6AAR
 
 | | Crystal structure of DAPK1 in complex with purpurin | | Descriptor: | Death-associated protein kinase 1, Purpurin | | Authors: | Yokoyama, T, Mizuguchi, M. | | Deposit date: | 2018-07-19 | | Release date: | 2019-07-24 | | Last modified: | 2024-03-27 | | Method: | X-RAY DIFFRACTION (1.95 Å) | | Cite: | Structural and thermodynamic analyses of interactions between death-associated protein kinase 1 and anthraquinones.
Acta Crystallogr D Struct Biol, 76, 2020
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6AJV
 | | Crystal structure of BRD4 in complex with isoliquiritigenin and DMSO (Cocktail No. 3) | | Descriptor: | 2',4,4'-TRIHYDROXYCHALCONE, Bromodomain-containing protein 4, DIMETHYL SULFOXIDE, ... | | Authors: | Yokoyama, T, Matsumoto, K, Nabeshima, Y, Mizuguchi, M. | | Deposit date: | 2018-08-28 | | Release date: | 2019-06-12 | | Last modified: | 2024-03-27 | | Method: | X-RAY DIFFRACTION (1.45 Å) | | Cite: | Structural and thermodynamic characterization of the binding of isoliquiritigenin to the first bromodomain of BRD4.
Febs J., 286, 2019
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6AA5
 | | Crystal structure of MTH1 in complex with 3-isomangostin | | Descriptor: | 5,9-dihydroxy-8-methoxy-2,2-dimethyl-7-(3-methylbut-2-en-1-yl)-3,4-dihydro-2H,6H-pyrano[3,2-b]xanthen-6-one, 7,8-dihydro-8-oxoguanine triphosphatase, SULFATE ION, ... | | Authors: | Yokoyama, T, Kitakami, R, Mizuguchi, M. | | Deposit date: | 2018-07-17 | | Release date: | 2019-03-06 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.901 Å) | | Cite: | Discovery of a new class of MTH1 inhibitor by X-ray crystallographic screening.
Eur J Med Chem, 167, 2019
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6AJX
 | | Crystal structure of BRD4 in complex with isoliquiritigenin in the absence of DMSO | | Descriptor: | 2',4,4'-TRIHYDROXYCHALCONE, Bromodomain-containing protein 4, SODIUM ION | | Authors: | Yokoyama, T, Matsumoto, K, Nabeshima, Y, Mizuguchi, M. | | Deposit date: | 2018-08-28 | | Release date: | 2019-06-12 | | Last modified: | 2024-03-27 | | Method: | X-RAY DIFFRACTION (1.887 Å) | | Cite: | Structural and thermodynamic characterization of the binding of isoliquiritigenin to the first bromodomain of BRD4.
Febs J., 286, 2019
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6AJY
 | | Crystal structure of BRD4 in complex with 2',4'-dihydroxy-2-methoxychalcone | | Descriptor: | 2',4'-dihydroxy-2-methoxychalcone, Bromodomain-containing protein 4, SODIUM ION | | Authors: | Yokoyama, T, Matsumoto, K, Nabeshima, Y, Mizuguchi, M. | | Deposit date: | 2018-08-28 | | Release date: | 2019-06-12 | | Last modified: | 2024-03-27 | | Method: | X-RAY DIFFRACTION (1.6 Å) | | Cite: | Structural and thermodynamic characterization of the binding of isoliquiritigenin to the first bromodomain of BRD4.
Febs J., 286, 2019
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6AJZ
 | | Joint nentron and X-ray structure of BRD4 in complex with colchicin | | Descriptor: | Bromodomain-containing protein 4, N-[(7S)-1,2,3,10-tetramethoxy-9-oxo-6,7-dihydro-5H-benzo[d]heptalen-7-yl]ethanamide, SODIUM ION | | Authors: | Yokoyama, T, Ostermann, A, Schrader, T.E, Nabeshima, Y, Mizuguchi, M. | | Deposit date: | 2018-08-28 | | Release date: | 2019-06-12 | | Last modified: | 2024-03-27 | | Method: | NEUTRON DIFFRACTION (1.301 Å), X-RAY DIFFRACTION | | Cite: | Structural and thermodynamic characterization of the binding of isoliquiritigenin to the first bromodomain of BRD4.
Febs J., 286, 2019
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6AJW
 | | Crystal structure of BRD4 in complex with DMSO (Cocktail No. 4) | | Descriptor: | Bromodomain-containing protein 4, DIMETHYL SULFOXIDE, SODIUM ION | | Authors: | Yokoyama, T, Matsumoto, K, Nabeshima, Y, Mizuguchi, M. | | Deposit date: | 2018-08-28 | | Release date: | 2019-06-12 | | Last modified: | 2024-03-27 | | Method: | X-RAY DIFFRACTION (1.401 Å) | | Cite: | Structural and thermodynamic characterization of the binding of isoliquiritigenin to the first bromodomain of BRD4.
