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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)
9BS8
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BU of 9bs8 by Molmil
Structure of the SARS-CoV-2 main protease in complex with inhibitor YR-B-107
Descriptor: 3C-like proteinase nsp5, benzyl (7S)-7-({(2R)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}carbamoyl)-6-azaspiro[3.4]octane-6-carboxylate
Authors:Blankenship, L.R, Liu, W.R.
Deposit date:2024-05-13
Release date:2025-05-14
Method:X-RAY DIFFRACTION (1.7 Å)
Cite:Structure of the SARS-CoV-2 main protease
To Be Published
9BSA
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BU of 9bsa by Molmil
Structure of the SARS-CoV-2 main protease in complex with inhibitor VB-B-112
Descriptor: 2,2-dichloro-N-(5-chloropyridin-3-yl)-N-phenylacetamide, 3C-like proteinase nsp5
Authors:Blankenship, L.R, Liu, W.R.
Deposit date:2024-05-13
Release date:2025-05-14
Method:X-RAY DIFFRACTION (1.7 Å)
Cite:Structure of the SARS-CoV-2 main protease
To Be Published
9BSE
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BU of 9bse by Molmil
Structure of the SARS-CoV-2 main protease in complex with inhibitor YR-B-165
Descriptor: (3S)-N-{(2S)-1-amino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-2-[(2R)-3,3-dimethyl-2-(2,2,2-trifluoroacetamido)butanoyl]-2-azaspiro[4.5]decane-3-carboxamide, 3C-like proteinase nsp5
Authors:Blankenship, L.R, Liu, W.R.
Deposit date:2024-05-13
Release date:2025-05-14
Method:X-RAY DIFFRACTION (1.85 Å)
Cite:Structure of the SARS-CoV-2 main protease
To Be Published
9BSF
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Structure of the SARS-CoV-2 main protease in complex with inhibitor SR-A-171
Descriptor: 3C-like proteinase nsp5, N-(4-tert-butylphenyl)-2,2-dichloro-N-(5-chloropyridin-3-yl)acetamide
Authors:Blankenship, L.R, Liu, W.R.
Deposit date:2024-05-13
Release date:2025-05-14
Method:X-RAY DIFFRACTION (1.75 Å)
Cite:Structure of the SARS-CoV-2 main protease
To Be Published
9BSG
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BU of 9bsg by Molmil
Structure of the SARS-CoV-2 main protease in complex with inhibitor VB-C-20
Descriptor: 3C-like proteinase nsp5, methyl 4-[(5-chloropyridin-3-yl)(phenyl)amino]-4-oxobutanoate
Authors:Blankenship, L.R, Liu, W.R.
Deposit date:2024-05-13
Release date:2025-05-14
Method:X-RAY DIFFRACTION (1.75 Å)
Cite:Structure of the SARS-CoV-2 main protease
To Be Published
9BSI
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BU of 9bsi by Molmil
Structure of the SARS-CoV-2 main protease in complex with inhibitor SR-B-7
Descriptor: 3C-like proteinase nsp5, N-[(1M)-3'-chloro[1,1'-biphenyl]-3-yl]-N-(5-chloropyridin-3-yl)-2-fluoroacetamide
Authors:Blankenship, L.R, Liu, W.R.
Deposit date:2024-05-13
Release date:2025-05-14
Method:X-RAY DIFFRACTION (1.7 Å)
Cite:Structure of the SARS-CoV-2 main protease
To Be Published
9BSO
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BU of 9bso by Molmil
Structure of the SARS-CoV-2 main protease in complex with inhibitor SR-B-13
Descriptor: 3C-like proteinase nsp5, N-[(1M)-3'-chloro[1,1'-biphenyl]-3-yl]-N-(5-chloropyridin-3-yl)-3-sulfanylpropanamide
Authors:Blankenship, L.R, Liu, W.R.
Deposit date:2024-05-13
Release date:2025-05-14
Method:X-RAY DIFFRACTION (1.7 Å)
Cite:Structure of the SARS-CoV-2 main protease
To Be Published
9BSP
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Structure of the SARS-CoV-2 main protease in complex with inhibitor VB-C-68
Descriptor: 3C-like proteinase nsp5, methyl 4-{[(1M)-3'-chloro[1,1'-biphenyl]-3-yl](5-chloropyridin-3-yl)amino}-4-oxobutanoate
Authors:Blankenship, L.R, Liu, W.R.
Deposit date:2024-05-13
Release date:2025-05-14
Method:X-RAY DIFFRACTION (1.6 Å)
Cite:Structure of the SARS-CoV-2 main protease
To Be Published
9BSQ
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BU of 9bsq by Molmil
Structure of the SARS-CoV-2 main protease in complex with inhibitor VB-C-70
Descriptor: (2R)-N-[(1M)-3'-chloro[1,1'-biphenyl]-3-yl]-N-(5-chloropyridin-3-yl)-2-hydroxy-2-sulfanylacetamide, 3C-like proteinase nsp5
Authors:Blankenship, L.R, Liu, W.R.
