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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 (5527)Repr. entries (2333)Latest entries (8)
7IK6
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Group deposition of SARS-CoV-2 NSP3 Macrodomain in complex with inhibitors from the O'Brien group -- Crystal Structure of SARS-CoV-2 NSP3 Macrodomain in complex with POB0217 (Mac1-x10585)
Descriptor: (2P)-2-[2-(methylamino)-1,3-benzothiazol-6-yl]cyclopent-1-ene-1-carboxylic acid, Papain-like protease nsp3
Authors:Aschenbrenner, J.C, Watt, G, Marples, P.G, Wang, X, Schuller, M, O'Brien, P, Fearon, D, von Delft, F.
Deposit date:2025-08-04
Release date:2025-08-13
Method:X-RAY DIFFRACTION (1.301 Å)
Cite:Group deposition of SARS-CoV-2 NSP3 Macrodomain in complex with inhibitors from the O'Brien group
To Be Published
7IK7
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Group deposition of SARS-CoV-2 NSP3 Macrodomain in complex with inhibitors from the O'Brien group -- Crystal Structure of SARS-CoV-2 NSP3 Macrodomain in complex with POB0218 (Mac1-x10586)
Descriptor: (2P)-2-[2-(ethylamino)-1,3-benzothiazol-6-yl]cyclopent-1-ene-1-carboxylic acid, DIMETHYL SULFOXIDE, Papain-like protease nsp3
Authors:Aschenbrenner, J.C, Watt, G, Marples, P.G, Wang, X, Schuller, M, O'Brien, P, Fearon, D, von Delft, F.
Deposit date:2025-08-04
Release date:2025-08-13
Method:X-RAY DIFFRACTION (1.229 Å)
Cite:Group deposition of SARS-CoV-2 NSP3 Macrodomain in complex with inhibitors from the O'Brien group
To Be Published
7IK8
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Group deposition of SARS-CoV-2 NSP3 Macrodomain in complex with inhibitors from the O'Brien group -- Crystal Structure of SARS-CoV-2 NSP3 Macrodomain in complex with POB0222 (Mac1-x10590)
Descriptor: (2P)-2-(quinolin-7-yl)cyclopent-1-ene-1-carboxylic acid, Papain-like protease nsp3
Authors:Aschenbrenner, J.C, Watt, G, Marples, P.G, Shaw, A, Wang, X, Schuller, M, O'Brien, P, Fearon, D, von Delft, F.
Deposit date:2025-08-04
Release date:2025-08-13
Method:X-RAY DIFFRACTION (1.151 Å)
Cite:Group deposition of SARS-CoV-2 NSP3 Macrodomain in complex with inhibitors from the O'Brien group
To Be Published
9J4S
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Structural basis for recognition of SARS-CoV-2 conserved nucleocapside epitopes by dominant T cell receptors
Descriptor: Beta-2-microglobulin, GLYCEROL, HLA class I histocompatibility antigen, ...
Authors:Yuan, P, Wu, D.C.
Deposit date:2024-08-10
Release date:2025-08-13
Method:X-RAY DIFFRACTION (2.95 Å)
Cite:Structural basis for recognition of SARS-CoV-2 conserved nucleocapside epitopes by dominant T cell receptors
To Be Published
9J4T
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BU of 9j4t by Molmil
Structural basis for recognition of SARS-CoV-2 conserved nucleocapside epitopes by dominant T cell receptors
Descriptor: Beta-2-microglobulin, HLA class I histocompatibility antigen, B alpha chain, ...
Authors:Yuan, P, Wu, D.C.
Deposit date:2024-08-10
Release date:2025-08-13
Method:X-RAY DIFFRACTION (2.04 Å)
Cite:Structural basis for recognition of SARS-CoV-2 conserved nucleocapside epitopes by dominant T cell receptors
To Be Published
9J4U
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Structural basis for recognition of SARS-CoV-2 conserved nucleocapside epitopes by dominant T cell receptors
Descriptor: Beta-2-microglobulin, LLL epitope specific TCR APHLA, LLL epitope specific TCR BETA, ...
Authors:Yuan, P, Wu, D.C.
Deposit date:2024-08-10
Release date:2025-08-13
Method:X-RAY DIFFRACTION (2.17 Å)
Cite:Structural basis for recognition of SARS-CoV-2 conserved nucleocapside epitopes by dominant T cell receptors
To Be Published
9J4V
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Structural basis for recognition of SARS-CoV-2 conserved nucleocapside epitopes by dominant T cell receptors
Descriptor: Beta-2-microglobulin, DI(HYDROXYETHYL)ETHER, GLYCEROL, ...
Authors:Yuan, P, Wu, D.C.
