Loading
PDBj
MenuPDBj@FacebookPDBj@X(formerly Twitter)PDBj@BlueSkyPDBj@YouTubewwPDB FoundationwwPDBDonate
RCSB PDBPDBeBMRBAdv. SearchSearch help
Search by PDB author
9J4G
DownloadVisualize
BU of 9j4g by Molmil
Crystal structure of SHMT from E. faecium with (+)-SHIN-2
Descriptor: (+)-SHIN-2, Serine hydroxymethyltransferase, [3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-SERINE
Authors:Hayashi, H, Murayama, K.
Deposit date:2024-08-09
Release date:2024-10-09
Method:X-RAY DIFFRACTION (1.95 Å)
Cite:SHIN-2 exerts potent activity against VanA-type vancomycin-resistant Enterococcus faecium in vitro by stabilizing the active site loop of serine hydroxymethyltransferase.
Arch.Biochem.Biophys., 761, 2024
1IX6
DownloadVisualize
BU of 1ix6 by Molmil
Aspartate Aminotransferase Active Site Mutant V39F
Descriptor: Aspartate Aminotransferase, PYRIDOXAL-5'-PHOSPHATE
Authors:Hayashi, H, Mizuguchi, H, Miyahara, I, Nakajima, Y, Hirotsu, K, Kagamiyama, H.
Deposit date:2002-06-14
Release date:2002-07-03
Last modified:2023-12-27
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:Conformational change in aspartate aminotransferase on substrate binding induces strain in the catalytic group and enhances catalysis
J.BIOL.CHEM., 278, 2003
1IX8
DownloadVisualize
BU of 1ix8 by Molmil
Aspartate Aminotransferase Active Site Mutant V39F/N194A
Descriptor: Aspartate Aminotransferase, PYRIDOXAL-5'-PHOSPHATE
Authors:Hayashi, H, Mizuguchi, H, Miyahara, I, Nakajima, Y, Hirotsu, K, Kagamiyama, H.
Deposit date:2002-06-14
Release date:2002-07-03
Last modified:2023-12-27
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:Conformational change in aspartate aminotransferase on substrate binding induces strain in the catalytic group and enhances catalysis
J.BIOL.CHEM., 278, 2003
1IX7
DownloadVisualize
BU of 1ix7 by Molmil
Aspartate Aminotransferase Active Site Mutant V39F maleate complex
Descriptor: Aspartate Aminotransferase, MALEIC ACID, PYRIDOXAL-5'-PHOSPHATE
Authors:Hayashi, H, Mizuguchi, H, Miyahara, I, Nakajima, Y, Hirotsu, K, Kagamiyama, H.
Deposit date:2002-06-14
Release date:2002-07-03
Last modified:2023-12-27
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:Conformational change in aspartate aminotransferase on substrate binding induces strain in the catalytic group and enhances catalysis
J.BIOL.CHEM., 278, 2003
9CTX
DownloadVisualize
BU of 9ctx by Molmil
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
9J4H
DownloadVisualize
BU of 9j4h by Molmil
Crystal structure of SHMT apo form
Descriptor: Serine hydroxymethyltransferase, TRIETHYLENE GLYCOL
Authors:Murayama, K, Hayashi, H.
Deposit date:2024-08-09
Release date:2024-10-09
Method:X-RAY DIFFRACTION (2.04 Å)
Cite:SHIN-2 exerts potent activity against VanA-type vancomycin-resistant Enterococcus faecium in vitro by stabilizing the active site loop of serine hydroxymethyltransferase.
Arch.Biochem.Biophys., 761, 2024
9KRO
DownloadVisualize
BU of 9kro by Molmil
Crystal structure of SHMT from E. faecium with mangiferin
Descriptor: Mangiferin, Serine hydroxymethyltransferase, [3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-SERINE
Authors:Murayama, K, Hayashi, H.
Deposit date:2024-11-28
Release date:2025-03-19
Method:X-RAY DIFFRACTION (2.25 Å)
Cite:Binding of a potential antibacterial drug, mangiferin, to serine hydroxymethyltransferase from Enterococcus faecium.
Biochem.Biophys.Res.Commun., 743, 2025
7V3D
DownloadVisualize
BU of 7v3d by Molmil
Complex structure of serine hydroxymethyltransferase from Enterococcus faecium and its inhibitor
Descriptor: (4R)-6-azanyl-4-[3-(hydroxymethyl)-5-phenyl-phenyl]-3-methyl-4-propan-2-yl-1H-pyrano[2,3-c]pyrazole-5-carbonitrile, CHLORIDE ION, PYRIDOXAL-5'-PHOSPHATE, ...
Authors:Hayashi, H, Murayama, K.
