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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
7F5R
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Crystal structure of SARS-CoV-2 Y453F-RBD bound to mink 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, Spike protein S1, ...
Authors:Wang, X.Q, Ding, Q, Lan, J, Ren, W.L.
Deposit date:2021-06-22
Release date:2022-06-22
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (3.01 Å)
Cite:Crystal structure of SARS-CoV-2 Y453F-RBD bound to mink ACE2
To Be Published
7FC5
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Crystal structure of SARS-CoV-2 RBD and horse ACE2
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Angiotensin-converting enzyme, Spike protein S1
Authors:Wang, X.Q, Lan, J, Ge, J.W.
Deposit date:2021-07-13
Release date:2022-06-22
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.894 Å)
Cite:Structural insights into the binding of SARS-CoV-2, SARS-CoV, and hCoV-NL63 spike receptor-binding domain to horse ACE2.
Structure, 30, 2022
7MB4
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SARS-CoV-2 Main Protease (Mpro) C145A in Complex with Cleavage Site Nsp4/5 (P6-P1)
Descriptor: 3C-like proteinase, THR-SER-ALA-VAL-LEU-GLN
Authors:Lockbaum, G.J, Schiffer, C.A.
Deposit date:2021-03-31
Release date:2022-06-22
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (1.83 Å)
Cite:Defining the substrate envelope of SARS-CoV-2 main protease to predict and avoid drug resistance.
Nat Commun, 13, 2022
7MB5
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SARS-CoV-2 Main Protease (Mpro) C145A in Complex with Cleavage Site Nsp5/6 (P6-P1)
Descriptor: 3C-like proteinase, SER-GLY-VAL-THR-PHE-GLN
Authors:Lockbaum, G.J, Schiffer, C.A.
Deposit date:2021-03-31
Release date:2022-06-22
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (1.6 Å)
Cite:Defining the substrate envelope of SARS-CoV-2 main protease to predict and avoid drug resistance.
Nat Commun, 13, 2022
7MB6
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SARS-CoV-2 Main Protease (Mpro) C145A in Complex with Cleavage Site Nsp6/7 (P6-P1)
Descriptor: 3C-like proteinase, LYS-VAL-ALA-THR-VAL-GLN
Authors:Lockbaum, G.J, Schiffer, C.A.
Deposit date:2021-03-31
Release date:2022-06-22
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (2.21 Å)
Cite:Defining the substrate envelope of SARS-CoV-2 main protease to predict and avoid drug resistance.
Nat Commun, 13, 2022
7MB7
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SARS-CoV-2 Main Protease (Mpro) C145A in Complex with Cleavage Site Nsp7/8 (P6-P1)
Descriptor: 3C-like proteinase, ASN-ARG-ALA-THR-LEU-GLN
Authors:Lockbaum, G.J, Schiffer, C.A.
Deposit date:2021-03-31
Release date:2022-06-22
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (2.02 Å)
Cite:Defining the substrate envelope of SARS-CoV-2 main protease to predict and avoid drug resistance.
Nat Commun, 13, 2022
7MB8
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SARS-CoV-2 Main Protease (Mpro) C145A in Complex with Cleavage Site Nsp8/9 (P6-P1)
Descriptor: 3C-like proteinase, SER-ALA-VAL-LYS-LEU-GLN
Authors:Lockbaum, G.J, Schiffer, C.A.
Deposit date:2021-03-31
Release date:2022-06-22
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (1.62 Å)
Cite:Defining the substrate envelope of SARS-CoV-2 main protease to predict and avoid drug resistance.
Nat Commun, 13, 2022
7MB9
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SARS-CoV-2 Main Protease (Mpro) C145A in Complex with Cleavage Site Nsp10/11 (P6-P1)
Descriptor: 3C-like proteinase, ARG-GLU-PRO-MET-LEU-GLN
Authors:Lockbaum, G.J, Schiffer, C.A.
Deposit date:2021-03-31
Release date:2022-06-22
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (1.81 Å)
Cite:Defining the substrate envelope of SARS-CoV-2 main protease to predict and avoid drug resistance.
Nat Commun, 13, 2022
7T70
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Co-crystal structure of SARS-CoV-2 Mpro C145A with substrate peptide 4/5
Descriptor: 3C-like proteinase, DIMETHYL SULFOXIDE, GLYCEROL, ...
Authors:Shaqra, A.M, Schiffer, C.A.
Deposit date:2021-12-14
Release date:2022-06-22
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (2.35 Å)
Cite:Defining the substrate envelope of SARS-CoV-2 main protease to predict and avoid drug resistance.
Nat Commun, 13, 2022
7T8M
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BU of 7t8m by Molmil
Co-crystal structure of SARS-CoV-2 Mpro C145A with substrate peptide 5/6
Descriptor: 3C-like proteinase, DIMETHYL SULFOXIDE, GLYCEROL, ...
