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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
9J8T
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BU of 9j8t by Molmil
Crystal structure of SARS-CoV-2 main protease in complex with Mp-4L2
Descriptor: 3C-like proteinase nsp5, TYR-DSG-DLE-DPN-DGN-ARG-DTH-DAS-DTR-DTH-ALO-DGN-DTY-CCJ-GLY-NH2
Authors:Shi, Y.S, Yang, J.Y, Wang, M.W.
Deposit date:2024-08-21
Release date:2025-07-02
Method:X-RAY DIFFRACTION (2.39 Å)
Cite:De novo discovery of a non-covalent cell-penetrating bicyclic peptide inhibitor targeting SARS-CoV-2 main protease
To Be Published
9J8U
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BU of 9j8u by Molmil
Crystal structure of SARS-CoV-2 main protease in complex with Mp-4D7
Descriptor: 3C-like proteinase nsp5, DTY-VAL-THR-PHE-HIS-ALO-2TL-2TL-PRO-PHE-LEU-DPR-PRO-CCJ-GLY-NH2
Authors:Shi, Y.S, Yang, J.Y, Wang, M.W.
Deposit date:2024-08-21
Release date:2025-07-02
Method:X-RAY DIFFRACTION (2.71 Å)
Cite:De novo discovery of a non-covalent cell-penetrating bicyclic pep-tide inhibitor targeting SARS-CoV-2 main protease
To Be Published
9P6P
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BU of 9p6p by Molmil
Crystal Structure of the SARS-CoV-2 2'-O-Methyltransferase with (m7GpppA)pUpU (Cap-0) and S-Adenosyl-L-homocysteine (SAH).
Descriptor: 2'-O-methyltransferase, 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE, CHLORIDE ION, ...
Authors:Minasov, G, Shuvalova, L, Maltseva, N, Kim, Y, Kiryukhina, O, Joachimiak, A, Satchell, K.J.F, Center for Structural Biology of Infectious Diseases (CSBID)
Deposit date:2025-06-19
Release date:2025-07-02
Method:X-RAY DIFFRACTION (1.95 Å)
Cite:Crystal Structure of the SARS-CoV-2 2'-O-Methyltransferase with (m7GpppA)pUpU (Cap-0) and S-Adenosyl-L-homocysteine (SAH).
To Be Published
9CJO
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BU of 9cjo by Molmil
X-ray crystal structure of SARS-CoV-2 main protease quadruple mutants
Descriptor: 3C-like proteinase nsp5
Authors:Esler, M.A, Shi, K, Harris, R.S, Aihara, H.
Deposit date:2024-07-07
Release date:2025-07-09
Method:X-RAY DIFFRACTION (2.33 Å)
Cite:X-ray crystal structure of SARS-CoV-2 main protease quadruple mutants
To Be Published
9CJP
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X-ray crystal structure of SARS-CoV-2 main protease quadruple mutants in complex with Nirmatrelvir
Descriptor: (1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide, 1,2-ETHANEDIOL, 3C-like proteinase nsp5, ...
Authors:Esler, M.A, Shi, K, Harris, R.S, Aihara, H.
Deposit date:2024-07-07
Release date:2025-07-09
Method:X-RAY DIFFRACTION (1.71 Å)
Cite:X-ray crystal structure of SARS-CoV-2 main protease quadruple mutants in complex with Nirmatrelvir
To Be Published
9CJQ
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BU of 9cjq by Molmil
X-ray crystal structure of SARS-CoV-2 main protease quadruple mutants in complex with Ensitrelvir
Descriptor: 1,2-ETHANEDIOL, 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, main protease
Authors:Esler, M.A, Shi, K, Harris, R.S, Aihara, H.
Deposit date:2024-07-07
Release date:2025-07-09
Method:X-RAY DIFFRACTION (2.24 Å)
Cite:X-ray crystal structure of SARS-CoV-2 main protease quadruple mutants in complex with Ensitrelvir
To Be Published
9CJR
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BU of 9cjr by Molmil
X-ray crystal structure of SARS-CoV-2 main protease double mutants in complex with Ensitrelvir
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, CHLORIDE ION, ...
