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COVID-19特辑

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冠状病毒
冠状病毒,2020. 由David S. Goodsell @ RCSB PDB原图修改

最近爆发的新型冠状病毒传染病(Novel Coronavirus disease 2019: COVID-19)对全世界的人们都构成了严重威胁。 为了尽早了解新病毒(Severe Acute Respiratory Syndrome Coronavirus 2: SARS-CoV-2)以开发出有效的抗病毒药物,已经有很多科研人員开始了相关蛋白结构的研究,并且将所获得的结构数据存储于PDB。 PDBj为用户提供了COVID-19相关数据一览的门户页面,并将于每周三更新当日新发布的相关数据。

有关该病毒蛋白质的解说,请参见下面的“当月的分子”页面。

“所有结构”标签的页面则逐一罗列了所有的结构数据,包括由同一研究组提交的系列数据群。 “代表性结构”标签的页面精选具有相同氨基酸序列的结构数据中的高分辨率数据,不重复选择具同一氨基酸序列的数据,即使该数据可能包含不同配体。 “最新条目”标签内包含本周新更新数据。


Created: 2020-09-03 (last edited: more than 1 year ago)2020-12-02
7GRS
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BU of 7grs by Molmil
Crystal structure of SARS-CoV-2 main protease in complex with cpd-15
Descriptor: 3C-like proteinase nsp5, DIMETHYL SULFOXIDE, SODIUM ION, ...
Authors:Huang, C.-Y, Metz, A, Sharpe, M, Sweeney, A.
Deposit date:2023-11-14
Release date:2024-02-14
Method:X-RAY DIFFRACTION (1.47 Å)
Cite:Fragment-based screening targeting an open form of the SARS-CoV-2 main protease binding pocket.
Acta Crystallogr D Struct Biol, 80, 2024
7GRT
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BU of 7grt by Molmil
Crystal structure of SARS-CoV-2 main protease in complex with cpd-16
Descriptor: 3C-like proteinase nsp5, DIMETHYL SULFOXIDE, N-[(2,3-dihydro-1-benzofuran-5-yl)methyl]benzamide, ...
Authors:Huang, C.-Y, Metz, A, Sharpe, M, Sweeney, A.
Deposit date:2023-11-14
Release date:2024-02-14
Last modified:2024-03-13
Method:X-RAY DIFFRACTION (1.71 Å)
Cite:Fragment-based screening targeting an open form of the SARS-CoV-2 main protease binding pocket.
Acta Crystallogr D Struct Biol, 80, 2024
7GRU
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BU of 7gru by Molmil
Crystal structure of SARS-CoV-2 main protease in complex with cpd-17
Descriptor: 3-(4-chlorophenyl)-1-methyl-1H-pyrazol-5-amine, 3C-like proteinase nsp5, CHLORIDE ION, ...
Authors:Huang, C.-Y, Metz, A, Sharpe, M, Sweeney, A.
Deposit date:2023-11-14
Release date:2024-02-14
Method:X-RAY DIFFRACTION (1.81 Å)
Cite:Fragment-based screening targeting an open form of the SARS-CoV-2 main protease binding pocket.
Acta Crystallogr D Struct Biol, 80, 2024
7GRV
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BU of 7grv by Molmil
Crystal structure of SARS-CoV-2 main protease in complex with cpd-18
Descriptor: (2S)-2-(2-fluorophenyl)-1,3-thiazolidin-4-one, 3C-like proteinase nsp5, CHLORIDE ION, ...
Authors:Huang, C.-Y, Metz, A, Sharpe, M, Sweeney, A.
Deposit date:2023-11-14
Release date:2024-02-14
Last modified:2024-03-13
Method:X-RAY DIFFRACTION (1.92 Å)
Cite:Fragment-based screening targeting an open form of the SARS-CoV-2 main protease binding pocket.
Acta Crystallogr D Struct Biol, 80, 2024
7GRW
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BU of 7grw by Molmil
Crystal structure of SARS-CoV-2 main protease in complex with cpd-19
Descriptor: (2S)-N-(3,5-dichlorophenyl)-2-hydroxypropanamide, 3C-like proteinase nsp5, DIMETHYL SULFOXIDE, ...
Authors:Huang, C.-Y, Metz, A, Sharpe, M, Sweeney, A.
Deposit date:2023-11-14
Release date:2024-02-14
Last modified:2024-03-13
Method:X-RAY DIFFRACTION (1.92 Å)
Cite:Fragment-based screening targeting an open form of the SARS-CoV-2 main protease binding pocket.
Acta Crystallogr D Struct Biol, 80, 2024
7GRX
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BU of 7grx by Molmil
Crystal structure of SARS-CoV-2 main protease in complex with cpd-20
Descriptor: 1-(2,4-difluorophenyl)pyrrolidine-2,5-dione, 3C-like proteinase nsp5, CHLORIDE ION, ...
