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COVID-19特輯

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冠狀病毒
冠狀病毒,2020. 由David S. Goodsell @ RCSB PDB原圖修改

最近爆發的新型冠狀病毒傳染病(Novel Coronavirus disease 2019: COVID-19)對全世界的人們都構成了嚴重威脅。 為了儘早了解新病毒(Severe Acute Respiratory Syndrome Coronavirus 2: SARS-CoV-2)以開發出有效的抗病毒藥物,已經有很多科研人員開始了相關蛋白結構的研究,並且將所獲得結構數據存儲與PDB。 PDBj為用戶提供了COVID-19相關數據一覽的門戶頁面,並將於每週三更新當日新發佈的相關數據。

有關該病毒蛋白質的解說,請參見下面的“當月的分子”頁面。

“所有結構”標籤的頁面則逐一羅列了所有的數據,包括由同一研究組提交的系列數據群。 “代表性結構”標籤的頁面精選具有相同胺基酸序列的結構數據中的高分辨率數據,不重複選擇具有同一胺基酸序列的數據,即使該數據可能包含不同的配體。 “最新條目”標籤內包含本週新更新數據。


Created: 2020-09-03 (last edited: more than 1 year ago)2022-09-02
7HFO
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BU of 7hfo by Molmil
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with AVI-0004309
Descriptor: (1S,3R)-1-{[(7H-pyrrolo[2,3-d]pyrimidin-4-yl)amino]methyl}-3-(trifluoromethyl)cyclohexan-1-ol, CHLORIDE ION, Non-structural protein 3
Authors:Correy, G.J, Fraser, J.S.
Deposit date:2024-08-15
Release date:2025-06-11
Method:X-RAY DIFFRACTION (0.99 Å)
Cite:Exploration of structure-activity relationships for the SARS-CoV-2 macrodomain from shape-based fragment linking and active learning.
Sci Adv, 11, 2025
7HFP
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BU of 7hfp by Molmil
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with AVI-0004318
Descriptor: 4-{[methyl(7H-pyrrolo[2,3-d]pyrimidin-4-yl)amino]methyl}oxan-4-ol, CHLORIDE ION, DIMETHYL SULFOXIDE, ...
Authors:Correy, G.J, Fraser, J.S.
Deposit date:2024-08-15
Release date:2025-06-11
Method:X-RAY DIFFRACTION (0.97 Å)
Cite:Exploration of structure-activity relationships for the SARS-CoV-2 macrodomain from shape-based fragment linking and active learning.
Sci Adv, 11, 2025
7HFQ
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BU of 7hfq by Molmil
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with AVI-0005994
Descriptor: Non-structural protein 3, [(2S)-4,4-dimethyl-1-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)piperidin-2-yl]methanol
Authors:Correy, G.J, Fraser, J.S.
Deposit date:2024-08-15
Release date:2025-06-11
Method:X-RAY DIFFRACTION (1 Å)
Cite:Exploration of structure-activity relationships for the SARS-CoV-2 macrodomain from shape-based fragment linking and active learning.
Sci Adv, 11, 2025
7HFR
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BU of 7hfr by Molmil
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with AVI-0005997
Descriptor: (3aS,6S,6aR)-1-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)octahydrocyclopenta[b]pyrrol-6-ol, DIMETHYL SULFOXIDE, Non-structural protein 3
Authors:Correy, G.J, Fraser, J.S.
Deposit date:2024-08-15
Release date:2025-06-11
Method:X-RAY DIFFRACTION (0.97 Å)
Cite:Exploration of structure-activity relationships for the SARS-CoV-2 macrodomain from shape-based fragment linking and active learning.
Sci Adv, 11, 2025
7HFS
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BU of 7hfs by Molmil
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with AVI-0005998
Descriptor: CHLORIDE ION, Non-structural protein 3, [(2S)-1-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)-1,2,5,6-tetrahydropyridin-2-yl]methanol
Authors:Correy, G.J, Fraser, J.S.
Deposit date:2024-08-15
Release date:2025-06-11
Method:X-RAY DIFFRACTION (1.02 Å)
Cite:Exploration of structure-activity relationships for the SARS-CoV-2 macrodomain from shape-based fragment linking and active learning.
Sci Adv, 11, 2025
7HFT
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BU of 7hft by Molmil
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with AVI-0006000