Authors:Esler, M.A, Shi, K, Harris, R.S, Aihara, H.
Deposit date:2024-07-07
Release date:2025-07-09
Method:X-RAY DIFFRACTION (1.65 Å)
Cite:X-ray crystal structure of SARS-CoV-2 main protease double mutants in complex with Ensitrelvir
To Be Published
9CJS
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X-ray crystal structure of SARS-CoV-2 main protease triple mutants 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:Esler, M.A, Shi, K, Harris, R.S, Aihara, H.
Deposit date:2024-07-07
Release date:2025-07-09
Method:X-RAY DIFFRACTION (2.09 Å)
Cite:X-ray crystal structure of SARS-CoV-2 main protease triple mutants in complex with Bofutrelvir
To Be Published
9CJT
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BU of 9cjt by Molmil
X-ray crystal structure of SARS-CoV-2 main protease quadruple mutants 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:Esler, M.A, Shi, K, Harris, R.S, Aihara, H.
Deposit date:2024-07-07
Release date:2025-07-09
Method:X-RAY DIFFRACTION (1.92 Å)
Cite:X-ray crystal structure of SARS-CoV-2 main protease quadruple mutants in complex with Bofutrelvir
To Be Published
9CJU
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BU of 9cju by Molmil
Structure of SARS-CoV-2 main protease in complex with Bofutrelvir in orthorhombic form
Descriptor: 1,2-ETHANEDIOL, DI(HYDROXYETHYL)ETHER, Non-structural protein 7, ...
Authors:Esler, M.A, Shi, K, Harris, R.S, Aihara, H.
Deposit date:2024-07-07
Release date:2025-07-09
Method:X-RAY DIFFRACTION (1.68 Å)
Cite:To be published
To Be Published
9CJV
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BU of 9cjv by Molmil
X-ray crystal structure of SARS-CoV-2 main protease complex with Bofutrelvir
Descriptor: 3C-like proteinase nsp5, DIMETHYL SULFOXIDE, ~{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:Esler, M.A, Shi, K, Aihara, H.
Deposit date:2024-07-07
Release date:2025-07-09
Method:X-RAY DIFFRACTION (1.91 Å)
Cite:X-ray crystal structure of SARS-CoV-2 main protease complex with Bofutrelvir
To Be Published
9E9Q
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BU of 9e9q by Molmil
SARS-CoV-2 SL5 crystal structure native
Descriptor: MAGNESIUM ION, RNA (101-MER)
Authors:Jones, C.P, Ferre-D'Amare, A.R.
Deposit date:2024-11-08
Release date:2025-07-09
Method:X-RAY DIFFRACTION (3.33 Å)
Cite:Crystallographic and cryoEM analyses reveal SARS-CoV-2 SL5 is a mobile T-shaped four-way junction with deep pockets.
Rna, 31, 2025
9FWH
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BU of 9fwh by Molmil
Crystal Structure of SARS-CoV-2 NSP10-ExoN in complex with VT00019
Descriptor: (4R)-4-phenyl-1,2-thiazolidine 1,1-dioxide, Guanine-N7 methyltransferase nsp14, Non-structural protein 10, ...
Authors:Krojer, T, Kozielski, F, Sele, C, Nyblom, M, Fisher, S.Z, Knecht, W.
Deposit date:2024-06-30
Release date:2025-07-09
Method:X-RAY DIFFRACTION (2.35 Å)
Cite:Crystal Structure of SARS-CoV-2 NSP10-ExoN in complex with VT00019
To Be Published
9FWI
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BU of 9fwi by Molmil
Ensemble model of ligand-free SARS-CoV-2 NSP10-NSP14 (ExoN) and in complex with partially bound VT00025
Descriptor: (3-oxidanylazetidin-1-yl)-phenyl-methanone, DIMETHYL SULFOXIDE, Guanine-N7 methyltransferase nsp14, ...
Authors:Krojer, T, Kozielski, F, Sele, C, Nyblom, M, Fisher, S.Z, Knecht, W.