Deposit date:2024-08-10
Release date:2025-08-13
Method:X-RAY DIFFRACTION (1.98 Å)
Cite:Structural basis for recognition of SARS-CoV-2 conserved nucleocapside epitopes by dominant T cell receptors
To Be Published
9QWI
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The N-terminal domain (44-180) of the SARS-CoV-2 nucleocapsid phosphoprotein using an automatic assignment/modeling software
Descriptor: Nucleoprotein
Authors:Schiavina, M, Bolognesi, T, Felli, I.C, Pierattelli, R.
Deposit date:2025-04-14
Release date:2025-08-13
Last modified:2025-09-17
Method:SOLUTION NMR
Cite:NMR insights on multidomain proteins: the case of the SARS-CoV-2 nucleoprotein.
Prog Nucl Magn Reson Spectrosc, 148-149, 2025
9RU5
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Cryo-EM structure of TCRpub/pMHC
Descriptor: MHC class I antigen, ORF3a protein, TCRpub alpha chain, ...
Authors:Akil, C, Zhu, Y, Hardenbrook, N, Zhang, P.
Deposit date:2025-07-03
Release date:2025-08-13
Method:ELECTRON MICROSCOPY (3.26 Å)
Cite:Cryo-EM structure of TCRpub/pMHC
To Be Published
7HC4
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PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodmain in complex with AVI-3367
Descriptor: CHLORIDE ION, Non-structural protein 3, ethyl {4-[(2-oxopyrrolidin-1-yl)amino]-9H-pyrimido[4,5-b]indol-8-yl}carbamate
Authors:Correy, G.J, Fraser, J.S.
Deposit date:2024-08-01
Release date:2025-08-20
Method:X-RAY DIFFRACTION (1 Å)
Cite:Ligand screen against SARS-CoV-2 NSP3 macrodomain
To be published
7HC5
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PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodmain in complex with AVI-3765
Descriptor: (5R)-1-[(7-fluoro-9H-pyrimido[4,5-b]indol-4-yl)amino]-5-methylpyrrolidin-2-one, CHLORIDE ION, Non-structural protein 3
Authors:Correy, G.J, Fraser, J.S.
Deposit date:2024-08-01
Release date:2025-08-20
Method:X-RAY DIFFRACTION (0.98 Å)
Cite:Ligand screen against SARS-CoV-2 NSP3 macrodomain
To be published
7HC6
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PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodmain in complex with AVI-3764
Descriptor: (5S)-1-[(7-fluoro-9H-pyrimido[4,5-b]indol-4-yl)amino]-5-methylpyrrolidin-2-one, CHLORIDE ION, Non-structural protein 3
Authors:Correy, G.J, Fraser, J.S.
Deposit date:2024-08-01
Release date:2025-08-20
Method:X-RAY DIFFRACTION (1.03 Å)
Cite:Ligand screen against SARS-CoV-2 NSP3 macrodomain
To be published
7HC7
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BU of 7hc7 by Molmil
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodmain in complex with AVI-4051
Descriptor: CHLORIDE ION, N-cyclopropyl-N'-{4-[(2-oxopyrrolidin-1-yl)amino]-9H-pyrimido[4,5-b]indol-8-yl}urea, Non-structural protein 3
Authors:Correy, G.J, Fraser, J.S.
Deposit date:2024-08-01
Release date:2025-08-20
Method:X-RAY DIFFRACTION (0.99 Å)
Cite:Ligand screen against SARS-CoV-2 NSP3 macrodomain
To be published
7HC8
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PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodmain in complex with AVI-3763
Descriptor: (5S)-1-[(7-fluoro-9H-pyrimido[4,5-b]indol-4-yl)amino]-5-phenylpyrrolidin-2-one, Non-structural protein 3
Authors:Correy, G.J, Fraser, J.S.
Deposit date:2024-08-01
Release date:2025-08-20
Method:X-RAY DIFFRACTION (1.01 Å)
Cite:Ligand screen against SARS-CoV-2 NSP3 macrodomain
To be published
7HC9
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BU of 7hc9 by Molmil
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodmain in complex with AVI-3762
Descriptor: (5R)-1-[(7-fluoro-9H-pyrimido[4,5-b]indol-4-yl)amino]-5-phenylpyrrolidin-2-one, Non-structural protein 3
Authors:Correy, G.J, Fraser, J.S.
Deposit date:2024-08-01
Release date:2025-08-20
Method:X-RAY DIFFRACTION (1.05 Å)
Cite:Ligand screen against SARS-CoV-2 NSP3 macrodomain
To be published
7HCA
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PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodmain in complex with AVI-4636
Descriptor: 1-[(7-fluoro-9H-pyrimido[4,5-b]indol-4-yl)amino]-5,5-dimethylpyrrolidin-2-one, Non-structural protein 3
Authors:Correy, G.J, Fraser, J.S.
Deposit date:2024-08-01
Release date:2025-08-20
Method:X-RAY DIFFRACTION (1.03 Å)
Cite:Ligand screen against SARS-CoV-2 NSP3 macrodomain
To be published
7HHS
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PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with AVI-0000411
Descriptor: 1-({6-[(1H-indazol-5-yl)amino]pyrimidin-4-yl}amino)pyrrolidin-2-one, Non-structural protein 3
Authors:Correy, G.J, Fraser, J.S.