Descriptor: 4-[(2R)-2-tert-butylpyrrolidin-1-yl]-7H-pyrrolo[2,3-d]pyrimidine, Non-structural protein 3
Authors:Correy, G.J, Fraser, J.S.
Deposit date:2024-08-15
Release date:2025-06-11
Method:X-RAY DIFFRACTION (1.01 Å)
Cite:Exploration of structure-activity relationships for the SARS-CoV-2 macrodomain from shape-based fragment linking and active learning.
Sci Adv, 11, 2025
7HFU
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BU of 7hfu by Molmil
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with AVI-0006002
Descriptor: Non-structural protein 3, [(2R)-1-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)piperidin-2-yl]methanol
Authors:Correy, G.J, Fraser, J.S.
Deposit date:2024-08-15
Release date:2025-06-11
Method:X-RAY DIFFRACTION (1 Å)
Cite:Exploration of structure-activity relationships for the SARS-CoV-2 macrodomain from shape-based fragment linking and active learning.
Sci Adv, 11, 2025
7HFV
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BU of 7hfv by Molmil
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with AVI-0005158
Descriptor: (2R,3R)-3-[(7H-pyrrolo[2,3-d]pyrimidin-4-yl)amino]butan-2-ol, (2S,3R)-3-[(7H-pyrrolo[2,3-d]pyrimidin-4-yl)amino]butan-2-ol, CHLORIDE ION, ...
Authors:Correy, G.J, Fraser, J.S.
Deposit date:2024-08-15
Release date:2025-06-11
Method:X-RAY DIFFRACTION (0.99 Å)
Cite:Exploration of structure-activity relationships for the SARS-CoV-2 macrodomain from shape-based fragment linking and active learning.
Sci Adv, 11, 2025
7HFW
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BU of 7hfw by Molmil
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with AVI-0005216
Descriptor: 4-[(2R)-2-(propan-2-yl)pyrrolidin-1-yl]-7H-pyrrolo[2,3-d]pyrimidine, CHLORIDE ION, Non-structural protein 3
Authors:Correy, G.J, Fraser, J.S.
Deposit date:2024-08-15
Release date:2025-06-11
Method:X-RAY DIFFRACTION (1 Å)
Cite:Exploration of structure-activity relationships for the SARS-CoV-2 macrodomain from shape-based fragment linking and active learning.
Sci Adv, 11, 2025
7HFX
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BU of 7hfx by Molmil
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with AVI-0005266
Descriptor: 2-methyl-2-[(7H-pyrrolo[2,3-d]pyrimidin-4-yl)amino]propan-1-ol, CHLORIDE ION, Non-structural protein 3
Authors:Correy, G.J, Fraser, J.S.
Deposit date:2024-08-15
Release date:2025-06-11
Method:X-RAY DIFFRACTION (1.02 Å)
Cite:Exploration of structure-activity relationships for the SARS-CoV-2 macrodomain from shape-based fragment linking and active learning.
Sci Adv, 11, 2025
7HFY
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BU of 7hfy by Molmil
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with AVI-0006217
Descriptor: 1-{[(7H-pyrrolo[2,3-d]pyrimidin-4-yl)amino]methyl}cyclohexan-1-ol, CHLORIDE ION, Non-structural protein 3
Authors:Correy, G.J, Fraser, J.S.
Deposit date:2024-08-15
Release date:2025-06-11
Method:X-RAY DIFFRACTION (1 Å)
Cite:Exploration of structure-activity relationships for the SARS-CoV-2 macrodomain from shape-based fragment linking and active learning.
Sci Adv, 11, 2025
7HFZ
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BU of 7hfz by Molmil
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with AVI-0006220
Descriptor: (1r,4r)-1-{[(7H-pyrrolo[2,3-d]pyrimidin-4-yl)amino]methyl}cyclohexane-1,4-diol, CHLORIDE ION, Non-structural protein 3
Authors:Correy, G.J, Fraser, J.S.
Deposit date:2024-08-15
Release date:2025-06-11
Method:X-RAY DIFFRACTION (1.02 Å)
Cite:Exploration of structure-activity relationships for the SARS-CoV-2 macrodomain from shape-based fragment linking and active learning.
