2KN7
| Structure of the XPF-single strand DNA complex | Descriptor: | DNA (5'-D(*CP*AP*GP*TP*GP*GP*CP*TP*GP*A)-3'), DNA repair endonuclease XPF | Authors: | Das, D, Folkers, G.E, van Dijk, M, Jaspers, N.G.J, Hoeijmakers, J.H.J, Kaptein, R, Boelens, R. | Deposit date: | 2009-08-16 | Release date: | 2010-08-04 | Last modified: | 2024-05-01 | Method: | SOLUTION NMR | Cite: | The structure of the XPF-ssDNA complex underscores the distinct roles of the XPF and ERCC1 helix- hairpin-helix domains in ss/ds DNA recognition Structure, 20, 2012
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1TD6
| Crystal structure of the conserved hypothetical protein MP506/MPN330 (gi: 1674200)from Mycoplasma pneumoniae | Descriptor: | Hypothetical protein MG237 homolog | Authors: | Das, D, Oganesyan, N, Yokota, H, Jancarik, J, Kim, R, Kim, S.H, Berkeley Structural Genomics Center (BSGC) | Deposit date: | 2004-05-21 | Release date: | 2004-12-07 | Last modified: | 2024-02-14 | Method: | X-RAY DIFFRACTION (2.5 Å) | Cite: | Crystal structure of the conserved hypothetical protein MPN330 (GI: 1674200) from Mycoplasma pneumoniae. Proteins, 58, 2004
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4MH8
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2AQ0
| Solution structure of the human homodimeric dna repair protein XPF | Descriptor: | DNA repair endonuclease XPF | Authors: | Das, D, Tripsianes, K, Folkers, G, Jaspers, N.G, Hoeijmakers, J.H, Kaptein, R, Boelens, R. | Deposit date: | 2005-08-17 | Release date: | 2006-10-03 | Last modified: | 2024-05-22 | Method: | SOLUTION NMR | Cite: | The HhH domain of the human DNA repair protein XPF forms stable homodimers Proteins, 70, 2008
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2HQL
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2I6W
| Crystal structure of the multidrug efflux transporter AcrB | Descriptor: | Acriflavine resistance protein B | Authors: | Das, D, Xu, Q.S, Kim, S.H. | Deposit date: | 2006-08-29 | Release date: | 2007-05-01 | Last modified: | 2024-02-21 | Method: | X-RAY DIFFRACTION (3.1 Å) | Cite: | Crystal structure of the multidrug efflux transporter AcrB at 3.1A resolution reveals the N-terminal region with conserved amino acids. J.Struct.Biol., 158, 2007
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9CTX
| X-ray crystal structure of multi-drug resistant HIV-1 protease (P51) in complex with Darunavir | Descriptor: | (3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YL(1S,2R)-3-[[(4-AMINOPHENYL)SULFONYL](ISOBUTYL)AMINO]-1-BENZYL-2-HYDROXYPROPYLCARBAMATE, GLYCEROL, Protease | Authors: | Hayashi, H, Yedidi, R, Bulut, H, Das, D, Mitsuya, H. | Deposit date: | 2024-07-25 | Release date: | 2024-08-07 | Method: | X-RAY DIFFRACTION (1.55 Å) | Cite: | Secondary amino-acid substitutions contribute to the emergence of HIV protease inhibitor resistance as directly as primary amino-acid substitutions. To Be Published
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8DPR