Deposit date:2024-06-30
Release date:2025-07-09
Method:X-RAY DIFFRACTION (1.533 Å)
Cite:Ensemble model of ligand-free SARS-CoV-2 NSP10-NSP14 (ExoN) and in complex with partially bound VT00025
To Be Published
9FWJ
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BU of 9fwj by Molmil
Ensemble model of ligand-free SARS-CoV-2 NSP10-NSP14 (ExoN) and in complex with partially bound VT00079
Descriptor: 2-methoxybenzamide, Guanine-N7 methyltransferase nsp14, MAGNESIUM ION, ...
Authors:Krojer, T, Kozielski, F, Sele, C, Nyblom, M, Fisher, S.Z, Knecht, W.
Deposit date:2024-06-30
Release date:2025-07-09
Method:X-RAY DIFFRACTION (2.424 Å)
Cite:Ensemble model of ligand-free SARS-CoV-2 NSP10-NSP14 (ExoN) and in complex with partially bound VT00079
To Be Published
9FWL
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BU of 9fwl by Molmil
Ensemble model of ligand-free SARS-CoV-2 NSP10-NSP14 (ExoN) and in complex with partially bound VT00025
Descriptor: 3-phenylthiophene-2-carboxamide, DIMETHYL SULFOXIDE, Guanine-N7 methyltransferase nsp14, ...
Authors:Krojer, T, Kozielski, F, Sele, C, Nyblom, M, Fisher, S.Z, Knecht, W.
Deposit date:2024-06-30
Release date:2025-07-09
Method:X-RAY DIFFRACTION (2.09 Å)
Cite:Ensemble model of ligand-free SARS-CoV-2 NSP10-NSP14 (ExoN) and in complex with partially bound VT00025
To Be Published
9FWM
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BU of 9fwm by Molmil
Crystal Structure of SARS-CoV-2 NSP10-NSP14 (ExoN) in complex with VT00180
Descriptor: 1H-indole-3-carboxamide, DIMETHYL SULFOXIDE, Guanine-N7 methyltransferase nsp14, ...
Authors:Krojer, T, Kozielski, F, Sele, C, Nyblom, M, Fisher, S.Z, Knecht, W.
Deposit date:2024-06-30
Release date:2025-07-09
Method:X-RAY DIFFRACTION (1.574 Å)
Cite:Crystal Structure of SARS-CoV-2 NSP10-NSP14 (ExoN) in complex with VT00180
To Be Published
9FWN
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BU of 9fwn by Molmil
Crystal Structure of SARS-CoV-2 NSP10-NSP14 (ExoN) in complex with VT00219
Descriptor: 1-methyl-1-(phenylmethyl)urea, DIMETHYL SULFOXIDE, Guanine-N7 methyltransferase nsp14, ...
Authors:Krojer, T, Kozielski, F, Sele, C, Nyblom, M, Fisher, S.Z, Knecht, W.
Deposit date:2024-06-30
Release date:2025-07-09
Method:X-RAY DIFFRACTION (1.866 Å)
Cite:Crystal Structure of SARS-CoV-2 NSP10-NSP14 (ExoN) in complex with VT00219
To Be Published
9FWO
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BU of 9fwo by Molmil
Crystal Structure of SARS-CoV-2 NSP10-NSP14 (ExoN) in complex with VT00216
Descriptor: 1-methylpyrrole-2-carboxamide, Guanine-N7 methyltransferase nsp14, MAGNESIUM ION, ...
Authors:Krojer, T, Kozielski, F, Sele, C, Nyblom, M, Fisher, S.Z, Knecht, W.
Deposit date:2024-06-30
Release date:2025-07-09
Method:X-RAY DIFFRACTION (2.179 Å)
Cite:Crystal Structure of SARS-CoV-2 NSP10-NSP14 (ExoN) in complex with VT00216
To Be Published
9FWP
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BU of 9fwp by Molmil
Crystal Structure of SARS-CoV-2 NSP10-NSP14 (ExoN) in complex with VT00198
Descriptor: Guanine-N7 methyltransferase nsp14, MAGNESIUM ION, N-methylbenzamide, ...
