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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
8I9H
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BU of 8i9h by Molmil
S-RBD (Omicron XBB.1) in complex with PD of ACE2
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Processed angiotensin-converting enzyme 2, ...
Authors:Li, Y.N, Shen, Y.P, Zhang, Y.Y, Yan, R.H.
Deposit date:2023-02-06
Release date:2024-02-07
Method:ELECTRON MICROSCOPY (3.6 Å)
Cite:Structural basis for the enhanced infectivity and immune evasion of Omicron subvariants
To Be Published
8IQJ
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BU of 8iqj by Molmil
Crystal structure of SARS-CoV2 N-NTD
Descriptor: Nucleoprotein
Authors:Hong, J.Y, Hou, M.H.
Deposit date:2023-03-16
Release date:2024-02-07
Last modified:2024-03-06
Method:X-RAY DIFFRACTION (2.3 Å)
Cite:Targeting protein-protein interaction interfaces with antiviral N protein inhibitor in SARS-CoV-2.
Biophys.J., 123, 2024
8IV3
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BU of 8iv3 by Molmil
Crystal structure of SARS-CoV2 N-NTD complexed with 5-Benzyloxygramine
Descriptor: N,N-dimethyl-1-(5-phenylmethoxy-1H-indol-3-yl)methanamine, Nucleoprotein
Authors:Hong, J.Y, Hou, M.H.
Deposit date:2023-03-25
Release date:2024-02-07
Last modified:2024-03-06
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:Targeting protein-protein interaction interfaces with antiviral N protein inhibitor in SARS-CoV-2.
Biophys.J., 123, 2024
8J6X
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BU of 8j6x by Molmil
Crystal structure of SARS-CoV2 N-NTD complexed with 5-Benzyloxygramine derivative (P3-8)
Descriptor: Nucleoprotein, ~{N}-methyl-~{N}-[(5-phenylmethoxy-1~{H}-indol-3-yl)methyl]propan-1-amine
Authors:Hong, J.Y, Hou, M.H.
Deposit date:2023-04-26
Release date:2024-02-07
Last modified:2024-03-06
Method:X-RAY DIFFRACTION (2.7 Å)
Cite:Targeting protein-protein interaction interfaces with antiviral N protein inhibitor in SARS-CoV-2.
Biophys.J., 123, 2024
8R11
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BU of 8r11 by Molmil
Structure of compound 7 bound to SARS-CoV-2 main protease
Descriptor: 1,2-ETHANEDIOL, 1-[(2~{S})-2-(3-chlorophenyl)pyrrolidin-1-yl]-2-(5-methylpyridin-3-yl)ethanone, 3C-like proteinase, ...
Authors:Mac Sweeney, A, Hazemann, J.
Deposit date:2023-11-01
Release date:2024-02-07
Last modified:2024-07-03
Method:X-RAY DIFFRACTION (1.31 Å)
Cite:Identification of SARS-CoV-2 Mpro inhibitors through deep reinforcement learning for de novo drug design and computational chemistry approaches.
Rsc Med Chem, 15, 2024
8R12
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BU of 8r12 by Molmil
Structure of compound 8 bound to SARS-CoV-2 main protease
Descriptor: 2-[[4-(5-chloranylpyridin-3-yl)carbonyl-1,4-diazepan-1-yl]methyl]benzenecarbonitrile, 3C-like proteinase, CHLORIDE ION, ...
Authors:Mac Sweeney, A, Hazemann, J.
Deposit date:2023-11-01
Release date:2024-02-07
Last modified:2024-07-03
Method:X-RAY DIFFRACTION (1.587 Å)
Cite:Identification of SARS-CoV-2 Mpro inhibitors through deep reinforcement learning for de novo drug design and computational chemistry approaches.
Rsc Med Chem, 15, 2024
8R14
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BU of 8r14 by Molmil
Structure of compound 11 bound to SARS-CoV-2 main protease
Descriptor: (5-chloranylpyridin-3-yl)-[4-[(2-chlorophenyl)methyl]-1,4-diazepan-1-yl]methanone, 3C-like proteinase, BROMIDE ION, ...