| Crystal structure of SARS-CoV-2 main protease in complex with inhibitor TKB-248 | Descriptor: | 2,2,2-trifluoro-N-{(2S)-1-[(1R,2S,5S)-2-({(2S)-1-(4-fluoro-1,3-benzothiazol-2-yl)-1-oxo-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}carbamothioyl)-6,6-dimethyl-3-azabicyclo[3.1.0]hexan-3-yl]-3,3-dimethyl-1-oxobutan-2-yl}acetamide, 3C-like proteinase nsp5, DIMETHYL SULFOXIDE, ... | Authors: | Bulut, H, Hayashi, H, Tsuji, K, Kuwata, N, Das, D, Tamamura, H, Mitsuya, H. | Deposit date: | 2022-07-16 | Release date: | 2022-08-24 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Identification of SARS-CoV-2 M pro inhibitors containing P1' 4-fluorobenzothiazole moiety highly active against SARS-CoV-2. Nat Commun, 14, 2023
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8DOY
| Crystal structure of SARS-CoV-2 main protease in complex with an inhibitor TKB-198 | Descriptor: | 2-(2-METHOXYETHOXY)ETHANOL, 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, 3C-like proteinase nsp5, ... | Authors: | Bulut, H, Hayashi, H, Tsuji, K, Kuwata, N, Das, D, Tamamura, H, Mitsuya, H. | Deposit date: | 2022-07-14 | Release date: | 2022-08-24 | Last modified: | 2023-10-25 | Method: | X-RAY DIFFRACTION (1.59 Å) | Cite: | Potent and biostable inhibitors of the main protease of SARS-CoV-2. Iscience, 25, 2022
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8DOX
| Crystal structure of SARS-CoV-2 main protease in complex with an inhibitor TKB-245 | Descriptor: | (1R,2S,5S)-N-{(1S,2S)-1-(4-fluoro-1,3-benzothiazol-2-yl)-1-hydroxy-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, DIMETHYL SULFOXIDE | Authors: | Bulut, H, Hayashi, H, Tsuji, K, Kuwata, N, Das, D, Tamamura, H, Mitsuya, H. | Deposit date: | 2022-07-14 | Release date: | 2022-09-21 | Last modified: | 2023-10-18 | Method: | X-RAY DIFFRACTION (1.46 Å) | Cite: | Identification of SARS-CoV-2 M pro inhibitors containing P1' 4-fluorobenzothiazole moiety highly active against SARS-CoV-2. Nat Commun, 14, 2023
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5TYS
| X-ray crystal structure of wild type HIV-1 protease in complex with GRL-142 | Descriptor: | (3S,3aR,5R,7aS,8S)-hexahydro-4H-3,5-methanofuro[2,3-b]pyran-8-yl [(2S,3R)-4-[{[2-(cyclopropylamino)-1,3-benzothiazol-6-yl]sulfonyl}(2-methylpropyl)amino]-1-(3,5-difluorophenyl)-3-hydroxybutan-2-yl]carbamate, Protease | Authors: | Yedidi, R.S, Hayashi, H, Aoki, M, Das, D, Ghosh, A.K, Mitsuya, H. | Deposit date: | 2016-11-21 | Release date: | 2017-10-18 | Last modified: | 2023-10-04 | Method: | X-RAY DIFFRACTION (2.007 Å) | Cite: | A novel central nervous system-penetrating protease inhibitor overcomes human immunodeficiency virus 1 resistance with unprecedented aM to pM potency. Elife, 6, 2017
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5TYR
| X-ray crystal structure of wild type HIV-1 protease in complex with GRL-121 | Descriptor: | (3S,3aR,5R,7aS,8S)-hexahydro-4H-3,5-methanofuro[2,3-b]pyran-8-yl {(2S,3R)-4-[{[2-(cyclopropylamino)-1,3-benzothiazol-6-yl]sulfonyl}(2-methylpropyl)amino]-3-hydroxy-1-phenylbutan-2-yl}carbamate, Protease | Authors: | Yedidi, R.S, Hayashi, H, Aoki, M, Das, D, Ghosh, A.K, Mitsuya, H. | Deposit date: | 2016-11-21 | Release date: | 2017-10-18 | Last modified: | 2023-10-04 | Method: | X-RAY DIFFRACTION (1.8 Å) | Cite: | A novel central nervous system-penetrating protease inhibitor overcomes human immunodeficiency virus 1 resistance with unprecedented aM to pM potency. Elife, 6, 2017