Authors:Huang, C.-Y, Metz, A, Sharpe, M, Sweeney, A.
Deposit date:2023-11-14
Release date:2024-02-14
Last modified:2024-03-13
Method:X-RAY DIFFRACTION (1.55 Å)
Cite:Fragment-based screening targeting an open form of the SARS-CoV-2 main protease binding pocket.
Acta Crystallogr D Struct Biol, 80, 2024
7GRY
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BU of 7gry by Molmil
Crystal structure of SARS-CoV-2 main protease in complex with cpd-21
Descriptor: 1-(3,5-dichlorophenyl)pyrrolidine-2,5-dione, 3C-like proteinase nsp5, CHLORIDE ION, ...
Authors:Huang, C.-Y, Metz, A, Sharpe, M, Sweeney, A.
Deposit date:2023-11-14
Release date:2024-02-14
Method:X-RAY DIFFRACTION (1.54 Å)
Cite:Fragment-based screening targeting an open form of the SARS-CoV-2 main protease binding pocket.
Acta Crystallogr D Struct Biol, 80, 2024
7GRZ
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BU of 7grz by Molmil
Crystal structure of SARS-CoV-2 main protease in complex with cpd-22
Descriptor: 3C-like proteinase nsp5, DIMETHYL SULFOXIDE, N,N-dimethyl-2-[(naphthalen-2-yl)oxy]acetamide, ...
Authors:Huang, C.-Y, Metz, A, Sharpe, M, Sweeney, A.
Deposit date:2023-11-14
Release date:2024-02-14
Method:X-RAY DIFFRACTION (1.86 Å)
Cite:Fragment-based screening targeting an open form of the SARS-CoV-2 main protease binding pocket.
Acta Crystallogr D Struct Biol, 80, 2024
7GS0
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BU of 7gs0 by Molmil
Crystal structure of SARS-CoV-2 main protease in complex with cpd-23
Descriptor: (pyridin-2-yl)(quinolin-2-yl)methanone, 3C-like proteinase nsp5, CHLORIDE ION, ...
Authors:Huang, C.-Y, Metz, A, Sharpe, M, Sweeney, A.
Deposit date:2023-11-14
Release date:2024-02-14
Method:X-RAY DIFFRACTION (1.69 Å)
Cite:Fragment-based screening targeting an open form of the SARS-CoV-2 main protease binding pocket.
Acta Crystallogr D Struct Biol, 80, 2024
7GS1
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BU of 7gs1 by Molmil
Crystal structure of SARS-CoV-2 main protease in complex with cpd-24
Descriptor: 2-cyano-~{N}-cyclohexyl-ethanamide, 3C-like proteinase nsp5, CHLORIDE ION, ...
Authors:Huang, C.-Y, Metz, A, Sharpe, M, Sweeney, A.
Deposit date:2023-11-14
Release date:2024-02-14
Method:X-RAY DIFFRACTION (1.74 Å)
Cite:Fragment-based screening targeting an open form of the SARS-CoV-2 main protease binding pocket.
Acta Crystallogr D Struct Biol, 80, 2024
7GS2
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BU of 7gs2 by Molmil
Crystal structure of SARS-CoV-2 main protease in complex with cpd-25
Descriptor: 3-(pyridin-3-yl)benzoic acid, 3C-like proteinase nsp5, DIMETHYL SULFOXIDE, ...
Authors:Huang, C.-Y, Metz, A, Sharpe, M, Sweeney, A.
Deposit date:2023-11-14
Release date:2024-02-14
Method:X-RAY DIFFRACTION (1.77 Å)
Cite:Fragment-based screening targeting an open form of the SARS-CoV-2 main protease binding pocket.
Acta Crystallogr D Struct Biol, 80, 2024
7GS3
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BU of 7gs3 by Molmil
Crystal structure of SARS-CoV-2 main protease in complex with cpd-26
Descriptor: (6-phenylpyridin-3-yl)methanamine, 3C-like proteinase nsp5, DIMETHYL SULFOXIDE, ...
Authors:Huang, C.-Y, Metz, A, Sharpe, M, Sweeney, A.
Deposit date:2023-11-14
Release date:2024-02-14
Last modified:2024-03-13
Method:X-RAY DIFFRACTION (1.89 Å)
Cite:Fragment-based screening targeting an open form of the SARS-CoV-2 main protease binding pocket.
Acta Crystallogr D Struct Biol, 80, 2024
7GS4
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BU of 7gs4 by Molmil
