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coronavirus
Coronavirus, 2020. Modified from the original illustration by David S. Goodsell@RCSB PDB

The recent outbreak of the Novel Coronavirus disease (COVID-19) is a serious threat to people all over the world. In order to understand and develop an effective drug against this virus (Severe Acute Respiratory Syndrome Coronavirus 2: SARS-CoV-2), structural work on the related proteins has already started and the resultant entries are accumulating in the PDB. PDBj provides a portal page for the COVID-19 related entries for our users. New entries will be added simultaneously with the public release from the wwPDB.

An explanation article covering one of the proteins of this virus is available on the "Molecules of the Month" page below:

The tab "All entries" contains all PDB IDs, in case you want to check all independent entries, including group depositions by the same authors. The "Repr. entries" tab contains only representative PDB entries with the highest resolution, excluding duplicate entries with 100% amino acid sequence identitiy, even if they contain a different ligand. Finally, the "Latest entries" tab contains the latest entries released this week.

Created: 2020-10-28 (last edited: more than 1 year ago)2022-09-02
All entries (5197)Repr. entries (2266)Latest entries (44)
7I16
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BU of 7i16 by Molmil
PanDDA analysis group deposition -- Main Protease (SARS-CoV-2) in complex with fragment C07 from the F2X-Entry Screen in orthorhombic space group
Descriptor: 3,4-dihydro-1~{H}-quinolin-2-one, 3C-like proteinase nsp5, CHLORIDE ION, ...
Authors:Barthel, T, Benz, L.S, Wollenhaupt, J, Weiss, M.S.
Deposit date:2025-02-03
Release date:2025-05-21
Method:X-RAY DIFFRACTION (2.13 Å)
Cite:Orthorhombic SARS-CoV-2 main protease crystals provide higher success rate in fragment screening
To be published
7I17
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BU of 7i17 by Molmil
PanDDA analysis group deposition -- Main Protease (SARS-CoV-2) in complex with fragment C10 from the F2X-Entry Screen in orthorhombic space group
Descriptor: 1,3-benzodioxole-5-carbothioamide, 3C-like proteinase nsp5, CHLORIDE ION, ...
Authors:Barthel, T, Benz, L.S, Wollenhaupt, J, Weiss, M.S.
Deposit date:2025-02-03
Release date:2025-05-21
Method:X-RAY DIFFRACTION (1.69 Å)
Cite:Orthorhombic SARS-CoV-2 main protease crystals provide higher success rate in fragment screening
To be published
7I18
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BU of 7i18 by Molmil
PanDDA analysis group deposition -- Main Protease (SARS-CoV-2) in complex with fragment D04 from the F2X-Entry Screen in orthorhombic space group
Descriptor: 3C-like proteinase nsp5, CHLORIDE ION, DIMETHYL SULFOXIDE, ...
Authors:Barthel, T, Benz, L.S, Wollenhaupt, J, Weiss, M.S.
Deposit date:2025-02-03
Release date:2025-05-21
Method:X-RAY DIFFRACTION (2 Å)
Cite:Orthorhombic SARS-CoV-2 main protease crystals provide higher success rate in fragment screening
To be published
7I19
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BU of 7i19 by Molmil
PanDDA analysis group deposition -- Main Protease (SARS-CoV-2) in complex with fragment D08 from the F2X-Entry Screen in orthorhombic space group
Descriptor: 3C-like proteinase nsp5, CHLORIDE ION, DIMETHYL SULFOXIDE, ...
Authors:Barthel, T, Benz, L.S, Wollenhaupt, J, Weiss, M.S.
Deposit date:2025-02-03
Release date:2025-05-21
Method:X-RAY DIFFRACTION (1.93 Å)
Cite:Orthorhombic SARS-CoV-2 main protease crystals provide higher success rate in fragment screening
To be published
7I1A
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BU of 7i1a by Molmil
PanDDA analysis group deposition -- Main Protease (SARS-CoV-2) in complex with fragment D11 from the F2X-Entry Screen in orthorhombic space group
Descriptor: 3-(1,3-thiazol-2-yl)propanoic acid, 3C-like proteinase nsp5, CHLORIDE ION, ...
