신종 코로나바이러스 특집 콘텐츠

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코로나 바이러스, 2020. David S. Goodsell @ RCSB PDB에 의한 오리지널 일러스트를 수정

신종 코로나바이러스 감염증 (Novel Coronavirus disease 2019:COVID-19)의 확산이 세계적으로 매우 큰 문제가 되고 있습니다. 시급히 새로운 바이러스（Severe Acute Respiratory Syndrome Coronavirus 2: SARS-CoV-2）를 이해하고 효과적인 약을 개발하기 위해, 신속하게 구조 생물학 연구가 시작되고 있습니다. PDBj는 사용자의 편의를 도모하기 위해 신종 코로나바이러스의 특집 페이지를 제공하고 있습니다. 매주 수요일에 최신 항목이 추가됩니다.

바이러스 단백질에 관한 해설기사는 아래의 「이달의 분자」 페이지를 참조하십시오.

「전체 엔트리」 탭에는, 모든 PDB ID가 포함되어 있습니다. 이용자가 전체의 독립된 엔트리를 검색하고 싶을 때 사용하실 수 있으며, 동일 저자에 의한 그룹등록의 엔트리도 전부 구별되어 있습니다. 「대표구조」 탭에는, 분해능이 가장 높은 대표구조만을 표지하고 있습니다. 아미노산 서열이 100 % 일치하는 PDB 엔트리의 경우, 다른 리간드를 포함하여도 대표구조에는 제외됩니다. 「최신 엔트리」 탭은, 이번주 공개된 가장 최근의 엔트리 입니다.

Created: 2020-09-03 (last edited: more than 1 year ago)

전체 엔트리 (5197)대표구조 (2266)최신 엔트리 (44)

8UE0

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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