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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 (5197)Repr. entries (2266)Latest entries (44)
9CDL
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SARS-CoV-2 Mpro E166V/L50F double mutant in complex with small molecule inhibitor Mpro61
Descriptor: (5P)-5-[(1P,3M,3'P)-3-{3-chloro-5-[(2-chlorophenyl)methoxy]-4-fluorophenyl}-2-oxo-2H-[1,3'-bipyridin]-5-yl]-1-methylpyrimidine-2,4(1H,3H)-dione, 3C-like proteinase nsp5
Authors:Tang, S, Kenneson, J.R, Huynh, K, Anderson, K.S.
Deposit date:2024-06-25
Release date:2025-02-05
Last modified:2025-03-12
Method:X-RAY DIFFRACTION (1.52 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
9CDM
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SARS-CoV-2 Mpro L50F mutant in complex with small molecule inhibitor Mpro61
Descriptor: (5P)-5-[(1P,3M,3'P)-3-{3-chloro-5-[(2-chlorophenyl)methoxy]-4-fluorophenyl}-2-oxo-2H-[1,3'-bipyridin]-5-yl]-1-methylpyrimidine-2,4(1H,3H)-dione, 3C-like proteinase nsp5, DIMETHYL SULFOXIDE
Authors:Tang, S, Kenneson, J.R, Huynh, K, Anderson, K.S.
Deposit date:2024-06-25
Release date:2025-02-05
Last modified:2025-03-12
Method:X-RAY DIFFRACTION (2.05 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
9G9C
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CryoEM structure of Enterococcus italicus Csm-crRNA-CTR (3.2) complex
Descriptor: CRISPR system Cms endoribonuclease Csm3, CRISPR system Cms protein Csm2, CRISPR system Cms protein Csm4, ...
Authors:Jungfer, K, Jinek, M.
Deposit date:2024-07-25
Release date:2025-02-05
Method:ELECTRON MICROSCOPY (2.72 Å)
Cite:Mechanistic determinants and dynamics of cA6 synthesis in type III CRISPR-Cas effector complexes.
Nucleic Acids Res., 53, 2025
9G9D
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CryoEM structure of Enterococcus italicus Csm-crRNA-CTR (4.3) complex
Descriptor: CRISPR system Cms endoribonuclease Csm3, CRISPR system Cms protein Csm2, CRISPR system Cms protein Csm4, ...
Authors:Jungfer, K, Jinek, M.
Deposit date:2024-07-25
Release date:2025-02-05
Method:ELECTRON MICROSCOPY (2.9 Å)
Cite:Mechanistic determinants and dynamics of cA6 synthesis in type III CRISPR-Cas effector complexes.
Nucleic Acids Res., 53, 2025
8XSD
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BA.5 Spike complex with CR9
Descriptor: CR9 heavy chain, CR9 light chain, Spike glycoprotein
Authors:Feng, L.L.
Deposit date:2024-01-09
Release date:2025-02-12
Last modified:2025-07-02
Method:ELECTRON MICROSCOPY (3.55 Å)
Cite:A broadly neutralizing antibody against the SARS-CoV-2 Omicron sub-variants BA.1, BA.2, BA.2.12.1, BA.4, and BA.5.
Signal Transduct Target Ther, 10, 2025
8Y42
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Crystal structure of SARS-CoV-2 3CL protease (3CLpro) in complex with compound 51
Descriptor: 3C-like proteinase nsp5, ~{N}-[(1~{S},2~{R})-2-[[4-cyclopropyl-2-(methylcarbamoyl)-6-nitro-phenyl]amino]cyclohexyl]-2-oxidanylidene-1~{H}-quinoline-4-carboxamide
Authors:Nie, T.Q, Su, H.X, Li, M.J, Xu, Y.C.
Deposit date:2024-01-30
Release date:2025-02-12
Last modified:2025-03-26
Method:X-RAY DIFFRACTION (2.35 Å)
Cite:Discovery of Novel Nonpeptidic and Noncovalent Small Molecule 3CL pro Inhibitors as anti-SARS-CoV-2 Drug Candidate.