Sci Adv, 11, 2025
8XCH
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BU of 8xch by Molmil
SARS-CoV-2 Replication-Transcription Complex has a dimer-of-dimeric architecture (ddRTC) in pre-capping initiation.
Descriptor: ADENOSINE-5'-DIPHOSPHATE, Helicase, MAGNESIUM ION, ...
Authors:Yan, L, Lou, Z.
Deposit date:2023-12-09
Release date:2025-06-11
Method:ELECTRON MICROSCOPY (3.4 Å)
Cite:Structural basis for template-product RNA duplex unwinding by SARS-CoV-2 helicase
To Be Published
8ZPQ
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BU of 8zpq by Molmil
Crystal structure of SARS-Cov-2-BQ1.1-RBD and 70fab
Descriptor: 70fab-H, 70fab-L, Spike protein S1
Authors:Wu, Y, Gao, F.
Deposit date:2024-05-31
Release date:2025-06-11
Method:X-RAY DIFFRACTION (2.75 Å)
Cite:Crystal structure of SARS-Cov-2-BQ1.1-RBD and 70fab
To Be Published
8ZQ8
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BU of 8zq8 by Molmil
SARS-Cov-2 3CL protease in complex with macrocyclic inhibitor CG-1039
Descriptor: 3C-like proteinase nsp5, CG-1039
Authors:Chen, X, Hou, K, Tang, X.
Deposit date:2024-06-01
Release date:2025-06-11
Method:X-RAY DIFFRACTION (1.77 Å)
Cite:SARS-Cov-2 3CL protease in complex with macrocyclic inhibitor CG-1039
To Be Published
8ZSE
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BU of 8zse by Molmil
Crystal Structure of SARS CoV-2 Papain-like Protease PLpro-C111S in Complex with GZNL-2002
Descriptor: 2-methyl-5-(4-methylpiperazin-1-yl)-~{N}-(1-quinolin-4-ylcyclopropyl)benzamide, Papain-like protease nsp3, ZINC ION
Authors:Lu, Y, Shang, J.
Deposit date:2024-06-05
Release date:2025-06-11
Method:X-RAY DIFFRACTION (2.8 Å)
Cite:Crystal Structure of SARS CoV-2 Papain-like Protease PLpro-C111S in Complex with GZNL-2002
To Be Published
8ZT9
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BU of 8zt9 by Molmil
The Crystal structure of mol066 bound to the main protease (3CLpro/Mpro) of SARS-CoV-2
Descriptor: 3C-like proteinase, 6-[(6-chloranyl-2-propan-2-yl-indazol-5-yl)amino]-3-[(1-methyl-1,2,4-triazol-3-yl)methyl]-1-[[2,4,5-tris(fluoranyl)phenyl]methyl]pyrimidine-2,4-dione, GLYCEROL
Authors:Yan, M, Zhang, H.
Deposit date:2024-06-06
Release date:2025-06-11
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Development of pyrimidone derivatives as nonpeptidic and noncovalent 3-chymotrypsin-like protease (3CL pro ) inhibitors with anti-coronavirus activities.
Bioorg.Chem., 154, 2025
8ZUB
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BU of 8zub by Molmil
The Crystal structure of mol075 bound to the main protease (3CLpro/Mpro) of SARS-CoV-2
Descriptor: 3C-like proteinase, 6-[(6-chloranyl-2-pentyl-indazol-5-yl)amino]-3-[(1-methyl-1,2,4-triazol-3-yl)methyl]-1-[[2,4,5-tris(fluoranyl)phenyl]methyl]pyrimidine-2,4-dione
Authors:Yan, M, Zhang, H.
Deposit date:2024-06-08
Release date:2025-06-11
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Development of pyrimidone derivatives as nonpeptidic and noncovalent 3-chymotrypsin-like protease (3CL pro ) inhibitors with anti-coronavirus activities.
Bioorg.Chem., 154, 2025
8ZUC
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BU of 8zuc by Molmil
The Crystal structure of mol080 bound to the main protease (3CLpro/Mpro) of SARS-CoV-2
Descriptor: 3C-like proteinase, 6-[[6-chloranyl-2-(3-methylbutyl)indazol-5-yl]amino]-3-[(1-methyl-1,2,4-triazol-3-yl)methyl]-1-[[2,4,5-tris(fluoranyl)phenyl]methyl]pyrimidine-2,4-dione
Authors:Yan, M, Zhang, H.
Deposit date:2024-06-08
Release date:2025-06-11
Method:X-RAY DIFFRACTION (2.1 Å)