Febs J., 286, 2019
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3BNV
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3D6L
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1V4W
 | | Crystal structure of bluefin tuna hemoglobin deoxy form at pH7.5 | | Descriptor: | PROTOPORPHYRIN IX CONTAINING FE, hemoglobin alpha chain, hemoglobin beta chain | | Authors: | Yokoyama, T, Chong, K.T, Miyazaki, Y, Nakatsukasa, T, Unzai, S, Miyazaki, G, Morimoto, H, Jeremy, R.H.T, Park, S.Y. | | Deposit date: | 2003-11-19 | | Release date: | 2004-07-06 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (1.7 Å) | | Cite: | Novel Mechanisms of pH Sensitivity in Tuna Hemoglobin: A STRUCTURAL EXPLANATION OF THE ROOT EFFECT
J.Biol.Chem., 279, 2004
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1V4U
 | | Crystal structure of bluefin tuna carbonmonoxy-hemoglobin | | Descriptor: | CARBON MONOXIDE, PROTOPORPHYRIN IX CONTAINING FE, hemoglobin alpha chain, ... | | Authors: | Yokoyama, T, Chong, K.T, Miyazaki, Y, Nakatsukasa, T, Unzai, S, Miyazaki, G, Morimoto, H, Jeremy, R.H.T, Park, S.Y. | | Deposit date: | 2003-11-19 | | Release date: | 2004-07-06 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Novel Mechanisms of pH Sensitivity in Tuna Hemoglobin: A STRUCTURAL EXPLANATION OF THE ROOT EFFECT
J.Biol.Chem., 279, 2004
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1V4X
 | | Crystal structure of bluefin tuna hemoglobin deoxy form at pH5.0 | | Descriptor: | PROTOPORPHYRIN IX CONTAINING FE, hemoglobin alpha chain, hemoglobin beta chain | | Authors: | Yokoyama, T, Chong, K.T, Miyazaki, Y, Nakatsukasa, T, Unzai, S, Miyazaki, G, Morimoto, H, Jeremy, R.H.T, Park, S.Y. | | Deposit date: | 2003-11-19 | | Release date: | 2004-07-06 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (1.6 Å) | | Cite: | Novel Mechanisms of pH Sensitivity in Tuna Hemoglobin: A STRUCTURAL EXPLANATION OF THE ROOT EFFECT
J.Biol.Chem., 279, 2004
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2D5Z
 | | Crystal structure of T-state human hemoglobin complexed with three L35 molecules | | Descriptor: | 2-[4-({[(3,5-DICHLOROPHENYL)AMINO]CARBONYL}AMINO)PHENOXY]-2-METHYLPROPANOIC ACID, Hemoglobin alpha subunit, Hemoglobin beta subunit, ... | | Authors: | Yokoyama, T, Neya, S, Tsuneshige, A, Yonetani, T, Park, S.Y, Tame, J.R. | | Deposit date: | 2005-11-08 | | Release date: | 2006-03-07 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (1.45 Å) | | Cite: | R-state haemoglobin with low oxygen affinity: crystal structures of deoxy human and carbonmonoxy horse haemoglobin bound to the effector molecule L35
J.Mol.Biol., 356, 2006
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2D60
 | | Crystal structure of deoxy human hemoglobin complexed with two L35 molecules | | Descriptor: | 2-[4-({[(3,5-DICHLOROPHENYL)AMINO]CARBONYL}AMINO)PHENOXY]-2-METHYLPROPANOIC ACID, Hemoglobin alpha subunit, Hemoglobin beta subunit, ... | | Authors: | Yokoyama, T, Neya, S, Tsuneshige, A, Yonetani, T, Park, S.Y, Tame, J.R. | | Deposit date: | 2005-11-08 | | Release date: | 2006-03-07 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (1.7 Å) | | Cite: | R-state haemoglobin with low oxygen affinity: crystal structures of deoxy human and carbonmonoxy horse haemoglobin bound to the effector molecule L35
J.Mol.Biol., 356, 2006
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2D5X
 | | Crystal structure of carbonmonoxy horse hemoglobin complexed with L35 | | Descriptor: | 2-[4-({[(3,5-DICHLOROPHENYL)AMINO]CARBONYL}AMINO)PHENOXY]-2-METHYLPROPANOIC ACID, CARBON MONOXIDE, Hemoglobin alpha subunit, ... | | Authors: | Yokoyama, T, Neya, S, Tsuneshige, A, Yonetani, T, Park, S.Y, Tame, J.R. | | Deposit date: | 2005-11-08 | | Release date: | 2006-03-07 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (1.45 Å) | | Cite: | R-state haemoglobin with low oxygen affinity: crystal structures of deoxy human and carbonmonoxy horse haemoglobin bound to the effector molecule L35
J.Mol.Biol., 356, 2006
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8IPB
 | | Wheat 80S ribosome pausing on AUG-Stop with cycloheximide | | Descriptor: | 18S ribosomal RNA, 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione, 40S ribosomal protein eL8, ... | | Authors: | Yokoyama, T, Tanaka, M, Saito, H, Nishimoto, M, Tsuda, K, Sotta, N, Shigematsu, H, Shirouzu, M, Iwasaki, S, Ito, T, Fujiwara, T. | | Deposit date: | 2023-03-14 | | Release date: | 2024-02-21 | | Method: | ELECTRON MICROSCOPY (3.4 Å) | | Cite: | Boric acid intercepts 80S ribosome migration from AUG-stop by stabilizing eRF1.