J.Med.Chem., 67, 2024
8Y44
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Crystal structure of SARS-CoV-2 3CL protease (3CLpro) in complex with compound 44
Descriptor: 3C-like proteinase nsp5, ~{N}-[(1~{S},2~{R})-2-[(4-bromanyl-2-morpholin-4-ylcarbonyl-6-nitro-phenyl)amino]cyclohexyl]-2-oxidanylidene-1~{H}-quinoline-4-carboxamide
Authors:Nie, T.Q, Su, H.X, Li, M.J, Xu, Y.C.
Deposit date:2024-01-30
Release date:2025-02-12
Last modified:2025-03-26
Method:X-RAY DIFFRACTION (1.91 Å)
Cite:Discovery of Novel Nonpeptidic and Noncovalent Small Molecule 3CL pro Inhibitors as anti-SARS-CoV-2 Drug Candidate.
J.Med.Chem., 67, 2024
8Z6Q
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SARS-CoV-2 XBB.1.16 Spike in complex with CYFN1006-1(S-CYFN1006-1 dimer trimer).
Descriptor: CYFN1006-1 heavy chain, CYFN1006-1 light chain, Spike glycoprotein,Fibritin,Expression Tag
Authors:Wang, Y.J, Sun, L.
Deposit date:2024-04-19
Release date:2025-02-12
Method:ELECTRON MICROSCOPY (5.41 Å)
Cite:SARS-CoV-2 XBB.1.16 Spike in complex with CYFN1006-1(S-CYFN1006-1 dimer trimer).
To Be Published
8Z6S
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Structure of XBB.1.16 S trimer with 2 down-RBDs complex with antibody CYFN1006-1.
Descriptor: CYFN1006-1 heavy chain, CYFN1006-1 light chain, Spike glycoprotein,Fibritin,Expression Tag
Authors:Wang, Y.J, Sun, L.
Deposit date:2024-04-19
Release date:2025-02-12
Method:ELECTRON MICROSCOPY (2.84 Å)
Cite:Structure of XBB.1.16 S trimer with 2 down-RBDs complex with antibody CYFN1006-1.
To Be Published
8Z6U
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SARS-CoV-2 EG.5.1 Spike in complex with CYFN1006-2(S-CYFN1006-2 dimer trimer).
Descriptor: CYFN1006-2 heavy chain, CYFN1006-2 light chain, Spike glycoprotein,Fibritin,Expression Tag
Authors:Wang, Y.J, Sun, L.
Deposit date:2024-04-19
Release date:2025-02-12
Method:ELECTRON MICROSCOPY (3.83 Å)
Cite:SARS-CoV-2 EG.5.1 Spike in complex with CYFN1006-2(S-CYFN1006-2 dimer trimer).
To Be Published
8Z6W
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Structure of EG.5.1 S trimer with 3 down-RBDs complex with antibody CYFN1006-2.
Descriptor: CYFN1006-2 heavy chain, CYFN1006-2 light chain, Spike glycoprotein,Fibritin,Expression Tag
Authors:Wang, Y.J, Sun, L.
Deposit date:2024-04-19
Release date:2025-02-12
Method:ELECTRON MICROSCOPY (3.04 Å)
Cite:Structure of EG.5.1 S trimer with 3 down-RBDs complex with antibody CYFN1006-2.
To Be Published
8Z86
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BA.5 RBD in complex with CR9
Descriptor: CR9 heavy chain, CR9 light chain, Spike protein S1
Authors:Feng, L.L.
Deposit date:2024-04-21
Release date:2025-02-12
Last modified:2025-06-18
Method:ELECTRON MICROSCOPY (3.87 Å)
Cite:A broadly neutralizing antibody against the SARS-CoV-2 Omicron sub-variants BA.1, BA.2, BA.2.12.1, BA.4, and BA.5.