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7JKV
| Crystal Structure of SARS-CoV-2 main protease in complex with an inhibitor GRL-2420 | Descriptor: | 3C-like proteinase, N-[(2S)-1-({(1S,2S)-1-(1,3-benzothiazol-2-yl)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide, PENTAETHYLENE GLYCOL | Authors: | Bulut, H, Hattori, S.I, Das, D, Murayama, K, Mitsuya, H. | Deposit date: | 2020-07-29 | Release date: | 2020-09-23 | Last modified: | 2023-10-18 | Method: | X-RAY DIFFRACTION (1.25 Å) | Cite: | A small molecule compound with an indole moiety inhibits the main protease of SARS-CoV-2 and blocks virus replication. Nat Commun, 12, 2021
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5COK
| X-ray crystal structure of wild type HIV-1 protease in complex with GRL-0476 | Descriptor: | (3aS,4S,7aR)-hexahydro-4H-furo[2,3-b]pyran-4-yl [(2S,3R)-3-hydroxy-4-{[(4-methoxyphenyl)sulfonyl](2-methylpropyl)amino}-1-phenylbutan-2-yl]carbamate, HIV-1 protease | Authors: | Yedidi, R.S, Hayashi, H, Aoki, M, Das, D, Ghosh, A.K, Mitsuya, H. | Deposit date: | 2015-07-20 | Release date: | 2016-01-13 | Last modified: | 2024-03-06 | Method: | X-RAY DIFFRACTION (1.801 Å) | Cite: | C-5-Modified Tetrahydropyrano-Tetrahydofuran-Derived Protease Inhibitors (PIs) Exert Potent Inhibition of the Replication of HIV-1 Variants Highly Resistant to Various PIs, including Darunavir. J.Virol., 90, 2015
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5COP
| X-ray crystal structure of wild type HIV-1 protease in complex with GRL-097 | Descriptor: | (3R,3aS,4S,7aS)-3-hydroxyhexahydro-4H-furo[2,3-b]pyran-4-yl [(2S,3R)-4-{[(4-aminophenyl)sulfonyl](2-methylpropyl)amino}-3-hydroxy-1-(4-methoxyphenyl)butan-2-yl]carbamate, HIV-1 protease | Authors: | Yedidi, R.S, Hayashi, H, Aoki, M, Das, D, Ghosh, A.K, Mitsuya, H. | Deposit date: | 2015-07-20 | Release date: | 2016-01-13 | Last modified: | 2024-03-06 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | C-5-Modified Tetrahydropyrano-Tetrahydofuran-Derived Protease Inhibitors (PIs) Exert Potent Inhibition of the Replication of HIV-1 Variants Highly Resistant to Various PIs, including Darunavir. J.Virol., 90, 2015
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5COO
| X-ray crystal structure of wild type HIV-1 protease in complex with GRL-085 | Descriptor: | (3R,3aS,4S,7aS)-3-hydroxyhexahydro-4H-furo[2,3-b]pyran-4-yl [(2S,3R)-3-hydroxy-1-(4-methoxyphenyl)-4-{[(4-methoxyphenyl)sulfonyl](2-methylpropyl)amino}butan-2-yl]carbamate, HIV-1 protease | Authors: | Yedidi, R.S, Hayashi, H, Aoki, M, Das, D, Ghosh, A.K, Mitsuya, H. | Deposit date: | 2015-07-20 | Release date: | 2016-01-13 | Last modified: | 2024-03-06 | Method: | X-RAY DIFFRACTION (1.8 Å) | Cite: | C-5-Modified Tetrahydropyrano-Tetrahydofuran-Derived Protease Inhibitors (PIs) Exert Potent Inhibition of the Replication of HIV-1 Variants Highly Resistant to Various PIs, including Darunavir. J.Virol., 90, 2015
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8UH8