Authors:Mac Sweeney, A, Hazemann, J.
Deposit date:2023-11-01
Release date:2024-02-07
Last modified:2024-07-03
Method:X-RAY DIFFRACTION (1.336 Å)
Cite:Identification of SARS-CoV-2 Mpro inhibitors through deep reinforcement learning for de novo drug design and computational chemistry approaches.
Rsc Med Chem, 15, 2024
8R16
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BU of 8r16 by Molmil
Structure of compound 12 bound to SARS-CoV-2 main protease
Descriptor: 1,2-ETHANEDIOL, 1-[6,7-bis(chloranyl)-3,4-dihydro-1H-isoquinolin-2-yl]-2-(5-methylpyridin-3-yl)ethanone, 3C-like proteinase, ...
Authors:Mac Sweeney, A, Hazemann, J.
Deposit date:2023-11-01
Release date:2024-02-07
Last modified:2024-07-03
Method:X-RAY DIFFRACTION (1.3 Å)
Cite:Identification of SARS-CoV-2 Mpro inhibitors through deep reinforcement learning for de novo drug design and computational chemistry approaches.
Rsc Med Chem, 15, 2024
8TYL
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BU of 8tyl by Molmil
Structural and biochemical rationale for Beta variant protein booster vaccine broad cross-neutralization of SARS-CoV-2
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein
Authors:Bruch, E.M, Rak, A.
Deposit date:2023-08-25
Release date:2024-02-07
Method:ELECTRON MICROSCOPY (2.85 Å)
Cite:Structural and biochemical rationale for Beta variant protein booster vaccine broad cross-neutralization of SARS-CoV-2.
Sci Rep, 14, 2024
8TYO
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BU of 8tyo by Molmil
Structural and biochemical rationale for Beta variant protein booster vaccine broad cross-neutralization of SARS-CoV-2
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein
Authors:Bruch, E.M, Rak, A.
Deposit date:2023-08-25
Release date:2024-02-07
Method:ELECTRON MICROSCOPY (2.75 Å)
Cite:Structural and biochemical rationale for Beta variant protein booster vaccine broad cross-neutralization of SARS-CoV-2.
Sci Rep, 14, 2024
8UAB
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BU of 8uab by Molmil
SARS-CoV-2 main protease (Mpro) complex with AC1115
Descriptor: 3C-like proteinase nsp5, N-[(2S)-1-({(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-1H-indole-2-carboxamide
Authors:DuPrez, K.T, Chao, A, Han, F.Q.
Deposit date:2023-09-20
Release date:2024-02-07
Method:X-RAY DIFFRACTION (1.781 Å)
Cite:SARS-CoV-2 main protease (Mpro) complex with AC1115
To Be Published
7GRE
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BU of 7gre by Molmil
Crystal structure of SARS-CoV-2 main protease in complex with cpd-1
Descriptor: 3C-like proteinase nsp5, 4-[3-(trifluoromethyl)-1H-pyrazol-5-yl]pyridine, CHLORIDE ION, ...
Authors:Huang, C.-Y, Metz, A, Sharpe, M, Sweeney, A.M.
Deposit date:2023-11-14
Release date:2024-02-14
Last modified:2024-03-13
Method:X-RAY DIFFRACTION (1.66 Å)
Cite:Fragment-based screening targeting an open form of the SARS-CoV-2 main protease binding pocket.
Acta Crystallogr D Struct Biol, 80, 2024
7GRF
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BU of 7grf by Molmil
Crystal structure of SARS-CoV-2 main protease in complex with cpd-2
Descriptor: 3C-like proteinase nsp5, 5-bromopyridin-3-amine, CHLORIDE ION, ...
Authors:Huang, C.-Y, Metz, A, Sharpe, M, Sweeney, A.
Deposit date:2023-11-14
Release date:2024-02-14
Method:X-RAY DIFFRACTION (1.84 Å)
Cite:Fragment-based screening targeting an open form of the SARS-CoV-2 main protease binding pocket.
