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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
8UDQ
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Crystal structure of SARS-CoV-2 3CL protease with inhibitor 1
Descriptor: 2-cyano-D-phenylalanyl-2,4-dichloro-N-[(2S)-4-{[2-(dimethylamino)ethyl]amino}-1-(4-fluorophenyl)-4-oxobutan-2-yl]-D-phenylalaninamide, 3C-like proteinase nsp5, SODIUM ION
Authors:Forouhar, F, Liu, H, Zack, A, Iketani, S, Williams, A, Vaz, D.R, Habashi, D.L, Resnick, S.J, Chavez, A, Ho, D.D, Stockwell, B.R.
Deposit date:2023-09-28
Release date:2024-12-25
Last modified:2025-01-15
Method:X-RAY DIFFRACTION (2.12 Å)
Cite:Development of small molecule non-covalent coronavirus 3CL protease inhibitors from DNA-encoded chemical library screening.
Nat Commun, 16, 2025
8UDW
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BU of 8udw by Molmil
Crystal structure of SARS-CoV-2 3CL protease with inhibitor 2
Descriptor: 2-cyano-D-phenylalanyl-2,4-dichloro-N-[(2S)-4-{[3-(dimethylamino)propyl]amino}-1-(4-fluorophenyl)-4-oxobutan-2-yl]-D-phenylalaninamide, 3C-like proteinase nsp5
Authors:Forouhar, F, Liu, H, Zack, A, Iketani, S, Williams, A, Vaz, D.R, Habashi, D.L, Resnick, S.J, Chavez, A, Ho, D.D, Stockwell, B.R.
Deposit date:2023-09-29
Release date:2024-12-25
Last modified:2025-01-15
Method:X-RAY DIFFRACTION (2.1 Å)
Cite:Development of small molecule non-covalent coronavirus 3CL protease inhibitors from DNA-encoded chemical library screening.
Nat Commun, 16, 2025
8ZPP
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BU of 8zpp by Molmil
Local CryoEM structure of the SARS-CoV-2 BA.5 in complex with ORB10 Fab
Descriptor: Spike glycoprotein,Fibritin, variable heavy chain of ORB10 Fab, variable light chain of ORB10 Fab
Authors:Cao, S, Leng, C, Hu, H.
Deposit date:2024-05-30
Release date:2024-12-25
Method:ELECTRON MICROSCOPY (3.6 Å)
Cite:Local CryoEM structure of the SARS-CoV-2 BA.5 in complex with ORB10 Fab
To Be Published
9BF9
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Human LAG-3-HLA-DR1 complex
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, DI(HYDROXYETHYL)ETHER, HLA class II histocompatibility antigen DR beta chain, ...
Authors:Petersen, J, Rossjohn, J.
Deposit date:2024-04-17
Release date:2024-12-25
Method:X-RAY DIFFRACTION (3.4 Å)
Cite:Crystal structure of the human LAG-3-HLA-DR1-peptide complex.
Sci Immunol, 9, 2024
8RI4
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Crystal structure of the SARS-CoV-2 Main Protease inhibited by (2-methylsulfanyl-6,7-dihydro-[1,4]dioxino[2,3-f]benzimidazol-3-yl)-(p-tolyl)methanone
Descriptor: 3C-like proteinase nsp5, 4-METHYLBENZOIC ACID, DIMETHYL SULFOXIDE, ...
Authors:Charton, J, Deprez, B, Hanoulle, X.
Deposit date:2023-12-18
Release date:2025-01-01
Method:X-RAY DIFFRACTION (1.7 Å)
Cite:Crystal structure of the SARS-CoV-2 Main Protease inhibited by (2-methylsulfanyl-6,7-dihydro-[1,4]dioxino[2,3-f]benzimidazol-3-yl)-(p-tolyl)methanone
To Be Published
8RJ5
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P1-15 T-cell Receptor bound to HLA A*2402-NF9 pMHC complex
Descriptor: Beta-2-microglobulin, MHC class I antigen, P1-15 T-cell Receptor Alpha Chain, ...