Nat.Chem.Biol., 2024
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8IP9
 | | Wheat 40S ribosome in complex with a tRNAi | | Descriptor: | 18S ribosomal RNA, 40S ribosomal protein S23, 40S ribosomal protein eS1, ... | | Authors: | Yokoyama, T, Tanaka, M, Saito, H, Nishimoto, M, Tsuda, K, Sotta, N, Shigematsu, H, Shirouzu, M, Iwasaki, S, Ito, T, Fujiwara, T. | | Deposit date: | 2023-03-14 | | Release date: | 2024-02-21 | | Method: | ELECTRON MICROSCOPY (3 Å) | | Cite: | Boric acid intercepts 80S ribosome migration from AUG-stop by stabilizing eRF1.
Nat.Chem.Biol., 2024
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8IP8
 | | Wheat 80S ribosome stalled on AUG-Stop boron dependently | | Descriptor: | 18S ribosomal RNA, 40S ribosomal protein eL8, 40S ribosomal protein eS1, ... | | Authors: | Yokoyama, T, Tanaka, M, Saito, H, Nishimoto, M, Tsuda, K, Sotta, N, Shigematsu, H, Shirouzu, M, Iwasaki, S, Ito, T, Fujiwara, T. | | Deposit date: | 2023-03-14 | | Release date: | 2024-02-21 | | Method: | ELECTRON MICROSCOPY (2.9 Å) | | Cite: | Boric acid intercepts 80S ribosome migration from AUG-stop by stabilizing eRF1.
Nat.Chem.Biol., 2024
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8IPA
 | | Wheat 80S ribosome stalled on AUG-Stop boron dependently with cycloheximide | | Descriptor: | 18S ribosomal RNA, 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione, 40S ribosomal protein eL8, ... | | Authors: | Yokoyama, T, Tanaka, M, Saito, H, Nishimoto, M, Tsuda, K, Sotta, N, Shigematsu, H, Shirouzu, M, Iwasaki, S, Ito, T, Fujiwara, T. | | Deposit date: | 2023-03-14 | | Release date: | 2024-02-21 | | Method: | ELECTRON MICROSCOPY (3.4 Å) | | Cite: | Boric acid intercepts 80S ribosome migration from AUG-stop by stabilizing eRF1.
Nat.Chem.Biol., 2024
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8I75
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8I76
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8I74
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7CPJ
 | | ycbZ-stalled 70S ribosome | | Descriptor: | 16S ribosomal RNA, 23S ribosomal RNA, 30S ribosomal protein S10, ... | | Authors: | Yokoyama, T, Shirouzu, M, Ito, T. | | Deposit date: | 2020-08-07 | | Release date: | 2021-12-08 | | Last modified: | 2023-04-05 | | Method: | ELECTRON MICROSCOPY (3.3 Å) | | Cite: | The landscape of translational stall sites in bacteria revealed by monosome and disome profiling.
Rna, 28, 2022
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8II1
 | | Crystal structure of V30M-TTR in complex with BID | | Descriptor: | Benziodarone, Transthyretin | | Authors: | Yokoyama, T. | | Deposit date: | 2023-02-24 | | Release date: | 2023-06-28 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.907 Å) | | Cite: | Benziodarone and 6-hydroxybenziodarone are potent and selective inhibitors of transthyretin amyloidogenesis.
Bioorg.Med.Chem., 90, 2023
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8II4
 | | Crystal structure of V30M-TTR in complex with 6-hydroxy BBM | | Descriptor: | Transthyretin, [3,5-bis(bromanyl)-4-oxidanyl-phenyl]-(2-ethyl-6-oxidanyl-1-benzofuran-3-yl)methanone | | Authors: | Yokoyama, T. | | Deposit date: | 2023-02-24 | | Release date: | 2023-06-28 | | Method: | X-RAY DIFFRACTION (1.499 Å) | | Cite: | Benziodarone and 6-hydroxybenziodarone are potent and selective inhibitors of transthyretin amyloidogenesis.
Bioorg.Med.Chem., 90, 2023
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