Loading
PDBj
English日本語简体中文繁體中文한국어
✖
MenuPDBj@FacebookPDBj@X(formerly Twitter)PDBj@BlueSkyPDBj@YouTubewwPDB FoundationwwPDBDonate
RCSB PDBPDBeBMRBAdv. SearchSearch help

COVID-19 featured content

This page is also available in: 日本語简体中文繁體中文한국어
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)
8UE0
DownloadVisualize
BU of 8ue0 by Molmil
Crystal structure of SARS-CoV-2 3CL protease with inhibitor 47
Descriptor: 2,4-dichloro-Nalpha-[(2R)-2-chloro-3-(2-cyanophenyl)propanoyl]-N-[(2S)-4-{[4-(dimethylamino)butyl]amino}-1-(4-fluorophenyl)-4-oxobutan-2-yl]-D-phenylalaninamide, 3C-like proteinase nsp5, CHLORIDE ION, ...
Authors:Forouhar, F, Liu, H, Zack, A, Iketani, S, Williams, A, Vaz, D.R, Habashi, D.L, Choi, K, Resnick, S.J, Chavez, A, Ho, D.D, Stockwell, B.R.
Deposit date:2023-09-29
Release date:2025-01-15
Method:X-RAY DIFFRACTION (2.16 Å)
Cite:Development of small molecule non-covalent coronavirus 3CL protease inhibitors from DNA-encoded chemical library screening.
Nat Commun, 16, 2025
8YDP
DownloadVisualize
BU of 8ydp by Molmil
Crystal structure of the receptor binding domain of SARS-CoV-2 spike protein in complex with Ce9
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, GLYCEROL, SARS-CoV-2 inhibiting peptide Ce9, ...
Authors:Nakamura, S, Numoto, N, Fujiyoshi, Y.
Deposit date:2024-02-21
Release date:2025-01-15
Method:X-RAY DIFFRACTION (2.3 Å)
Cite:Development of a short-peptide inhibiting any SARS-CoV-2 variants based on structural biology
To Be Published
8YDQ
DownloadVisualize
BU of 8ydq by Molmil
Crystal structure of the receptor binding domain of SARS-CoV-2 Omicron BA.2 variant spike protein in complex with Ce149
Descriptor: GLYCEROL, SARS-CoV-2 inhibiting peptide Ce149, Spike protein S1
Authors:Nakamura, S, Numoto, N, Fujiyoshi, Y.
Deposit date:2024-02-21
Release date:2025-01-15
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:Development of a short-peptide inhibiting any SARS-CoV-2 variants based on structural biology
To Be Published
8YDR
DownloadVisualize
BU of 8ydr by Molmil
Crystal structure of the receptor binding domain of SARS-CoV-2 Alpha variant spike protein in complex with Ce59
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, SARS-CoV-2 inhibiting peptide Ce59, Spike protein S1
Authors:Nakamura, S, Numoto, N, Fujiyoshi, Y.
Deposit date:2024-02-21
Release date:2025-01-15
Method:X-RAY DIFFRACTION (2.3 Å)
Cite:Development of a short-peptide inhibiting any SARS-CoV-2 variants based on structural biology
To Be Published
8YDS
DownloadVisualize
BU of 8yds by Molmil
Crystal structure of the receptor binding domain of SARS-CoV-2 Delta variant spike protein in complex with Ce59
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, GLYCEROL, SARS-CoV-2 inhibiting peptide Ce59, ...
Authors:Nakamura, S, Numoto, N, Fujiyoshi, Y.
Deposit date:2024-02-21
Release date:2025-01-15
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:Development of a short-peptide inhibiting any SARS-CoV-2 variants based on structural biology
To Be Published
8YDT
DownloadVisualize
BU of 8ydt by Molmil
Crystal structure of the receptor binding domain of SARS-CoV-2 Alpha variant spike protein in complex with Ce41
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, SARS-CoV-2 inhibiting peptide Ce41, Spike protein S1
Authors:Nakamura, S, Numoto, N, Fujiyoshi, Y.