Crystal structure of SARS-CoV-2 main protease in complex with cpd-27
Descriptor: 3C-like proteinase nsp5, 7-(hydroxymethyl)-3-methyl-6~{H}-[1,3]thiazolo[3,2-a]pyrimidin-5-one, CHLORIDE ION, ...
Authors:Huang, C.-Y, Metz, A, Sharpe, M, Sweeney, A.
Deposit date:2023-11-14
Release date:2024-02-14
Last modified:2024-03-13
Method:X-RAY DIFFRACTION (1.86 Å)
Cite:Fragment-based screening targeting an open form of the SARS-CoV-2 main protease binding pocket.
Acta Crystallogr D Struct Biol, 80, 2024
7GS5
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BU of 7gs5 by Molmil
Crystal structure of SARS-CoV-2 main protease in complex with cpd-28
Descriptor: (3R)-5-fluoro-3-hydroxy-1,3-dihydro-2H-indol-2-one, 3C-like proteinase nsp5, DIMETHYL SULFOXIDE, ...
Authors:Huang, C.-Y, Metz, A, Sharpe, M, Sweeney, A.
Deposit date:2023-11-14
Release date:2024-02-14
Last modified:2024-03-13
Method:X-RAY DIFFRACTION (1.88 Å)
Cite:Fragment-based screening targeting an open form of the SARS-CoV-2 main protease binding pocket.
Acta Crystallogr D Struct Biol, 80, 2024
7GS6
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BU of 7gs6 by Molmil
Crystal structure of SARS-CoV-2 main protease in complex with cpd-29
Descriptor: (3S)-4,7-dichloro-3-hydroxy-1,3-dihydro-2H-indol-2-one, 3C-like proteinase nsp5, DIMETHYL SULFOXIDE, ...
Authors:Huang, C.-Y, Metz, A, Sharpe, M, Sweeney, A.
Deposit date:2023-11-14
Release date:2024-02-14
Last modified:2024-03-13
Method:X-RAY DIFFRACTION (1.62 Å)
Cite:Fragment-based screening targeting an open form of the SARS-CoV-2 main protease binding pocket.
Acta Crystallogr D Struct Biol, 80, 2024
8RV4
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BU of 8rv4 by Molmil
SARS-CoV-2 nsp16-nsp10 in complex with SAM derivative inhibitor 2
Descriptor: 2'-O-methyltransferase nsp16, 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, 5-[[(2~{S},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methylsulfanylmethyl]-2-phenyl-benzoic acid, ...
Authors:Kalnins, G.
Deposit date:2024-01-31
Release date:2024-02-14
Method:X-RAY DIFFRACTION (2.35 Å)
Cite:SARS-CoV-2 nsp16-nsp10 in complex with SAM derivative inhibitor 2
To Be Published
8RV5
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BU of 8rv5 by Molmil
SARS-CoV-2 nsp16-nsp10 in complex with SAM derivative inhibitor 1
Descriptor: 2'-O-methyltransferase nsp16, 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, 5'-DEOXY-5'-METHYLTHIOADENOSINE, ...
Authors:Kalnins, G.
Deposit date:2024-01-31
Release date:2024-02-14
Method:X-RAY DIFFRACTION (2.05 Å)
Cite:SARS-CoV-2 nsp16-nsp10 in complex with SAM derivative inhibitor 1
To Be Published
8RV6
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BU of 8rv6 by Molmil
SARS-CoV-2 nsp16-nsp10 in complex with SAM derivative inhibitor 2
Descriptor: 2'-O-methyltransferase nsp16, 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, 3-[[(2~{S},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methylsulfanylmethyl]-5-(4-hydroxyphenyl)benzoic acid, ...
Authors:Kalnins, G.
Deposit date:2024-01-31
Release date:2024-02-14
Method:X-RAY DIFFRACTION (2.25 Å)
Cite:SARS-CoV-2 nsp16-nsp10 in complex with SAM derivative inhibitor 3
To Be Published
8RV7
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BU of 8rv7 by Molmil
SARS-CoV-2 nsp16-nsp10 in complex with SAM derivative inhibitor 4
Descriptor: 2'-O-methyltransferase nsp16, 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, 3-[[(2~{S},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methylsulfanylmethyl]-5-(3-oxidanylprop-1-ynyl)benzoic acid, ...
