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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)

All entries (4406)Repr. entries (1944)Latest entries (19)

8F02

SARS-CoV-2 Main Protease (Mpro) in Complex with ML2006a4
Descriptor:	(1R,2S,5S)-N-{(2S,3R)-4-(3,3-dimethylazetidin-1-yl)-3-hydroxy-4-oxo-1-[(3S)-2-oxopiperidin-3-yl]butan-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:	Westberg, M, Fernandez, D, Lin, M.Z.
Deposit date:	2022-11-01
Release date:	2023-10-11
Last modified:	2024-03-20
Method:	X-RAY DIFFRACTION (2 Å)
Cite:	An orally bioavailable SARS-CoV-2 main protease inhibitor exhibits improved affinity and reduced sensitivity to mutations. Sci Transl Med, 16, 2024

8F2C

SARS-CoV-2 Main Protease (Mpro) in Complex with ML3006a
Descriptor:	(1R,2S,5S)-N-[(2S,3R)-4-(azetidin-1-yl)-3-hydroxy-4-oxo-1-(2-oxopyrrolidin-1-yl)butan-2-yl]-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide, 3C-like proteinase nsp5, CHLORIDE ION
Authors:	Westberg, M, Fernandez, D, Lin, M.Z.
Deposit date:	2022-11-07
Release date:	2023-10-11
Last modified:	2024-03-20
Method:	X-RAY DIFFRACTION (1.95 Å)
Cite:	An orally bioavailable SARS-CoV-2 main protease inhibitor exhibits improved affinity and reduced sensitivity to mutations. Sci Transl Med, 16, 2024

8F2D

SARS-CoV-2 Main Protease (Mpro) in Complex with ML4006a
Descriptor:	(1R,2S,5S)-N-[(2S,3R)-4-(azetidin-1-yl)-3-hydroxy-4-oxo-1-(2-oxopiperidin-1-yl)butan-2-yl]-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide, 3C-like proteinase nsp5, CHLORIDE ION
Authors:	Westberg, M, Fernandez, D, Lin, M.Z.
Deposit date:	2022-11-07
Release date:	2023-10-11
Last modified:	2024-03-20
Method:	X-RAY DIFFRACTION (1.95 Å)
Cite:	An orally bioavailable SARS-CoV-2 main protease inhibitor exhibits improved affinity and reduced sensitivity to mutations. Sci Transl Med, 16, 2024

8H3G

Crystal Structure of SARS-CoV-2 Main Protease (Mpro) E166V Mutant in Complex with Inhibitor Enstrelvir
Descriptor:	3C-like proteinase nsp5, 6-[(6-chloranyl-2-methyl-indazol-5-yl)amino]-3-[(1-methyl-1,2,4-triazol-3-yl)methyl]-1-[[2,4,5-tris(fluoranyl)phenyl]methyl]-1,3,5-triazine-2,4-dione, GLYCEROL
Authors:	Wang, H, Lin, M, Duan, Y, Zhang, X, Zhou, H, Bian, Q, Liu, X, Rao, Z, Yang, H.
Deposit date:	2022-10-08
Release date:	2023-10-11
Last modified:	2023-10-25
Method:	X-RAY DIFFRACTION (1.46 Å)
Cite:	Molecular mechanisms of SARS-CoV-2 resistance to nirmatrelvir. Nature, 622, 2023

8H3K

Crystal Structure of SARS-CoV-2 Main Protease (Mpro) Double Mutant (L50F and E166V) in Complex with Inhibitor Enstrelvir
Descriptor:	3-(4-AMINO-2-METHYL-PYRIMIDIN-5-YLMETHYL)-5-(2-HYDROXY-ETHYL)-4-METHYL-THIAZOL-3-IUM, 3C-like proteinase nsp5, 6-[(6-chloranyl-2-methyl-indazol-5-yl)amino]-3-[(1-methyl-1,2,4-triazol-3-yl)methyl]-1-[[2,4,5-tris(fluoranyl)phenyl]methyl]-1,3,5-triazine-2,4-dione, ...
Authors:	Wang, H, Lin, M, Duan, Y, Zhang, X, Zhou, H, Bian, Q, Liu, X, Rao, Z, Yang, H.
Deposit date:	2022-10-08
Release date:	2023-10-11
Last modified:	2023-10-25
Method:	X-RAY DIFFRACTION (1.8 Å)
Cite:	Molecular mechanisms of SARS-CoV-2 resistance to nirmatrelvir. Nature, 622, 2023