Deposit date:2024-02-21
Release date:2025-01-15
Method:X-RAY DIFFRACTION (2.5 Å)
Cite:Development of a short-peptide inhibiting any SARS-CoV-2 variants based on structural biology
To Be Published
8YDU
DownloadVisualize
BU of 8ydu by Molmil
Crystal structure of the receptor binding domain of SARS-CoV-2 Omicron BA.2 variant spike protein in complex with CeSPIACE
Descriptor: GLYCEROL, SARS-CoV-2 inhibiting peptide CeSPIACE, Spike protein S1
Authors:Nakamura, S, Numoto, N, Fujiyoshi, Y.
Deposit date:2024-02-21
Release date:2025-01-15
Method:X-RAY DIFFRACTION (1.7 Å)
Cite:Development of a short-peptide inhibiting any SARS-CoV-2 variants based on structural biology
To Be Published
8YDV
DownloadVisualize
BU of 8ydv by Molmil
Crystal structure of the receptor binding domain of SARS-CoV-2 Omicron BA.5 variant spike protein in complex with CeSPIACE
Descriptor: GLYCEROL, SARS-CoV-2 inhibiting peptide CeSPIACE, Spike protein S1
Authors:Nakamura, S, Numoto, N, Fujiyoshi, Y.
Deposit date:2024-02-21
Release date:2025-01-15
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:Development of a short-peptide inhibiting any SARS-CoV-2 variants based on structural biology
To Be Published
8YDW
DownloadVisualize
BU of 8ydw by Molmil
Crystal structure of the receptor binding domain of SARS-CoV-2 Omicron XBB.1.5 variant spike protein in complex with CeSPIACE
Descriptor: GLYCEROL, SARS-CoV-2 inhibiting peptide CeSPIACE, SODIUM ION, ...
Authors:Nakamura, S, Numoto, N, Fujiyoshi, Y.
Deposit date:2024-02-21
Release date:2025-01-15
Method:X-RAY DIFFRACTION (2 Å)
Cite:Development of a short-peptide inhibiting any SARS-CoV-2 variants based on structural biology
To Be Published
8YDX
DownloadVisualize
BU of 8ydx by Molmil
Cryo-EM structure of SARS-CoV-2 spike ectodomain (HexaPro, Omicron BA.2 variant) in complex with CeSPIACE
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, CeSPIACE, Spike glycoprotein
Authors:Suzuki, H, Nakamura, S, Fujiyoshi, Y.
Deposit date:2024-02-21
Release date:2025-01-15
Method:ELECTRON MICROSCOPY (4.9 Å)
Cite:Development of a short-peptide inhibiting any SARS-CoV-2 variants based on structural biology
To Be Published
8YDY
DownloadVisualize
BU of 8ydy by Molmil
Cryo-EM structure of SARS-CoV-2 spike ectodomain (HexaPro, Omicron BA.5 variant) in complex with CeSPIACE, class 1
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, CeSPIACE, Spike glycoprotein
Authors:Suzuki, H, Nakamura, S, Fujiyoshi, Y.
Deposit date:2024-02-21
Release date:2025-01-15
Method:ELECTRON MICROSCOPY (8 Å)
Cite:Development of a short-peptide inhibiting any SARS-CoV-2 variants based on structural biology
To Be Published
8YDZ
DownloadVisualize
BU of 8ydz by Molmil
Cryo-EM structure of SARS-CoV-2 spike ectodomain (HexaPro, Omicron BA.5 variant) in complex with CeSPIACE, class 2
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, CeSPIACE, Spike glycoprotein
Authors:Suzuki, H, Nakamura, S, Fujiyoshi, Y.
Deposit date:2024-02-21
Release date:2025-01-15
Method:ELECTRON MICROSCOPY (5.2 Å)
Cite:Development of a short-peptide inhibiting any SARS-CoV-2 variants based on structural biology
To Be Published
9CEC
DownloadVisualize
BU of 9cec by Molmil
SARS-CoV-2 3CL Protease complexed with covalent inhibitor BC671
Descriptor: 3C-like proteinase nsp5, DIMETHYL SULFOXIDE, N-[(2S)-1-{[(2S)-1-hydroxy-3-(2-oxo-1,2-dihydropyridin-3-yl)propan-2-yl]amino}-4-methyl-1-oxopentan-2-yl]-1H-indole-2-carboxamide
Authors:Farzandh, S, Hoffpauir, Z.A, Meneely, K.M, Lamb, A.L.