Acta Crystallogr D Struct Biol, 80, 2024
7GRG
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BU of 7grg by Molmil
Crystal structure of SARS-CoV-2 main protease in complex with cpd-3
Descriptor: 3,5-dichloropyridin-4-amine, 3C-like proteinase nsp5, CHLORIDE ION, ...
Authors:Huang, C.-Y, Metz, A, Sharpe, M, Sweeney, A.
Deposit date:2023-11-14
Release date:2024-02-14
Method:X-RAY DIFFRACTION (1.54 Å)
Cite:Fragment-based screening targeting an open form of the SARS-CoV-2 main protease binding pocket.
Acta Crystallogr D Struct Biol, 80, 2024
7GRH
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BU of 7grh by Molmil
Crystal structure of SARS-CoV-2 main protease in complex with cpd-4
Descriptor: 3C-like proteinase nsp5, 5-chloropyridin-3-ol, DIMETHYL SULFOXIDE, ...
Authors:Huang, C.-Y, Metz, A, Sharpe, M, Sweeney, A.
Deposit date:2023-11-14
Release date:2024-02-14
Method:X-RAY DIFFRACTION (1.87 Å)
Cite:Fragment-based screening targeting an open form of the SARS-CoV-2 main protease binding pocket.
Acta Crystallogr D Struct Biol, 80, 2024
7GRI
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BU of 7gri by Molmil
Crystal structure of SARS-CoV-2 main protease in complex with cpd-5
Descriptor: (1S)-1-(1H-pyrazol-5-yl)ethan-1-ol, 3C-like proteinase nsp5, DIMETHYL SULFOXIDE, ...
Authors:Huang, C.-Y, Metz, A, Sharpe, M, Sweeney, A.
Deposit date:2023-11-14
Release date:2024-02-14
Last modified:2024-03-13
Method:X-RAY DIFFRACTION (1.79 Å)
Cite:Fragment-based screening targeting an open form of the SARS-CoV-2 main protease binding pocket.
Acta Crystallogr D Struct Biol, 80, 2024
7GRJ
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BU of 7grj by Molmil
Crystal structure of SARS-CoV-2 main protease in complex with cpd-6
Descriptor: (5-chloro-1-benzothiophen-3-yl)methanol, 3C-like proteinase nsp5, DIMETHYL SULFOXIDE, ...
Authors:Huang, C.-Y, Metz, A, Sharpe, M, Sweeney, A.
Deposit date:2023-11-14
Release date:2024-02-14
Method:X-RAY DIFFRACTION (1.74 Å)
Cite:Fragment-based screening targeting an open form of the SARS-CoV-2 main protease binding pocket.
Acta Crystallogr D Struct Biol, 80, 2024
7GRK
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BU of 7grk by Molmil
Crystal structure of SARS-CoV-2 main protease in complex with cpd-7
Descriptor: (6-fluoro-2H,4H-1,3-benzodioxin-8-yl)methanol, 3C-like proteinase nsp5, CHLORIDE ION, ...
Authors:Huang, C.-Y, Metz, A, Sharpe, M, Sweeney, A.
Deposit date:2023-11-14
Release date:2024-02-14
Last modified:2024-03-13
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Fragment-based screening targeting an open form of the SARS-CoV-2 main protease binding pocket.
Acta Crystallogr D Struct Biol, 80, 2024
7GRL
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BU of 7grl by Molmil
Crystal structure of SARS-CoV-2 main protease in complex with cpd-8
Descriptor: 3C-like proteinase nsp5, 4-(4,5-dibromo-2H-1,2,3-triazol-2-yl)butan-2-one, CHLORIDE ION, ...
Authors:Huang, C.-Y, Metz, A, Sharpe, M, Sweeney, A.
Deposit date:2023-11-14
Release date:2024-02-14
Method:X-RAY DIFFRACTION (1.68 Å)
Cite:Fragment-based screening targeting an open form of the SARS-CoV-2 main protease binding pocket.
