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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
9ARU
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BU of 9aru by Molmil
COVA2-15 fragment antigen binding in complex with SARS-CoV-2 6P-mut7 S protein
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, COVA2-15 heavy chain variable region, ...
Authors:Ozorowski, G, Turner, H.L, Ward, A.B.
Deposit date:2024-02-23
Release date:2025-01-29
Last modified:2025-05-28
Method:ELECTRON MICROSCOPY (3.9 Å)
Cite:Plant-produced SARS-CoV-2 antibody engineered towards enhanced potency and in vivo efficacy.
Plant Biotechnol J, 23, 2025
9F2X
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BU of 9f2x by Molmil
Crystal structure of SARS-CoV-2 Mpro in complex with RHTCR03
Descriptor: 3C-like proteinase nsp5, ~{tert}-butyl ~{N}-[4-[(2~{S})-1-[[(2~{S},3~{R})-4-azanyl-3-oxidanyl-4-oxidanylidene-1-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]butan-2-yl]amino]-3-cyclopropyl-1-oxidanylidene-propan-2-yl]-3-oxidanylidene-pyrazin-2-yl]carbamate
Authors:El kilani, H, Hilgenfeld, R.
Deposit date:2024-04-24
Release date:2025-01-29
Last modified:2025-02-26
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:Structure-Based Optimization of Pyridone alpha-Ketoamides as Inhibitors of the SARS-CoV-2 Main Protease.
J.Med.Chem., 68, 2025
9F39
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BU of 9f39 by Molmil
Crystal structure of SARS-CoV-2 Mpro in complex with RK-54
Descriptor: (2R,3R)-3-[[(2S)-3-cyclopropyl-2-[3-(2-methylpropanoylamino)-2-oxidanylidene-pyridin-1-yl]propanoyl]amino]-N-methyl-2-oxidanyl-4-[(3S)-2-oxidanylidenepyrrolidin-3-yl]butanamide, 3C-like proteinase nsp5
Authors:El kilani, H, Hilgenfeld, R.
Deposit date:2024-04-25
Release date:2025-01-29
Last modified:2025-02-26
Method:X-RAY DIFFRACTION (2.45 Å)
Cite:Structure-Based Optimization of Pyridone alpha-Ketoamides as Inhibitors of the SARS-CoV-2 Main Protease.
J.Med.Chem., 68, 2025
9F3A
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BU of 9f3a by Molmil
Crystal structure of SARS-CoV-2 Mpro in complex with RK-325
Descriptor: 3C-like proteinase nsp5, tert-butyl N-[1-[(2S)-3-cyclopropyl-1-[[(2S,3R)-4-(methylamino)-3-oxidanyl-4-oxidanylidene-1-[(3S)-2-oxidanylidenepyrrolidin-3-yl]butan-2-yl]amino]-1-oxidanylidene-propan-2-yl]-5-fluoranyl-2-oxidanylidene-pyridin-3-yl]carbamate
Authors:El kilani, H, Hilgenfeld, R.
Deposit date:2024-04-25
Release date:2025-01-29
Last modified:2025-02-26
Method:X-RAY DIFFRACTION (2.15 Å)
Cite:Structure-Based Optimization of Pyridone alpha-Ketoamides as Inhibitors of the SARS-CoV-2 Main Protease.
J.Med.Chem., 68, 2025
9FHQ
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BU of 9fhq by Molmil
Crystal structure of SARS-CoV-2 Mpro in complex with RHTCR04
Descriptor: 3C-like proteinase nsp5, ~{tert}-butyl ~{N}-[1-[(2~{S})-1-[[(2~{S})-4-azanyl-3-oxidanyl-4-oxidanylidene-1-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]butan-2-yl]amino]-3-cyclopropyl-1-oxidanylidene-propan-2-yl]-6-oxidanylidene-pyrimidin-5-yl]carbamate
Authors:El kilani, H, Hilgenfeld, R.
Deposit date:2024-05-28
Release date:2025-01-29
Last modified:2025-02-26
Method:X-RAY DIFFRACTION (1.696 Å)
Cite:Structure-Based Optimization of Pyridone alpha-Ketoamides as Inhibitors of the SARS-CoV-2 Main Protease.
