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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
8ZYF
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BU of 8zyf by Molmil
Crystal structure of ZW2G10 Fab in complex with omicron RBD
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Spike protein S1, ZW2G10 fab heavy chain, ...
Authors:Yuan, H.Y, Li, J.M.
Deposit date:2024-06-17
Release date:2025-03-26
Last modified:2025-04-16
Method:X-RAY DIFFRACTION (2.6 Å)
Cite:Nasal delivery of secretory IgA confers enhanced neutralizing activity against Omicron variants compared to its IgG counterpart.
Mol.Ther., 33, 2025
9D2K
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BU of 9d2k by Molmil
SARS-CoV-2 Papain-like Protease (PLpro) complex with covalent inhibitor Jun13567
Descriptor: 2,3-DIHYDROXY-1,4-DITHIOBUTANE, 2-(3-{2-[4-(3,3-dimethylazetidin-1-yl)-4-oxobutanoyl]hydrazin-1-yl}-3-oxopropyl)-N-{(1R)-1-[(3P,5P)-3-(1-ethyl-1H-pyrazol-3-yl)-5-(1-methyl-1H-pyrazol-4-yl)phenyl]ethyl}benzamide, CHLORIDE ION, ...
Authors:Ansari, A, Tan, B, Ruiz, F.X, Arnold, E, Wang, J.
Deposit date:2024-08-08
Release date:2025-03-26
Method:X-RAY DIFFRACTION (2.7 Å)
Cite:Structure-Based Design of Covalent SARS-CoV-2 Papain-like Protease Inhibitors.
J.Med.Chem., 67, 2024
9GXE
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BU of 9gxe by Molmil
Structure of the SARS-CoV spike glycoprotein in complex with a homotrimeric Bicycle molecule
Descriptor: 2,4,6-tris(chloromethyl)-1,3,5-triazine, 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:Drulyte, I, Pellegrino, S, Harman, M, Bezerra, G.A.
Deposit date:2024-09-30
Release date:2025-03-26
Method:ELECTRON MICROSCOPY (2.3 Å)
Cite:Structure of the SARS-CoV spike glycoprotein in complex with a homotrimeric Bicycle molecule
To Be Published
9GXG
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BU of 9gxg by Molmil
Structure of the SARS-CoV spike glycoprotein in complex with a biparatopic Bicycle molecule
Descriptor: 1-[3,5-bis(2-chloranylethanoyl)-1,3,5-triazinan-1-yl]-2-chloranyl-ethanone, 2,4,6-tris(chloromethyl)-1,3,5-triazine, 2-acetamido-2-deoxy-beta-D-glucopyranose, ...
Authors:Drulyte, I, Pellegrino, S, Harman, M, Bezerra, G.A.
Deposit date:2024-09-30
Release date:2025-03-26
Last modified:2025-07-02
Method:ELECTRON MICROSCOPY (1.92 Å)
Cite:Structure of the SARS-CoV spike glycoprotein in complex with a biparatopic Bicycle molecule
To Be Published
8YWE
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BU of 8ywe by Molmil
Local refinement of SARS-CoV-2 Omicron BA.2.86 S complexed with Abs G7-Fc
Descriptor: 7F3 scFv, GW01 scFv, Spike protein S1
Authors:Ma, Y, Liu, Q, Rehati, P, Zhang, Z.
Deposit date:2024-03-31
Release date:2025-04-02
Method:ELECTRON MICROSCOPY (2.69 Å)
Cite:Impact of scFv Sequence and Position on the Functionality of Bispecific Antibodies against Omicron Variants EG.5 and BA.2.86
To Be Published
8ZFV
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BU of 8zfv by Molmil
Crystal Structure of C-terminal domain of nucleocapsid protein from SARS-CoV-2 in complex with ceftriaxone
Descriptor: Ceftriaxone, DI(HYDROXYETHYL)ETHER, Nucleoprotein, ...
Authors:Dhaka, P, Mahto, J.K, Tomar, S, Kumar, P.
