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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
9LUG
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BU of 9lug by Molmil
Crystal structure of SARS-Cov-2 main protease E166V mutant in complex with Bofutrelvir
Descriptor: ORF1a polyprotein, ~{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:Zhou, X.L, Li, J.
Deposit date:2025-02-08
Release date:2025-04-09
Method:X-RAY DIFFRACTION (2.13 Å)
Cite:Inhibitory efficacy and structural insights of Bofutrelvir against SARS-CoV-2 M pro mutants and MERS-CoV M pro.
Commun Biol, 8, 2025
9B4X
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BU of 9b4x by Molmil
SARS CoV-2 full-length spike protein with Lys1269Ala and His1271Ala substitutions in the coatomer binding motif, 1RBD-up conformation (SPIKE-AXA)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:Singh, S, Hasan, S.S.
Deposit date:2024-03-21
Release date:2025-04-16
Method:ELECTRON MICROSCOPY (3.33 Å)
Cite:Cryo-EM structure of SARS CoV-2 full-length spike with Lys1269Ala and His1271Ala substitutions in the coatomer binding motif, 1RBD-up conformation
To Be Published
9B8F
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BU of 9b8f by Molmil
SARS CoV-2 full-length spike protein with Lys1269Ala and His1271Ala substitutions in the coatomer binding motif, 2RBD-up conformation (SPIKE-AXA)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:Singh, S, Hasan, S.S.
Deposit date:2024-03-29
Release date:2025-04-16
Method:ELECTRON MICROSCOPY (4.15 Å)
Cite:Structure of SARS CoV-2 full-length spike protein with Lys1269Ala and His1271Ala substitutions in the coatomer binding motif, 2RBD-up conformation
To Be Published
9B9U
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BU of 9b9u by Molmil
SARS-CoV-2 full-length spike protein with His1271Lys substitution in the coatomer binding motif, 1RBD-up conformation (SPIKE-KXK)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:Singh, S, Hasan, S.S.
Deposit date:2024-04-03
Release date:2025-04-16
Method:ELECTRON MICROSCOPY (2.86 Å)
Cite:SARS CoV-2 full-length spike protein with His1271Lys substitution in the coatomer binding motif, 1RBD-up conformation
To Be Published
9BBK
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BU of 9bbk by Molmil
SARS-CoV-2 full-length spike protein with His1271Lys substitution in the coatomer binding motif, 2RBD-up conformation (SPIKE-KxK)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:Singh, S, Hasan, S.S.
Deposit date:2024-04-06
Release date:2025-04-16
Method:ELECTRON MICROSCOPY (2.95 Å)
Cite:Structure of SARS CoV-2 full-length spike protein with His1271Lys substitution in the coatomer binding motif, 2RBD-up conformation
To Be Published
9BBP
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BU of 9bbp by Molmil
SARS-CoV-2 Mpro in complex with compound 12d inhibitor
Descriptor: 3C-like proteinase nsp5, GLYCINE, N-{(2R)-1-amino-3-[(2R,3S)-2-hydroxypyrrolidin-3-yl]propan-2-yl}-N~2~-[4-(6-fluoropyridin-3-yl)benzoyl]-L-leucinamide, ...
Authors:Afsar, M, Bury, P, Olsen, S.K.
Deposit date:2024-04-07
Release date:2025-04-16
Last modified:2025-05-14
Method:X-RAY DIFFRACTION (1.81 Å)
Cite:SARS-CoV-2 Mpro in complex with compound 12d inhibitor
To Be Published
9BBQ
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BU of 9bbq by Molmil
SARS-CoV-2 Mpro in complex with compound 6c inhibitor
Descriptor: 3C-like proteinase nsp5, N-[(2R)-1-({(2S)-1-amino-3-[(2S,3R)-2-hydroxypyrrolidin-3-yl]propan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-4'-ethoxy[1,1'-biphenyl]-4-carboxamide
Authors:Afsar, M, Bury, P, Olsen, S.K.