Authors:Wall, A, Sewell, A.K, Motozono, C, Rizkallah, P.J, Fuller, A.
Deposit date:2023-12-20
Release date:2025-01-01
Method:X-RAY DIFFRACTION (3.02 Å)
Cite:NF9 T-cell Receptor bound to HLA A*2402-NF9 pMHC complex (Paper Pending)
To Be Published
8RJH
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HLA A*2402-NF9_6F pMHC complex
Descriptor: ASN-TYR-ASN-TYR-LEU-PHE-ARG-LEU-PHE, Beta-2-microglobulin, MHC class I antigen
Authors:Wall, A, Sewell, A.K, Motozono, C, Rizkallah, P.J, Fuller, A.
Deposit date:2023-12-21
Release date:2025-01-01
Method:X-RAY DIFFRACTION (2.6 Å)
Cite:HLA A*2402-NF9_6F pMHC complex
To Be Published
8RJI
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HLA A*2402-NF9_5R pMHC complex
Descriptor: Beta-2-microglobulin, MHC class I antigen, Spike glycoprotein
Authors:Wall, A, Motozono, C, Sewell, A.K, Rizkallah, P.J, Fuller, A.
Deposit date:2023-12-21
Release date:2025-01-01
Method:X-RAY DIFFRACTION (2.3 Å)
Cite:HLA A*2402-NF9_5R pMHC complex
To Be Published
8UDM
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Crystal structure of SARS-CoV-2 3CL protease with inhibitor 16
Descriptor: 1,2-ETHANEDIOL, 2-cyano-D-phenylalanyl-N-[(2S)-4-({3-[(5-amino-4H-1,2,4-triazol-3-yl)amino]propyl}amino)-1-(4-fluorophenyl)-4-oxobutan-2-yl]-2,4-dichloro-D-phenylalaninamide, 3C-like proteinase nsp5
Authors:Forouhar, F, Liu, H, Zack, A, Iketani, S, Williams, A, Vaz, D.R, Habashi, D.L, Resnick, S.J, Chavez, A, Ho, D.D, Stockwell, B.R.
Deposit date:2023-09-28
Release date:2025-01-01
Last modified:2025-01-15
Method:X-RAY DIFFRACTION (1.55 Å)
Cite:Development of small molecule non-covalent coronavirus 3CL protease inhibitors from DNA-encoded chemical library screening.
Nat Commun, 16, 2025
8UDO
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BU of 8udo by Molmil
Crystal structure of SARS-CoV-2 3CL protease with inhibitor 15
Descriptor: 2-cyano-D-phenylalanyl-2,4-dichloro-N-[(2S)-4-{[5-(dimethylamino)pentyl]amino}-1-(4-fluorophenyl)-4-oxobutan-2-yl]-D-phenylalaninamide, 3C-like proteinase nsp5
Authors:Forouhar, F, Liu, H, Zack, A, Iketani, S, Williams, A, Vaz, D.R, Habashi, D.L, Resnick, S.J, Chavez, A, Ho, D.D, Stockwell, B.R.
Deposit date:2023-09-28
Release date:2025-01-01
Last modified:2025-01-15
Method:X-RAY DIFFRACTION (1.78 Å)
Cite:Development of small molecule non-covalent coronavirus 3CL protease inhibitors from DNA-encoded chemical library screening.
Nat Commun, 16, 2025
8UDP
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BU of 8udp by Molmil
Crystal structure of SARS-CoV-2 3CL protease with inhibitor 14
Descriptor: 2-cyano-D-phenylalanyl-2,4-dichloro-N-[(2S)-4-{[4-(dimethylamino)butyl]amino}-1-(4-fluorophenyl)-4-oxobutan-2-yl]-D-phenylalaninamide, 3C-like proteinase nsp5
Authors:Forouhar, F, Liu, H, Zack, A, Iketani, S, Williams, A, Vaz, D.R, Habashi, D.L, Resnick, S.J, Chavez, A, Ho, D.D, Stockwell, B.R.
