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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
8Z9L
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BU of 8z9l by Molmil
Crystal structure of SARS-CoV-2 RBD bound to Rhinolophus affinis ACE2
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Angiotensin-converting enzyme, Spike protein S1, ...
Authors:Lan, J, Wang, C.H.
Deposit date:2024-04-23
Release date:2025-04-30
Last modified:2025-05-14
Method:X-RAY DIFFRACTION (3.598 Å)
Cite:Molecular mechanisms of RaTG13 and SARS-CoV-2 RBD bound to Rhinolophus affinis bat ACE2.
Protein Sci., 34, 2025
8ZBF
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BU of 8zbf by Molmil
Crystal structure of the A58-T10 DNA aptamer in complex with SARS-CoV-2 N-NTD
Descriptor: DNA (40-MER), Nucleoprotein, SODIUM ION
Authors:Chen, X, Huang, L.
Deposit date:2024-04-26
Release date:2025-04-30
Last modified:2025-05-07
Method:X-RAY DIFFRACTION (2.8 Å)
Cite:Molecular characterization and broad-spectrum mechanism of coronavirus N protein aptamer
To Be Published
9DTZ
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BU of 9dtz by Molmil
SARS-CoV-2 Mpro in complex with compound 5
Descriptor: 3C-like proteinase nsp5, N-[(2S)-3-cyclopropyl-1-({(2R)-1-imino-3-[(3R)-2-oxopyrrolidin-3-yl]propan-2-yl}amino)-1-oxopropan-2-yl]-4-methoxy-1H-indole-2-carboxamide, SODIUM ION
Authors:Bigelow, L, Tang, H, Boguslaw, N, Duda, D.M.
Deposit date:2024-10-02
Release date:2025-04-30
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:Inhibition of Dimeric SARS-CoV-2 Mpro by Aldehyde and Nitrilebased Inhibitors Displays Positive Cooperativity and a Mixture of Covalent and Non-covalent Binding.
To Be Published
9DU2
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BU of 9du2 by Molmil
SARS-CoV-2 Mpro in complex with compound 7
Descriptor: 3C-like proteinase nsp5, N-[(2S)-3-cyclopropyl-1-{[(1Z,2S)-1-imino-4-(methanesulfonyl)butan-2-yl]amino}-1-oxopropan-2-yl]-4-methoxy-1H-indole-2-carboxamide
Authors:Bigelow, L, Tang, H, Boguslaw, N, Duda, D.M.
Deposit date:2024-10-02
Release date:2025-04-30
Method:X-RAY DIFFRACTION (1.86 Å)
Cite:Inhibition of Dimeric SARS-CoV-2 Mpro by Aldehyde and Nitrilebased Inhibitors Displays Positive Cooperativity and a Mixture of Covalent and Non-covalent Binding.
To Be Published
9DU3
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BU of 9du3 by Molmil
SARS-CoV-2 Mpro in complex with compound 1
Descriptor: 3C-like proteinase nsp5, N-[(2S)-3-cyclopropyl-1-({(2R)-1-hydroxy-3-[(3R)-2-oxopyrrolidin-3-yl]propan-2-yl}amino)-1-oxopropan-2-yl]-4-methoxy-1H-indole-2-carboxamide
Authors:Bigelow, L, Tang, H, Boguslaw, N, Duda, D.M.
Deposit date:2024-10-02
Release date:2025-04-30
Method:X-RAY DIFFRACTION (2.07 Å)
Cite:Inhibition of Dimeric SARS-CoV-2 Mpro by Aldehyde and Nitrilebased Inhibitors Displays Positive Cooperativity and a Mixture of Covalent and Non-covalent Binding.
To Be Published
9DU4
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BU of 9du4 by Molmil
SARS-CoV-2 Mpro in complex with compound 3
Descriptor: 3C-like proteinase nsp5, N-[(2S)-3-cyclopropyl-1-{[(2R)-1-hydroxy-4-(methanesulfonyl)butan-2-yl]amino}-1-oxopropan-2-yl]-4-methoxy-1H-indole-2-carboxamide
Authors:Bigelow, L, Tang, H, Boguslaw, N, Duda, D.M.
