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PDB: 163 results

6IP5
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BU of 6ip5 by Molmil
Cryo-EM structure of the CMV-stalled human 80S ribosome (Structure ii)
Descriptor: 18S ribosomal RNA, 28S ribosomal RNA, 40S ribosomal protein S10, ...
Authors:Yokoyama, T, Shigematsu, H, Shirouzu, M, Imataka, H, Ito, T.
Deposit date:2018-11-02
Release date:2019-05-29
Last modified:2019-11-06
Method:ELECTRON MICROSCOPY (3.9 Å)
Cite:HCV IRES Captures an Actively Translating 80S Ribosome.
Mol.Cell, 74, 2019
4PWK
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BU of 4pwk by Molmil
Crystal structure of V30M mutant human transthyretin complexed with dihydroguaiaretic acid
Descriptor: 4,4'-[(2R,3R)-2,3-dimethylbutane-1,4-diyl]bis(2-methoxyphenol), Transthyretin
Authors:Yokoyama, T, Kosaka, Y, Mizuguchi, M.
Deposit date:2014-03-20
Release date:2014-11-26
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (1.59 Å)
Cite:Inhibitory Activities of Propolis and Its Promising Component, Caffeic Acid Phenethyl Ester, against Amyloidogenesis of Human Transthyretin
J.Med.Chem., 57, 2014
4PWG
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BU of 4pwg by Molmil
Crystal structure of V30M mutant human transthyretin complexed with caffeic acid ethyl ester
Descriptor: CALCIUM ION, Transthyretin, ethyl (2E)-3-(3,4-dihydroxyphenyl)prop-2-enoate
Authors:Yokoyama, T, Kosaka, Y, Mizuguchi, M.
Deposit date:2014-03-20
Release date:2014-11-26
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (1.798 Å)
Cite:Inhibitory Activities of Propolis and Its Promising Component, Caffeic Acid Phenethyl Ester, against Amyloidogenesis of Human Transthyretin
J.Med.Chem., 57, 2014
8IG1
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BU of 8ig1 by Molmil
Crystal structure of wild-type transthyretin in complex with rafoxanide
Descriptor: SODIUM ION, Transthyretin, ~{N}-[3-chloranyl-4-(4-chloranylphenoxy)phenyl]-3,5-bis(iodanyl)-2-oxidanyl-benzamide
Authors:Yokoyama, T.
Deposit date:2023-02-20
Release date:2023-08-16
Last modified:2023-11-15
Method:X-RAY DIFFRACTION (1.451 Å)
Cite:Rafoxanide, a salicylanilide anthelmintic, interacts with human plasma protein transthyretin.
Febs J., 290, 2023
5CG5
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BU of 5cg5 by Molmil
Neutron crystal structure of human farnesyl pyrophosphate synthase in complex with risedronate
Descriptor: 1-HYDROXY-2-(3-PYRIDINYL)ETHYLIDENE BIS-PHOSPHONIC ACID, Farnesyl pyrophosphate synthase, MAGNESIUM ION
Authors:Yokoyama, T, Mizuguchi, M, Ostermann, A, Kusaka, K, Niimura, N, Schrader, T.E, Tanaka, I.
Deposit date:2015-07-09
Release date:2015-10-14
Last modified:2024-04-03
Method:NEUTRON DIFFRACTION (1.402 Å), X-RAY DIFFRACTION
Cite:Protonation State and Hydration of Bisphosphonate Bound to Farnesyl Pyrophosphate Synthase
J.Med.Chem., 58, 2015
5CG6
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BU of 5cg6 by Molmil
Neutron crystal structure of human farnesyl pyrophosphate synthase in complex with risedronate and isopentenyl pyrophosphate
Descriptor: 1-HYDROXY-2-(3-PYRIDINYL)ETHYLIDENE BIS-PHOSPHONIC ACID, 3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE, Farnesyl pyrophosphate synthase, ...
Authors:Yokoyama, T, Mizuguchi, M, Ostermann, A, Kusaka, K, Niimura, N, Schrader, T.E, Tanaka, I.
Deposit date:2015-07-09
Release date:2015-10-14
Last modified:2024-04-03
Method:NEUTRON DIFFRACTION (1.7 Å), X-RAY DIFFRACTION
Cite:Protonation State and Hydration of Bisphosphonate Bound to Farnesyl Pyrophosphate Synthase
J.Med.Chem., 58, 2015
6IMY
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BU of 6imy by Molmil
Crystal structure of V30M mutated transthyretin in complex with 4'-caroboxybenzo-18-Crown-6
Descriptor: 2,3,5,6,8,9,11,12,14,15-decahydro-1,4,7,10,13,16-benzohexaoxacyclooctadecine-18-carboxylic acid, Transthyretin
Authors:Yokoyama, T, Kosaka, Y, Matsumoto, K, Kitakami, R, Nabeshima, Y, Mizuguchi, M.
Deposit date:2018-10-24
Release date:2019-03-13
Last modified:2024-03-27
Method:X-RAY DIFFRACTION (1.501 Å)
Cite:Crown Ethers as Transthyretin Amyloidogenesis Inhibitors.