Authors:Barthel, T, Benz, L.S, Wollenhaupt, J, Weiss, M.S.
Deposit date:2025-02-03
Release date:2025-05-21
Method:X-RAY DIFFRACTION (1.73 Å)
Cite:Orthorhombic SARS-CoV-2 main protease crystals provide higher success rate in fragment screening
To be published
7I1C
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BU of 7i1c by Molmil
PanDDA analysis group deposition -- Main Protease (SARS-CoV-2) in complex with fragment E11 from the F2X-Entry Screen in orthorhombic space group
Descriptor: 3C-like proteinase nsp5, CHLORIDE ION, [2-(morpholin-4-yl)-1,3-thiazol-5-yl]methanol
Authors:Barthel, T, Benz, L.S, Wollenhaupt, J, Weiss, M.S.
Deposit date:2025-02-03
Release date:2025-05-21
Method:X-RAY DIFFRACTION (1.95 Å)
Cite:Orthorhombic SARS-CoV-2 main protease crystals provide higher success rate in fragment screening
To be published
7I1D
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BU of 7i1d by Molmil
PanDDA analysis group deposition -- Main Protease (SARS-CoV-2) in complex with fragment F04 from the F2X-Entry Screen in orthorhombic space group
Descriptor: 3C-like proteinase nsp5, CHLORIDE ION, DIMETHYL SULFOXIDE, ...
Authors:Barthel, T, Benz, L.S, Wollenhaupt, J, Weiss, M.S.
Deposit date:2025-02-03
Release date:2025-05-21
Method:X-RAY DIFFRACTION (2 Å)
Cite:Orthorhombic SARS-CoV-2 main protease crystals provide higher success rate in fragment screening
To be published
7I1E
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BU of 7i1e by Molmil
PanDDA analysis group deposition -- Main Protease (SARS-CoV-2) in complex with fragment G03 from the F2X-Entry Screen in orthorhombic space group
Descriptor: 3-ethoxybenzene-1-carboximidamide, 3C-like proteinase nsp5, CHLORIDE ION, ...
Authors:Barthel, T, Benz, L.S, Wollenhaupt, J, Weiss, M.S.
Deposit date:2025-02-03
Release date:2025-05-21
Method:X-RAY DIFFRACTION (1.88 Å)
Cite:Orthorhombic SARS-CoV-2 main protease crystals provide higher success rate in fragment screening
To be published
7I1F
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BU of 7i1f by Molmil
PanDDA analysis group deposition -- Main Protease (SARS-CoV-2) in complex with fragment G04 from the F2X-Entry Screen in orthorhombic space group
Descriptor: 3C-like proteinase nsp5, CHLORIDE ION, DIMETHYL SULFOXIDE, ...
Authors:Barthel, T, Benz, L.S, Wollenhaupt, J, Weiss, M.S.
Deposit date:2025-02-03
Release date:2025-05-21
Method:X-RAY DIFFRACTION (1.77 Å)
Cite:Orthorhombic SARS-CoV-2 main protease crystals provide higher success rate in fragment screening
To be published
7I1G
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BU of 7i1g by Molmil
PanDDA analysis group deposition -- Main Protease (SARS-CoV-2) in complex with fragment G09 from the F2X-Entry Screen in orthorhombic space group
Descriptor: (2R)-2-(acetylamino)-4-phenylbutanoic acid, 3C-like proteinase nsp5, CHLORIDE ION, ...
Authors:Barthel, T, Benz, L.S, Wollenhaupt, J, Weiss, M.S.