Deposit date:2024-05-08
Release date:2025-04-02
Method:X-RAY DIFFRACTION (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
9IN1
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BU of 9in1 by Molmil
Crystal Structure of C-terminal domain of nucleocapsid protein from SARS-CoV-2
Descriptor: Nucleoprotein
Authors:Dhaka, P, Mahto, J.K, Tomar, S, Kumar, P.
Deposit date:2024-07-05
Release date:2025-04-02
Method:X-RAY DIFFRACTION (1.4 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
9KR5
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BU of 9kr5 by Molmil
Crystal structure of SARS-CoV-2 main protease in complex with compound 3
Descriptor: (6~{E})-6-(6-chloranyl-2-methyl-indazol-5-yl)imino-3-[5-[(3~{S})-oxolan-3-yl]oxypyridin-3-yl]-1-[[2,4,5-tris(fluoranyl)phenyl]methyl]-1,3,5-triazinane-2,4-dione, 3C-like proteinase nsp5
Authors:Zhong, Y, Zhao, L, Zhang, W, Peng, W.
Deposit date:2024-11-27
Release date:2025-04-02
Method:X-RAY DIFFRACTION (1.92 Å)
Cite:Expanding the utilization of binding pockets proves to be effective for noncovalent small molecule inhibitors against SARS-CoV-2 M pro.
Eur.J.Med.Chem., 289, 2025
9KSH
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BU of 9ksh by Molmil
Crystal structure of SARS-CoV-2 main protease in complex with compound 1
Descriptor: 3C-like proteinase nsp5, 6-[(6-chloranyl-2-methyl-indazol-5-yl)amino]-3-pyridin-3-yl-1-[[2,4,5-tris(fluoranyl)phenyl]methyl]-1,3,5-triazine-2,4-dione
Authors:Zhong, Y, Zhao, L, Zhang, W, Peng, W.
Deposit date:2024-11-29
Release date:2025-04-02
Method:X-RAY DIFFRACTION (1.91 Å)
Cite:Expanding the utilization of binding pockets proves to be effective for noncovalent small molecule inhibitors against SARS-CoV-2 M pro.
Eur.J.Med.Chem., 289, 2025
9KSI
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BU of 9ksi by Molmil
Crystal Structure of SARS-CoV-2 main protease in complex with compound 5
Descriptor: (6E)-1-[[5-chloranyl-4-fluoranyl-2-(4-fluoranylphenoxy)phenyl]methyl]-6-(6-chloranyl-2-methyl-indazol-5-yl)imino-3-(5-methoxypyridin-3-yl)-1,3,5-triazinane-2,4-dione, 3C-like proteinase nsp5
Authors:Zhong, Y, Zhao, L, Zhang, W, Peng, W.
Deposit date:2024-11-29
Release date:2025-04-02
Method:X-RAY DIFFRACTION (2.3 Å)
Cite:Expanding the utilization of binding pockets proves to be effective for noncovalent small molecule inhibitors against SARS-CoV-2 M pro.
Eur.J.Med.Chem., 289, 2025
9KSJ
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BU of 9ksj by Molmil
Crystal structure of SARS-CoV-2 main protease in complex with compound 8
Descriptor: 3-[[(6E)-6-(6-chloranyl-2-methyl-indazol-5-yl)imino-3-[5-(2-methoxyethoxy)pyridin-3-yl]-2,4-bis(oxidanylidene)-1,3,5-triazinan-1-yl]methyl]-4-methyl-benzenecarbonitrile, 3C-like proteinase nsp5
Authors:Zhong, Y, Zhao, L, Zhang, W, Peng, W.
Deposit date:2024-11-29
Release date:2025-04-02
Method:X-RAY DIFFRACTION (1.67 Å)
Cite:Expanding the utilization of binding pockets proves to be effective for noncovalent small molecule inhibitors against SARS-CoV-2 M pro.
Eur.J.Med.Chem., 289, 2025
9KSK
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BU of 9ksk by Molmil
Crystal structure of SARS-CoV-2 main protease in complex with compound 10
Descriptor: 3C-like proteinase, 4-[4-chloranyl-2-[[(6E)-6-(6-chloranyl-2-methyl-indazol-5-yl)imino-3-(5-methylpyridin-3-yl)-2,4-bis(oxidanylidene)-1,3,5-triazinan-1-yl]methyl]-5-fluoranyl-phenoxy]-2-fluoranyl-benzenecarbonitrile
Authors:Zhong, Y, Zhao, L, Zhang, W, Peng, W.
