19
公開日2025-02-12
実験手法ELECTRON MICROSCOPY (5.41 Å)
主引用文献SARS-CoV-2 XBB.1.16 Spike in complex with CYFN1006-1(S-CYFN1006-1 dimer trimer).
To Be Published
8Z6S
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BU of 8z6s by Molmil
Structure of XBB.1.16 S trimer with 2 down-RBDs complex with antibody CYFN1006-1.
分子名称: CYFN1006-1 heavy chain, CYFN1006-1 light chain, Spike glycoprotein,Fibritin,Expression Tag
著者Wang, Y.J, Sun, L.
登録日2024-04-19
公開日2025-02-12
実験手法ELECTRON MICROSCOPY (2.84 Å)
主引用文献Structure of XBB.1.16 S trimer with 2 down-RBDs complex with antibody CYFN1006-1.
To Be Published
8Z6U
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BU of 8z6u by Molmil
SARS-CoV-2 EG.5.1 Spike in complex with CYFN1006-2(S-CYFN1006-2 dimer trimer).
分子名称: CYFN1006-2 heavy chain, CYFN1006-2 light chain, Spike glycoprotein,Fibritin,Expression Tag
著者Wang, Y.J, Sun, L.
登録日2024-04-19
公開日2025-02-12
実験手法ELECTRON MICROSCOPY (3.83 Å)
主引用文献SARS-CoV-2 EG.5.1 Spike in complex with CYFN1006-2(S-CYFN1006-2 dimer trimer).
To Be Published
8Z6W
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BU of 8z6w by Molmil
Structure of EG.5.1 S trimer with 3 down-RBDs complex with antibody CYFN1006-2.
分子名称: CYFN1006-2 heavy chain, CYFN1006-2 light chain, Spike glycoprotein,Fibritin,Expression Tag
著者Wang, Y.J, Sun, L.
登録日2024-04-19
公開日2025-02-12
実験手法ELECTRON MICROSCOPY (3.04 Å)
主引用文献Structure of EG.5.1 S trimer with 3 down-RBDs complex with antibody CYFN1006-2.
To Be Published
8Z86
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BU of 8z86 by Molmil
BA.5 RBD in complex with CR9
分子名称: CR9 heavy chain, CR9 light chain, Spike protein S1
著者Feng, L.L.
登録日2024-04-21
公開日2025-02-12
実験手法ELECTRON MICROSCOPY (3.87 Å)
主引用文献A broadly neutralizing antibody against the SARS-CoV-2 Omicron sub-variants BA.1, BA.2, BA.2.12.1, BA.4, and BA.5.
Signal Transduct Target Ther, 10, 2025
9BNT
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BU of 9bnt by Molmil
Crystal Structure of T21I SARS-CoV-2 Main Protease
分子名称: 3C-like proteinase
著者Papini, C, Anderson, K.S.
登録日2024-05-03
公開日2025-02-12
最終更新日2025-03-12
実験手法X-RAY DIFFRACTION (1.83 Å)
主引用文献Exploring Possible Drug-Resistant Variants of SARS-CoV-2 Main Protease (M pro ) with Noncovalent Preclinical Candidate, Mpro61.
Acs Bio Med Chem Au, 5, 2025
9BNU
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BU of 9bnu by Molmil
Crystal Structure of T190I SARS-CoV-2 Main Protease
分子名称: 3C-like proteinase nsp5
著者Papini, C, Anderson, K.S.
登録日2024-05-03
公開日2025-02-12
最終更新日2025-03-12
実験手法X-RAY DIFFRACTION (1.55 Å)
主引用文献Exploring Possible Drug-Resistant Variants of SARS-CoV-2 Main Protease (M pro ) with Noncovalent Preclinical Candidate, Mpro61.
Acs Bio Med Chem Au, 5, 2025
9BNV
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BU of 9bnv by Molmil
Crystal Structure of A173V SARS-CoV-2 Main Protease
分子名称: 3C-like proteinase nsp5
著者Papini, C, Kenneson, J, Anderson, K.S.