Deposit date:2024-10-02
Release date:2025-04-30
Method:X-RAY DIFFRACTION (2.42 Å)
Cite:Inhibition of Dimeric SARS-CoV-2 Mpro by Aldehyde and Nitrilebased Inhibitors Displays Positive Cooperativity and a Mixture of Covalent and Non-covalent Binding.
To Be Published
8WZ0
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BU of 8wz0 by Molmil
SARS-CoV-2 3CLpro bound to covalent inhibitor
Descriptor: (2~{R})-~{N}-[4,4-bis(fluoranyl)cyclohexyl]-2-[(2-chloranyl-2-fluoranyl-ethanoyl)-[4-(trifluoromethyloxy)phenyl]amino]-2-pyrimidin-5-yl-propanamide, 3C-like proteinase nsp5
Authors:Peng, J, Sun, D, Ding, X.
Deposit date:2023-11-01
Release date:2025-05-07
Method:X-RAY DIFFRACTION (2.45 Å)
Cite:SARS-CoV-2 3CLpro bound to covalent inhibitor
To Be Published
9BF8
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BU of 9bf8 by Molmil
SARS-CoV-2 Papain-like Protease (PLpro) Untagged Crystal Structure
Descriptor: 1,2-ETHANEDIOL, ORF1a polyprotein, PHOSPHATE ION, ...
Authors:Al-Homoudi, A.I, Engel, J, Brunzelle, J.S, Gavande, N, Kovari, L.C.
Deposit date:2024-04-17
Release date:2025-05-07
Method:X-RAY DIFFRACTION (1.85 Å)
Cite:Human Structural Homologues of SARS-CoV-2 PL pro as Anti-Targets: A Strategic Panel Analysis.
MicroPubl Biol, 2025, 2025
9FM4
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BU of 9fm4 by Molmil
Dynamic structure of the apical stem loop of the stem loop 2 motif (s2m) from SCoV-2 Delta variant.
Descriptor: RNA (25-MER)
Authors:Wirtz Martin, M.A, Matzel, T, Makowski, J, Kensinger, A, Herr, A, Wacker, A, Richter, C, Jonker, H.R.A, Evanseck, J, Schwalbe, H.
Deposit date:2024-06-05
Release date:2025-05-07
Last modified:2025-06-04
Method:SOLUTION NMR, SOLUTION SCATTERING
Cite:Characterization of structure and dynamics of the apical stem loop of s2m from SCoV-2 Delta by NMR spectroscopy, validated by MD and SAXS
To Be Published
8X1X
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BU of 8x1x by Molmil
SARS-CoV-2 Papain like protease (PLpro) in complex with inhibitor Lithocholic acid
Descriptor: (3beta,5beta,14beta,17alpha)-3-hydroxycholan-24-oic acid, GLYCEROL, Papain-like protease nsp3, ...
Authors:Choudhary, S, Verma, S, Kumar, P, Tomar, S.
Deposit date:2023-11-09
Release date:2025-05-14
Method:X-RAY DIFFRACTION (2.3 Å)
Cite:SARS-CoV-2 Papain like protease (PLpro) in complex with inhibitor Lithocholic acid
To Be Published
9BLF
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BU of 9blf by Molmil
SARS-CoV-2 core polymerase complex inhibited by araCTP
Descriptor: 4-amino-1-{5-O-[(S)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-arabinofuranosyl}pyrimidin-2(1H)-one, MAGNESIUM ION, Non-structural protein 7, ...
Authors:Anderson, T.K, Kirchdeorfer, R.N.