Acta Crystallogr D Struct Biol, 80, 2024
7GRM
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BU of 7grm by Molmil
Crystal structure of SARS-CoV-2 main protease in complex with cpd-9
Descriptor: 3C-like proteinase nsp5, CHLORIDE ION, DIMETHYL SULFOXIDE, ...
Authors:Huang, C.-Y, Metz, A, Sharpe, M, Sweeney, A.
Deposit date:2023-11-14
Release date:2024-02-14
Last modified:2024-03-13
Method:X-RAY DIFFRACTION (1.7 Å)
Cite:Fragment-based screening targeting an open form of the SARS-CoV-2 main protease binding pocket.
Acta Crystallogr D Struct Biol, 80, 2024
7GRN
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BU of 7grn by Molmil
Crystal structure of SARS-CoV-2 main protease in complex with cpd-10
Descriptor: 2-[(3S)-pyrrolidin-3-yl]-5-(trifluoromethyl)-1H-benzimidazole, 3C-like proteinase nsp5, DIMETHYL SULFOXIDE, ...
Authors:Huang, C.-Y, Metz, A, Sharpe, M, Sweeney, A.
Deposit date:2023-11-14
Release date:2024-02-14
Method:X-RAY DIFFRACTION (1.92 Å)
Cite:Fragment-based screening targeting an open form of the SARS-CoV-2 main protease binding pocket.
Acta Crystallogr D Struct Biol, 80, 2024
7GRO
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BU of 7gro by Molmil
Crystal structure of SARS-CoV-2 main protease in complex with cpd-11
Descriptor: 3C-like proteinase nsp5, CHLORIDE ION, DIMETHYL SULFOXIDE, ...
Authors:Huang, C.-Y, Metz, A, Sharpe, M, Sweeney, A.
Deposit date:2023-11-14
Release date:2024-02-14
Method:X-RAY DIFFRACTION (1.55 Å)
Cite:Fragment-based screening targeting an open form of the SARS-CoV-2 main protease binding pocket.
Acta Crystallogr D Struct Biol, 80, 2024
7GRP
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BU of 7grp by Molmil
Crystal structure of SARS-CoV-2 main protease in complex with cpd-12
Descriptor: 1-(2,3-dihydro-1-benzofuran-5-yl)methanamine, 3C-like proteinase nsp5, CHLORIDE ION, ...
Authors:Huang, C.-Y, Metz, A, Sharpe, M, Sweeney, A.
Deposit date:2023-11-14
Release date:2024-02-14
Last modified:2024-03-13
Method:X-RAY DIFFRACTION (1.56 Å)
Cite:Fragment-based screening targeting an open form of the SARS-CoV-2 main protease binding pocket.
Acta Crystallogr D Struct Biol, 80, 2024
7GRQ
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BU of 7grq by Molmil
Crystal structure of SARS-CoV-2 main protease in complex with cpd-13
Descriptor: 3C-like proteinase nsp5, CHLORIDE ION, DIMETHYL SULFOXIDE, ...
Authors:Huang, C.-Y, Metz, A, Sharpe, M, Sweeney, A.
Deposit date:2023-11-14
Release date:2024-02-14
Method:X-RAY DIFFRACTION (1.67 Å)
Cite:Fragment-based screening targeting an open form of the SARS-CoV-2 main protease binding pocket.
Acta Crystallogr D Struct Biol, 80, 2024
7GRR
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BU of 7grr by Molmil
Crystal structure of SARS-CoV-2 main protease in complex with cpd-14
Descriptor: 3C-like proteinase nsp5, 5-(3-cyclohexylprop-1-yn-1-yl)pyridine-3-carboxylic acid, DIMETHYL SULFOXIDE, ...
Authors:Huang, C.-Y, Metz, A, Sharpe, M, Sweeney, A.
Deposit date:2023-11-14
Release date:2024-02-14
Method:X-RAY DIFFRACTION (1.68 Å)
Cite:Fragment-based screening targeting an open form of the SARS-CoV-2 main protease binding pocket.
Acta Crystallogr D Struct Biol, 80, 2024

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