登録日2024-05-03
公開日2025-02-12
最終更新日2025-03-12
実験手法X-RAY DIFFRACTION (1.67 Å)
主引用文献Exploring Possible Drug-Resistant Variants of SARS-CoV-2 Main Protease (M pro ) with Noncovalent Preclinical Candidate, Mpro61.
Acs Bio Med Chem Au, 5, 2025
9BNW
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BU of 9bnw by Molmil
Crystal Structure of A173V/L50F SARS-CoV-2 Main Protease
分子名称: 3C-like proteinase nsp5
著者Papini, C, Kenneson, J, Anderson, K.S.
登録日2024-05-03
公開日2025-02-12
最終更新日2025-03-12
実験手法X-RAY DIFFRACTION (1.3 Å)
主引用文献Exploring Possible Drug-Resistant Variants of SARS-CoV-2 Main Protease (M pro ) with Noncovalent Preclinical Candidate, Mpro61.
Acs Bio Med Chem Au, 5, 2025
9BNX
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BU of 9bnx by Molmil
Crystal Structure of L50F SARS-CoV-2 Main Protease
分子名称: 3C-like proteinase nsp5
著者Papini, C, Kenneson, J, Anderson, K.S.
登録日2024-05-03
公開日2025-02-12
最終更新日2025-03-12
実験手法X-RAY DIFFRACTION (2.48 Å)
主引用文献Exploring Possible Drug-Resistant Variants of SARS-CoV-2 Main Protease (M pro ) with Noncovalent Preclinical Candidate, Mpro61.
Acs Bio Med Chem Au, 5, 2025
9BNY
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BU of 9bny by Molmil
Crystal Structure of E166V/L50F SARS-CoV-2 Main Protease
分子名称: 3C-like proteinase nsp5
著者Papini, C, Kenneson, J, Anderson, K.S.
登録日2024-05-03
公開日2025-02-12
最終更新日2025-03-12
実験手法X-RAY DIFFRACTION (1.83 Å)
主引用文献Exploring Possible Drug-Resistant Variants of SARS-CoV-2 Main Protease (M pro ) with Noncovalent Preclinical Candidate, Mpro61.
Acs Bio Med Chem Au, 5, 2025
9BNZ
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BU of 9bnz by Molmil
Crystal Structure of E166V SARS-CoV-2 Main Protease
分子名称: 3C-like proteinase nsp5
著者Kenneson, J, Papini, C, Anderson, K.S.
登録日2024-05-03
公開日2025-02-12
最終更新日2025-03-12
実験手法X-RAY DIFFRACTION (2.08 Å)
主引用文献Exploring Possible Drug-Resistant Variants of SARS-CoV-2 Main Protease (M pro ) with Noncovalent Preclinical Candidate, Mpro61.
Acs Bio Med Chem Au, 5, 2025
9BO0
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BU of 9bo0 by Molmil
Crystal Structure of T21I SARS-CoV-2 Main Protease in Complex with Compound Mpro61
分子名称: (5P)-5-[(1P,3M,3'P)-3-{3-chloro-5-[(2-chlorophenyl)methoxy]-4-fluorophenyl}-2-oxo-2H-[1,3'-bipyridin]-5-yl]-1-methylpyrimidine-2,4(1H,3H)-dione, 3C-like proteinase
著者Papini, C, Zhang, C.H, Jorgensen, W.L, Anderson, K.S.
登録日2024-05-03
公開日2025-02-12
最終更新日2025-03-12
実験手法X-RAY DIFFRACTION (2.16 Å)
主引用文献Exploring Possible Drug-Resistant Variants of SARS-CoV-2 Main Protease (M pro ) with Noncovalent Preclinical Candidate, Mpro61.