Signal Transduct Target Ther, 10, 2025
9BNT
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BU of 9bnt by Molmil
Crystal Structure of T21I SARS-CoV-2 Main Protease
Descriptor: 3C-like proteinase
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 (1.83 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
9BNU
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BU of 9bnu by Molmil
Crystal Structure of T190I SARS-CoV-2 Main Protease
Descriptor: 3C-like proteinase nsp5
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 (1.55 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
9BNV
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Crystal Structure of A173V SARS-CoV-2 Main Protease
Descriptor: 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 (1.67 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
9BNW
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Crystal Structure of A173V/L50F SARS-CoV-2 Main Protease
Descriptor: 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 (1.3 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
9BNX
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Crystal Structure of L50F SARS-CoV-2 Main Protease
Descriptor: 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 (2.48 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
9BNY
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Crystal Structure of E166V/L50F SARS-CoV-2 Main Protease
Descriptor: 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 (1.83 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
9BNZ
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Crystal Structure of E166V SARS-CoV-2 Main Protease
Descriptor: 3C-like proteinase nsp5
Authors:Kenneson, J, Papini, C, Anderson, K.S.
Deposit date:2024-05-03
Release date:2025-02-12
Last modified:2025-03-12
Method:X-RAY DIFFRACTION (2.08 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
9BO0
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BU of 9bo0 by Molmil
Crystal Structure of T21I SARS-CoV-2 Main Protease in Complex with Compound Mpro61
Descriptor: (5P)-5-[(1P,3M,3'P)-3-{3-chloro-5-[(2-chlorophenyl)methoxy]-4-fluorophenyl}-2-oxo-2H-[1,3'-bipyridin]-5-yl]-1-methylpyrimidine-2,4(1H,3H)-dione, 3C-like proteinase
Authors:Papini, C, Zhang, C.H, Jorgensen, W.L, Anderson, K.S.
Deposit date:2024-05-03
Release date:2025-02-12
Last modified:2025-03-12
Method:X-RAY DIFFRACTION (2.16 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
9BO1
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BU of 9bo1 by Molmil
Crystal Structure of T190I SARS-CoV-2 Main Protease in Complex with Compound Mpro61
Descriptor: (5P)-5-[(1P,3M,3'P)-3-{3-chloro-5-[(2-chlorophenyl)methoxy]-4-fluorophenyl}-2-oxo-2H-[1,3'-bipyridin]-5-yl]-1-methylpyrimidine-2,4(1H,3H)-dione, 3C-like proteinase nsp5
Authors:Papini, C, Zhang, C.H, Jorgensen, W.L, Anderson, K.S.
Deposit date:2024-05-03
Release date:2025-02-12
Last modified:2025-03-12
Method:X-RAY DIFFRACTION (1.96 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
9BO2
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BU of 9bo2 by Molmil
Crystal Structure of A173V/L50F SARS-CoV-2 Main Protease in Complex with Compound Mpro61
Descriptor: (5P)-5-[(1P,3M,3'P)-3-{3-chloro-5-[(2-chlorophenyl)methoxy]-4-fluorophenyl}-2-oxo-2H-[1,3'-bipyridin]-5-yl]-1-methylpyrimidine-2,4(1H,3H)-dione, 3C-like proteinase nsp5
Authors:Papini, C, Kenneson, J, Zhang, C.H, Jorgensen, W.L, 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
9BO3
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BU of 9bo3 by Molmil
Crystal Structure of E166V SARS-CoV-2 Main Protease in Complex with Compound Mpro61
Descriptor: (5P)-5-[(1P,3M,3'P)-3-{3-chloro-5-[(2-chlorophenyl)methoxy]-4-fluorophenyl}-2-oxo-2H-[1,3'-bipyridin]-5-yl]-1-methylpyrimidine-2,4(1H,3H)-dione, 3C-like proteinase nsp5
Authors:Papini, C, Kenneson, J, Zhang, C.H, Jorgensen, W.L, Anderson, K.S.
Deposit date:2024-05-03
Release date:2025-02-12
Last modified:2025-03-12
Method:X-RAY DIFFRACTION (2.78 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
9BO4
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Crystal Structure of T21I 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
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 (2.28 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
9BO5
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Crystal Structure of T190I 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, Anderson, K.S.
Deposit date:2024-05-03
Release date:2025-02-12
Last modified:2025-03-12
Method:X-RAY DIFFRACTION (1.84 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

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