Deposit date:2024-06-26
Release date:2025-01-15
Last modified:2025-01-22
Method:X-RAY DIFFRACTION (2.36 Å)
Cite:Dual Inhibitors of SARS-CoV-2 3CL Protease and Human Cathepsin L Containing Glutamine Isosteres Are Anti-CoV-2 Agents.
J.Am.Chem.Soc., 147, 2025
9CED
DownloadVisualize
BU of 9ced by Molmil
SARS-CoV-2 3CL Protease complexed with covalent inhibitor VK13
Descriptor: 3C-like proteinase nsp5, N-[(2S)-1-{[(2S)-1-hydroxy-3-(2-oxo-1,2-dihydropyridin-3-yl)propan-2-yl]amino}-4-methyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide
Authors:Hoffpauir, Z.A, Meneely, K.M, Lamb, A.L.
Deposit date:2024-06-26
Release date:2025-01-15
Last modified:2025-01-22
Method:X-RAY DIFFRACTION (1.82 Å)
Cite:Dual Inhibitors of SARS-CoV-2 3CL Protease and Human Cathepsin L Containing Glutamine Isosteres Are Anti-CoV-2 Agents.
J.Am.Chem.Soc., 147, 2025
9CEK
DownloadVisualize
BU of 9cek by Molmil
SARS-CoV-2 3CL Protease complexed with covalent inhibitor VK20
Descriptor: 3C-like proteinase nsp5, L(+)-TARTARIC ACID, N-[(2S)-1-amino-4-methyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide, ...
Authors:Hoffpauir, Z.A, Meneely, K.M, Lamb, A.L.
Deposit date:2024-06-26
Release date:2025-01-15
Last modified:2025-01-22
Method:X-RAY DIFFRACTION (1.38 Å)
Cite:Dual Inhibitors of SARS-CoV-2 3CL Protease and Human Cathepsin L Containing Glutamine Isosteres Are Anti-CoV-2 Agents.
J.Am.Chem.Soc., 147, 2025
9CF9
DownloadVisualize
BU of 9cf9 by Molmil
SARS-CoV-2 3CL Protease complexed with covalent inhibitor BC787
Descriptor: 3C-like proteinase nsp5, N-[(2S)-1-{[(2S)-1-hydroxy-3-(pyridin-3-yl)propan-2-yl]amino}-4-methyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide
Authors:Hoffpauir, Z.A, Meneely, K.M, Lamb, A.L.
Deposit date:2024-06-27
Release date:2025-01-15
Last modified:2025-01-22
Method:X-RAY DIFFRACTION (2 Å)
Cite:Dual Inhibitors of SARS-CoV-2 3CL Protease and Human Cathepsin L Containing Glutamine Isosteres Are Anti-CoV-2 Agents.
J.Am.Chem.Soc., 147, 2025
9CFB
DownloadVisualize
BU of 9cfb by Molmil
SARS-CoV-2 3CL Protease complexed with covalent inhibitor BC674
Descriptor: 3C-like proteinase nsp5, N-[(2S)-3-cyclohexyl-1-{[(2S)-1-hydroxy-3-(2-oxo-1,2-dihydropyridin-3-yl)propan-2-yl]amino}-1-oxopropan-2-yl]-1H-indole-2-carboxamide, SODIUM ION
Authors:Hoffpauir, Z.A, Meneely, K.M, Lamb, A.L.
Deposit date:2024-06-27
Release date:2025-01-15
Last modified:2025-01-22
Method:X-RAY DIFFRACTION (1.45 Å)
Cite:Dual Inhibitors of SARS-CoV-2 3CL Protease and Human Cathepsin L Containing Glutamine Isosteres Are Anti-CoV-2 Agents.
J.Am.Chem.Soc., 147, 2025
9IUP
DownloadVisualize
BU of 9iup by Molmil
KP.3 RBD in complex with ACE2
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Processed angiotensin-converting enzyme 2, Spike protein S1
Authors:Feng, L.L.
Deposit date:2024-07-22
Release date:2025-01-15
Last modified:2025-07-02
Method:ELECTRON MICROSCOPY (3.3 Å)
Cite:Structural and molecular basis of the epistasis effect in enhanced affinity between SARS-CoV-2 KP.3 and ACE2.