Deposit date:2024-09-16
Release date:2025-08-20
Method:X-RAY DIFFRACTION (0.98 Å)
Cite:Expanding automated multiconformer ligand modeling to macrocycles and fragments.
Elife, 14, 2025
7HHT
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PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with AVI-0000372
Descriptor: 1-{[(5P)-5-(3-fluoropyridin-2-yl)pyrimidin-4-yl]amino}pyrrolidin-2-one, BROMIDE ION, DIMETHYL SULFOXIDE, ...
Authors:Correy, G.J, Fraser, J.S.
Deposit date:2024-09-16
Release date:2025-08-20
Method:X-RAY DIFFRACTION (1.02 Å)
Cite:Expanding automated multiconformer ligand modeling to macrocycles and fragments.
Elife, 14, 2025
7HHU
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PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with AVI-0000528
Descriptor: (3R)-3-(2,4-difluorophenyl)-3-[(6,7-dihydro-5H-cyclopenta[c]pyridine-4-carbonyl)amino]propanoic acid, Non-structural protein 3
Authors:Correy, G.J, Fraser, J.S.
Deposit date:2024-09-16
Release date:2025-08-20
Method:X-RAY DIFFRACTION (1.03 Å)
Cite:Expanding automated multiconformer ligand modeling to macrocycles and fragments.
Elife, 14, 2025
7HHV
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PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with AVI-0000527
Descriptor: (3R)-3-(2,4-difluorophenyl)-3-{[(4R)-[1,2,4]triazolo[1,5-a]pyridine-5-carbonyl]amino}propanoic acid, DIMETHYL SULFOXIDE, Non-structural protein 3
Authors:Correy, G.J, Fraser, J.S.
Deposit date:2024-09-16
Release date:2025-08-20
Method:X-RAY DIFFRACTION (1.02 Å)
Cite:Expanding automated multiconformer ligand modeling to macrocycles and fragments.
Elife, 14, 2025
7HHW
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PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with AVI-0000724
Descriptor: (5S)-1-[(5-iodo-7H-pyrrolo[2,3-d]pyrimidin-4-yl)amino]-5-(thiophen-2-yl)pyrrolidin-2-one, Non-structural protein 3
Authors:Correy, G.J, Fraser, J.S.
Deposit date:2024-09-16
Release date:2025-08-20
Method:X-RAY DIFFRACTION (1.03 Å)
Cite:Expanding automated multiconformer ligand modeling to macrocycles and fragments.
Elife, 14, 2025
7HHX
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PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with AVI-0000729
Descriptor: 4-{[(5S)-2-oxo-5-(thiophen-2-yl)pyrrolidin-1-yl]amino}-7H-pyrrolo[2,3-d]pyrimidine-5-carboxamide, DIMETHYL SULFOXIDE, Non-structural protein 3
Authors:Correy, G.J, Fraser, J.S.
Deposit date:2024-09-16
Release date:2025-08-20
Method:X-RAY DIFFRACTION (1.01 Å)
Cite:Expanding automated multiconformer ligand modeling to macrocycles and fragments.
Elife, 14, 2025
7HHY
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PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with AVI-0000700
Descriptor: (5S)-1-[(5-ethyl-7H-pyrrolo[2,3-d]pyrimidin-4-yl)amino]-5-phenylpyrrolidin-2-one, Non-structural protein 3
Authors:Correy, G.J, Fraser, J.S.
Deposit date:2024-09-16
Release date:2025-08-20
Method:X-RAY DIFFRACTION (1.01 Å)
Cite:Expanding automated multiconformer ligand modeling to macrocycles and fragments.
Elife, 14, 2025
7HHZ
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BU of 7hhz by Molmil
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with AVI-0000703
Descriptor: (5S)-1-[(5-bromo-7H-pyrrolo[2,3-d]pyrimidin-4-yl)amino]-5-phenylpyrrolidin-2-one, Non-structural protein 3
Authors:Correy, G.J, Fraser, J.S.
Deposit date:2024-09-16
Release date:2025-08-20
Method:X-RAY DIFFRACTION (1.01 Å)
Cite:Expanding automated multiconformer ligand modeling to macrocycles and fragments.
Elife, 14, 2025
7HI0
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BU of 7hi0 by Molmil
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with AVI-0000708
Descriptor: (5S)-1-[(5-ethyl-7H-pyrrolo[2,3-d]pyrimidin-4-yl)amino]-5-methylpyrrolidin-2-one, CHLORIDE ION, Non-structural protein 3
Authors:Correy, G.J, Fraser, J.S.
Deposit date:2024-09-16
Release date:2025-08-20
Method:X-RAY DIFFRACTION (1 Å)
Cite:Expanding automated multiconformer ligand modeling to macrocycles and fragments.
Elife, 14, 2025

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