Deposit date:2023-09-28
Release date:2025-01-01
Last modified:2025-01-15
Method:X-RAY DIFFRACTION (1.75 Å)
Cite:Development of small molecule non-covalent coronavirus 3CL protease inhibitors from DNA-encoded chemical library screening.
Nat Commun, 16, 2025
8UDX
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Crystal structure of SARS-CoV-2 3CL protease with C145 sulfinic acid in complex with inhibitor 17
Descriptor: 2-cyano-D-phenylalanyl-2,4-dichloro-N-[(2S)-1-(4-fluorophenyl)-4-{[3-(4-methylpiperazin-1-yl)propyl]amino}-4-oxobutan-2-yl]-D-phenylalaninamide, 3C-like proteinase
Authors:Forouhar, F, Liu, H, Zack, A, Iketani, S, Williams, A, Vaz, D.R, Habashi, D.L, Resnick, S.J, Chavez, A, Ho, D.D, Stockwell, B.R.
Deposit date:2023-09-29
Release date:2025-01-01
Last modified:2025-01-15
Method:X-RAY DIFFRACTION (1.79 Å)
Cite:Development of small molecule non-covalent coronavirus 3CL protease inhibitors from DNA-encoded chemical library screening.
Nat Commun, 16, 2025
8UEA
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BU of 8uea by Molmil
Crystal structure of SARS-CoV-2 3CL protease with inhibitor 29
Descriptor: 1,2-ETHANEDIOL, 2-cyano-D-phenylalanyl-2,4-dichloro-N-[(2S)-1-(4-fluorophenyl)-4-oxo-4-{[3-(pyridin-3-yl)propyl]amino}butan-2-yl]-D-phenylalaninamide, 3C-like proteinase nsp5, ...
Authors:Forouhar, F, Liu, H, Zack, A, Iketani, S, Williams, A, Vaz, D.R, Habashi, D.L, Choi, K, Resnick, S.J, Chavez, A, Ho, D.D, Stockwell, B.R.
Deposit date:2023-09-30
Release date:2025-01-01
Last modified:2025-01-15
Method:X-RAY DIFFRACTION (1.94 Å)
Cite:Development of small molecule non-covalent coronavirus 3CL protease inhibitors from DNA-encoded chemical library screening.
Nat Commun, 16, 2025
8UEB
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BU of 8ueb by Molmil
Crystal structure of SARS-CoV-2 3CL protease with inhibitor 30
Descriptor: 1,2-ETHANEDIOL, 2-cyano-D-phenylalanyl-2,4-dichloro-N-[(2S)-1-(4-fluorophenyl)-4-oxo-4-{[3-(pyridin-4-yl)propyl]amino}butan-2-yl]-D-phenylalaninamide, 3C-like proteinase nsp5, ...
Authors:Forouhar, F, Liu, H, Zack, A, Iketani, S, Williams, A, Vaz, D.R, Habashi, D.L, Choi, K, Resnick, S.J, Chavez, A, Ho, D.D, Stockwell, B.R.
Deposit date:2023-09-30
Release date:2025-01-01
Last modified:2025-01-15
Method:X-RAY DIFFRACTION (2.03 Å)
Cite:Development of small molecule non-covalent coronavirus 3CL protease inhibitors from DNA-encoded chemical library screening.
Nat Commun, 16, 2025
8UEF
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BU of 8uef by Molmil
Crystal structure of SARS-CoV-2 3CL protease with inhibitor 32
Descriptor: 2-cyano-D-phenylalanyl-2,4-dichloro-N-{(2S)-1-(4-fluorophenyl)-4-[(4-methoxybutyl)amino]-4-oxobutan-2-yl}-D-phenylalaninamide, 3C-like proteinase nsp5
Authors:Forouhar, F, Liu, H, Zack, A, Iketani, S, Williams, A, Vaz, D.R, Habashi, D.L, Choi, K, Resnick, S.J, Chavez, A, Ho, D.D, Stockwell, B.R.
Deposit date:2023-10-01
Release date:2025-01-01
Last modified:2025-01-15
Method:X-RAY DIFFRACTION (1.96 Å)
Cite:Development of small molecule non-covalent coronavirus 3CL protease inhibitors from DNA-encoded chemical library screening.