Deposit date:2024-11-29
Release date:2025-04-02
Method:X-RAY DIFFRACTION (2.45 Å)
Cite:Expanding the utilization of binding pockets proves to be effective for noncovalent small molecule inhibitors against SARS-CoV-2 M pro.
Eur.J.Med.Chem., 289, 2025
9LBS
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BU of 9lbs by Molmil
Cryo-EM structure of Omicron BA.1 RBD complexed with ConBA-998,S309 and S304Fabs
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose, Heavy chain of ConBA-998, Heavy chain of S304 Fab, ...
Authors:Zhang, Z, Ju, B, Liu, C.
Deposit date:2025-01-03
Release date:2025-04-02
Method:ELECTRON MICROSCOPY (3.41 Å)
Cite:Cryo-EM structure of Omicron BA.1 RBD complexed with ConBA-998,S309 and S304Fabs
To Be Published
9LDS
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BU of 9lds by Molmil
Crystal structure of nanobody H145 bound to SARS-CoV-2 spike stem-helix
Descriptor: H145, Spike protein S2'
Authors:Lu, G.W, Guo, L.Y, Lin, S.
Deposit date:2025-01-06
Release date:2025-04-02
Last modified:2025-07-02
Method:X-RAY DIFFRACTION (1.6 Å)
Cite:Structural basis and mode of action for two broadly neutralizing nanobodies targeting the highly conserved spike stem-helix of sarbecoviruses including SARS-CoV-2 and its variants.
Plos Pathog., 21, 2025
9LYO
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BU of 9lyo by Molmil
Alpha SARS-CoV-2 spike protein in complex with REGN10987 Fab homologue.
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, REGN10987 Fab homologue (Heavy chain), ...
Authors:Kocharovskaya, M.V, Pichkur, E.B, Shenkarev, Z.O, Lyukmanova, E.N.
Deposit date:2025-02-20
Release date:2025-04-02
Method:ELECTRON MICROSCOPY (3.07 Å)
Cite:Structure and dynamics of Alpha B.1.1.7 SARS-CoV-2 S-protein in complex with Fab of neutralizing antibody REGN10987.
Biochem.Biophys.Res.Commun., 755, 2025
9LYP
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BU of 9lyp by Molmil
Alpha SARS-CoV-2 spike protein RBD-down in complex with REGN10987 Fab homologue (local refinement)
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, REGN10987 Fab homologue (Heavy chain), REGN10987 Fab homologue (Light chain), ...
Authors:Kocharovskaya, M.V, Pichkur, E.B, Shenkarev, Z.O, Lyukmanova, E.N.
Deposit date:2025-02-20
Release date:2025-04-02
Method:ELECTRON MICROSCOPY (3.6 Å)
Cite:Structure and dynamics of Alpha B.1.1.7 SARS-CoV-2 S-protein in complex with Fab of neutralizing antibody REGN10987.
Biochem.Biophys.Res.Commun., 755, 2025
9Q8H
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BU of 9q8h by Molmil
SARS-CoV-2 methyltransferase nsp10-16 in complex with SAM and theophylline derivative BDH 34019023
Descriptor: 1,2-ETHANEDIOL, 2'-O-methyltransferase nsp16, 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, ...
Authors:Kremling, V, Sprenger, J, Turk, D, Oberthuer, D, Kiene, A.
Deposit date:2025-02-24
Release date:2025-04-02
Method:X-RAY DIFFRACTION (1.802 Å)
Cite:Crystal structures of SARS-CoV-2 methyltransferase nsp10-16 with Cap0-site binders
To Be Published
8YWY
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BU of 8ywy by Molmil
Crystal structure of SARS-Cov-2 main protease E166N mutant in complex with Bofutrelvir
Descriptor: 3C-like proteinase nsp5, ~{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, Wang, W.W, Zhang, J, Li, J.