8H3L

Crystal Structure of SARS-CoV-2 Main Protease (Mpro) Double Mutant (T21I and E166V) in Complex with Inhibitor Enstrelvir
Descriptor:	3C-like proteinase nsp5, 6-[(6-chloranyl-2-methyl-indazol-5-yl)amino]-3-[(1-methyl-1,2,4-triazol-3-yl)methyl]-1-[[2,4,5-tris(fluoranyl)phenyl]methyl]-1,3,5-triazine-2,4-dione
Authors:	Wang, H, Lin, M, Duan, Y, Zhang, X, Zhou, H, Bian, Q, Liu, X, Rao, Z, Yang, H.
Deposit date:	2022-10-08
Release date:	2023-10-11
Last modified:	2023-10-25
Method:	X-RAY DIFFRACTION (2.3 Å)
Cite:	Molecular mechanisms of SARS-CoV-2 resistance to nirmatrelvir. Nature, 622, 2023

8H4Y

Crystal Structure of SARS-CoV-2 Main Protease (Mpro) F140L Mutant in Complex with Inhibitor 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:	Lin, M, Liu, X.
Deposit date:	2022-10-11
Release date:	2023-10-11
Last modified:	2023-10-25
Method:	X-RAY DIFFRACTION (2.25 Å)
Cite:	Molecular mechanisms of SARS-CoV-2 resistance to nirmatrelvir. Nature, 622, 2023

8H51

Crystal Structure of SARS-CoV-2 Main Protease (Mpro) Double Mutant (T21I and E166V) in Complex with Inhibitor 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:	Lin, M, Liu, X.
Deposit date:	2022-10-11
Release date:	2023-10-11
Last modified:	2023-10-25
Method:	X-RAY DIFFRACTION (2.18 Å)
Cite:	Molecular mechanisms of SARS-CoV-2 resistance to nirmatrelvir. Nature, 622, 2023

8H57

Crystal Structure of SARS-CoV-2 Main Protease (Mpro) A193P Mutant in Complex with Inhibitor 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:	Lin, M, Liu, X.
Deposit date:	2022-10-12
Release date:	2023-10-11
Last modified:	2023-10-25
Method:	X-RAY DIFFRACTION (1.55 Å)
Cite:	Molecular mechanisms of SARS-CoV-2 resistance to nirmatrelvir. Nature, 622, 2023

8H5F

Crystal Structure of SARS-CoV-2 Main Protease (Mpro) L167F Mutant in Complex with Inhibitor 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:	Lin, M, Liu, X.
Deposit date:	2022-10-13
Release date:	2023-10-11
Last modified:	2023-10-25
Method:	X-RAY DIFFRACTION (1.79 Å)
Cite:	Molecular mechanisms of SARS-CoV-2 resistance to nirmatrelvir. Nature, 622, 2023

8H5P

Crystal Structure of SARS-CoV-2 Main Protease (Mpro) Double Mutant (L50F and E166V) in Complex with Inhibitor 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:	Lin, M, Liu, X.
Deposit date:	2022-10-13
Release date:	2023-10-11
Last modified:	2023-10-25
Method:	X-RAY DIFFRACTION (1.67 Å)
Cite:	Molecular mechanisms of SARS-CoV-2 resistance to nirmatrelvir. Nature, 622, 2023

8H6I

The crystal structure of SARS-CoV-2 3C-like protease Double Mutant (L50F and E166V) in complex with a traditional Chinese Medicine Inhibitors
Descriptor:	(1beta,6beta,7beta,8alpha,9beta,10alpha,13alpha,14R,16beta)-1,6,7,14-tetrahydroxy-7,20-epoxykauran-15-one, 3C-like proteinase nsp5
Authors:	Lin, M, Liu, X.
Deposit date:	2022-10-17
Release date:	2023-10-11
Last modified:	2023-10-25
Method:	X-RAY DIFFRACTION (1.9 Å)
Cite:	Molecular mechanisms of SARS-CoV-2 resistance to nirmatrelvir. Nature, 622, 2023

8H6N

Crystal structure of SARS-CoV-2 main protease (Mpro) Mutant (T21I) in complex with protease inhibitor 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, 2-(diethylamino)-N-(2,6-dimethylphenyl)ethanamide, 3C-like proteinase nsp5
Authors:	Lin, M, Liu, X.
Deposit date:	2022-10-18
Release date:	2023-10-11
Last modified:	2023-10-25
Method:	X-RAY DIFFRACTION (1.65 Å)
Cite:	Molecular mechanisms of SARS-CoV-2 resistance to nirmatrelvir. Nature, 622, 2023

