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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)
9JEB
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BU of 9jeb by Molmil
Crystal structure of SARS-CoV-2 RBD in complex with a neutralizing antibody scFv N1
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, N1 scFv, Spike protein S1
Authors:Guo, K, Zhang, N, Guo, Y.
Deposit date:2024-09-03
Release date:2025-09-03
Method:X-RAY DIFFRACTION (2.3 Å)
Cite:Mining antibody functionality via AI-guided structural landscape profiling
To Be Published
8ZRD
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BU of 8zrd by Molmil
The complex structure of SARS-CoV-2 RBD and llama single-domain antibody S4
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Spike protein S1, llama single-domain antibody S4
Authors:Chen, L.
Deposit date:2024-06-04
Release date:2025-09-10
Method:X-RAY DIFFRACTION (2.715 Å)
Cite:Identification of a potent SARS-CoV-2 neutralizing nanobody targeting the receptor-binding domain of the spike protein.
Int.J.Biol.Macromol., 281, 2024
9DDF
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SARS-CoV-2 main protease with inhibitor
Descriptor: 3C-like proteinase nsp5, N-{(3S,4S)-1-[(4S)-imidazo[1,5-a]pyridine-8-carbonyl]-4-phenylpiperidin-3-yl}-1H-pyrrole-2-carboxamide
Authors:Bell, J.A.
Deposit date:2024-08-28
Release date:2025-09-10
Last modified:2025-10-22
Method:X-RAY DIFFRACTION (1.549 Å)
Cite:Discovery of Highly Potent Noncovalent Inhibitors of SARS-CoV-2 Main Protease through Computer-Aided Drug Design.
J.Med.Chem., 2025
9DDG
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SARS-CoV-2 main protease with inhibitor
Descriptor: 3C-like proteinase nsp5, [(4R)-imidazo[1,5-a]pyridin-8-yl]{4-[(1M)-3'-nitro[1,1'-biphenyl]-2-yl]piperazin-1-yl}methanone
Authors:Bell, J.A, Lane, W.
Deposit date:2024-08-28
Release date:2025-09-10
Last modified:2025-10-22
Method:X-RAY DIFFRACTION (1.4 Å)
Cite:Discovery of Highly Potent Noncovalent Inhibitors of SARS-CoV-2 Main Protease through Computer-Aided Drug Design.
J.Med.Chem., 2025
7IIW
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PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z5398393122
Descriptor: (3R)-3-(4-bromophenyl)-3-[(7H-pyrrolo[2,3-d]pyrimidine-4-carbonyl)amino]propanoic acid, (3S)-3-(4-bromophenyl)-3-[(7H-pyrrolo[2,3-d]pyrimidine-4-carbonyl)amino]propanoic acid, Non-structural protein 3
Authors:Correy, G.J, Fraser, J.S.
Deposit date:2025-07-22
Release date:2025-09-17
Method:X-RAY DIFFRACTION (0.97 Å)
Cite:Ligand screen against SARS-CoV-2 NSP3 macrodomain
To be published
7IIX
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PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z7691912366
Descriptor: (3R)-3-(4-bromophenyl)-3-[(2-methyl-7H-pyrrolo[2,3-d]pyrimidine-4-carbonyl)amino]propanoic acid, (3S)-3-(4-bromophenyl)-3-[(2-methyl-7H-pyrrolo[2,3-d]pyrimidine-4-carbonyl)amino]propanoic acid, Non-structural protein 3
Authors:Correy, G.J, Fraser, J.S.
Deposit date:2025-07-22
Release date:2025-09-17
Method:X-RAY DIFFRACTION (1.02 Å)
Cite:Ligand screen against SARS-CoV-2 NSP3 macrodomain
To be published
7IIY
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PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z8598075283
Descriptor: (3R)-3-(4-bromophenyl)-3-[(5-methyl-7H-pyrrolo[2,3-d]pyrimidine-4-carbonyl)amino]propanoic acid, (3S)-3-(4-bromophenyl)-3-[(5-methyl-7H-pyrrolo[2,3-d]pyrimidine-4-carbonyl)amino]propanoic acid, Non-structural protein 3
Authors:Correy, G.J, Fraser, J.S.
Deposit date:2025-07-22
Release date:2025-09-17
Method:X-RAY DIFFRACTION (1.01 Å)
Cite:Ligand screen against SARS-CoV-2 NSP3 macrodomain
To be published
7IIZ
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BU of 7iiz by Molmil
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z8598075280
Descriptor: (3R)-3-(4-bromophenyl)-3-[(9H-purine-6-carbonyl)amino]propanoic acid, (3S)-3-(4-bromophenyl)-3-[(9H-purine-6-carbonyl)amino]propanoic acid, Non-structural protein 3
Authors:Correy, G.J, Fraser, J.S.