Nat Commun, 16, 2025
8UEG
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BU of 8ueg by Molmil
Crystal structure of SARS-CoV-2 3CL protease with inhibitor 27
Descriptor: 2-cyano-D-phenylalanyl-2,4-dichloro-N-{(2S)-1-(4-fluorophenyl)-4-oxo-4-[(pent-4-yn-1-yl)amino]butan-2-yl}-D-phenylalaninamide, 3C-like proteinase nsp5
Authors:Forouhar, F, Liu, H, Zack, A, Iketani, S, Williams, A, Vaz, D.R, Habashi, D.L, Choi, K, Resnick, S.J, Chavez, A, Ho, D.D, Stockwell, B.R.
Deposit date:2023-10-01
Release date:2025-01-01
Last modified:2025-01-15
Method:X-RAY DIFFRACTION (2.21 Å)
Cite:Development of small molecule non-covalent coronavirus 3CL protease inhibitors from DNA-encoded chemical library screening.
Nat Commun, 16, 2025
8UEH
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BU of 8ueh by Molmil
Crystal structure of SARS-CoV-2 3CL protease with inhibitor 31
Descriptor: 2-cyano-D-phenylalanyl-2,4-dichloro-N-{(2S)-1-(4-fluorophenyl)-4-oxo-4-[(2-phenylethyl)amino]butan-2-yl}-D-phenylalaninamide, 3C-like proteinase nsp5, CHLORIDE ION
Authors:Forouhar, F, Liu, H, Zack, A, Iketani, S, Williams, A, Vaz, D.R, Habashi, D.L, Choi, K, Resnick, S.J, Chavez, A, Ho, D.D, Stockwell, B.R.
Deposit date:2023-10-01
Release date:2025-01-01
Last modified:2025-01-15
Method:X-RAY DIFFRACTION (1.88 Å)
Cite:Development of small molecule non-covalent coronavirus 3CL protease inhibitors from DNA-encoded chemical library screening.
Nat Commun, 16, 2025
8UEI
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BU of 8uei by Molmil
Crystal structure of SARS-CoV-2 3CL protease with inhibitor 28
Descriptor: 2-cyano-D-phenylalanyl-2,4-dichloro-N-[(2S)-1-(4-fluorophenyl)-4-oxo-4-{[4-(pyrrolidin-1-yl)butyl]amino}butan-2-yl]-D-phenylalaninamide, 3C-like proteinase nsp5
Authors:Forouhar, F, Liu, H, Zack, A, Iketani, S, Williams, A, Vaz, D.R, Habashi, D.L, Choi, K, Resnick, S.J, Chavez, A, Ho, D.D, Stockwell, B.R.
Deposit date:2023-10-01
Release date:2025-01-01
Last modified:2025-01-15
Method:X-RAY DIFFRACTION (1.71 Å)
Cite:Development of small molecule non-covalent coronavirus 3CL protease inhibitors from DNA-encoded chemical library screening.
Nat Commun, 16, 2025
8Y4D
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BU of 8y4d by Molmil
Crystal structure of SARS-Cov-2 main protease in complex with Bofutrelvir
Descriptor: 3C-like proteinase nsp5, ~{N}-[(2~{S})-3-cyclohexyl-1-oxidanylidene-1-[[(2~{S})-1-oxidanylidene-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]propan-2-yl]-1~{H}-indole-2-carboxamide
Authors:Zhou, X.L, Wang, W.W, Zhang, J, Li, J.
Deposit date:2024-01-30
Release date:2025-01-08
Method:X-RAY DIFFRACTION (1.91 Å)
Cite:Crystal structure of SARS-Cov-2 main protease in complex with Bofutrelvir
To Be Published
8Y4G
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BU of 8y4g by Molmil
Crystal structure of SARS-Cov-2 main protease G15S mutant in complex with Bofutrelvir
Descriptor: 3C-like proteinase nsp5, ~{N}-[(2~{S})-3-cyclohexyl-1-oxidanylidene-1-[[(2~{S})-1-oxidanylidene-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]propan-2-yl]-1~{H}-indole-2-carboxamide
Authors:Zeng, P, Wang, W.W, Zhang, J, Li, J.
