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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 (4459)Repr. entries (1984)Latest entries (16)
5RV1
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BU of 5rv1 by Molmil
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINC000000251609
Descriptor: Non-structural protein 3, trifluoroacetic acid
Authors:Correy, G.J, Young, I.D, Thompson, M.C, Fraser, J.S.
Deposit date:2020-09-28
Release date:2020-12-16
Last modified:2024-05-22
Method:X-RAY DIFFRACTION (1 Å)
Cite:Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.
Sci Adv, 7, 2021
5RV2
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BU of 5rv2 by Molmil
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINC000000311783
Descriptor: N-benzylpyrazine-2-carboxamide, Non-structural protein 3
Authors:Correy, G.J, Young, I.D, Thompson, M.C, Fraser, J.S.
Deposit date:2020-09-28
Release date:2020-12-16
Last modified:2024-05-22
Method:X-RAY DIFFRACTION (1.01 Å)
Cite:Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.
Sci Adv, 7, 2021
5RV3
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BU of 5rv3 by Molmil
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINC000000057162
Descriptor: (5-methoxy-1H-indol-3-yl)acetic acid, Non-structural protein 3
Authors:Correy, G.J, Young, I.D, Thompson, M.C, Fraser, J.S.
Deposit date:2020-09-28
Release date:2020-12-16
Last modified:2024-05-22
Method:X-RAY DIFFRACTION (1.02 Å)
Cite:Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.
Sci Adv, 7, 2021
5RV4
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BU of 5rv4 by Molmil
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINC000000039224
Descriptor: Non-structural protein 3, quinolin-3-amine
Authors:Correy, G.J, Young, I.D, Thompson, M.C, Fraser, J.S.
Deposit date:2020-09-28
Release date:2020-12-16
Last modified:2024-05-22
Method:X-RAY DIFFRACTION (1 Å)
Cite:Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.
Sci Adv, 7, 2021
5RV5
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BU of 5rv5 by Molmil
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINC000008578948
Descriptor: BENZOFURO[3,2-D]PYRIMIDIN-4(3H)-ONE, Non-structural protein 3
Authors:Correy, G.J, Young, I.D, Thompson, M.C, Fraser, J.S.
Deposit date:2020-09-28
Release date:2020-12-16
Last modified:2024-05-22
Method:X-RAY DIFFRACTION (1 Å)
Cite:Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.
Sci Adv, 7, 2021
5RV6
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BU of 5rv6 by Molmil
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINC000000158540
Descriptor: 1,3-benzodioxole-5-carboxylic acid, Non-structural protein 3
Authors:Correy, G.J, Young, I.D, Thompson, M.C, Fraser, J.S.
Deposit date:2020-09-28
Release date:2020-12-16
Last modified:2024-05-22
Method:X-RAY DIFFRACTION (1 Å)
Cite:Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.
Sci Adv, 7, 2021
5RV7
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BU of 5rv7 by Molmil
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINC000003954002
Descriptor: 1H-indazol-3-amine, Non-structural protein 3
Authors:Correy, G.J, Young, I.D, Thompson, M.C, Fraser, J.S.
Deposit date:2020-09-28
Release date:2020-12-16
Last modified:2024-05-22
Method:X-RAY DIFFRACTION (1 Å)
Cite:Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.
Sci Adv, 7, 2021
5RV8
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BU of 5rv8 by Molmil
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINC000000039575
Descriptor: 6-methylpyridine-3-carboxamide, Non-structural protein 3
Authors:Correy, G.J, Young, I.D, Thompson, M.C, Fraser, J.S.
Deposit date:2020-09-28
Release date:2020-12-16
Last modified:2024-05-22
Method:X-RAY DIFFRACTION (1 Å)
Cite:Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.
Sci Adv, 7, 2021
5RV9
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BU of 5rv9 by Molmil
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINC000000388150
Descriptor: 4-tert-butylbenzene-1,2-diol, Non-structural protein 3
Authors:Correy, G.J, Young, I.D, Thompson, M.C, Fraser, J.S.