8H7K

SARS-CoV-2 Mpro Double Mutant (H41A and T21I) in complex with nsp4/5 peptidyl substrate
Descriptor:	3C-like proteinase nsp5, nsp4/5 peptidyl substrate
Authors:	Lin, M, Liu, X.
Deposit date:	2022-10-20
Release date:	2023-10-11
Last modified:	2023-10-25
Method:	X-RAY DIFFRACTION (1.45 Å)
Cite:	Molecular mechanisms of SARS-CoV-2 resistance to nirmatrelvir. Nature, 622, 2023

8H7W

Crystal structure of SARS-CoV-2 main protease (Mpro) Mutant (S144A) in complex with protease inhibitor 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:	Lin, M, Liu, X.
Deposit date:	2022-10-21
Release date:	2023-10-11
Last modified:	2023-10-25
Method:	X-RAY DIFFRACTION (1.6 Å)
Cite:	Molecular mechanisms of SARS-CoV-2 resistance to nirmatrelvir. Nature, 622, 2023

8H82

Crystal structure of SARS-CoV-2 main protease (Mpro) Mutant (E166V) in complex with protease inhibitor 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:	Lin, M, Liu, X.
Deposit date:	2022-10-21
Release date:	2023-10-11
Last modified:	2023-10-25
Method:	X-RAY DIFFRACTION (1.93 Å)
Cite:	Molecular mechanisms of SARS-CoV-2 resistance to nirmatrelvir. Nature, 622, 2023

8HBK

The crystal structure of SARS-CoV-2 3CL protease in complex with Ensitrelvir
Descriptor:	3C-like proteinase nsp5, 6-[(6-chloranyl-2-methyl-indazol-5-yl)amino]-3-[(1-methyl-1,2,4-triazol-3-yl)methyl]-1-[[2,4,5-tris(fluoranyl)phenyl]methyl]-1,3,5-triazine-2,4-dione
Authors:	Lin, M.
Deposit date:	2022-10-29
Release date:	2023-10-11
Last modified:	2023-10-25
Method:	X-RAY DIFFRACTION (1.8 Å)
Cite:	Molecular mechanisms of SARS-CoV-2 resistance to nirmatrelvir. Nature, 622, 2023

8F4S

Crystal Structure of the SARS-CoV-2 2'-O-Methyltransferase with Compound 5a bound to the Cryptic Pocket of nsp16
Descriptor:	2'-O-methyltransferase, 4-[(E)-2-(2,4-dichlorophenyl)ethenyl]-6-(trifluoromethyl)pyrimidin-2-ol, FORMIC ACID, ...
Authors:	Minasov, G, Shuvalova, L, Brunzelle, J.S, Rosas-Lemus, M, Kiryukhina, O, Satchell, K.J.F, Center for Structural Biology of Infectious Diseases (CSBID)
Deposit date:	2022-11-11
Release date:	2023-10-18
Last modified:	2023-10-25
Method:	X-RAY DIFFRACTION (2.15 Å)
Cite:	Discovery of a Druggable, Cryptic Pocket in SARS-CoV-2 nsp16 Using Allosteric Inhibitors. Acs Infect Dis., 9, 2023

8F4Y

Crystal Structure of SARS-CoV-2 2'-O-Methyltransferase in Complex with Compound 5a covalently bound to nsp16 and nsp10
Descriptor:	2'-O-methyltransferase, 4-[(E)-2-(2,4-dichlorophenyl)ethenyl]-6-(trifluoromethyl)pyrimidin-2-ol, 4-[2-(2,4-dichlorophenyl)ethyl]-6-(trifluoromethyl)pyrimidin-2-ol, ...
Authors:	Minasov, G, Shuvalova, L, Brunzelle, J.S, Rosas-Lemus, M, Kiryukhina, O, Satchell, K.J.F, Center for Structural Biology of Infectious Diseases (CSBID)
Deposit date:	2022-11-11
Release date:	2023-10-18
Last modified:	2023-10-25
Method:	X-RAY DIFFRACTION (2.13 Å)
Cite:	Discovery of a Druggable, Cryptic Pocket in SARS-CoV-2 nsp16 Using Allosteric Inhibitors. Acs Infect Dis., 9, 2023