Deposit date:2025-02-03
Release date:2025-05-21
Method:X-RAY DIFFRACTION (1.83 Å)
Cite:Orthorhombic SARS-CoV-2 main protease crystals provide higher success rate in fragment screening
To be published
7I1H
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BU of 7i1h by Molmil
PanDDA analysis group deposition -- Main Protease (SARS-CoV-2) in complex with fragment G10 from the F2X-Entry Screen in orthorhombic space group
Descriptor: 1-phenyl-1H-tetrazole, 3C-like proteinase nsp5, CHLORIDE ION, ...
Authors:Barthel, T, Benz, L.S, Wollenhaupt, J, Weiss, M.S.
Deposit date:2025-02-03
Release date:2025-05-21
Method:X-RAY DIFFRACTION (1.98 Å)
Cite:Orthorhombic SARS-CoV-2 main protease crystals provide higher success rate in fragment screening
To be published
7I1I
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BU of 7i1i by Molmil
PanDDA analysis group deposition -- Main Protease (SARS-CoV-2) in complex with fragment H03 from the F2X-Entry Screen in orthorhombic space group
Descriptor: 3C-like proteinase nsp5, CHLORIDE ION, DIMETHYL SULFOXIDE, ...
Authors:Barthel, T, Benz, L.S, Wollenhaupt, J, Weiss, M.S.
Deposit date:2025-02-03
Release date:2025-05-21
Method:X-RAY DIFFRACTION (1.88 Å)
Cite:Orthorhombic SARS-CoV-2 main protease crystals provide higher success rate in fragment screening
To be published
7I1J
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BU of 7i1j by Molmil
PanDDA analysis group deposition -- Main Protease (SARS-CoV-2) in complex with fragment H11 from the F2X-Entry Screen in orthorhombic space group
Descriptor: 3C-like proteinase nsp5, CHLORIDE ION, DIMETHYL SULFOXIDE, ...
Authors:Barthel, T, Benz, L.S, Wollenhaupt, J, Weiss, M.S.
Deposit date:2025-02-03
Release date:2025-05-21
Method:X-RAY DIFFRACTION (1.85 Å)
Cite:Orthorhombic SARS-CoV-2 main protease crystals provide higher success rate in fragment screening
To be published
9BTE
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BU of 9bte by Molmil
Structure of the SARS-CoV-2 main protease in complex with inhibitor CID5573_0017
Descriptor: 3C-like proteinase nsp5, 4-[5-[4-[oxidanyl(oxidanylidene)-$l^{4}-azanyl]-1,2,5-oxadiazol-3-yl]-1~{H}-1,2,4-triazol-3-yl]-1,2,5-oxadiazole-3-thiol
Authors:Blankenship, L.R, Liu, W.R.
Deposit date:2024-05-15
Release date:2025-05-21
Method:X-RAY DIFFRACTION (1.6 Å)
Cite:Structure of the SARS-CoV-2 main protease
To Be Published
9BTF
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BU of 9btf by Molmil
Structure of the SARS-CoV-2 main protease in complex with inhibitor SR-B-77
Descriptor: (1R,2S,5S)-N-[(1R)-1-(5-fluoropyridin-3-yl)-2-iminoethyl]-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide, 3C-like proteinase nsp5
Authors:Blankenship, L.R, Liu, W.R.
Deposit date:2024-05-15
Release date:2025-05-21
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Structure of the SARS-CoV-2 main protease
To Be Published
9BTK
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Structure of the SARS-CoV-2 main protease in complex with inhibitor YR-C-108T
Descriptor: (1R,2S,5R)-N-[(1R)-2-imino-1-(isoquinolin-4-yl)ethyl]-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-D-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide, 3C-like proteinase nsp5
Authors:Blankenship, L.R, Liu, W.R.
Deposit date:2024-05-15
Release date:2025-05-21
Method:X-RAY DIFFRACTION (1.79 Å)
Cite:Structure of the SARS-CoV-2 main protease
To Be Published
9BTR
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Structure of the SARS-CoV-2 main protease in complex with inhibitor YR-C-163
Descriptor: 2-chloro-N-[(3P)-3-(5-chloro-2-methyl-2H-indazol-7-yl)phenyl]-N-(5-chloropyridin-3-yl)acetamide, 3C-like proteinase nsp5
Authors:Blankenship, L.R, Liu, W.R.