Authors:Shaqra, A.M, Schiffer, C.A.
Deposit date:2021-12-16
Release date:2022-06-22
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (1.6 Å)
Cite:Defining the substrate envelope of SARS-CoV-2 main protease to predict and avoid drug resistance.
Nat Commun, 13, 2022
7T8R
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Co-crystal structure of SARS-CoV-2 Mpro C145A with substrate peptide 7/8
Descriptor: 1,2-ETHANEDIOL, 3C-like proteinase, GLYCEROL, ...
Authors:Shaqra, A.M, Schiffer, C.A.
Deposit date:2021-12-16
Release date:2022-06-22
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (1.74 Å)
Cite:Defining the substrate envelope of SARS-CoV-2 main protease to predict and avoid drug resistance.
Nat Commun, 13, 2022
7T9Y
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BU of 7t9y by Molmil
Co-crystal structure of SARS-CoV-2 Mpro C145A with substrate peptide 8/9
Descriptor: 3C-like proteinase, GLYCEROL, Nonstructural protein 8/9
Authors:Shaqra, A.M, Schiffer, C.A.
Deposit date:2021-12-20
Release date:2022-06-22
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (2.18 Å)
Cite:Defining the substrate envelope of SARS-CoV-2 main protease to predict and avoid drug resistance.
Nat Commun, 13, 2022
7TA4
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BU of 7ta4 by Molmil
Co-crystal structure of SARS-CoV-2 Mpro C145A with substrate peptide 9/10
Descriptor: 3C-like proteinase, Nonstructural protein 9/10
Authors:Shaqra, A.M, Schiffer, C.A.
Deposit date:2021-12-20
Release date:2022-06-22
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (1.78 Å)
Cite:Defining the substrate envelope of SARS-CoV-2 main protease to predict and avoid drug resistance.
Nat Commun, 13, 2022
7TA7
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BU of 7ta7 by Molmil
Co-crystal structure of SARS-CoV-2 Mpro C145A with substrate peptide 10/11
Descriptor: 3C-like proteinase, GLYCEROL, Nonstructural protein 10/11
Authors:Shaqra, A.M, Schiffer, C.A.
Deposit date:2021-12-20
Release date:2022-06-22
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (2.28 Å)
Cite:Defining the substrate envelope of SARS-CoV-2 main protease to predict and avoid drug resistance.
Nat Commun, 13, 2022
7TB2
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BU of 7tb2 by Molmil
Co-crystal structure of SARS-CoV-2 Mpro C145A with substrate peptide 12/13
Descriptor: 3C-like proteinase, Nonstructural protein 12/13
Authors:Shaqra, A.M, Schiffer, C.A.
Deposit date:2021-12-21
Release date:2022-06-22
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Defining the substrate envelope of SARS-CoV-2 main protease to predict and avoid drug resistance.
Nat Commun, 13, 2022
7TBT
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BU of 7tbt by Molmil
Co-crystal structure of SARS-CoV-2 Mpro C145A with substrate peptide 13/14
Descriptor: 3C-like proteinase, Nonstructural protein 13/14
Authors:Shaqra, A.M, Schiffer, C.A.
Deposit date:2021-12-22
Release date:2022-06-22
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (2.45 Å)
Cite:Defining the substrate envelope of SARS-CoV-2 main protease to predict and avoid drug resistance.
Nat Commun, 13, 2022
7TC4
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Co-crystal structure of SARS-CoV-2 Mpro C145A with substrate peptide 15/16
Descriptor: 3C-like proteinase, GLYCEROL, Nonstructural protein 15/16
Authors:Shaqra, A.M, Schiffer, C.A.
Deposit date:2021-12-22
Release date:2022-06-22
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (1.94 Å)
Cite:Defining the substrate envelope of SARS-CoV-2 main protease to predict and avoid drug resistance.
Nat Commun, 13, 2022
7TQ2
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Structure of SARS-CoV-2 3CL protease in complex with the cyclopropane based inhibitor 1c
Descriptor: 3C-like proteinase, N-{(2S)-1-oxo-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-N~2~-({[(1R,2R)-2-phenylcyclopropyl]methoxy}carbonyl)-L-leucinamide
Authors:Lovell, S, Kashipathy, M.M, Battaile, K.P, Nguyen, H.N, Chamandi, S.D, Picard, H.R, Madden, T.K, Thruman, H.A, Kim, Y, Groutas, W.C, Chang, K.O.
Deposit date:2022-01-26
Release date:2022-06-22
Last modified:2023-10-25
Method:X-RAY DIFFRACTION (2.3 Å)
Cite:Broad-Spectrum Cyclopropane-Based Inhibitors of Coronavirus 3C-like Proteases: Biochemical, Structural, and Virological Studies.
