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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 (5963)Repr. entries (2425)Latest entries (16)
9RXL
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BU of 9rxl by Molmil
SARS-CoV-2 nucleocapsid C-terminal domain in complex with BCY00018176
Descriptor: 1-[3,5-bis(3-bromanylpropanoyl)-1,3,5-triazinan-1-yl]-3-bromanyl-propan-1-one, BCY00018176, GLYCEROL, ...
Authors:Brear, P, Lulla, A, Dods, R, Bezerra, G.A, Hyvonen, M.
Deposit date:2025-07-11
Release date:2026-03-04
Method:X-RAY DIFFRACTION (1.46 Å)
Cite:Utilizing Constrained Bicyclic Peptides for In Vitro Diagnostics.
Acs Nano, 2026
9KH3
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BU of 9kh3 by Molmil
Crystal structure of SARS-Cov-2 main protease Y54C mutant in complex with S217622
Descriptor: 3C-like proteinase nsp5, 6-[(6-chloranyl-2-methyl-indazol-5-yl)amino]-3-[(1-methyl-1,2,4-triazol-3-yl)methyl]-1-[[2,4,5-tris(fluoranyl)phenyl]methyl]-1,3,5-triazine-2,4-dione
Authors:Zhou, X.L, Zhang, J, Li, J.
Deposit date:2024-11-09
Release date:2026-03-04
Method:X-RAY DIFFRACTION (1.49 Å)
Cite:Crystal structure of SARS-Cov-2 main protease Y54C mutant in complex with S217622
To Be Published
9KH1
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BU of 9kh1 by Molmil
Crystal structure of SARS-Cov-2 main protease V186F mutant in complex with S217622
Descriptor: 3C-like proteinase nsp5, 6-[(6-chloranyl-2-methyl-indazol-5-yl)amino]-3-[(1-methyl-1,2,4-triazol-3-yl)methyl]-1-[[2,4,5-tris(fluoranyl)phenyl]methyl]-1,3,5-triazine-2,4-dione
Authors:Zhou, X.L, Zhang, J, Li, J.
Deposit date:2024-11-09
Release date:2026-03-04
Method:X-RAY DIFFRACTION (1.51 Å)
Cite:Crystal structure of SARS-Cov-2 main protease V186F mutant in complex with S217622
To Be Published
28WF
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BU of 28wf by Molmil
SARS-CoV-2 nsp16-nsp10 in complex with SAM derivative ligand AD1
Descriptor: 2'-O-methyltransferase nsp16, 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, Non-structural protein 10, ...
Authors:Kalnins, G.
Deposit date:2026-02-24
Release date:2026-03-04
Method:X-RAY DIFFRACTION (1.7 Å)
Cite:SARS-CoV-2 nsp16-nsp10 in complex with SAM derivative inhibitor 3
To Be Published
9KH0
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BU of 9kh0 by Molmil
Crystal structure of SARS-Cov-2 main protease S46F mutant in complex with S217622
Descriptor: 3C-like proteinase nsp5, 6-[(6-chloranyl-2-methyl-indazol-5-yl)amino]-3-[(1-methyl-1,2,4-triazol-3-yl)methyl]-1-[[2,4,5-tris(fluoranyl)phenyl]methyl]-1,3,5-triazine-2,4-dione
Authors:Zhou, X.L, Zhang, J, Li, J.
Deposit date:2024-11-09
Release date:2026-03-04
Method:X-RAY DIFFRACTION (1.76 Å)
Cite:Crystal structure of SARS-Cov-2 main protease S46F mutant in complex with S217622
To Be Published
9P6F
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Structure of the SARS-CoV-2 main protease in complex with inhibitor SR-B-78
Descriptor: (1R,2S,5S)-N-[(1S,2Z)-2-imino-1-(5-methoxypyridin-3-yl)ethyl]-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:2025-06-18
Release date:2026-03-04
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:From nicotine to SARS-CoV-2 antivirals with potent in vivo efficacy and a broad anti-coronavirus spectrum.
Nat Commun, 2026
9OBH
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BU of 9obh by Molmil
Co-Structure of SARS-CoV-2 with Compound 34
Descriptor: (4S)-4-(iminomethyl)-3-(isoquinolin-4-yl)-1-[(1s,3R)-3-(trifluoromethyl)cyclobutyl]imidazolidin-2-one, 3C-like proteinase nsp5
Authors:Knapp, M.S, Ornelas, E.
Deposit date:2025-04-22
Release date:2026-03-04
Method:X-RAY DIFFRACTION (1.871 Å)
Cite:Discovery of EGT710, an Oral Nonpeptidomimetic Reversible Covalent SARS-CoV-2 Main Protease Inhibitor.
J.Med.Chem., 2026
9M29
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BU of 9m29 by Molmil
Crystal Structure of the SARS-CoV-2 (COVID-19) main protease with inhibitor AD05
Descriptor: 3C-like proteinase nsp5, inhibitor AD05
Authors:Yin, W, Kong, W.P, Wong, K.Y.
Deposit date:2025-02-27
Release date:2026-03-04
Method:X-RAY DIFFRACTION (1.967 Å)