Deposit date:2024-01-30
Release date:2025-01-08
Last modified:2025-04-09
Method:X-RAY DIFFRACTION (1.93 Å)
Cite:Inhibitory efficacy and structural insights of Bofutrelvir against SARS-CoV-2 M pro mutants and MERS-CoV M pro.
Commun Biol, 8, 2025
8Y4H
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Crystal structure of SARS-Cov-2 main protease K90R mutant in complex with Bofutrelvir
Descriptor: 3C-like proteinase nsp5, ~{N}-[(2~{S})-3-cyclohexyl-1-oxidanylidene-1-[[(2~{S})-1-oxidanylidene-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]propan-2-yl]-1~{H}-indole-2-carboxamide
Authors:Guo, L, Wang, W.W, Zhang, J, Li, J.
Deposit date:2024-01-30
Release date:2025-01-08
Last modified:2025-04-09
Method:X-RAY DIFFRACTION (1.93 Å)
Cite:Inhibitory efficacy and structural insights of Bofutrelvir against SARS-CoV-2 M pro mutants and MERS-CoV M pro.
Commun Biol, 8, 2025
7HUC
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BU of 7huc by Molmil
PanDDA analysis group deposition -- Main Protease (SARS-CoV-2) in complex with fragment B07 from the F2X-Entry Screen in monoclinic space group
Descriptor: 3C-like proteinase nsp5, DIMETHYL SULFOXIDE, N-[3-(diethylamino)phenyl]ethanamide
Authors:Barthel, T, Benz, L.S, Wollenhaupt, J, Weiss, M.S.
Deposit date:2025-01-07
Release date:2025-01-15
Method:X-RAY DIFFRACTION (1.52 Å)
Cite:Orthorhombic SARS-CoV-2 main protease crystals provide higher success rate in fragment screening
To be published
7HUD
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BU of 7hud by Molmil
PanDDA analysis group deposition -- Main Protease (SARS-CoV-2) in complex with fragment B08 from the F2X-Entry Screen in monoclinic 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:2025-01-07
Release date:2025-01-15
Method:X-RAY DIFFRACTION (1.61 Å)
Cite:Orthorhombic SARS-CoV-2 main protease crystals provide higher success rate in fragment screening
To be published
7HUE
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BU of 7hue by Molmil
PanDDA analysis group deposition -- Main Protease (SARS-CoV-2) in complex with fragment D08 from the F2X-Entry Screen in monoclinic space group
Descriptor: 3C-like proteinase nsp5, DIMETHYL SULFOXIDE, N-[(3R)-1,1-dioxo-1lambda~6~-thiolan-3-yl]-N,N',N'-trimethylurea
Authors:Barthel, T, Benz, L.S, Wollenhaupt, J, Weiss, M.S.
Deposit date:2025-01-07
Release date:2025-01-15
Method:X-RAY DIFFRACTION (1.7 Å)
Cite:Orthorhombic SARS-CoV-2 main protease crystals provide higher success rate in fragment screening
To be published
8UDY
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Crystal structure of SARS-CoV-2 3CL protease with inhibitor 25
Descriptor: 2-cyano-D-phenylalanyl-2,4-dichloro-N-{(2S)-1-(4-fluorophenyl)-4-oxo-4-[(prop-2-yn-1-yl)amino]butan-2-yl}-D-phenylalaninamide, 3C-like proteinase nsp5, CALCIUM ION, ...
Authors:Forouhar, F, Liu, H, Zack, A, Iketani, S, Williams, A, Vaz, D.R, Habashi, D.L, Resnick, S.J, Chavez, A, Ho, D.D, Stockwell, B.R.
Deposit date:2023-09-29
Release date:2025-01-15
Method:X-RAY DIFFRACTION (1.91 Å)
Cite:Development of small molecule non-covalent coronavirus 3CL protease inhibitors from DNA-encoded chemical library screening.
Nat Commun, 16, 2025

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