Deposit date:2024-04-30
Release date:2025-05-14
Method:ELECTRON MICROSCOPY (3.31 Å)
Cite:Structure of the SARS-CoV-2 core-RTC bound to RNA, araCMP, and araCTP
To Be Published
9BQF
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BU of 9bqf by Molmil
Structure of the SARS-CoV-2 main protease in complex with inhibitor 78
Descriptor: 3C-like proteinase nsp5, N-[(BENZYLOXY)CARBONYL]-O-(TERT-BUTYL)-L-THREONYL-3-CYCLOHEXYL-N-[(1S)-2-HYDROXY-1-{[(3S)-2-OXOPYRROLIDIN-3-YL]METHYL}ETHYL]-L-ALANINAMIDE
Authors:Blankenship, L.R, Liu, W.R.
Deposit date:2024-05-09
Release date:2025-05-14
Method:X-RAY DIFFRACTION (1.7 Å)
Cite:Structure of the SARS-CoV-2 main protease in complex with inhibitor 78
To Be Published
9BQG
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BU of 9bqg by Molmil
Structure of the SARS-CoV-2 main protease in complex with inhibitor k68
Descriptor: 3C-like proteinase nsp5, benzyl (2S,4S)-4-tert-butoxy-2-({(2R)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}carbamoyl)pyrrolidine-1-carboxylate
Authors:Blankenship, L.R, Liu, W.R.
Deposit date:2024-05-09
Release date:2025-05-14
Method:X-RAY DIFFRACTION (1.65 Å)
Cite:Structure of the SARS-CoV-2 main protease in complex with inhibitor k68
To Be Published
9BQL
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BU of 9bql by Molmil
Structure of the SARS-CoV-2 main protease in complex with inhibitor VB-A-32
Descriptor: 3C-like proteinase nsp5, O-tert-butyl-N-[(cyclopropylmethoxy)carbonyl]-L-threonyl-3-cyclohexyl-N-{(2R)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-alaninamide
Authors:Blankenship, L.R, Liu, W.R.
Deposit date:2024-05-10
Release date:2025-05-14
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Structure of the SARS-CoV-2 main protease
To Be Published
9BQM
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BU of 9bqm by Molmil
Structure of the SARS-CoV-2 main protease in complex with inhibitor VB-A-26
Descriptor: 3C-like proteinase nsp5, O-tert-butyl-N-{[(propan-2-yl)oxy]carbonyl}-L-threonyl-3-cyclohexyl-N-{(2R)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-alaninamide
Authors:Blankenship, L.R, Liu, W.R.
Deposit date:2024-05-10
Release date:2025-05-14
Method:X-RAY DIFFRACTION (2.1 Å)
Cite:Structure of the SARS-CoV-2 main protease
To Be Published
9BQN
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BU of 9bqn by Molmil
Structure of the SARS-CoV-2 main protease in complex with inhibitor VB-A-28
Descriptor: 3C-like proteinase nsp5, O-tert-butyl-N-[(2,2,2-trifluoroethoxy)carbonyl]-L-threonyl-3-cyclohexyl-N-{(2R)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-alaninamide
Authors:Blankenship, L.R, Liu, W.R.
Deposit date:2024-05-10
Release date:2025-05-14
Method:X-RAY DIFFRACTION (2 Å)
Cite:To be determined
To Be Published
9BQO
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BU of 9bqo by Molmil
Structure of the SARS-CoV-2 main protease in complex with inhibitor k88
Descriptor: 3C-like proteinase nsp5, N-[(benzyloxy)carbonyl]-O-tert-butyl-L-threonyl-3-cyclohexyl-N-{(2R)-1-hydroxy-3-[(3S)-2-oxopiperidin-3-yl]propan-2-yl}-L-alaninamide
Authors:Blankenship, L.R, Liu, W.R.
Deposit date:2024-05-10
Release date:2025-05-14
Method:X-RAY DIFFRACTION (2.5 Å)
Cite:Structure of the SARS-CoV-2 main protease
To Be Published
9BQP
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BU of 9bqp by Molmil
Structure of the SARS-CoV-2 main protease in complex with inhibitor R79
Descriptor: 3C-like proteinase nsp5, propan-2-yl {(2R)-1-[(1R,2S,5R)-2-({(2R)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}carbamoyl)-6,6-dimethyl-3-azabicyclo[3.1.0]hexan-3-yl]-3,3-dimethyl-1-oxobutan-2-yl}carbamate
Authors:Blankenship, L.R, Liu, W.R.