| Crystal structure of SARS-CoV-2 main protease E166V (Apo structure) | Descriptor: | ORF1a polyprotein | Authors: | Bulut, H, Hayashi, H, Kuwata, N, Tsuji, K, Das, D, Tamamura, H, Mitsuya, H. | Deposit date: | 2023-10-07 | Release date: | 2024-01-24 | Method: | X-RAY DIFFRACTION (1.9 Å) | Cite: | TKB272, an Orally Available SARS-CoV-2-Mpro Inhibitor Containing 5-Fluorobenzothiazole, Potently Blocks SARS-CoV-2 Replication without Ritonavir To Be Published
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8UH5
| Crystal structure of SARS-CoV-2 main protease in complex with an inhibitor TKB-272 | Descriptor: | (1R,2S,5S)-N-{(1S,2S)-1-(5-fluoro-1,3-benzothiazol-2-yl)-1-hydroxy-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, DI(HYDROXYETHYL)ETHER | Authors: | Bulut, H, Hayashi, H, Kuwata, N, Tsuji, K, Das, D, Tamamura, H, Mitsuya, H. | Deposit date: | 2023-10-06 | Release date: | 2023-12-13 | Method: | X-RAY DIFFRACTION (1.74 Å) | Cite: | TKB272, an Orally Available SARS-CoV-2-Mpro Inhibitor Containing 5-Fluorobenzothiazole, Potently Blocks SARS-CoV-2 Replication without Ritonavir To Be Published
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8UH9
| Crystal structure of SARS-CoV-2 main protease E166V mutant in complex with an inhibitor TKB-272 | Descriptor: | (1R,2S,5S)-N-{(1S,2S)-1-(5-fluoro-1,3-benzothiazol-2-yl)-1-hydroxy-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, DI(HYDROXYETHYL)ETHER | Authors: | Bulut, H, Hayashi, H, Kuwata, N, Tsuji, K, Das, D, Tamamura, H, Mitsuya, H. | Deposit date: | 2023-10-07 | Release date: | 2023-12-20 | Method: | X-RAY DIFFRACTION (2.067 Å) | Cite: | TKB272, an Orally Available SARS-CoV-2-Mpro Inhibitor Containing 5-Fluorobenzothiazole, Potently Blocks SARS-CoV-2 Replication without Ritonavir To Be Published
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5CON
| X-ray crystal structure of wild type HIV-1 protease in complex with GRL-015 | Descriptor: | (3R,3aS,4S,7aS)-3-hydroxyhexahydro-4H-furo[2,3-b]pyran-4-yl [(2S,3R)-3-hydroxy-4-{[(4-methoxyphenyl)sulfonyl](2-methylpropyl)amino}-1-phenylbutan-2-yl]carbamate, HIV-1 protease | Authors: | Yedidi, R.S, Hayashi, H, Aoki, M, Das, D, Ghosh, A.K, Mitsuya, H. | Deposit date: | 2015-07-20 | Release date: | 2016-01-13 | Last modified: | 2024-03-06 | Method: | X-RAY DIFFRACTION (1.8 Å) | Cite: | C-5-Modified Tetrahydropyrano-Tetrahydofuran-Derived Protease Inhibitors (PIs) Exert Potent Inhibition of the Replication of HIV-1 Variants Highly Resistant to Various PIs, including Darunavir. J.Virol., 90, 2015
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6MK9
| X-ray crystal structure of darunavir-resistant-P51 HIV-1 protease in complex with GRL-121 | Descriptor: | (3S,3aR,5R,7aS,8S)-hexahydro-4H-3,5-methanofuro[2,3-b]pyran-8-yl {(2S,3R)-4-[{[2-(cyclopropylamino)-1,3-benzothiazol-6-yl]sulfonyl}(2-methylpropyl)amino]-3-hydroxy-1-phenylbutan-2-yl}carbamate, Protease | Authors: | Yedidi, R.S, Hayashi, H, Das, D, Mitsuya, H. | Deposit date: | 2018-09-25 | Release date: | 2019-10-02 | Last modified: | 2023-10-11 | Method: | X-RAY DIFFRACTION (1.7 Å) | Cite: | X-ray crystal structure of darunavir-resistant-P51 HIV-1 protease in complex with GRL-121 To Be Published
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6MKL