Deposit date:2025-07-22
Release date:2025-09-17
Method:X-RAY DIFFRACTION (0.99 Å)
Cite:Ligand screen against SARS-CoV-2 NSP3 macrodomain
To be published
7IJ0
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PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z8598075284
Descriptor: (3R)-3-(4-bromo-2-methylphenyl)-3-[(7H-pyrrolo[2,3-d]pyrimidine-4-carbonyl)amino]propanoic acid, Non-structural protein 3
Authors:Correy, G.J, Fraser, J.S.
Deposit date:2025-07-22
Release date:2025-09-17
Method:X-RAY DIFFRACTION (0.98 Å)
Cite:Ligand screen against SARS-CoV-2 NSP3 macrodomain
To be published
7IJ1
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BU of 7ij1 by Molmil
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z8598075302
Descriptor: (3R)-3-(4-hydroxyphenyl)-3-[(7H-pyrrolo[2,3-d]pyrimidine-4-carbonyl)amino]propanoic acid, (3S)-3-(4-hydroxyphenyl)-3-[(7H-pyrrolo[2,3-d]pyrimidine-4-carbonyl)amino]propanoic acid, Non-structural protein 3
Authors:Correy, G.J, Fraser, J.S.
Deposit date:2025-07-22
Release date:2025-09-17
Method:X-RAY DIFFRACTION (1.01 Å)
Cite:Ligand screen against SARS-CoV-2 NSP3 macrodomain
To be published
7IJ2
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BU of 7ij2 by Molmil
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z8727396638
Descriptor: (2R,3S)-2-methyl-3-phenyl-3-[(7H-pyrrolo[2,3-d]pyrimidine-4-carbonyl)amino]propanoic acid, (2S,3R)-2-methyl-3-phenyl-3-[(7H-pyrrolo[2,3-d]pyrimidine-4-carbonyl)amino]propanoic acid, DIMETHYL SULFOXIDE, ...
Authors:Correy, G.J, Fraser, J.S.
Deposit date:2025-07-22
Release date:2025-09-17
Method:X-RAY DIFFRACTION (0.97 Å)
Cite:Ligand screen against SARS-CoV-2 NSP3 macrodomain
To be published
7IJ3
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BU of 7ij3 by Molmil
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z8727396582
Descriptor: (3R)-3-(3-methylphenyl)-3-[(7H-pyrrolo[2,3-d]pyrimidine-4-carbonyl)amino]propanoic acid, Non-structural protein 3
Authors:Correy, G.J, Fraser, J.S.
Deposit date:2025-07-22
Release date:2025-09-17
Method:X-RAY DIFFRACTION (0.97 Å)
Cite:Ligand screen against SARS-CoV-2 NSP3 macrodomain
To be published
7IJ4
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BU of 7ij4 by Molmil
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z7692046343
Descriptor: (3S)-3-(4-chlorophenyl)-3-[(7H-pyrrolo[2,3-d]pyrimidine-4-carbonyl)amino]propanoic acid, DIMETHYL SULFOXIDE, Non-structural protein 3
Authors:Correy, G.J, Fraser, J.S.
Deposit date:2025-07-22
Release date:2025-09-17
Method:X-RAY DIFFRACTION (1.01 Å)
Cite:Ligand screen against SARS-CoV-2 NSP3 macrodomain
To be published
7IJ5
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BU of 7ij5 by Molmil
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z7692056627
Descriptor: (3S)-3-(pyridin-2-yl)-3-[(7H-pyrrolo[2,3-d]pyrimidine-4-carbonyl)amino]propanoic acid, Non-structural protein 3
Authors:Correy, G.J, Fraser, J.S.
Deposit date:2025-07-22
Release date:2025-09-17
Method:X-RAY DIFFRACTION (0.99 Å)
Cite:Ligand screen against SARS-CoV-2 NSP3 macrodomain
To be published
7IJ6
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BU of 7ij6 by Molmil
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z7140729870
Descriptor: (3S)-3-(4-methylphenyl)-3-[(7H-pyrrolo[2,3-d]pyrimidine-4-carbonyl)amino]propanoic acid, Non-structural protein 3
Authors:Correy, G.J, Fraser, J.S.
Deposit date:2025-07-22
Release date:2025-09-17
Method:X-RAY DIFFRACTION (1.02 Å)
Cite:Ligand screen against SARS-CoV-2 NSP3 macrodomain
To be published
7IJ7
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BU of 7ij7 by Molmil
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z7691912473
Descriptor: (3R)-3-(pyridin-4-yl)-3-[(7H-pyrrolo[2,3-d]pyrimidine-4-carbonyl)amino]propanoic acid, DIMETHYL SULFOXIDE, Non-structural protein 3
Authors:Correy, G.J, Fraser, J.S.
Deposit date:2025-07-22
Release date:2025-09-17
Method:X-RAY DIFFRACTION (1.01 Å)
Cite:Ligand screen against SARS-CoV-2 NSP3 macrodomain
To be published
7IJ8
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BU of 7ij8 by Molmil
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z8928826043
Descriptor: (3R)-3-phenyl-3-[(7H-pyrrolo[2,3-d]pyrimidine-4-carbonyl)amino]butanoic acid, Non-structural protein 3
Authors:Correy, G.J, Fraser, J.S.