J.Med.Chem., 68, 2025
9G9F
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BU of 9g9f by Molmil
CryoEM structure of Enterococcus italicus Csm-crRNA-CTR complex bound to AMPNPP
Descriptor: 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine, CRISPR system Cms endoribonuclease Csm3, CRISPR system Cms protein Csm2, ...
Authors:Jungfer, K, Jinek, M.
Deposit date:2024-07-25
Release date:2025-01-29
Method:ELECTRON MICROSCOPY (2.93 Å)
Cite:Mechanistic determinants and dynamics of cA6 synthesis in type III CRISPR-Cas effector complexes.
Nucleic Acids Res., 53, 2025
9G9G
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BU of 9g9g by Molmil
CryoEM structure of Enterococcus italicus Csm-crRNA-CTR1 complex (4.3) bound to AMPNPP
Descriptor: 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine, CRISPR system Cms endoribonuclease Csm3, CRISPR system Cms protein Csm2, ...
Authors:Jungfer, K, Jinek, M.
Deposit date:2024-07-25
Release date:2025-01-29
Method:ELECTRON MICROSCOPY (3.38 Å)
Cite:Mechanistic determinants and dynamics of cA6 synthesis in type III CRISPR-Cas effector complexes.
Nucleic Acids Res., 53, 2025
9G9H
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BU of 9g9h by Molmil
CryoEM structure of Enterococcus italicus Csm-crRNA-CTR1 complex bound to pNppA3 and AMPNPP
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:2025-01-29
Method:ELECTRON MICROSCOPY (2.99 Å)
Cite:Mechanistic determinants and dynamics of cA6 synthesis in type III CRISPR-Cas effector complexes.
Nucleic Acids Res., 53, 2025
9G9I
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BU of 9g9i by Molmil
CryoEM structure of Enterococcus italicus Csm-crRNA-CTR2 complex bound to pNppA3 and AMPNPP
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:2025-01-29
Method:ELECTRON MICROSCOPY (3.31 Å)
Cite:Mechanistic determinants and dynamics of cA6 synthesis in type III CRISPR-Cas effector complexes.
Nucleic Acids Res., 53, 2025
9G9K
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BU of 9g9k by Molmil
CryoEM structure of Enterococcus italicus Csm-crRNA-CTR2 complex (4.3) bound to AMPNPP
Descriptor: 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine, CRISPR system Cms endoribonuclease Csm3, CRISPR system Cms protein Csm2, ...
Authors:Jungfer, K, Jinek, M.
Deposit date:2024-07-25
Release date:2025-01-29
Method:ELECTRON MICROSCOPY (3.34 Å)
Cite:Mechanistic determinants and dynamics of cA6 synthesis in type III CRISPR-Cas effector complexes.
Nucleic Acids Res., 53, 2025
9GMQ
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BU of 9gmq by Molmil
Crystal structure of the Mpro of SARS COV-2 in complex with the MG-87 inhibitor
Descriptor: 3C-like proteinase nsp5, CHLORIDE ION, ~{tert}-butyl ~{N}-[1-[(2~{S})-1-[[(2~{S},3~{R})-4-azanyl-3-oxidanyl-4-oxidanylidene-1-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]butan-2-yl]amino]-3-cyclopropyl-1-oxidanylidene-propan-2-yl]-2-oxidanylidene-pyridin-3-yl]carbamate
Authors:El Kilani, H, Hilgenfeld, R.
Deposit date:2024-08-29
Release date:2025-01-29
Last modified:2025-02-26
Method:X-RAY DIFFRACTION (2.19 Å)
Cite:Structure-Based Optimization of Pyridone alpha-Ketoamides as Inhibitors of the SARS-CoV-2 Main Protease.
J.Med.Chem., 68, 2025
9GV2
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BU of 9gv2 by Molmil
Crystal structure of SARS-CoV-2 main protease (MPro) in complex with the covalently bound inhibitor FP237 (compound 8p in publication)
Descriptor: (2S)-2-[2-(3-methoxyphenoxy)ethanoylamino]-4-methyl-N-[(2S)-3-oxidanylidene-1-phenyl-pentan-2-yl]pentanamide, 1,2-ETHANEDIOL, 3C-like proteinase nsp5, ...