Deposit date:2024-05-13
Release date:2025-05-14
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Structure of the SARS-CoV-2 main protease
To Be Published
9BSR
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Structure of the SARS-CoV-2 main protease in complex with inhibitor YR-B-136B
Descriptor: (1R,2S,5R)-N-[(1R)-1-(7-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:Blankenship, L.R, Liu, W.R.
Deposit date:2024-05-13
Release date:2025-05-14
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:Structure of the SARS-CoV-2 main protease
To Be Published
9BST
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Structure of the SARS-CoV-2 main protease in complex with inhibitor CID8009_5647
Descriptor: 3C-like proteinase nsp5, [3-[2,6-bis(chloranyl)phenyl]-5-methyl-1,2-oxazol-4-yl]methanol
Authors:Blankenship, L.R, Liu, W.R.
Deposit date:2024-05-13
Release date:2025-05-14
Method:X-RAY DIFFRACTION (1.6 Å)
Cite:Structure of the SARS-CoV-2 main protease
To Be Published
9C2H
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BU of 9c2h by Molmil
SARS-CoV-2 Nucleocapsid Dimerization Domain bound to Fab-NP1E9 and Fab-NP3B4
Descriptor: Antibody Fab NP1-E9 Heavy Chain (variable region), Antibody Fab NP1-E9 Light Chain (variable region), Antibody Fab NP3-B4 Heavy Chain (variable region), ...
Authors:Landeras-Bueno, S, Hariharan, C, Diaz Avalos, R, Ollmann Saphire, E.
Deposit date:2024-05-31
Release date:2025-05-14
Method:ELECTRON MICROSCOPY (3.7 Å)
Cite:Structural stabilization of the intrinsically disordered SARS-CoV-2 N by binding to RNA sequences engineered from the viral genome
To Be Published
9F7P
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SARS-CoV-2 papain-like protease (PLpro) C112S mutant
Descriptor: CHLORIDE ION, DI(HYDROXYETHYL)ETHER, MALONATE ION, ...
Authors:Camara-Artigas, A.
Deposit date:2024-05-04
Release date:2025-05-14
Method:X-RAY DIFFRACTION (1.7 Å)
Cite:SARS-CoV-2 papain-like protease (PLpro) C112S mutant
To Be Published
9F7Q
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SARS-CoV-2 papain-like protease (PLpro) C112S mutant
Descriptor: GLYCEROL, Replicase polyprotein 1ab, SULFATE ION, ...
Authors:Camara-Artigas, A.
Deposit date:2024-05-04
Release date:2025-05-14
Method:X-RAY DIFFRACTION (2.3 Å)
Cite:SARS-CoV-2 papain-like protease (PLpro) C112S mutant
To Be Published
9F7R
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SARS-CoV-2 papain-like protease (PLpro) C112S mutant
Descriptor: GLYCEROL, PHOSPHATE ION, Replicase polyprotein 1ab, ...
Authors:Camara-Artigas, A.
Deposit date:2024-05-04
Release date:2025-05-14
Method:X-RAY DIFFRACTION (1.5 Å)
Cite:SARS-CoV-2 papain-like protease (PLpro) C112S mutant
To Be Published
9F7S
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SARS-CoV-2 papain-like protease (PLpro) C112S-K191D-K229R mutant
Descriptor: CHLORIDE ION, DI(HYDROXYETHYL)ETHER, MALONATE ION, ...
Authors:Camara-Artigas, A.
Deposit date:2024-05-04
Release date:2025-05-14
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:SARS-CoV-2 papain-like protease (PLpro) C112S-K191D-K229R mutant
To Be Published
9F7T
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SARS-CoV-2 papain-like protease (PLpro) C112S-K191D-K229R mutant: dimer
Descriptor: CHLORIDE ION, DI(HYDROXYETHYL)ETHER, Replicase polyprotein 1ab, ...
Authors:Camara-Artigas, A.
Deposit date:2024-05-04
Release date:2025-05-14
Method:X-RAY DIFFRACTION (2.05 Å)
Cite:SARS-CoV-2 papain-like protease (PLpro) C112S-K191D-K229R mutant
To Be Published
9F7U
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SARS-CoV-2 papain-like protease (PLpro) C112S-K191D-Q222D-K229R-Q230R-C271S mutant
Descriptor: CHLORIDE ION, GLYCEROL, MALONIC ACID, ...
Authors:Camara-Artigas, A.
Deposit date:2024-05-05
Release date:2025-05-14
Method:X-RAY DIFFRACTION (1.6 Å)
Cite:SARS-CoV-2 papain-like protease (PLpro) C112S-K191D-Q222D-K229R-Q230R-C271S mutant
To Be Published
9F7Y
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BU of 9f7y by Molmil
SARS-CoV-2 papain-like protease (PLpro) C112S-K191D-Q222D-K229R-Q230R-C271S mutant
Descriptor: CHLORIDE ION, MALONIC ACID, Replicase polyprotein 1ab, ...