Authors:Kalnins, G.
Deposit date:2024-01-31
Release date:2024-02-14
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:SARS-CoV-2 nsp16-nsp10 in complex with SAM derivative inhibitor 4
To Be Published
8RV8
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BU of 8rv8 by Molmil
SARS-CoV-2 nsp16-nsp10 in complex with SAM derivative inhibitor 5
Descriptor: 2'-O-methyltransferase nsp16, 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, 5-[[(2~{S},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methylsulfanyl]-2-chloranyl-benzoic acid, ...
Authors:Kalnins, G.
Deposit date:2024-01-31
Release date:2024-02-14
Method:X-RAY DIFFRACTION (1.7 Å)
Cite:SARS-CoV-2 nsp16-nsp10 in complex with SAM derivative inhibitor 5
To Be Published
8RV9
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BU of 8rv9 by Molmil
SARS-CoV-2 nsp16-nsp10 in complex with SAM derivative inhibitor 6
Descriptor: 2'-O-methyltransferase nsp16, 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, 5-[[(2~{S},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methylsulfanylmethyl]-2-chloranyl-benzoic acid, ...
Authors:Kalnins, G.
Deposit date:2024-01-31
Release date:2024-02-14
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:SARS-CoV-2 nsp16-nsp10 in complex with SAM derivative inhibitor 6
To Be Published
8RVA
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BU of 8rva by Molmil
SARS-CoV-2 nsp16-nsp10 in complex with SAM derivative inhibitor 7
Descriptor: 2'-O-methyltransferase nsp16, 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, 3-[[(2~{S},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methylsulfanylmethyl]benzoic acid, ...
Authors:Kalnins, G.
Deposit date:2024-01-31
Release date:2024-02-14
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:SARS-CoV-2 nsp16-nsp10 in complex with SAM derivative inhibitor 7
To Be Published
8RVB
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BU of 8rvb by Molmil
SARS-CoV-2 nsp16-nsp10 in complex with SAM derivative inhibitor 8
Descriptor: (2~{R},3~{R},4~{S},5~{S})-2-(6-aminopurin-9-yl)-5-[2-(1~{H}-1,2,3-triazol-4-yl)ethylsulfanylmethyl]oxolane-3,4-diol, 2'-O-methyltransferase nsp16, 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, ...
Authors:Kalnins, G.
Deposit date:2024-01-31
Release date:2024-02-14
Method:X-RAY DIFFRACTION (1.95 Å)
Cite:SARS-CoV-2 nsp16-nsp10 in complex with SAM derivative inhibitor 8
To Be Published
8UIA
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BU of 8uia by Molmil
Crystal structure of SARS CoV-2 3CL protease in complex with GSK4365097A
Descriptor: 3C-like proteinase nsp5, CHLORIDE ION, GLYCEROL, ...
Authors:Concha, N.O, Williams, S.P.
Deposit date:2023-10-10
Release date:2024-02-14
Method:X-RAY DIFFRACTION (1.75 Å)
Cite:Exploration of the P1 residue in 3CL protease inhibitors leading to the discovery of a 2-tetrahydrofuran P1 replacement.
Bioorg.Med.Chem., 100, 2024
8UIF
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BU of 8uif by Molmil
Crystal structure of SARS CoV-2 3CL protease in complex with GSK4365096A
Descriptor: 3C-like proteinase nsp5, N-[(benzyloxy)carbonyl]-4-fluoro-L-phenylalanyl-N-{(2R)-1-[(2S)-oxolan-2-yl]-3-[(3S)-2-oxooxolan-3-yl]propan-2-yl}-L-leucinamide
Authors:Concha, N.O, Williams, S.P.
Deposit date:2023-10-10
Release date:2024-02-14
Method:X-RAY DIFFRACTION (2.02 Å)
Cite:Exploration of the P1 residue in 3CL protease inhibitors leading to the discovery of a 2-tetrahydrofuran P1 replacement.
Bioorg.Med.Chem., 100, 2024

223532

数据于2024-08-07公开中

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