Deposit date:2020-09-28
Release date:2020-12-16
Last modified:2022-05-25
Method:X-RAY DIFFRACTION (1 Å)
Cite:Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.
Sci Adv, 7, 2021
5RVA
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BU of 5rva by Molmil
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINC000016343276
Descriptor: 3-HYDROXY-2-METHYLQUINOLIN-4(1H)-ONE, Non-structural protein 3
Authors:Correy, G.J, Young, I.D, Thompson, M.C, Fraser, J.S.
Deposit date:2020-09-28
Release date:2020-12-16
Last modified:2024-05-22
Method:X-RAY DIFFRACTION (1 Å)
Cite:Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.
Sci Adv, 7, 2021
5RVB
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BU of 5rvb by Molmil
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINC000014419577
Descriptor: 2-aminopteridine-4,7(3H,8H)-dione, Non-structural protein 3
Authors:Correy, G.J, Young, I.D, Thompson, M.C, Fraser, J.S.
Deposit date:2020-09-28
Release date:2020-12-16
Last modified:2024-05-22
Method:X-RAY DIFFRACTION (1 Å)
Cite:Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.
Sci Adv, 7, 2021
5RVC
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BU of 5rvc by Molmil
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINC000933940912
Descriptor: (1R,5R)-N-methyl-N-(1H-pyrazol-4-yl)bicyclo[3.1.0]hexane-1-carboxamide, Non-structural protein 3
Authors:Correy, G.J, Young, I.D, Thompson, M.C, Fraser, J.S.
Deposit date:2020-09-28
Release date:2020-12-16
Last modified:2024-05-22
Method:X-RAY DIFFRACTION (1 Å)
Cite:Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.
Sci Adv, 7, 2021
5RVD
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BU of 5rvd by Molmil
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINC000263980802
Descriptor: 4-[(2R)-2-cyclobutylpyrrolidin-1-yl]-7H-pyrrolo[2,3-d]pyrimidine, Non-structural protein 3
Authors:Correy, G.J, Young, I.D, Thompson, M.C, Fraser, J.S.
Deposit date:2020-09-28
Release date:2020-12-16
Last modified:2024-05-22
Method:X-RAY DIFFRACTION (1 Å)
Cite:Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.
Sci Adv, 7, 2021
5RVE
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BU of 5rve by Molmil
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINC000736709772
Descriptor: Non-structural protein 3, {[(2S)-1-oxo-1-(2-oxoimidazolidin-1-yl)propan-2-yl]sulfanyl}acetic acid
Authors:Correy, G.J, Young, I.D, Thompson, M.C, Fraser, J.S.
Deposit date:2020-09-28
Release date:2020-12-16
Last modified:2024-05-22
Method:X-RAY DIFFRACTION (1 Å)
Cite:Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.
Sci Adv, 7, 2021
5RVF
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BU of 5rvf by Molmil
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINC000082473428_N3
Descriptor: 3-{[(2R)-oxolan-2-yl]methyl}-3H-purin-6-amine, Non-structural protein 3
Authors:Correy, G.J, Young, I.D, Thompson, M.C, Fraser, J.S.
Deposit date:2020-09-28
Release date:2020-12-16
Last modified:2024-05-22
Method:X-RAY DIFFRACTION (1 Å)
Cite:Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.
Sci Adv, 7, 2021
5RVG
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BU of 5rvg by Molmil
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINC000400552187_N3
Descriptor: 3-{3-[(3S)-oxolan-3-yl]propyl}-3H-purin-6-amine, Non-structural protein 3
Authors:Correy, G.J, Young, I.D, Thompson, M.C, Fraser, J.S.
Deposit date:2020-09-28
Release date:2020-12-16
Last modified:2024-05-22
Method:X-RAY DIFFRACTION (1 Å)
Cite:Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.
Sci Adv, 7, 2021
5RVH
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BU of 5rvh by Molmil
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINC000000265642
Descriptor: Non-structural protein 3, quinoline-3-carboxylic acid
Authors:Correy, G.J, Young, I.D, Thompson, M.C, Fraser, J.S.