Acs Bio Med Chem Au, 5, 2025
9BO1
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BU of 9bo1 by Molmil
Crystal Structure of T190I SARS-CoV-2 Main Protease in Complex with Compound Mpro61
分子名称: (5P)-5-[(1P,3M,3'P)-3-{3-chloro-5-[(2-chlorophenyl)methoxy]-4-fluorophenyl}-2-oxo-2H-[1,3'-bipyridin]-5-yl]-1-methylpyrimidine-2,4(1H,3H)-dione, 3C-like proteinase nsp5
著者Papini, C, Zhang, C.H, Jorgensen, W.L, Anderson, K.S.
登録日2024-05-03
公開日2025-02-12
最終更新日2025-03-12
実験手法X-RAY DIFFRACTION (1.96 Å)
主引用文献Exploring Possible Drug-Resistant Variants of SARS-CoV-2 Main Protease (M pro ) with Noncovalent Preclinical Candidate, Mpro61.
Acs Bio Med Chem Au, 5, 2025
9BO2
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BU of 9bo2 by Molmil
Crystal Structure of A173V/L50F SARS-CoV-2 Main Protease in Complex with Compound Mpro61
分子名称: (5P)-5-[(1P,3M,3'P)-3-{3-chloro-5-[(2-chlorophenyl)methoxy]-4-fluorophenyl}-2-oxo-2H-[1,3'-bipyridin]-5-yl]-1-methylpyrimidine-2,4(1H,3H)-dione, 3C-like proteinase nsp5
著者Papini, C, Kenneson, J, Zhang, C.H, Jorgensen, W.L, Anderson, K.S.
登録日2024-05-03
公開日2025-02-12
最終更新日2025-03-12
実験手法X-RAY DIFFRACTION (1.91 Å)
主引用文献Exploring Possible Drug-Resistant Variants of SARS-CoV-2 Main Protease (M pro ) with Noncovalent Preclinical Candidate, Mpro61.
Acs Bio Med Chem Au, 5, 2025
9BO3
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BU of 9bo3 by Molmil
Crystal Structure of E166V SARS-CoV-2 Main Protease in Complex with Compound Mpro61
分子名称: (5P)-5-[(1P,3M,3'P)-3-{3-chloro-5-[(2-chlorophenyl)methoxy]-4-fluorophenyl}-2-oxo-2H-[1,3'-bipyridin]-5-yl]-1-methylpyrimidine-2,4(1H,3H)-dione, 3C-like proteinase nsp5
著者Papini, C, Kenneson, J, Zhang, C.H, Jorgensen, W.L, Anderson, K.S.
登録日2024-05-03
公開日2025-02-12
最終更新日2025-03-12
実験手法X-RAY DIFFRACTION (2.78 Å)
主引用文献Exploring Possible Drug-Resistant Variants of SARS-CoV-2 Main Protease (M pro ) with Noncovalent Preclinical Candidate, Mpro61.
Acs Bio Med Chem Au, 5, 2025
9BO4
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BU of 9bo4 by Molmil
Crystal Structure of T21I SARS-CoV-2 Main Protease in Complex with Nirmatrelvir
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
著者Papini, C, Anderson, K.S.
登録日2024-05-03
公開日2025-02-12
最終更新日2025-03-12
実験手法X-RAY DIFFRACTION (2.28 Å)
主引用文献Exploring Possible Drug-Resistant Variants of SARS-CoV-2 Main Protease (M pro ) with Noncovalent Preclinical Candidate, Mpro61.
Acs Bio Med Chem Au, 5, 2025
9BO5
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BU of 9bo5 by Molmil
Crystal Structure of T190I SARS-CoV-2 Main Protease in Complex with Nirmatrelvir
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Papini, C, Anderson, K.S.
登録日2024-05-03
公開日2025-02-12
最終更新日2025-03-12
実験手法X-RAY DIFFRACTION (1.84 Å)
主引用文献Exploring Possible Drug-Resistant Variants of SARS-CoV-2 Main Protease (M pro ) with Noncovalent Preclinical Candidate, Mpro61.
Acs Bio Med Chem Au, 5, 2025

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件を2025-06-04に公開中

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