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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
9BO6
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Crystal Structure of A173V/L50F SARS-CoV-2 Main Protease in Complex with Nirmatrelvir
Descriptor: (1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide, 3C-like proteinase nsp5
Authors:Papini, C, Kenneson, J, Anderson, K.S.
Deposit date:2024-05-03
Release date:2025-02-12
Last modified:2025-03-12
Method:X-RAY DIFFRACTION (1.61 Å)
Cite:Exploring Possible Drug-Resistant Variants of SARS-CoV-2 Main Protease (M pro ) with Noncovalent Preclinical Candidate, Mpro61.
Acs Bio Med Chem Au, 5, 2025
9BO7
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Crystal Structure of L50F SARS-CoV-2 Main Protease in Complex with Nirmatrelvir
Descriptor: (1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide, 3C-like proteinase nsp5
Authors:Papini, C, Kenneson, J, Anderson, K.S.
Deposit date:2024-05-03
Release date:2025-02-12
Last modified:2025-03-12
Method:X-RAY DIFFRACTION (1.54 Å)
Cite:Exploring Possible Drug-Resistant Variants of SARS-CoV-2 Main Protease (M pro ) with Noncovalent Preclinical Candidate, Mpro61.
Acs Bio Med Chem Au, 5, 2025
9BO8
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Crystal Structure of T21I SARS-CoV-2 Main Protease in Complex with GC376
Descriptor: 3C-like proteinase, N~2~-[(benzyloxy)carbonyl]-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-leucinamide
Authors:Papini, C, Anderson, K.S.
Deposit date:2024-05-03
Release date:2025-02-12
Last modified:2025-03-12
Method:X-RAY DIFFRACTION (1.49 Å)
Cite:Exploring Possible Drug-Resistant Variants of SARS-CoV-2 Main Protease (M pro ) with Noncovalent Preclinical Candidate, Mpro61.
Acs Bio Med Chem Au, 5, 2025
9BO9
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Crystal Structure of T190I SARS-CoV-2 Main Protease in Complex with GC376
Descriptor: 3C-like proteinase nsp5, N~2~-[(benzyloxy)carbonyl]-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-leucinamide
Authors:Papini, C, Anderson, K.S.
Deposit date:2024-05-03
Release date:2025-02-12
Last modified:2025-03-12
Method:X-RAY DIFFRACTION (1.98 Å)
Cite:Exploring Possible Drug-Resistant Variants of SARS-CoV-2 Main Protease (M pro ) with Noncovalent Preclinical Candidate, Mpro61.
Acs Bio Med Chem Au, 5, 2025
9BOA
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Crystal Structure of A173V SARS-CoV-2 Main Protease in Complex with GC376
Descriptor: 3C-like proteinase nsp5, N~2~-[(benzyloxy)carbonyl]-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-leucinamide
Authors:Papini, C, Kenneson, J, Anderson, K.S.
Deposit date:2024-05-03
Release date:2025-02-12
Last modified:2025-03-12
Method:X-RAY DIFFRACTION (1.7 Å)
Cite:Exploring Possible Drug-Resistant Variants of SARS-CoV-2 Main Protease (M pro ) with Noncovalent Preclinical Candidate, Mpro61.
Acs Bio Med Chem Au, 5, 2025
9BOB
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Crystal Structure of A173V/L50F SARS-CoV-2 Main Protease in Complex with GC376
Descriptor: 3C-like proteinase nsp5, N~2~-[(benzyloxy)carbonyl]-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-leucinamide
Authors:Papini, C, Kenneson, J, Anderson, K.S.
Deposit date:2024-05-03
Release date:2025-02-12
Last modified:2025-03-12
Method:X-RAY DIFFRACTION (1.87 Å)
Cite:Exploring Possible Drug-Resistant Variants of SARS-CoV-2 Main Protease (M pro ) with Noncovalent Preclinical Candidate, Mpro61.