Cite:Crystal Structure of the SARS-CoV-2 (COVID-19) main protease with inhibitor AD05
To Be Published
9M2U
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BU of 9m2u by Molmil
Crystal Structure of the SARS-CoV-2 (COVID-19) main protease with inhibitor AD06
Descriptor: 3C-like proteinase nsp5, AD06 peptide
Authors:Yin, W, Kong, W.P, Wong, K.Y.
Deposit date:2025-02-28
Release date:2026-03-04
Method:X-RAY DIFFRACTION (1.967 Å)
Cite:Crystal Structure of the SARS-CoV-2 (COVID-19) main protease with inhibitor AD06
To Be Published
9LZP
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BU of 9lzp by Molmil
Crystal structure of SARS-Cov-2 main protease P132H mutant in complex with Pomotrelvir
Descriptor: 3C-like proteinase nsp5, Pomotrelvir bound form
Authors:Jiang, H.H, Zhang, J, Li, J.
Deposit date:2025-02-22
Release date:2026-03-04
Method:X-RAY DIFFRACTION (1.97 Å)
Cite:Crystal structure of SARS-Cov-2 main protease P132H mutant in complex with Pomotrelvir
To Be Published
9IB0
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BU of 9ib0 by Molmil
Cryo-EM consensus map of prefusion SARS-CoV-2 spike (RBDs: 1 up & 2 down) bound to RBD-targeting MO176-117 antibody
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein
Authors:Schulte, T, Wallden, W, Andrell, J, Ohlin, M.
Deposit date:2025-02-11
Release date:2026-03-04
Method:ELECTRON MICROSCOPY (2.9 Å)
Cite:A stochastic codon deletion generates a SARS-CoV-2-neutralizing antibody
To Be Published
9IB2
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BU of 9ib2 by Molmil
Cryo-EM consensus map of prefusion SARS-CoV-2 spike (RBDs: 2 up & 1 down) bound to RBD-targeting MO176-117 antibody
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein
Authors:Schulte, T, Wallden, W, Andrell, J, Ohlin, M.
Deposit date:2025-02-11
Release date:2026-03-04
Method:ELECTRON MICROSCOPY (2.9 Å)
Cite:A stochastic codon deletion generates a SARS-CoV-2-neutralizing antibody
To Be Published
9LVS
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BU of 9lvs by Molmil
Cryo-EM structure of the SARS-CoV-2 spike protein in complex with S416
Descriptor: 2-[(E)-[[4-(2-chlorophenyl)-1,3-thiazol-2-yl]-methyl-hydrazinylidene]methyl]benzoic acid, 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:Fang, Y, Binghao, Z.
Deposit date:2025-02-12
Release date:2026-03-04
Method:ELECTRON MICROSCOPY (2.95 Å)
Cite:Cryo-EM structure of the SARS-CoV-2 spike protein(one RBD up state)
To Be Published
9IB1
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BU of 9ib1 by Molmil
Cryo-EM focus map of prefusion SARS-CoV-2 spike (RBDs: 1 up & 2 down) bound to RBD-targeting MO176-117 antibody
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Heavy chain of antibody MO176-117, Light chain of antibody MO176-117, ...
Authors:Schulte, T, Wallden, W, Andrell, J, Ohlin, M.
Deposit date:2025-02-11
Release date:2026-03-04
Method:ELECTRON MICROSCOPY (3.2 Å)
Cite:A stochastic codon deletion generates a SARS-CoV-2-neutralizing antibody
To Be Published
9IB3
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BU of 9ib3 by Molmil
Cryo-EM focus map of prefusion SARS-CoV-2 spike (RBDs: 2 up & 1 down) bound to RBD-targeting MO176-117 antibody
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Heavy chain of antibody MO176-117, Light chain of antibody MO176-117, ...
Authors:Schulte, T, Wallden, W, Andrell, J, Ohlin, M.
Deposit date:2025-02-11
Release date:2026-03-04
Method:ELECTRON MICROSCOPY (3.3 Å)
Cite:A stochastic codon deletion generates a SARS-CoV-2-neutralizing antibody
To Be Published
9T74
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BU of 9t74 by Molmil
2'-fluoro-modified pyrimidine (FY) RNA aptamer binding to the receptor binding domain (RBD) of the SARS-CoV-2 spike protein. (focus map: RBD-aptamer)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, DNA/RNA (51-MER), MAGNESIUM ION, ...
Authors:Kristoffersen, E.L, Andersen, E.S, Zwergious, N.H.
Deposit date:2025-11-10
Release date:2026-03-04
Method:ELECTRON MICROSCOPY (3.46 Å)
Cite:Serum-stable RNA origami nano-devices
To Be Published

250059

PDB entries from 2026-03-04

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