Deposit date:2020-09-28
Release date:2020-12-16
Last modified:2024-05-22
Method:X-RAY DIFFRACTION (0.98 Å)
Cite:Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.
Sci Adv, 7, 2021
5RVI
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BU of 5rvi by Molmil
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINC000084843283
Descriptor: CHLORZOXAZONE, Non-structural protein 3
Authors:Correy, G.J, Young, I.D, Thompson, M.C, Fraser, J.S.
Deposit date:2020-09-28
Release date:2020-12-16
Last modified:2024-05-22
Method:X-RAY DIFFRACTION (0.94 Å)
Cite:Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.
Sci Adv, 7, 2021
5RVJ
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BU of 5rvj by Molmil
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINC000001612349
Descriptor: 6-amino-2H-chromen-2-one, Non-structural protein 3
Authors:Correy, G.C, Young, I.D, Thompson, M.C, Fraser, J.S.
Deposit date:2020-10-02
Release date:2020-12-16
Last modified:2024-05-22
Method:X-RAY DIFFRACTION (1.2 Å)
Cite:Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.
Sci Adv, 7, 2021
5RVK
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BU of 5rvk by Molmil
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINC000002977810
Descriptor: 7-bromo-5-methyl-1H-indole-2,3-dione, Non-structural protein 3
Authors:Correy, G.C, Young, I.D, Thompson, M.C, Fraser, J.S.
Deposit date:2020-10-02
Release date:2020-12-16
Last modified:2024-05-22
Method:X-RAY DIFFRACTION (1.46 Å)
Cite:Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.
Sci Adv, 7, 2021
5RVL
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BU of 5rvl by Molmil
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINC000000149580
Descriptor: 4-METHYLPYRIDIN-2-AMINE, Non-structural protein 3
Authors:Correy, G.C, Young, I.D, Thompson, M.C, Fraser, J.S.
Deposit date:2020-10-02
Release date:2020-12-16
Last modified:2024-05-22
Method:X-RAY DIFFRACTION (1.36 Å)
Cite:Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.
Sci Adv, 7, 2021
5RVM
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BU of 5rvm by Molmil
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINC000000157088
Descriptor: 4-HYDROXYBENZAMIDE, Non-structural protein 3
Authors:Correy, G.C, Young, I.D, Thompson, M.C, Fraser, J.S.
Deposit date:2020-10-02
Release date:2020-12-16
Last modified:2024-05-22
Method:X-RAY DIFFRACTION (1.03 Å)
Cite:Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.
Sci Adv, 7, 2021
5RVN
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BU of 5rvn by Molmil
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINC000000332748
Descriptor: 4-METHOXYBENZOIC ACID, Non-structural protein 3
Authors:Correy, G.C, Young, I.D, Thompson, M.C, Fraser, J.S.
Deposit date:2020-10-02
Release date:2020-12-16
Last modified:2024-05-22
Method:X-RAY DIFFRACTION (1.26 Å)
Cite:Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.
Sci Adv, 7, 2021
5RVO
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BU of 5rvo by Molmil
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINC000013514509
Descriptor: 2-AMINOQUINAZOLIN-4(3H)-ONE, Non-structural protein 3
Authors:Correy, G.C, Young, I.D, Thompson, M.C, Fraser, J.S.
Deposit date:2020-10-02
Release date:2020-12-16
Last modified:2024-05-22
Method:X-RAY DIFFRACTION (1.52 Å)
Cite:Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.
Sci Adv, 7, 2021
5RVP
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BU of 5rvp by Molmil
PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINC000000154817
Descriptor: ISOQUINOLIN-1-AMINE, Non-structural protein 3
Authors:Correy, G.C, Young, I.D, Thompson, M.C, Fraser, J.S.
Deposit date:2020-10-02
Release date:2020-12-16
Last modified:2024-05-22
Method:X-RAY DIFFRACTION (1.04 Å)
Cite:Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.
Sci Adv, 7, 2021

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