Acs Bio Med Chem Au, 5, 2025
9BOC
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Crystal Structure of L50F SARS-CoV-2 Main Protease in Complex with GC376
Descriptor: 3C-like proteinase nsp5, N~2~-[(benzyloxy)carbonyl]-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-leucinamide
Authors:Papini, C, Kenneson, J, Anderson, K.S.
Deposit date:2024-05-03
Release date:2025-02-12
Last modified:2025-03-12
Method:X-RAY DIFFRACTION (1.68 Å)
Cite:Exploring Possible Drug-Resistant Variants of SARS-CoV-2 Main Protease (M pro ) with Noncovalent Preclinical Candidate, Mpro61.
Acs Bio Med Chem Au, 5, 2025
9BOD
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Crystal Structure of E166V/L50F SARS-CoV-2 Main Protease in Complex with GC376
Descriptor: 3C-like proteinase nsp5, N~2~-[(benzyloxy)carbonyl]-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-leucinamide
Authors:Papini, C, Kenneson, J, Anderson, K.S.
Deposit date:2024-05-03
Release date:2025-02-12
Last modified:2025-03-12
Method:X-RAY DIFFRACTION (1.91 Å)
Cite:Exploring Possible Drug-Resistant Variants of SARS-CoV-2 Main Protease (M pro ) with Noncovalent Preclinical Candidate, Mpro61.
Acs Bio Med Chem Au, 5, 2025
9BOE
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Crystal Structure of E166V SARS-CoV-2 Main Protease in Complex with GC376
Descriptor: 3C-like proteinase nsp5, N~2~-[(benzyloxy)carbonyl]-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-leucinamide
Authors:Papini, C, Kenneson, J, Anderson, K.S.
Deposit date:2024-05-03
Release date:2025-02-12
Last modified:2025-03-12
Method:X-RAY DIFFRACTION (2.02 Å)
Cite:Exploring Possible Drug-Resistant Variants of SARS-CoV-2 Main Protease (M pro ) with Noncovalent Preclinical Candidate, Mpro61.
Acs Bio Med Chem Au, 5, 2025
9EX8
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Free form of a mutant of SARS-CoV-2 main protease Mpro.
Descriptor: Non-structural protein 7
Authors:Battistutta, R, Fornasier, E, Giachin, G.
Deposit date:2024-04-05
Release date:2025-02-12
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Allostery in homodimeric SARS-CoV-2 main protease.
Commun Biol, 7, 2024
9EXU
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Complex of a mutant of the SARS-CoV-2 main protease Mpro with the nsp4/5 substrate peptide (cocrystallization).
Descriptor: Non-structural protein 7, THR-SER-ALA-VAL-LEU-GLN-SER-GLY-PHE-ARG-LYS
Authors:Battistutta, R, Fornasier, E, Giachin, G.
Deposit date:2024-04-08
Release date:2025-02-12
Method:X-RAY DIFFRACTION (1.78 Å)
Cite:Allostery in homodimeric SARS-CoV-2 main protease.
Commun Biol, 7, 2024
9EYA
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Complex of a mutant of the SARS-CoV-2 main protease Mpro with the nsp4/5 substrate peptide (soaking).
Descriptor: Non-structural protein 7, THR-SER-ALA-VAL-LEU-GLN-SER-GLY-PHE-ARG-LYS
Authors:Battistutta, R, Fornasier, E, Giachin, G.
Deposit date:2024-04-09
Release date:2025-02-12
Method:X-RAY DIFFRACTION (1.7 Å)
Cite:Allostery in homodimeric SARS-CoV-2 main protease.
Commun Biol, 7, 2024
9EZ4
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Complex of a mutant of the SARS-CoV-2 main protease Mpro with the nsp5/6 substrate peptide.
Descriptor: 1,2-ETHANEDIOL, DI(HYDROXYETHYL)ETHER, GLUTAMINE, ...
Authors:Battistutta, R, Fornasier, E, Giachin, G.
Deposit date:2024-04-10
Release date:2025-02-12
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Allostery in homodimeric SARS-CoV-2 main protease.