Deposit date:2025-07-22
Release date:2025-09-17
Method:X-RAY DIFFRACTION (1 Å)
Cite:Ligand screen against SARS-CoV-2 NSP3 macrodomain
To be published
7IJ9
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BU of 7ij9 by Molmil
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z8928826033
Descriptor: (3R)-3-(3-fluorophenyl)-3-[(7H-pyrrolo[2,3-d]pyrimidine-4-carbonyl)amino]propanoic acid, DIMETHYL SULFOXIDE, Non-structural protein 3
Authors:Correy, G.J, Fraser, J.S.
Deposit date:2025-07-22
Release date:2025-09-17
Method:X-RAY DIFFRACTION (1 Å)
Cite:Ligand screen against SARS-CoV-2 NSP3 macrodomain
To be published
7IJA
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BU of 7ija by Molmil
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z8929429249
Descriptor: (3S)-3-(2-methylphenyl)-3-[(7H-pyrrolo[2,3-d]pyrimidine-4-carbonyl)amino]propanoic acid, Non-structural protein 3
Authors:Correy, G.J, Fraser, J.S.
Deposit date:2025-07-22
Release date:2025-09-17
Method:X-RAY DIFFRACTION (1 Å)
Cite:Ligand screen against SARS-CoV-2 NSP3 macrodomain
To be published
7IJB
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BU of 7ijb by Molmil
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z8768700676
Descriptor: (3S)-3-(2-chlorophenyl)-3-[(7H-pyrrolo[2,3-d]pyrimidine-4-carbonyl)amino]propanoic acid, DIMETHYL SULFOXIDE, Non-structural protein 3
Authors:Correy, G.J, Fraser, J.S.
Deposit date:2025-07-22
Release date:2025-09-17
Method:X-RAY DIFFRACTION (1 Å)
Cite:Ligand screen against SARS-CoV-2 NSP3 macrodomain
To be published
7IJC
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BU of 7ijc by Molmil
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z8929428675
Descriptor: (3S)-3-(pyridin-3-yl)-3-[(7H-pyrrolo[2,3-d]pyrimidine-4-carbonyl)amino]propanoic acid, DIMETHYL SULFOXIDE, Non-structural protein 3
Authors:Correy, G.J, Fraser, J.S.
Deposit date:2025-07-22
Release date:2025-09-17
Method:X-RAY DIFFRACTION (1 Å)
Cite:Ligand screen against SARS-CoV-2 NSP3 macrodomain
To be published
7IJD
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BU of 7ijd by Molmil
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z7692056404
Descriptor: (3S)-3-(4-fluorophenyl)-3-[(7H-pyrrolo[2,3-d]pyrimidine-4-carbonyl)amino]propanoic acid, DIMETHYL SULFOXIDE, Non-structural protein 3
Authors:Correy, G.J, Fraser, J.S.
Deposit date:2025-07-22
Release date:2025-09-17
Method:X-RAY DIFFRACTION (1 Å)
Cite:Ligand screen against SARS-CoV-2 NSP3 macrodomain
To be published
7IJE
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BU of 7ije by Molmil
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z8990523169
Descriptor: (3S)-3-phenyl-3-[(9H-purine-6-carbonyl)amino]propanoic acid, DIMETHYL SULFOXIDE, Non-structural protein 3
Authors:Correy, G.J, Fraser, J.S.
Deposit date:2025-07-22
Release date:2025-09-17
Method:X-RAY DIFFRACTION (1 Å)
Cite:Ligand screen against SARS-CoV-2 NSP3 macrodomain
To be published
7IJF
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BU of 7ijf by Molmil
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z8727401304
Descriptor: (3S)-3-(3-chlorophenyl)-3-[(7H-pyrrolo[2,3-d]pyrimidine-4-carbonyl)amino]propanoic acid, DIMETHYL SULFOXIDE, Non-structural protein 3
Authors:Correy, G.J, Fraser, J.S.
Deposit date:2025-07-22
Release date:2025-09-17
Method:X-RAY DIFFRACTION (1 Å)
Cite:Ligand screen against SARS-CoV-2 NSP3 macrodomain
To be published
7IJG
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BU of 7ijg by Molmil
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z8990527720
Descriptor: (3R)-3-(2-fluorophenyl)-3-[(7H-pyrrolo[2,3-d]pyrimidine-4-carbonyl)amino]propanoic acid, DIMETHYL SULFOXIDE, Non-structural protein 3
Authors:Correy, G.J, Fraser, J.S.
Deposit date:2025-07-22
Release date:2025-09-17
Method:X-RAY DIFFRACTION (1.02 Å)
Cite:Ligand screen against SARS-CoV-2 NSP3 macrodomain
To be published

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