8H5T

Crystal structure of SARS-CoV-2 spike receptor-binding domain in complex with neutralizing nanobody Nb-015
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, Nanobody Nb-015, Spike protein S1
Authors:	Yang, J, Lin, S, Lu, G.W.
Deposit date:	2022-10-13
Release date:	2023-10-18
Last modified:	2023-12-13
Method:	X-RAY DIFFRACTION (2 Å)
Cite:	Development of a bispecific nanobody conjugate broadly neutralizes diverse SARS-CoV-2 variants and structural basis for its broad neutralization. Plos Pathog., 19, 2023

8H5U

Crystal structure of SARS-CoV-2 spike receptor-binding domain in complex with neutralizing nanobody Nb-021
Descriptor:	2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Nanobody Nb-021, ...
Authors:	Yang, J, Lin, S, Lu, G.W.
Deposit date:	2022-10-13
Release date:	2023-10-18
Last modified:	2023-12-13
Method:	X-RAY DIFFRACTION (2.401 Å)
Cite:	Development of a bispecific nanobody conjugate broadly neutralizes diverse SARS-CoV-2 variants and structural basis for its broad neutralization. Plos Pathog., 19, 2023

8IFP

SARS-CoV-2 3CL protease (3CLpro) in complex with compound 1
Descriptor:	(1R,2S,5S)-3-[(2S)-2-(tert-butylcarbamoylamino)-3,3-dimethyl-butanoyl]-6,6-dimethyl-N-[(2S)-1-oxidanylidene-3-[(3S)-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]-3-azabicyclo[3.1.0]hexane-2-carboxamide, 3C-like proteinase nsp5
Authors:	Su, H.X, Zhao, W.F, Xie, H, Nie, T.Q, Li, M.J, Xu, Y.C.
Deposit date:	2023-02-19
Release date:	2023-10-18
Last modified:	2024-05-08
Method:	X-RAY DIFFRACTION (1.78 Å)
Cite:	Structure-based development and preclinical evaluation of the SARS-CoV-2 3C-like protease inhibitor simnotrelvir. Nat Commun, 14, 2023

8IFQ

SARS-CoV-2 3CL protease (3CLpro) in complex with compound 2
Descriptor:	(1R,2S,5S)-3-[N-(tert-butylcarbamoyl)-3-methyl-L-valyl]-N-{(1Z,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2-carboxamide, 3C-like proteinase nsp5
Authors:	Su, H.X, Zhao, W.F, Xie, H, Nie, T.Q, Li, M.J, Xu, Y.C.
Deposit date:	2023-02-19
Release date:	2023-10-18
Last modified:	2024-05-08
Method:	X-RAY DIFFRACTION (1.96 Å)
Cite:	Structure-based development and preclinical evaluation of the SARS-CoV-2 3C-like protease inhibitor simnotrelvir. Nat Commun, 14, 2023

8IFR

SARS-CoV-2 3CL protease (3CLpro) in complex with compound 3
Descriptor:	(1R,2S,5S)-3-[(2S)-2-(tert-butylcarbamoylamino)-3,3-dimethyl-butanoyl]-6,6-dimethyl-N-[(2S)-5-oxidanylidene-1-[(3S)-2-oxidanylidenepyrrolidin-3-yl]hex-3-en-2-yl]-3-azabicyclo[3.1.0]hexane-2-carboxamide, 3C-like proteinase nsp5
Authors:	Su, H.X, Zhao, W.F, Xie, H, Nie, T.Q, Li, M.J, Xu, Y.C.
Deposit date:	2023-02-19
Release date:	2023-10-18
Last modified:	2024-05-08
Method:	X-RAY DIFFRACTION (1.66 Å)
Cite:	Structure-based development and preclinical evaluation of the SARS-CoV-2 3C-like protease inhibitor simnotrelvir. Nat Commun, 14, 2023

8IFS

SARS-CoV-2 3CL protease (3CLpro) in complex with compound 7
Descriptor:	(8~{S})-7-[(2~{S})-2-(~{tert}-butylcarbamoylamino)-3,3-dimethyl-butanoyl]-~{N}-[(1~{S})-1-cyano-2-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]ethyl]-1,4-dithia-7-azaspiro[4.4]nonane-8-carboxamide, 3C-like proteinase nsp5
Authors:	Su, H.X, Zhao, W.F, Xie, H, Nie, T.Q, Li, M.J, Xu, Y.C.
Deposit date:	2023-02-19
Release date:	2023-10-18
Last modified:	2024-05-08
Method:	X-RAY DIFFRACTION (2.46 Å)
Cite:	Structure-based development and preclinical evaluation of the SARS-CoV-2 3C-like protease inhibitor simnotrelvir. Nat Commun, 14, 2023

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Total results:	4406
Displayed results:	25
Sorted by:	Release date (from oldest)