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COVID-19特輯

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冠狀病毒
冠狀病毒,2020. 由David S. Goodsell @ RCSB PDB原圖修改

最近爆發的新型冠狀病毒傳染病(Novel Coronavirus disease 2019: COVID-19)對全世界的人們都構成了嚴重威脅。 為了儘早了解新病毒(Severe Acute Respiratory Syndrome Coronavirus 2: SARS-CoV-2)以開發出有效的抗病毒藥物,已經有很多科研人員開始了相關蛋白結構的研究,並且將所獲得結構數據存儲與PDB。 PDBj為用戶提供了COVID-19相關數據一覽的門戶頁面,並將於每週三更新當日新發佈的相關數據。

有關該病毒蛋白質的解說,請參見下面的“當月的分子”頁面。

“所有結構”標籤的頁面則逐一羅列了所有的數據,包括由同一研究組提交的系列數據群。 “代表性結構”標籤的頁面精選具有相同胺基酸序列的結構數據中的高分辨率數據,不重複選擇具有同一胺基酸序列的數據,即使該數據可能包含不同的配體。 “最新條目”標籤內包含本週新更新數據。


Created: 2020-09-03 (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

238582

數據於2025-07-09公開中

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