Deposit date:2024-04-07
Release date:2025-04-16
Last modified:2025-05-14
Method:X-RAY DIFFRACTION (1.78 Å)
Cite:SARS-CoV-2 Mpro in complex with compound 6c inhibitor
To Be Published
9BBR
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BU of 9bbr by Molmil
SARS-CoV-2 Mpro in complex with compound 6b inhibitor
Descriptor: 3C-like proteinase nsp5, 4'-fluoro-N-[(2S)-1-({(2R)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}amino)-4-methyl-1-oxopentan-2-yl][1,1'-biphenyl]-4-carboxamide
Authors:Afsar, M, Bury, P, Olsen, S.K.
Deposit date:2024-04-07
Release date:2025-04-16
Last modified:2025-05-14
Method:X-RAY DIFFRACTION (2.15 Å)
Cite:SARS-CoV-2 Mpro in complex with compound 6b inhibitor
To Be Published
9BBS
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BU of 9bbs by Molmil
SARS-CoV-2 Mpro in complex with compound 6d inhibitor
Descriptor: 3C-like proteinase nsp5, N-[(2S)-1-({(2R)-1-imino-3-[(3R)-2-oxopyrrolidin-3-yl]propan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-4'-methoxy[1,1'-biphenyl]-4-carboxamide
Authors:Afsar, M, Bury, P, Olsen, S.K, Nayak, A.
Deposit date:2024-04-07
Release date:2025-04-16
Last modified:2025-05-14
Method:X-RAY DIFFRACTION (1.95 Å)
Cite:SARS-CoV-2 Mpro in complex with compound 6d inhibitor
To Be Published
9BBT
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BU of 9bbt by Molmil
SARS-CoV-2 Mpro in complex with compound 6f inhibitor
Descriptor: 3C-like proteinase nsp5, N-[(2S)-1-({(2R)-1-imino-3-[(3R)-2-oxopyrrolidin-3-yl]propan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-3',4'-dimethoxy[1,1'-biphenyl]-4-carboxamide
Authors:Afsar, M, Bury, P, Olsen, S.K, Nayak, A.
Deposit date:2024-04-07
Release date:2025-04-16
Last modified:2025-05-14
Method:X-RAY DIFFRACTION (2.57 Å)
Cite:SARS-CoV-2 Mpro in complex with compound 6f inhibitor
To Be Published
9BBU
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BU of 9bbu by Molmil
SARS-CoV-2 Mpro in complex with compound 6h inhibitor
Descriptor: 1,2-ETHANEDIOL, 3C-like proteinase nsp5, N~2~-[4-(5-chloropyridin-3-yl)benzoyl]-N-{(1Z,2S)-1-imino-3-[(3R)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-leucinamide
Authors:Nayak, A, Afsar, M, Nayak, D, Olsen, S.K.
Deposit date:2024-04-07
Release date:2025-04-16
Last modified:2025-05-14
Method:X-RAY DIFFRACTION (2 Å)
Cite:SARS-CoV-2 Mpro in complex with compound 6h inhibitor
To Be Published
9BBV
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BU of 9bbv by Molmil
SARS-CoV-2 Mpro in complex with compound 6j inhibitor
Descriptor: 3C-like proteinase nsp5, N-{(1E,2R)-1-imino-3-[(3R)-2-oxopyrrolidin-3-yl]propan-2-yl}-N~2~-[4-(2-methyl-2H-indazol-4-yl)benzoyl]-L-leucinamide
Authors:Nayak, A, Afsar, M, Nayak, D, Olsen, S.K.
Deposit date:2024-04-07
Release date:2025-04-16
Last modified:2025-05-14
Method:X-RAY DIFFRACTION (2.46 Å)
Cite:SARS-CoV-2 Mpro in complex with compound 6j inhibitor
To Be Published
9BBW
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BU of 9bbw by Molmil
SARS-CoV-2 Mpro in complex with compound 6k inhibitor
Descriptor: 3C-like proteinase nsp5, N-{(2R)-1-imino-3-[(3R)-2-oxopyrrolidin-3-yl]propan-2-yl}-N~2~-[4-(6-methoxypyridin-3-yl)benzoyl]-L-leucinamide
Authors:Afsar, M, Bury, P, Olsen, S.K, Nayak, A.