Authors:Krojer, T, Kozielski, F, Sele, C, Nyblom, M, Fisher, S.Z, Knecht, W.
Deposit date:2024-06-30
Release date:2025-07-09
Method:X-RAY DIFFRACTION (2.381 Å)
Cite:Crystal Structure of SARS-CoV-2 NSP10-NSP14 (ExoN) in complex with VT00198
To Be Published
9FWQ
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BU of 9fwq by Molmil
Crystal Structure of SARS-CoV-2 NSP10-NSP14 (ExoN) in complex with VT00218
Descriptor: 5,6,7,8-tetrahydro-[1,2,4]triazolo[4,3-a]pyridine, Guanine-N7 methyltransferase nsp14, MAGNESIUM ION, ...
Authors:Krojer, T, Kozielski, F, Sele, C, Nyblom, M, Fisher, S.Z, Knecht, W.
Deposit date:2024-06-30
Release date:2025-07-09
Method:X-RAY DIFFRACTION (2.322 Å)
Cite:Crystal Structure of SARS-CoV-2 NSP10-NSP14 (ExoN) in complex with VT00218
To Be Published
9FWR
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BU of 9fwr by Molmil
Crystal Structure of SARS-CoV-2 NSP10-NSP14 (ExoN) in complex with VT00249
Descriptor: (4R)-4-phenyl-1,3-oxazolidin-2-one, Guanine-N7 methyltransferase nsp14, MAGNESIUM ION, ...
Authors:Krojer, T, Kozielski, F, Sele, C, Nyblom, M, Fisher, S.Z, Knecht, W.
Deposit date:2024-06-30
Release date:2025-07-09
Method:X-RAY DIFFRACTION (2.294 Å)
Cite:Crystal Structure of SARS-CoV-2 NSP10-NSP14 (ExoN) in complex with VT00249
To Be Published
9FWS
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BU of 9fws by Molmil
Crystal Structure of SARS-CoV-2 NSP10-NSP14 (ExoN) in complex with VT00258
Descriptor: 7-METHOXY-1H-INDAZOLE, DIMETHYL SULFOXIDE, Guanine-N7 methyltransferase nsp14, ...
Authors:Krojer, T, Kozielski, F, Sele, C, Nyblom, M, Fisher, S.Z, Knecht, W.
Deposit date:2024-06-30
Release date:2025-07-09
Method:X-RAY DIFFRACTION (1.433 Å)
Cite:Crystal Structure of SARS-CoV-2 NSP10-NSP14 (ExoN) in complex with VT00258
To Be Published
9FWT
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BU of 9fwt by Molmil
Ensemble model of ligand-free SARS-CoV-2 NSP10-NSP14 (ExoN) and in complex with partially bound VT00259
Descriptor: DIMETHYL SULFOXIDE, Guanine-N7 methyltransferase nsp14, Non-structural protein 10, ...
Authors:Krojer, T, Kozielski, F, Sele, C, Nyblom, M, Fisher, S.Z, Knecht, W.
Deposit date:2024-06-30
Release date:2025-07-09
Method:X-RAY DIFFRACTION (1.639 Å)
Cite:Ensemble model of ligand-free SARS-CoV-2 NSP10-NSP14 (ExoN) and in complex with partially bound VT00259
To Be Published
9FWU
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BU of 9fwu by Molmil
Crystal Structure of SARS-CoV-2 NSP10-NSP14 (ExoN) in complex with VT00421
Descriptor: DIMETHYL SULFOXIDE, Guanine-N7 methyltransferase nsp14, N,N-dimethyl-3-oxidanyl-benzamide, ...
Authors:Krojer, T, Kozielski, F, Sele, C, Nyblom, M, Fisher, S.Z, Knecht, W.
Deposit date:2024-06-30
Release date:2025-07-09
Method:X-RAY DIFFRACTION (1.425 Å)
Cite:Crystal Structure of SARS-CoV-2 NSP10-NSP14 (ExoN) in complex with VT00421
To Be Published

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