Commun Biol, 7, 2024
9EZ6
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Complex of a mutant of the SARS-CoV-2 main protease Mpro with the nsp14/15 substrate peptide.
Descriptor: 1,2-ETHANEDIOL, DI(HYDROXYETHYL)ETHER, DIMETHYL SULFOXIDE, ...
Authors:Battistutta, R, Fornasier, E, Giachin, G.
Deposit date:2024-04-10
Release date:2025-02-12
Method:X-RAY DIFFRACTION (1.87 Å)
Cite:Allostery in homodimeric SARS-CoV-2 main protease.
Commun Biol, 7, 2024
9J19
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BU of 9j19 by Molmil
The crystal structure of COVID-19 main protease in complex with an inhibitor minocycline
Descriptor: (4S,4AS,5AR,12AS)-4,7-BIS(DIMETHYLAMINO)-3,10,12,12A-TETRAHYDROXY-1,11-DIOXO-1,4,4A,5,5A,6,11,12A-OCTAHYDROTETRACENE-2- CARBOXAMIDE, 3C-like proteinase nsp5
Authors:Singh, A, Jangid, K, Dhaka, P, Tomar, S, Kumar, P.
Deposit date:2024-08-04
Release date:2025-02-12
Last modified:2025-04-09
Method:X-RAY DIFFRACTION (2.7 Å)
Cite:Structural and Mechanistic Insights into the Main Protease (Mpro) Dimer Interface Destabilization Inhibitor: Unveiling New Therapeutic Avenues against SARS-CoV-2.
Biochemistry, 64, 2025
9LAE
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Locally refined region of SARS-CoV-2 spike in complex with antibodies 9G11 and 3E2.
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Heavy chain of 3E2, Heavy chain of 9G11, ...
Authors:Jiang, Y, Sun, H, Zheng, Q, Li, S.
Deposit date:2025-01-02
Release date:2025-02-12
Last modified:2025-02-19
Method:ELECTRON MICROSCOPY (3.46 Å)
Cite:Structural insight into broadening SARS-CoV-2 neutralization by an antibody cocktail harbouring both NTD and RBD potent antibodies.
Emerg Microbes Infect, 13, 2024
8VYA
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BU of 8vya by Molmil
SARS-CoV-2 Omicron Variant Spike Glycoprotein Fusion Core (Q954H)
Descriptor: SARS-CoV-2 Omicron variant spike glycoprotein C-terminal heptad repeat domain, SARS-CoV-2 Omicron variant spike glycoprotein N-terminal heptad repeat domain (Q954H)
Authors:Outlaw, V.K, Apurba, R, Vithanage, N.
Deposit date:2024-02-07
Release date:2025-02-19
Method:X-RAY DIFFRACTION (2.12 Å)
Cite:SARS-CoV-2 Omicron Variant Spike Glycoprotein Mutation Q954H Enhances Fusion Core Stability
to be published
8Z46
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SARS-CoV-2 3CL protease (3CL pro) in complex with a novel inhibitor
Descriptor: (2~{S})-~{N}-(3-azanyl-3-oxidanylidene-propyl)-4-[4-[[(1~{S})-1-(2-chlorophenyl)-3-oxidanyl-propyl]amino]-6-(methylamino)-1,3,5-triazin-2-yl]-1-ethanoyl-piperazine-2-carboxamide, 3C-like proteinase nsp5
Authors:Zhao, W.F, Xiong, L.W, Xu, Y.C.
Deposit date:2024-04-16
Release date:2025-02-26
Method:X-RAY DIFFRACTION (1.57 Å)
Cite:Covalent DNA-Encoded Library Workflow Drives Discovery of SARS-CoV-2 Nonstructural Protein Inhibitors.
J.Am.Chem.Soc., 146, 2024
8Z4W
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Crystal structures of SARS-CoV-2 papain-like protease in complex with covalent inhibitors
Descriptor: 1-[4-[[[4-(isoquinolin-5-ylamino)-6-(methylamino)-1,3,5-triazin-2-yl]amino]methyl]piperidin-1-yl]ethanone, GLYCEROL, Non-structural protein 3, ...