Deposit date:2024-04-07
Release date:2025-04-16
Last modified:2025-05-14
Method:X-RAY DIFFRACTION (2.31 Å)
Cite:SARS-CoV-2 Mpro in complex with compound 6k inhibitor
To Be Published
9BBX
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BU of 9bbx by Molmil
SARS-CoV-2 Mpro in complex with compound 6l inhibitor
Descriptor: 3C-like proteinase nsp5, N-{(2R)-1-imino-3-[(3R)-2-oxopyrrolidin-3-yl]propan-2-yl}-N~2~-[4-(1-methyl-1H-indazol-5-yl)benzoyl]-L-leucinamide
Authors:Afsar, M, Bury, P, Olsen, S.K, Nayak, A.
Deposit date:2024-04-07
Release date:2025-04-16
Last modified:2025-05-14
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:SARS-CoV-2 Mpro in complex with compound 6l inhibitor
To Be Published
9BBY
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BU of 9bby by Molmil
SARS-CoV-2 Mpro in complex with compound 18b inhibitor
Descriptor: 3-fluoro-N-[(2S)-1-({(2R)-1-imino-3-[(3R)-2-oxopyrrolidin-3-yl]propan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-4'-methoxy[1,1'-biphenyl]-4-carboxamide, 3C-like proteinase nsp5
Authors:Afsar, M, Bury, P, Olsen, S.K.
Deposit date:2024-04-07
Release date:2025-04-16
Last modified:2025-05-14
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:SARS-CoV-2 Mpro in complex with compound 18b inhibitor
To Be Published
9BBZ
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BU of 9bbz by Molmil
SARS-CoV-2 Mpro in complex with compound 18d inhibitor
Descriptor: 3C-like proteinase nsp5, N~2~-[(4M)-2-fluoro-4-(1-methyl-1H-indazol-5-yl)benzene-1-carbonyl]-N-{(1E,2S)-1-imino-3-[(3R)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-leucinamide
Authors:Afsar, M, Bury, P, Olsen, S.K.
Deposit date:2024-04-07
Release date:2025-04-16
Last modified:2025-05-14
Method:X-RAY DIFFRACTION (1.62 Å)
Cite:SARS-CoV-2 Mpro in complex with compound 18d inhibitor
To Be Published
9BC0
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BU of 9bc0 by Molmil
SARS-CoV-2 Mpro in complex with compound 18r inhibitor
Descriptor: 3-chloro-N-[(2R)-1-({(1Z,2S)-1-imino-3-[(3R)-2-oxopyrrolidin-3-yl]propan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-4'-methoxy[1,1'-biphenyl]-4-carboxamide, 3C-like proteinase nsp5
Authors:Afsar, M, Bury, P, Olsen, S.K.
Deposit date:2024-04-07
Release date:2025-04-16
Last modified:2025-05-14
Method:X-RAY DIFFRACTION (2.08 Å)
Cite:SARS-CoV-2 Mpro in complex with compound 18r inhibitor
To Be Published
9BD9
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BU of 9bd9 by Molmil
SARS CoV-2 full-length WT spike protein, 1RBD-up conformation (SPIKE-WT)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:Singh, S, Hasan, S.S.
Deposit date:2024-04-11
Release date:2025-04-16
Method:ELECTRON MICROSCOPY (2.95 Å)
Cite:Structure of SARS CoV-2 full-length spike protein, 1RBD-up conformation
To Be Published
9BEA
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BU of 9bea by Molmil
Structure of SARS-CoV-2 full-length WT spike protein with internal tag, 2RBD-up conformation (SPIKE-WT)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:Singh, S, Hasan, S.S.