Authors:Camara-Artigas, A.
Deposit date:2024-05-05
Release date:2025-05-14
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:SARS-CoV-2 papain-like protease (PLpro) C112S-K191D-Q222D-K229R-Q230R-C271S mutant
To Be Published
9LVR
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BU of 9lvr by Molmil
Crystal structure of SARS-CoV-2 3CL protease in complex with compound 1
Descriptor: 1,2-ETHANEDIOL, 3C-like proteinase nsp5, 6-(1,3-dihydroisoindol-2-yl)-3-(5-methylpyridin-3-yl)-1-[[3,4,5-tris(fluoranyl)phenyl]methyl]-1,3,5-triazine-2,4-dione
Authors:Unoh, Y, Hirai, K, Uehara, S, Kawashima, S, Nobori, H, Sato, J, Shibayama, H, Hori, A, Nakahara, K, Kurahashi, K, Takamatsu, M, Yamamoto, S, Zhang, O, Tanimura, M, Dodo, R, Maruyama, Y, Sawa, H, Watari, R, Miyano, T, Kato, T, Sato, T, Tachibana, Y.
Deposit date:2025-02-12
Release date:2025-05-14
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:Discovery of The Clinical Candidate S-892216: A Second-Generation of SARS-CoV-2 3CL Protease Inhibitor for Treating COVID-19
To Be Published
9LVT
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Crystal structure of SARS-CoV-2 3CL protease in complex with compound 4
Descriptor: 1-(2-azanylideneethyl)-6-(1,3-dihydroisoindol-2-yl)-3-(5-methylpyridin-3-yl)-5-[[3,4,5-tris(fluoranyl)phenyl]methyl]pyrimidine-2,4-dione, 3C-like proteinase
Authors:Unoh, Y, Hirai, K, Uehara, S, Kawashima, S, Nobori, H, Sato, J, Shibayama, H, Hori, A, Nakahara, K, Kurahashi, K, Takamatsu, M, Yamamoto, S, Zhang, O, Tanimura, M, Dodo, R, Maruyama, Y, Sawa, H, Watari, R, Miyano, T, Kato, T, Sato, T, Tachibana, Y.
Deposit date:2025-02-12
Release date:2025-05-14
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:Discovery of The Clinical Candidate S-892216: A Second-Generation of SARS-CoV-2 3CL Protease Inhibitor for Treating COVID-19
To Be Published
9LVV
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Crystal structure of SARS-CoV-2 3CL protease in complex with compound 17 (S-892216)
Descriptor: 1-(2-azanylideneethyl)-6-[6,6-bis(fluoranyl)-2-azaspiro[3.3]heptan-2-yl]-5-(3-chloranyl-4-fluoranyl-phenyl)-3-(5-chloranylpyridin-3-yl)pyrimidine-2,4-dione, 3C-like proteinase
Authors:Unoh, Y, Hirai, K, Uehara, S, Kawashima, S, Nobori, H, Sato, J, Shibayama, H, Hori, A, Nakahara, K, Kurahashi, K, Takamatsu, M, Yamamoto, S, Zhang, O, Tanimura, M, Dodo, R, Maruyama, Y, Sawa, H, Watari, R, Miyano, T, Kato, T, Sato, T, Tachibana, Y.
Deposit date:2025-02-12
Release date:2025-05-14
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:Discovery of The Clinical Candidate S-892216: A Second-Generation of SARS-CoV-2 3CL Protease Inhibitor for Treating COVID-19
To Be Published
7I13
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PanDDA analysis group deposition -- Main Protease (SARS-CoV-2) in complex with fragment B05 from the F2X-Entry Screen in orthorhombic space group
Descriptor: 2-acetylbenzoic 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 (2 Å)
Cite:Orthorhombic SARS-CoV-2 main protease crystals provide higher success rate in fragment screening
To be published
7I14
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BU of 7i14 by Molmil
PanDDA analysis group deposition -- Main Protease (SARS-CoV-2) in complex with fragment B08 from the F2X-Entry Screen in orthorhombic space group
Descriptor: 3C-like proteinase nsp5, DIMETHYL SULFOXIDE, ethyl 1,3-dihydro-2H-pyrrolo[3,4-c]pyridine-2-carboxylate
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
7I15
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PanDDA analysis group deposition -- Main Protease (SARS-CoV-2) in complex with fragment C02 from the F2X-Entry Screen in orthorhombic space group
Descriptor: 2,4,5-tris(fluoranyl)-3-methoxy-benzoic 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 (2 Å)
Cite:Orthorhombic SARS-CoV-2 main protease crystals provide higher success rate in fragment screening
To be published

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