Deposit date:2021-08-10
Release date:2022-07-06
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.28 Å)
Cite:Serine hydroxymethyltransferase as a potential target of antibacterial agents acting synergistically with one-carbon metabolism-related inhibitors.
Commun Biol, 5, 2022
1L6G
DownloadVisualize
BU of 1l6g by Molmil
Alanine racemase bound with N-(5'-phosphopyridoxyl)-D-alanine
Descriptor: N-(5'-PHOSPHOPYRIDOXYL)-D-ALANINE, alanine racemase
Authors:Watanabe, A, Yoshimura, T, Mikami, B, Hayashi, H, Kagamiyama, H, Esaki, N.
Deposit date:2002-03-10
Release date:2002-06-05
Last modified:2023-11-15
Method:X-RAY DIFFRACTION (2 Å)
Cite:Reaction mechanism of alanine racemase from Bacillus stearothermophilus: x-ray crystallographic studies of the enzyme bound with N-(5'-phosphopyridoxyl)alanine.
J.Biol.Chem., 277, 2002
5TYR
DownloadVisualize
BU of 5tyr by Molmil
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
5TYS
DownloadVisualize
BU of 5tys by Molmil
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
9NWB
DownloadVisualize
BU of 9nwb by Molmil
Crystal structure of SARS-CoV-2 main protease in complex with an inhibitor TKB-280-5I
Descriptor: (1R,2S,5S)-N-{(1S,2R)-1-hydroxy-1-(5-iodo-1,3-benzothiazol-2-yl)-3-[(3R)-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, ORF1a polyprotein
Authors:Bulut, H, Hayashi, H, Hattori, S, Li, M, Das, D, Wlodawer, A, Tamamura, H, Mitsuya, H.
Deposit date:2025-03-21
Release date:2025-06-04
Method:X-RAY DIFFRACTION (2.01 Å)
Cite:Impact of Single Halogen Atom Substitutions on Potency of Inhibitors Targeting SARS-CoV-2 Main Protease
To Be Published
9NWA
DownloadVisualize
BU of 9nwa by Molmil
Crystal structure of SARS-CoV-2 main protease in complex with an inhibitor TKB-277-5Cl
Descriptor: (1R,2S,5S)-N-{(1S,2S)-1-(5-chloro-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
Authors:Bulut, H, Kuwata, N, Hayashi, H, Aoki, H, Das, D, Li, M, Wlodawer, A, Misumi, S, Tamamura, H, Mitsuya, H.
Deposit date:2025-03-21
Release date:2025-06-04
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Impact of Single Halogen Atom Substitutions on Potency of Inhibitors Targeting SARS-CoV-2 Main Protease
To Be Published
9NWC
DownloadVisualize
BU of 9nwc by Molmil
Crystal structure of SARS-CoV-2 main protease in complex with an inhibitor TKB-276-5Br
Descriptor: (1R,2S,5S)-N-{(1S,2S)-1-(5-bromo-1,3-benzothiazol-2-yl)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-D-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide, 3C-like proteinase nsp5
Authors:Bulut, H, Kuwata, N, Hayashi, H, Aoki, H, Hattori, S, Li, M, Das, D, Misumi, S, Wlodawer, A, Tamamura, H, Mitsuya, H.
Deposit date:2025-03-21
Release date:2025-06-04
Method:X-RAY DIFFRACTION (1.79 Å)
Cite:Impact of Single Halogen Atom Substitutions on Potency of Inhibitors Targeting SARS-CoV-2 Main Protease
To Be Published
3K8U
DownloadVisualize
BU of 3k8u by Molmil
Crystal Structure of the Peptidase Domain of Streptococcus ComA, a Bi-functional ABC Transporter Involved in Quorum Sensing Pathway
Descriptor: Putative ABC transporter, ATP-binding protein ComA
Authors:Ishii, S, Yano, T, Ebihara, A, Okamoto, A, Manzoku, M, Hayashi, H.
Deposit date:2009-10-14
Release date:2010-02-23
Last modified:2024-03-20
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:Crystal structure of the peptidase domain of Streptococcus ComA, a bifunctional ATP-binding cassette transporter involved in the quorum-sensing pathway
J.Biol.Chem., 285, 2010
8DOX
DownloadVisualize
BU of 8dox by Molmil
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:2024-10-23
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
8DPR
DownloadVisualize
BU of 8dpr by Molmil
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:2024-11-20
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
8DOY
DownloadVisualize
BU of 8doy by Molmil
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:2024-10-09
Method:X-RAY DIFFRACTION (1.59 Å)
Cite:Potent and biostable inhibitors of the main protease of SARS-CoV-2.