Acs Pharmacol Transl Sci, 6, 2023
7TQ3
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BU of 7tq3 by Molmil
Structure of SARS-CoV-2 3CL protease in complex with the cyclopropane based inhibitor 5c
Descriptor: 3C-like proteinase, N~2~-({[(1R,2R)-2-(3-fluorophenyl)cyclopropyl]methoxy}carbonyl)-N-{(2S)-1-oxo-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-leucinamide
Authors:Lovell, S, Battaile, K.P, Nguyen, H.N, Chamandi, S.D, Picard, H.R, Madden, T.K, Thruman, H.A, Kim, Y, Groutas, W.C, Chang, K.O.
Deposit date:2022-01-26
Release date:2022-06-22
Last modified:2023-10-25
Method:X-RAY DIFFRACTION (2 Å)
Cite:Broad-Spectrum Cyclopropane-Based Inhibitors of Coronavirus 3C-like Proteases: Biochemical, Structural, and Virological Studies.
Acs Pharmacol Transl Sci, 6, 2023
7TQ4
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Structure of SARS-CoV-2 3CL protease in complex with the cyclopropane based inhibitor 6c
Descriptor: 3C-like proteinase, N~2~-({[(1R,2R)-2-(3-chlorophenyl)cyclopropyl]methoxy}carbonyl)-N-{(2S)-1-oxo-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-leucinamide
Authors:Lovell, S, Battaile, K.P, Nguyen, H.N, Chamandi, S.D, Picard, H.R, Madden, T.K, Thruman, H.A, Kim, Y, Groutas, W.C, Chang, K.O.
Deposit date:2022-01-26
Release date:2022-06-22
Last modified:2023-10-25
Method:X-RAY DIFFRACTION (2.45 Å)
Cite:Broad-Spectrum Cyclopropane-Based Inhibitors of Coronavirus 3C-like Proteases: Biochemical, Structural, and Virological Studies.
Acs Pharmacol Transl Sci, 6, 2023
7UXX
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Crystal structure of SARS-CoV-2 nucleocapsid protein C-terminal domain
Descriptor: ACETATE ION, GLYCEROL, Nucleoprotein
Authors:Bezerra, E.H.S, Tonoli, C.C.C, Soprano, A.S, Franchini, K.G, Trivella, D.B.B, Benedetti, C.E.
Deposit date:2022-05-06
Release date:2022-06-22
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (1.85 Å)
Cite:Discovery and structural characterization of chicoric acid as a SARS-CoV-2 nucleocapsid protein ligand and RNA binding disruptor.
Sci Rep, 12, 2022
7UXZ
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Crystal structure of SARS-CoV-2 nucleocapsid protein C-terminal domain complexed with Chicoric acid
Descriptor: (2R,3R)-2,3-bis{[(2E)-3-(3,4-dihydroxyphenyl)prop-2-enoyl]oxy}butanedioic acid, CHLORIDE ION, DI(HYDROXYETHYL)ETHER, ...
Authors:Bezerra, E.H.S, Tonoli, C.C.C, Soprano, A.S, Franchini, K.G, Trivella, D.B.B, Benedetti, C.E.
Deposit date:2022-05-06
Release date:2022-06-22
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (1.733 Å)
Cite:Discovery and structural characterization of chicoric acid as a SARS-CoV-2 nucleocapsid protein ligand and RNA binding disruptor.
Sci Rep, 12, 2022
7V61
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BU of 7v61 by Molmil
ACE2 -Targeting Monoclonal Antibody as Potent and Broad-Spectrum Coronavirus Blocker
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 3E8, ...
Authors:Yan, R.H, Zhang, Y.Y, Li, Y.N, Zhou, Q.
Deposit date:2021-08-18
Release date:2022-06-22
Method:ELECTRON MICROSCOPY (3.2 Å)
Cite:ACE2-targeting monoclonal antibody as potent and broad-spectrum coronavirus blocker.
Signal Transduct Target Ther, 6, 2021
7VRV
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BU of 7vrv by Molmil
VAS5 Spike (1 RBD up)
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:Zhen, C, Wang, X.
Deposit date:2021-10-25
Release date:2022-06-22
Method:ELECTRON MICROSCOPY (4.2 Å)
Cite:VAS5 Spike(1 RBD up)
To Be Published
7VRW
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VAS5 Spike (3 RBD down)
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:Zhen, C, Wang, X.
Deposit date:2021-10-25
Release date:2022-06-22
Method:ELECTRON MICROSCOPY (3.6 Å)
Cite:VAS5 Spike (3-RBD down)
To Be Published

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