Deposit date:2024-05-10
Release date:2025-05-14
Method:X-RAY DIFFRACTION (2 Å)
Cite:Structure of the SARS-CoV-2 main protease
To Be Published
9BQQ
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BU of 9bqq by Molmil
Structure of the SARS-CoV-2 main protease in complex with inhibitor R81
Descriptor: 3C-like proteinase nsp5, N-[(benzyloxy)carbonyl]-O-tert-butyl-L-threonyl-3-cyclohexyl-N-{(2R)-3-oxo-1-[(3S)-2-oxopyrrolidin-3-yl]butan-2-yl}-L-alaninamide
Authors:Blankenship, L.R, Liu, W.R.
Deposit date:2024-05-10
Release date:2025-05-14
Method:X-RAY DIFFRACTION (2 Å)
Cite:Structure of the SARS-CoV-2 main protease
To Be Published
9BQT
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BU of 9bqt by Molmil
Structure of the SARS-CoV-2 main protease in complex with inhibitor R80
Descriptor: 3C-like proteinase nsp5, N-[(benzyloxy)carbonyl]-O-tert-butyl-L-threonyl-3-cyclohexyl-N-{(2R)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-alaninamide
Authors:Blankenship, L.R, Liu, W.R.
Deposit date:2024-05-10
Release date:2025-05-14
Method:X-RAY DIFFRACTION (2.1 Å)
Cite:Structure of the SARS-CoV-2 main protease
To Be Published
9BQY
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BU of 9bqy by Molmil
Structure of the SARS-CoV-2 main protease in complex with inhibitor R70
Descriptor: (1R,2S,5R)-3-[N-(3,3-dimethylbutanoyl)-3-methyl-L-valyl]-N-{(1E,2R)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2-carboxamide, 3C-like proteinase nsp5
Authors:Blankenship, L.R, Liu, W.R.
Deposit date:2024-05-10
Release date:2025-05-14
Method:X-RAY DIFFRACTION (2.5 Å)
Cite:Structure of the SARS-CoV-2 main protease
To Be Published
9BQZ
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BU of 9bqz by Molmil
Structure of the SARS-CoV-2 main protease in complex with inhibitor x11
Descriptor: (1H-indol-4-yl)methanol, 3C-like proteinase nsp5
Authors:Blankenship, L.R, Liu, W.R.
Deposit date:2024-05-10
Release date:2025-05-14
Method:X-RAY DIFFRACTION (1.7 Å)
Cite:Structure of the SARS-CoV-2 main protease
To Be Published
9BR0
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BU of 9br0 by Molmil
Structure of the SARS-CoV-2 main protease in complex with inhibitor YR-B-84
Descriptor: 3C-like proteinase nsp5, O-tert-butyl-N-(trifluoroacetyl)-L-threonyl-3-cyclohexyl-N-{(2R)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-alaninamide
Authors:Blankenship, L.R, Liu, W.R.
Deposit date:2024-05-10
Release date:2025-05-14
Method:X-RAY DIFFRACTION (2.5 Å)
Cite:Structure of the SARS-CoV-2 main protease
To Be Published
9BR1
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BU of 9br1 by Molmil
Structure of the SARS-CoV-2 main protease in complex with inhibitor VB-A-70
Descriptor: 3C-like proteinase nsp5, N-[(benzyloxy)carbonyl]-O-tert-butyl-L-threonyl-N-{(1S,2R)-1-(1,3-benzoxazol-2-yl)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-3-cyclohexyl-L-alaninamide
Authors:Blankenship, L.R, Liu, W.R.
Deposit date:2024-05-10
Release date:2025-05-14
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:Structure of the SARS-CoV-2 main protease
To Be Published
9BS7
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BU of 9bs7 by Molmil
Structure of the SARS-CoV-2 main protease in complex with inhibitor Vinylpyridine
Descriptor: 3-ethenylpyridine, 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

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