Iscience, 25, 2022
8UH8
DownloadVisualize
BU of 8uh8 by Molmil
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
Last modified:2025-02-19
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:An orally available P1'-5-fluorinated M pro inhibitor blocks SARS-CoV-2 replication without booster and exhibits high genetic barrier.
Pnas Nexus, 4, 2025
8UH5
DownloadVisualize
BU of 8uh5 by Molmil
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
Last modified:2025-02-19
Method:X-RAY DIFFRACTION (1.74 Å)
Cite:An orally available P1'-5-fluorinated M pro inhibitor blocks SARS-CoV-2 replication without booster and exhibits high genetic barrier.
Pnas Nexus, 4, 2025
8UH9
DownloadVisualize
BU of 8uh9 by Molmil
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
Last modified:2025-02-19
Method:X-RAY DIFFRACTION (2.067 Å)
Cite:An orally available P1'-5-fluorinated M pro inhibitor blocks SARS-CoV-2 replication without booster and exhibits high genetic barrier.
Pnas Nexus, 4, 2025
5XN0
DownloadVisualize
BU of 5xn0 by Molmil
HIV-1 reverse transcriptase Q151M:DNA binary complex
Descriptor: 38-MER DNA aptamer, GLYCEROL, Pol protein, ...
Authors:Yasutake, Y, Tamura, N, Hayashi, H, Maeda, K.
Deposit date:2017-05-17
Release date:2018-02-07
Last modified:2023-11-22
Method:X-RAY DIFFRACTION (2.596 Å)
Cite:HIV-1 with HBV-associated Q151M substitution in RT becomes highly susceptible to entecavir: structural insights into HBV-RT inhibition by entecavir.
Sci Rep, 8, 2018
5XN1
DownloadVisualize
BU of 5xn1 by Molmil
HIV-1 reverse transcriptase Q151M:DNA:entecavir-triphosphate ternary complex
Descriptor: 38-MER DNA aptamer, GLYCEROL, MAGNESIUM ION, ...
Authors:Yasutake, Y, Tamura, N, Hayashi, H, Maeda, K.
Deposit date:2017-05-17
Release date:2018-02-07
Last modified:2023-11-22
Method:X-RAY DIFFRACTION (2.446 Å)
Cite:HIV-1 with HBV-associated Q151M substitution in RT becomes highly susceptible to entecavir: structural insights into HBV-RT inhibition by entecavir.
Sci Rep, 8, 2018
6UWC
DownloadVisualize
BU of 6uwc by Molmil
X-ray crystal structure of wild type HIV-1 protease in complex with GRL-08613
Descriptor: (3aS,4S,7aR)-hexahydro-4H-furo[2,3-b]pyran-4-yl {(2S,3R)-1-(4-fluorophenyl)-3-hydroxy-4-[(2-methylpropyl)({2-[(propan-2-yl)amino]-1,3-benzothiazol-6-yl}sulfonyl)amino]butan-2-yl}carbamate, Protease
Authors:Yedidi, R.S, Hayashi, H, Ghosh, A.K, Mitsuya, H.
Deposit date:2019-11-05
Release date:2020-11-18
Last modified:2023-10-11
Method:X-RAY DIFFRACTION (1.95 Å)
Cite:Fluorine Modifications Contribute to Potent Antiviral Activity against Highly Drug-Resistant HIV-1 and Favorable Blood-Brain Barrier Penetration Property of Novel Central Nervous System-Targeting HIV-1 Protease Inhibitors In Vitro.
Antimicrob.Agents Chemother., 66, 2022
6UWB
DownloadVisualize
BU of 6uwb by Molmil
X-ray crystal structure of wild type HIV-1 protease in complex with GRL-08513
Descriptor: (3aS,4S,7aR)-hexahydro-4H-furo[2,3-b]pyran-4-yl {(2S,3R)-1-(3,5-difluorophenyl)-3-hydroxy-4-[(2-methylpropyl)({2-[(propan-2-yl)amino]-1,3-benzothiazol-6-yl}sulfonyl)amino]butan-2-yl}carbamate, Protease
Authors:Yedidi, R.S, Hayashi, H, Ghosh, A.K, Mitsuya, H.
Deposit date:2019-11-05
Release date:2020-11-18
Last modified:2023-10-11
Method:X-RAY DIFFRACTION (1.95 Å)
Cite:Fluorine Modifications Contribute to Potent Antiviral Activity against Highly Drug-Resistant HIV-1 and Favorable Blood-Brain Barrier Penetration Property of Novel Central Nervous System-Targeting HIV-1 Protease Inhibitors In Vitro.
Antimicrob.Agents Chemother., 66, 2022

238582

PDB entries from 2025-07-09

PDB statisticsPDBj update infoContact PDBjnumon