Deposit date:2024-04-01
Release date:2025-04-09
Method:X-RAY DIFFRACTION (1.95 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
8YWZ
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BU of 8ywz by Molmil
Crystal structure of SARS-Cov-2 main protease H163A mutant in complex with Bofutrelvir
Descriptor: 3C-like proteinase nsp5, ~{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:Zou, X.F, Wang, W.W, Zhang, J, Li, J.
Deposit date:2024-04-01
Release date:2025-04-09
Method:X-RAY DIFFRACTION (1.91 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
9CYB
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BU of 9cyb by Molmil
SARS-CoV-2 PLpro in complex with inhibitor WEHI-P1
Descriptor: Papain-like protease, SUCCINIC ACID, [(3R)-1-cyclopentylpiperidin-3-yl](6-methoxynaphthalen-2-yl)methanone
Authors:Calleja, D.J, Lechtenberg, B.C, Kuchel, N.W, Devine, S.M, Bader, S.M, Doerflinger, M, Mitchell, J.P, Lessene, G, Komander, D.
Deposit date:2024-08-01
Release date:2025-04-09
Last modified:2025-04-16
Method:X-RAY DIFFRACTION (1.98 Å)
Cite:A novel PLpro inhibitor improves outcomes in a pre-clinical model of long COVID.
Nat Commun, 16, 2025
9CYC
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BU of 9cyc by Molmil
SARS-CoV-2 PLpro in complex with inhibitor WEHI-P2
Descriptor: (E)-1-[(3R)-1-cyclopentylpiperidin-3-yl]-N-methoxy-1-(6-methoxynaphthalen-2-yl)methanimine, ACETIC ACID, GLYCEROL, ...
Authors:Calleja, D.J, Lechtenberg, B.C, Kuchel, N.W, Devine, S.M, Bader, S.M, Doerflinger, M, Mitchel, J.P, Lessene, G, Komander, D.
Deposit date:2024-08-01
Release date:2025-04-09
Last modified:2025-04-16
Method:X-RAY DIFFRACTION (2.01 Å)
Cite:A novel PLpro inhibitor improves outcomes in a pre-clinical model of long COVID.
Nat Commun, 16, 2025
9CYD
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BU of 9cyd by Molmil
SARS-CoV-2 PLpro in complex with inhibitor WEHI-P4
Descriptor: (1S,4s)-4-{(3R)-3-[(E)-(methoxyimino)(6-methoxynaphthalen-2-yl)methyl]piperidin-1-yl}cyclohexan-1-ol, CHLORIDE ION, Papain-like protease, ...
Authors:Calleja, D.J, Lechtenberg, B.C, Kuchel, N.W, Devine, S.M, Bader, S.M, Doerflinger, M, Mitchell, J.P, Lessene, G, Komander, D.
Deposit date:2024-08-02
Release date:2025-04-09
Last modified:2025-04-16
Method:X-RAY DIFFRACTION (2.8 Å)
Cite:A novel PLpro inhibitor improves outcomes in a pre-clinical model of long COVID.
Nat Commun, 16, 2025
9CYK
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BU of 9cyk by Molmil
SARS-CoV-2 PLpro in complex with inhibitor WEHI-P24
Descriptor: ACETIC ACID, GLYCEROL, Papain-like protease, ...
Authors:Calleja, D.J, Lechtenberg, B.C, Kuchel, N.W, Devine, S.M, Bader, S.M, Doerflinger, M, Mitchell, J.P, Lessene, G, Komander, D.
Deposit date:2024-08-02
Release date:2025-04-09
Last modified:2025-04-16
Method:X-RAY DIFFRACTION (1.88 Å)
Cite:A novel PLpro inhibitor improves outcomes in a pre-clinical model of long COVID.
Nat Commun, 16, 2025
9INL
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BU of 9inl by Molmil
Crystal structure of SARS-Cov-2 main protease E166R mutant in complex with Bofutrelvir
Descriptor: Replicase polyprotein 1a, ~{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:2024-07-08
Release date:2025-04-09
Method:X-RAY DIFFRACTION (2.04 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
9LUF
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BU of 9luf by Molmil
Crystal structure of SARS-Cov-2 main protease S144A 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 (1.99 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

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PDB entries from 2025-07-09

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