| X-ray crystal structure of darunavir-resistant-P51 HIV-1 protease in complex with GRL-142 | Descriptor: | (3S,3aR,5R,7aS,8S)-hexahydro-4H-3,5-methanofuro[2,3-b]pyran-8-yl [(2S,3R)-4-[{[2-(cyclopropylamino)-1,3-benzothiazol-6-yl]sulfonyl}(2-methylpropyl)amino]-1-(3,5-difluorophenyl)-3-hydroxybutan-2-yl]carbamate, Protease | Authors: | Yedidi, R.S, Hayashi, H, Das, D, Mitsuya, H. | Deposit date: | 2018-09-25 | Release date: | 2019-10-02 | Last modified: | 2023-10-11 | Method: | X-RAY DIFFRACTION (1.7 Å) | Cite: | Structure-function analysis of darunavir-resistant-P51 HIV-1 protease in complex with GRL-142. To Be Published
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3H98
| Crystal structure of HCV NS5b 1b with (1,1-dioxo-2H-[1,2,4]benzothiadiazin-3-yl) azolo[1,5-a]pyrimidine derivative | Descriptor: | GLYCEROL, N-{3-[5-hydroxy-8-(3-methylbutyl)-7-oxo-7,8-dihydroimidazo[1,2-a]pyrimidin-6-yl]-1,1-dioxido-4H-1,2,4-benzothiadiazin-7-yl}methanesulfonamide, RNA-directed RNA polymerase | Authors: | Wang, G, Lei, H, Wang, X, Das, D, Mackinnon, C, Montalbetti, C.A.G, Mears, R, Gai, X, Bailey, S, Ruhrmund, D, Hooi, L, Misialek, S, Rajagopalan, R, Cheng, R.K.Y, Barker, J.L, Felicetti, B, Stoycheva, A, Buckman, B, Kossen, K, Seiwert, S, Beigelmana, L. | Deposit date: | 2009-04-30 | Release date: | 2009-10-13 | Last modified: | 2023-09-06 | Method: | X-RAY DIFFRACTION (1.9 Å) | Cite: | HCV NS5B polymerase inhibitors 2: Synthesis and in vitro activity of (1,1-dioxo-2H-[1,2,4]benzothiadiazin-3-yl) azolo[1,5-a]pyridine and azolo[1,5-a]pyrimidine derivatives. Bioorg.Med.Chem.Lett., 19, 2009
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4RVJ
| Crystal structure of multidrug-resistant clinical isolate A02 HIV-1 protease in complex with amprenavir | Descriptor: | HIV-1 protease, {3-[(4-AMINO-BENZENESULFONYL)-ISOBUTYL-AMINO]-1-BENZYL-2-HYDROXY-PROPYL}-CARBAMIC ACID TETRAHYDRO-FURAN-3-YL ESTER | Authors: | Yedidi, R.S, Garimella, H, Kaufman, J.D, Das, D, Wingfield, P.T, Mitsuya, H. | Deposit date: | 2014-11-26 | Release date: | 2016-05-04 | Last modified: | 2024-02-28 | Method: | X-RAY DIFFRACTION (1.6 Å) | Cite: | Enhanced antiviral activity by the P2-tris-tetrahydrofuran moiety of GRL-0519, a novel nonpeptidic HIV-1 protease inhibitor (PI), against multi-PI-resistant and highly darunavir-resistant strains of HIV-1 To be Published
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4RVI
| Crystal structure of multidrug-resistant clinical isolate A02 HIV-1 protease in complex with non-peptidic inhibitor, GRL0519 | Descriptor: | (3R,3aS,3bR,6aS,7aS)-octahydrodifuro[2,3-b:3',2'-d]furan-3-yl [(1S,2R)-1-benzyl-2-hydroxy-3-{[(4-methoxyphenyl)sulfonyl](2-methylpropyl)amino}propyl]carbamate, HIV-1 protease | Authors: | Yedidi, R.S, Garimella, H, Kaufman, J.D, Das, D, Wingfield, P.T, Ghosh, A.K, Mitsuya, H. | Deposit date: | 2014-11-26 | Release date: | 2016-05-04 | Last modified: | 2024-02-28 | Method: | X-RAY DIFFRACTION (1.99 Å) | Cite: | Enhanced antiviral activity by the P2-tris-tetrahydrofuran moiety of GRL-0519, a novel nonpeptidic HIV-1 protease inhibitor (PI), against multi-PI-resistant and highly darunavir-resistant strains of HIV-1 To be Published
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