Cite:Development of pyrimidone derivatives as nonpeptidic and noncovalent 3-chymotrypsin-like protease (3CL pro ) inhibitors with anti-coronavirus activities.
Bioorg.Chem., 154, 2025
9FC2
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BU of 9fc2 by Molmil
The crystal structure of the SARS-CoV-2 receptor binding domain in complex with the neutralizing nanobody 4.
Descriptor: 1,2-ETHANEDIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose, ACETATE ION, ...
Authors:Casasnovas, J.M, Fernandez, L.A, Silva, K.
Deposit date:2024-05-15
Release date:2025-06-11
Method:X-RAY DIFFRACTION (1.21 Å)
Cite:Integrating immune library probing with structure-based computational design to develop potent neutralizing nanobodies against emerging SARS-CoV-2 variants.
Mabs, 17, 2025
9GUB
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BU of 9gub by Molmil
SARS-CoV-2 Mac1 in complex with MCD-628
Descriptor: (2~{S})-3-(1~{H}-indol-3-yl)-2-(7~{H}-pyrrolo[2,3-d]pyrimidin-4-ylamino)propanoic acid, Papain-like protease nsp3
Authors:Duong, M, Paakkonen, J, Lehtio, L.
Deposit date:2024-09-19
Release date:2025-06-11
Last modified:2025-06-25
Method:X-RAY DIFFRACTION (1.1 Å)
Cite:Identification of a series of pyrrolo-pyrimidine-based SARS-CoV-2 Mac1 inhibitors that repress coronavirus replication.
Mbio, 16, 2025
9H0F
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BU of 9h0f by Molmil
SARS-CoV-2 Mpro in complex with a silicon-containing inhibitor
Descriptor: 3C-like proteinase nsp5, CHLORIDE ION, DIMETHYL SULFOXIDE, ...
Authors:Andrews-Clark, T.C, Laczi, D, Schoenbauer, S, Brewitz, L, Schofield, C.J, Walsh, M.
Deposit date:2024-10-08
Release date:2025-06-11
Method:X-RAY DIFFRACTION (2.09 Å)
Cite:Silaproline-bearing nirmatrelvir derivatives are potent inhibitors of the SARS-CoV-2 main protease highlighting the value of silicon-derivatives in structure-activity-relationship studies.
Eur J Med Chem, 291, 2025
9I1S
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BU of 9i1s by Molmil
Crystal structure of the SARS-CoV-2 helicase NSP13 in complex with myricetin
Descriptor: 3,5,7-TRIHYDROXY-2-(3,4,5-TRIHYDROXYPHENYL)-4H-CHROMEN-4-ONE, 3[N-MORPHOLINO]PROPANE SULFONIC ACID, Helicase nsp13, ...
Authors:Kloskowski, P, Neumann, P, Ficner, R.
Deposit date:2025-01-16
Release date:2025-06-11
Method:X-RAY DIFFRACTION (2.09 Å)
Cite:Myricetin-bound crystal structure of the SARS-CoV-2 helicase NSP13 facilitates the discovery of novel natural inhibitors.
Acta Crystallogr D Struct Biol, 81, 2025
9I4V
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BU of 9i4v by Molmil
Crystal structure of the SARS-CoV-2 helicase NSP13
Descriptor: 3[N-MORPHOLINO]PROPANE SULFONIC ACID, PHOSPHATE ION, SARS-CoV-2 helicase NSP13, ...
Authors:Kloskowski, P, Neumann, P, Ficner, R.
Deposit date:2025-01-27
Release date:2025-06-11
Method:X-RAY DIFFRACTION (2.33 Å)
Cite:Myricetin-bound crystal structure of the SARS-CoV-2 helicase NSP13 facilitates the discovery of novel natural inhibitors.
Acta Crystallogr D Struct Biol, 81, 2025
9NPX
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BU of 9npx by Molmil
SARS-CoV-2 nsp1 bound to the Rhinolophus lepidus 40S ribosomal subunit (local refinement of the 40S body)
Descriptor: 18S ribosomal RNA, 40S ribosomal protein S11, 40S ribosomal protein S13, ...
Authors:Gen, R, Seattle Structural Genomics Center for Infectious Disease (SSGCID), Veesler, D.
Deposit date:2025-03-11
Release date:2025-06-11
Method:ELECTRON MICROSCOPY (2.1 Å)
Cite:SARS-CoV-2 nsp1 mediates broad inhibition of translation in mammals.
Cell Rep, 44, 2025

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數據於2025-07-09公開中

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