Deposit date:2024-05-15
Release date:2025-05-21
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:Structure of the SARS-CoV-2 main protease
To Be Published
9BTT
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Structure of the SARS-CoV-2 main protease in complex with inhibitor SR-B-51T
Descriptor: (1R,2S,5S)-N-[(1R)-1-(5-chloropyridin-3-yl)-2-iminoethyl]-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide, 3C-like proteinase nsp5
Authors:Blankenship, L.R, Liu, W.R.
Deposit date:2024-05-15
Release date:2025-05-21
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Structure of the SARS-CoV-2 main protease
To Be Published
9BVW
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BU of 9bvw by Molmil
SARS-CoV-2 main protease bound to inhibitor SR-B-103
Descriptor: (1R,2S,5R)-N-[(1R)-1-(8-fluoroisoquinolin-4-yl)-2-iminoethyl]-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-D-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide, 3C-like proteinase nsp5
Authors:Liu, W.R, Blankenship, L.R.
Deposit date:2024-05-20
Release date:2025-05-21
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:SARS-CoV-2 main protease
To Be Published
9BVX
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BU of 9bvx by Molmil
SARS-CoV-2 main protease bound to inhibitor YR-C-155
Descriptor: (1R,2S,5R)-N-[(1R)-1-(5-fluoroisoquinolin-4-yl)-2-iminoethyl]-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide, 3C-like proteinase nsp5
Authors:Liu, W.R, Blankenship, L.R.
Deposit date:2024-05-20
Release date:2025-05-21
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:SARS-CoV-2 main protease
To Be Published
9BVZ
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BU of 9bvz by Molmil
SARS-CoV-2 main protease bound to inhibitor AR-A-135
Descriptor: 3C-like proteinase nsp5, [2-(iminomethyl)pyridin-3-yl]boronic acid
Authors:Liu, W.R, Blankenship, L.R.
Deposit date:2024-05-20
Release date:2025-05-21
Method:X-RAY DIFFRACTION (2 Å)
Cite:SARS-CoV-2 main protease
To Be Published
9D6B
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BU of 9d6b by Molmil
Crystal structure of SARS-CoV-2 NSP3 macrodmain in complex with AVI-607
Descriptor: 2-[(2R)-1-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)pyrrolidin-2-yl]propan-2-ol, CHLORIDE ION, DIMETHYL SULFOXIDE, ...
Authors:Correy, G.J, Fraser, J.S.
Deposit date:2024-08-14
Release date:2025-05-21
Last modified: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
9D6G
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BU of 9d6g by Molmil
Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with AVI-3716
Descriptor: DIMETHYL SULFOXIDE, Non-structural protein 3, [(2R,3S)-3-methyl-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:2025-05-21
Last modified: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
9D6H
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BU of 9d6h by Molmil
Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with AVI-1504
Descriptor: (2R)-3-methyl-2-[(7H-pyrrolo[2,3-d]pyrimidin-4-yl)amino]butan-1-ol, CHLORIDE ION, DIMETHYL SULFOXIDE, ...
Authors:Correy, G.J, Fraser, J.S.
Deposit date:2024-08-15
Release date:2025-05-21
Last modified: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
9D6I
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BU of 9d6i by Molmil
Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with AVI-4317
Descriptor: (3R)-3-hydroxy-3-{[(7H-pyrrolo[2,3-d]pyrimidin-4-yl)amino]methyl}-1lambda~6~-thiane-1,1-dione, CHLORIDE ION, DIMETHYL SULFOXIDE, ...
Authors:Correy, G.J, Fraser, J.S.
Deposit date:2024-08-15
Release date:2025-05-21
Last modified: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

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