Deposit date:2024-04-15
Release date:2025-04-16
Method:ELECTRON MICROSCOPY (3.85 Å)
Cite:Structure of SARS CoV-2 full-length spike protein with internal tag, 2RBD-up conformation
To Be Published
9DHY
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BU of 9dhy by Molmil
Structure of SARS-CoV-2 spike in complex with antibody Fab COVIC-154
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Antibody Fab COVIC-154 Heavy Chain, ...
Authors:Yu, X, Saphire, E.O.
Deposit date:2024-09-04
Release date:2025-04-16
Method:ELECTRON MICROSCOPY (2.7 Å)
Cite:A global collaboration for systematic analysis of broad-ranging antibodies against the SARS-CoV-2 spike protein.
Cell Rep, 44, 2025
8WTS
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BU of 8wts by Molmil
SARS-CoV-2 3CLpro bound to covalent inhibitor
Descriptor: (2~{R})-2-[[4-[chloranyl-bis(fluoranyl)methoxy]phenyl]-(2-chloranyl-2-fluoranyl-ethanoyl)amino]-~{N}-(oxan-4-yl)-2-pyrimidin-5-yl-propanamide, 1,2-ETHANEDIOL, 3C-like proteinase, ...
Authors:Peng, J, Sun, D, Ding, X.
Deposit date:2023-10-19
Release date:2025-04-23
Last modified:2025-05-28
Method:X-RAY DIFFRACTION (1.56 Å)
Cite:A novel, covalent broad-spectrum inhibitor targeting human coronavirus M pro.
Nat Commun, 16, 2025
8Z2E
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BU of 8z2e by Molmil
Crystal structure of nanobody Tnb04-1 with antibody 1F11 fab and SARS-CoV-2 RBD
Descriptor: 1F11-H, 1F11-L, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:Wang, X.Q, Zhang, L.Q, Chen, J, Dong, H.D.
Deposit date:2024-04-12
Release date:2025-04-23
Method:X-RAY DIFFRACTION (2.3 Å)
Cite:Crystal structure of nanobody Tnb04-1 with antibody 1F11 fab and SARS-CoV-2 RBD
To Be Published
9BC1
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BU of 9bc1 by Molmil
SARS-CoV-2 Mpro in complex with peptide mimetic inhibitor
Descriptor: 3C-like proteinase nsp5, peptide mimetic inhibitor
Authors:Afsar, M, Priscila, B, Olsen, S.K.
Deposit date:2024-04-07
Release date:2025-04-23
Method:X-RAY DIFFRACTION (1.72 Å)
Cite:SARS-CoV-2 Mpro in complex with peptide mimetic inhibitor
To Be Published
9GF7
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BU of 9gf7 by Molmil
SARS-CoV2 Main Protease (Mpro) in complex with the covalent inhibitor 28a
Descriptor: 3C-like proteinase nsp5, ~{N}-[(2~{S})-4-methyl-1-oxidanylidene-1-[[(2~{S})-1-oxidanylidene-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]pentan-2-yl]quinoline-8-carboxamide
Authors:Lolicato, M, Arrigoni, C.
Deposit date:2024-08-08
Release date:2025-04-23
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:Synthesis and biological investigation of peptidomimetic SARS-CoV-2 main protease inhibitors bearing quinoline-based heterocycles at P 3.
Arch Pharm, 358, 2025
9KN1
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BU of 9kn1 by Molmil
Crystal structure of SARS-CoV-2 nucleocapsid phosphoprotein N-terminal domain(N-NTD) in complex with UMP
Descriptor: Nucleoprotein, PHOSPHATE ION, URIDINE-5'-MONOPHOSPHATE
Authors:Higashiura, A, Yamamoto, A, Ito, H.
Deposit date:2024-11-18
Release date:2025-04-23
Method:X-RAY DIFFRACTION (2.12 Å)
Cite:Structural insights into nucleocapsid protein variability: Implications for PJ34 efficacy against SARS-CoV-2.
Virology, 604, 2025

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PDB entries from 2025-07-09

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