Authors:Strater, N, Sylvester, K, Muller, C.E, Flury, P, Kruger, N, Breidenbach, J, Guetschow, M, Laufer, S.A, Pillaiyar, T.
Deposit date:2024-09-20
Release date:2025-01-29
Last modified:2025-02-26
Method:X-RAY DIFFRACTION (2.56 Å)
Cite:Design, Synthesis, and Unprecedented Interactions of Covalent Dipeptide-Based Inhibitors of SARS-CoV-2 Main Protease and Its Variants Displaying Potent Antiviral Activity.
J.Med.Chem., 68, 2025
9KT3
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BU of 9kt3 by Molmil
Structure of EG.5.1 S trimer with 2 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:2024-12-01
Release date:2025-01-29
Method:ELECTRON MICROSCOPY (3.63 Å)
Cite:Structure of EG.5.1 S trimer with 2 down-RBDs complex with antibody CYFN1006-2.
To Be Published
8VUO
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BU of 8vuo by Molmil
Crystal structure of SARS-CoV-2 nsp16/nsp10 in complex with Cap-1 RNA
Descriptor: 1,2-ETHANEDIOL, 2'-O-methyltransferase, 7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE, ...
Authors:Misra, A, Rahisuddin, R, Gupta, Y.K.
Deposit date:2024-01-29
Release date:2025-02-05
Method:X-RAY DIFFRACTION (2.39 Å)
Cite:Crystal structure of SARS-CoV-2 nsp16/nsp10 in complex with Cap-1 RNA
To Be Published
8Y7T
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BU of 8y7t by Molmil
Crystal structure of SARS-CoV-2 main protease in complex with C2
Descriptor: 3C-like proteinase nsp5, 6-(iminomethyl)-4-(2-pyridin-2-ylethyl)-2-[4-(trifluoromethyl)phenyl]-1,2,4-triazine-3,5-dione
Authors:Zeng, R, Deng, X.Y, Yang, Z.Y, Wang, K, Jiang, Y.Y, Lei, J.
Deposit date:2024-02-05
Release date:2025-02-05
Last modified:2025-04-23
Method:X-RAY DIFFRACTION (2.5 Å)
Cite:A deep learning model for structure-based bioactivity optimization and its application in the bioactivity optimization of a SARS-CoV-2 main protease inhibitor.
Eur.J.Med.Chem., 291, 2025
8Y7U
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BU of 8y7u by Molmil
Crystal structure of SARS-CoV-2 main protease in complex with C5
Descriptor: 2-(3-fluoro-4-(trifluoromethyl)phenyl)-6-(iminomethyl)-4-(2-oxo-2-(pyridin-2-yl)ethyl)-1,2,4-triazine-3,5(2H,4H)-dione, 3C-like proteinase nsp5
Authors:Zeng, R, Deng, X.Y, Yang, Z.Y, Wang, K, Jiang, Y.Y, Lei, J.
Deposit date:2024-02-05
Release date:2025-02-05
Last modified:2025-04-23
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:A deep learning model for structure-based bioactivity optimization and its application in the bioactivity optimization of a SARS-CoV-2 main protease inhibitor.
Eur.J.Med.Chem., 291, 2025
8Z3W
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BU of 8z3w by Molmil
Cryo-EM structure of SARS-CoV-2 D614G S with one ACE2 receptor binding (RB1) in prefusion 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, Angiotensin-converting enzyme 2, ...
Authors:Liu, Z, Xing, L.
Deposit date:2024-04-16
Release date:2025-02-05
Method:ELECTRON MICROSCOPY (3.45 Å)
Cite:Cryo-EM structure of SARS-CoV-2 D614G S with one ACE2 receptor binding (RB1) in prefusion conformation
To Be Published
8Z4X
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BU of 8z4x by Molmil
Cryo-EM structure of SARS-CoV-2 D614G S with two ACE2 receptors binding (RB2) in prefusion 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, Angiotensin-converting enzyme 2, ...