Authors:Hu, H.C, Xu, Y.C.
Deposit date:2024-04-17
Release date:2025-02-26
Method:X-RAY DIFFRACTION (2.33 Å)
Cite:Covalent DNA-Encoded Library Workflow Drives Discovery of SARS-CoV-2 Nonstructural Protein Inhibitors.
J.Am.Chem.Soc., 146, 2024
9MZB
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X-ray crystallographic structure of Orf9b Apo Homodimer
Descriptor: GLYCINE, ORF9b protein
Authors:San Felipe, C.J, Fraser, J.S.
Deposit date:2025-01-22
Release date:2025-02-26
Method:X-RAY DIFFRACTION (2.8 Å)
Cite:X-ray Crystallographic Structure of Refolded Apo-Orf9b Homodimer
To Be Published
8W6W
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Crystal Structure of C-terminal domain of nucleocapsid protein from SARS-CoV-2 in complex with ampicillin
Descriptor: (2S,5R,6R)-6-{[(2R)-2-AMINO-2-PHENYLETHANOYL]AMINO}-3,3-DIMETHYL-7-OXO-4-THIA-1-AZABICYCLO[3.2.0]HEPTANE-2-CARBOXYLIC ACID, 1,2-ETHANEDIOL, Nucleoprotein
Authors:Dhaka, P, Mahto, J.K, Tomar, S, Kumar, P.
Deposit date:2023-08-30
Release date:2025-03-05
Last modified:2025-04-02
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:Structural insights into the RNA binding inhibitors of the C-terminal domain of the SARS-CoV-2 nucleocapsid.
J.Struct.Biol., 217, 2025
9B0Y
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SARS CoV-2 Spike protein Ectodomain with internal tag, all RBD-down conformation
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:2024-03-12
Release date:2025-03-05
Last modified:2025-03-19
Method:ELECTRON MICROSCOPY (2.32 Å)
Cite:Production and cryo-electron microscopy structure of an internally tagged SARS-CoV-2 spike ecto-domain construct.
J Struct Biol X, 11, 2025
9B2V
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BU of 9b2v by Molmil
SARS CoV-2 Spike protein Ectodomain with internal tag, 1RBD-up conformation
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:Singh, S, Hasan, S.S.
Deposit date:2024-03-17
Release date:2025-03-05
Last modified:2025-03-19
Method:ELECTRON MICROSCOPY (2.55 Å)
Cite:Production and cryo-electron microscopy structure of an internally tagged SARS-CoV-2 spike ecto-domain construct.
J Struct Biol X, 11, 2025
9BJ2
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Structure of the SARS-CoV-2 S 6P trimer complex with the human neutralizing antibody Fab fragment, C1533 (local refinement of NTD and C1533)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, C1533 Heavy Chain, C1533 Light Chain, ...
Authors:Rubio, A.A, Abernathy, M.E, Barnes, C.O.
Deposit date:2024-04-24
Release date:2025-03-05
Last modified:2025-03-19
Method:ELECTRON MICROSCOPY (2.8 Å)
Cite:Bispecific antibodies targeting the N-terminal and receptor binding domains potently neutralize SARS-CoV-2 variants of concern.
Sci Transl Med, 17, 2025
9BJ3
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BU of 9bj3 by Molmil
Structure of the SARS-CoV-2 S 6P trimer complex with the human neutralizing antibody Fab fragment, C1596
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, C1596 Fab Heavy Chain, ...
Authors:Rubio, A.A, Abernathy, M.E, Barnes, C.O.
Deposit date:2024-04-24
Release date:2025-03-05
Last modified:2025-03-19
Method:ELECTRON MICROSCOPY (3.04 Å)
Cite:Bispecific antibodies targeting the N-terminal and receptor binding domains potently neutralize SARS-CoV-2 variants of concern.
Sci Transl Med, 17, 2025

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