Cell Discov, 10, 2024
9IUQ
DownloadVisualize
BU of 9iuq by Molmil
KP.2 RBD in complex with ACE2
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Processed angiotensin-converting enzyme 2, Spike protein S1
Authors:Feng, L.L.
Deposit date:2024-07-22
Release date:2025-01-15
Last modified:2025-06-25
Method:ELECTRON MICROSCOPY (3.3 Å)
Cite:Structural and molecular basis of the epistasis effect in enhanced affinity between SARS-CoV-2 KP.3 and ACE2.
Cell Discov, 10, 2024
9IUU
DownloadVisualize
BU of 9iuu by Molmil
JN.1 RBD with Q493E in complex with ACE2
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, Angiotensin-converting enzyme 2, CHLORIDE ION, ...
Authors:Feng, L.L.
Deposit date:2024-07-22
Release date:2025-01-15
Last modified:2025-07-02
Method:ELECTRON MICROSCOPY (3.29 Å)
Cite:Structural and molecular basis of the epistasis effect in enhanced affinity between SARS-CoV-2 KP.3 and ACE2.
Cell Discov, 10, 2024
9JJ7
DownloadVisualize
BU of 9jj7 by Molmil
The crystal structure of SARS-CoV-2 NSP5 in complex with eIF4G2
Descriptor: 3C-like proteinase nsp5, Eukaryotic translation initiation factor 4 gamma 2
Authors:Yan, X, Jin, Z, Wang, Y, Zhang, J.
Deposit date:2024-09-13
Release date:2025-01-15
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Coronavirus NSP5 is an Evolutionarily Conserved Inhibitor of Host Translation
To Be Published
8XAL
DownloadVisualize
BU of 8xal by Molmil
Cryo-EM structure of SARS-CoV-2 S-BQ.1 in complex with 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,Green fluorescent protein (Fragment), ...
Authors:Hsu, H.F, Wu, M.H, Chang, Y.C, Hsu, S.T.D.
Deposit date:2023-12-04
Release date:2025-01-22
Last modified:2025-07-02
Method:ELECTRON MICROSCOPY (3.2 Å)
Cite:Functional and structural investigation of a broadly neutralizing SARS-CoV-2 antibody.
JCI Insight, 9, 2024
8XWR
DownloadVisualize
BU of 8xwr by Molmil
Crystal structure of SARS-CoV-2 3CLpro-T21I/L50F double mutant with its peptidyl substrate
Descriptor: 3C-like proteinase nsp5, cleaved N-terminal product of nsp5/6 substrate peptide
Authors:Zhang, L.J, Hu, Q.
Deposit date:2024-01-16
Release date:2025-01-22
Method:X-RAY DIFFRACTION (1.7 Å)
Cite:Crystal structure of SARS-CoV-2 3CLpro-T21I/L50F double mutant with its peptidyl substrate
To Be Published
8XWT
DownloadVisualize
BU of 8xwt by Molmil
Crystal structure of SARS-CoV-2 3CLpro-L50F mutant with its peptidyl substrate
Descriptor: 3C-like proteinase nsp5, CYS-SER-GLY-VAL-THR-PHE-GLN-SER-ALA-VAL-LYS-ARG-THR-ILE
Authors:Zhang, L.J, Hu, Q.
Deposit date:2024-01-16
Release date:2025-01-22
Method:X-RAY DIFFRACTION (1.7 Å)
Cite:Crystal structure of SARS-CoV-2 3CLpro-L50F mutant with its peptidyl substrate
To Be Published
8XY9
DownloadVisualize
BU of 8xy9 by Molmil
Crystal structure of SARS-CoV-2 BF.7 RBD and human ACE2 complex
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Processed angiotensin-converting enzyme 2, ...
Authors:Lan, J, Wang, C.H.
Deposit date:2024-01-19
Release date:2025-01-22
Last modified:2025-04-16
Method:X-RAY DIFFRACTION (3.64 Å)
Cite:Receptor binding mechanism and immune evasion capacity of SARS-CoV-2 BQ.1.1 lineage.
Virology, 600, 2024

238582

PDB entries from 2025-07-09

PDB statisticsPDBj update infoContact PDBjnumon