Authors:Liu, Z, Xing, L.
Deposit date:2024-04-17
Release date:2025-02-05
Method:ELECTRON MICROSCOPY (3.4 Å)
Cite:Cryo-EM structure of SARS-CoV-2 D614G S with two ACE2 receptors binding (RB2) in prefusion conformation
To Be Published
8Z64
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BU of 8z64 by Molmil
Cryo-EM structure of SARS-CoV-2 D614G S with three ACE2 receptors binding (RB3) in prefusion conformation (focused refinement of NTD-SD1-RBD-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, Angiotensin-converting enzyme 2, ...
Authors:Liu, Z, Xing, L.
Deposit date:2024-04-18
Release date:2025-02-05
Last modified:2025-07-02
Method:ELECTRON MICROSCOPY (3.53 Å)
Cite:Cryo-EM structure of SARS-CoV-2 D614G S with three ACE2 receptors binding (RB3) in prefusion conformation (focused refinement of NTD-SD1-RBD-ACE2)
To Be Published
8Z6A
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BU of 8z6a by Molmil
Cryo-EM structure of SARS-CoV-2 D614G S with three ACE2 receptors binding (RB3) in prefusion 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, Angiotensin-converting enzyme 2, ...
Authors:Liu, Z, Xing, L.
Deposit date:2024-04-18
Release date:2025-02-05
Method:ELECTRON MICROSCOPY (2.99 Å)
Cite:Cryo-EM structure of SARS-CoV-2 D614G S with three ACE2 receptors binding (RB3) in prefusion conformation
To Be Published
8Z7B
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BU of 8z7b by Molmil
Cryo-EM structure of SARS-CoV-2 S trimer in the early fusion intermediate conformation (E-FIC) (focused refinement of NTD-SD1-RBD-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, Angiotensin-converting enzyme 2, ...
Authors:Liu, Z, Xing, L.
Deposit date:2024-04-19
Release date:2025-02-05
Method:ELECTRON MICROSCOPY (3.3 Å)
Cite:Cryo-EM structure of SARS-CoV-2 S trimer in the early fusion intermediate conformation (E-FIC) (focused refinement of NTD-SD1-RBD-ACE2)
To Be Published
8Z7G
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BU of 8z7g by Molmil
Cryo-EM structure of SARS-CoV-2 S trimer in the early fusion intermediate conformation (E-FIC) (focused refinement of intact S2)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein
Authors:Liu, Z, Xing, L.
Deposit date:2024-04-20
Release date:2025-02-05
Method:ELECTRON MICROSCOPY (3.06 Å)
Cite:Cryo-EM structure of SARS-CoV-2 S trimer in the early fusion intermediate conformation (E-FIC) (focused refinement of intact S2)
To Be Published
8Z7L
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BU of 8z7l by Molmil
Cryo-EM structure of SARS-CoV-2 S trimer in the early fusion intermediate conformation (E-FIC) (focused refinement of S-bottom)
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:Liu, Z, Xing, L.
Deposit date:2024-04-20
Release date:2025-02-05
Method:ELECTRON MICROSCOPY (3.42 Å)
Cite:Cryo-EM structure of SARS-CoV-2 S trimer in the early fusion intermediate conformation (E-FIC) (focused refinement of S-bottom)
To Be Published
8Z7P
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BU of 8z7p by Molmil
Cryo-EM structure of SARS-CoV-2 S trimer in the early fusion intermediate conformation (E-FIC)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Angiotensin-converting enzyme 2, ...
Authors:Liu, Z, Xing, L.
Deposit date:2024-04-20
Release date:2025-02-05
Method:ELECTRON MICROSCOPY (3.45 Å)
Cite:Cryo-EM structure of SARS-CoV-2 S trimer in the early fusion intermediate conformation (E-FIC)
To Be Published
9CDK
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BU of 9cdk by Molmil
SARS-CoV-2 Mpro A173V 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, CHLORIDE ION, ...
Authors:Tang, S, Kenneson, J.R, Anderson, K.S.
Deposit date:2024-06-25
Release date:2025-02-05
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

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PDB entries from 2025-07-09

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