J. Med. Chem., 62, 2019
6IN2
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BU of 6in2 by Molmil
Crystal structure of BRD1 in complex with 18-Crown-6
Descriptor: 1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE, ACETATE ION, Bromodomain-containing protein 1
Authors:Yokoyama, T, Kosaka, Y, Matsumoto, K, Kitakami, R, Nabeshima, Y, Mizuguchi, M.
Deposit date:2018-10-24
Release date:2019-10-30
Last modified:2024-03-27
Method:X-RAY DIFFRACTION (1.75 Å)
Cite:Crown Ethers as Transthyretin Amyloidogenesis Inhibitor
To Be Published
7FH2
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BU of 7fh2 by Molmil
Crystal structure of the first bromodomain of BRD4 in complex with 16D10
Descriptor: Bromodomain-containing protein 4, CHLORIDE ION, N-[2-[2-[(E)-3-(2,5-dimethoxyphenyl)prop-2-enoyl]-4,5-dimethoxy-phenyl]ethyl]ethanamide
Authors:Yokoyama, T, Hirasawa, N.
Deposit date:2021-07-29
Release date:2022-08-03
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.492 Å)
Cite:A chalcone derivative suppresses TSLP induction in mice and human keratinocytes through binding to BET family proteins.
Biochem Pharmacol, 194, 2021
8WGT
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BU of 8wgt by Molmil
Crystal structure of V30M-TTR in complex with compound 7
Descriptor: Transthyretin, [4,7-bis(chloranyl)-2-ethyl-1-benzofuran-3-yl]-[3,5-bis(iodanyl)-4-oxidanyl-phenyl]methanone
Authors:Yokoyama, T.
Deposit date:2023-09-22
Release date:2024-05-15
Last modified:2024-05-29
Method:X-RAY DIFFRACTION (1.696 Å)
Cite:Development of Benziodarone Analogues with Enhanced Potency for Selective Binding to Transthyretin in Human Plasma.
J.Med.Chem., 67, 2024
8WGS
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BU of 8wgs by Molmil
Crystal structure of V30M-TTR in complex with compound 4
Descriptor: Transthyretin, [3,5-bis(iodanyl)-4-oxidanyl-phenyl]-(2-ethyl-4-iodanyl-1-benzofuran-3-yl)methanone
Authors:Yokoyama, T.
Deposit date:2023-09-22
Release date:2024-05-15
Last modified:2024-05-29
Method:X-RAY DIFFRACTION (1.801 Å)
Cite:Development of Benziodarone Analogues with Enhanced Potency for Selective Binding to Transthyretin in Human Plasma.
J.Med.Chem., 67, 2024
8WGU
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BU of 8wgu by Molmil
Crystal structure of V30M-TTR in complex with compound 20
Descriptor: Transthyretin, [3,5-bis(iodanyl)-4-oxidanyl-phenyl]-[2-ethyl-4,7-bis(fluoranyl)-1-benzofuran-3-yl]methanone
Authors:Yokoyama, T.
Deposit date:2023-09-22
Release date:2024-05-15
Last modified:2024-05-29
Method:X-RAY DIFFRACTION (1.508 Å)
Cite:Development of Benziodarone Analogues with Enhanced Potency for Selective Binding to Transthyretin in Human Plasma.
J.Med.Chem., 67, 2024
8IE6
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BU of 8ie6 by Molmil
Crystal structure of DAPK1 in complex with pinostilbene
Descriptor: 3-[(E)-2-(4-hydroxyphenyl)ethenyl]-5-methoxy-phenol, Death-associated protein kinase 1, SULFATE ION
Authors:Yokoyama, T.
Deposit date:2023-02-15
Release date:2023-05-24
Last modified:2023-10-04
Method:X-RAY DIFFRACTION (1.701 Å)
Cite:Characterization of the molecular interactions between resveratrol derivatives and death-associated protein kinase 1.
Febs J., 290, 2023
8IE5
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BU of 8ie5 by Molmil
Crystal structure of DAPK1 in complex with oxyresveratrol
Descriptor: Death-associated protein kinase 1, SULFATE ION, trans-oxyresveratrol
Authors:Yokoyama, T.
Deposit date:2023-02-15
Release date:2023-05-24
Last modified:2023-10-04
Method:X-RAY DIFFRACTION (1.803 Å)
Cite:Characterization of the molecular interactions between resveratrol derivatives and death-associated protein kinase 1.
Febs J., 290, 2023
8IE8
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BU of 8ie8 by Molmil
Crystal structure of DAPK1 in complex with isorhapontigenin
Descriptor: 5-[(~{E})-2-(3-methoxy-4-oxidanyl-phenyl)ethenyl]benzene-1,3-diol, Death-associated protein kinase 1, SULFATE ION
Authors:Yokoyama, T.
Deposit date:2023-02-15
Release date:2023-05-24
Last modified:2023-10-04
Method:X-RAY DIFFRACTION (1.75 Å)
Cite:Characterization of the molecular interactions between resveratrol derivatives and death-associated protein kinase 1.
Febs J., 290, 2023
8IE7
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BU of 8ie7 by Molmil
Crystal structure of DAPK1 in complex with pterostilbene
Descriptor: Death-associated protein kinase 1, Pterostilbene, SULFATE ION
Authors:Yokoyama, T.
Deposit date:2023-02-15
Release date:2023-05-24
Last modified:2023-10-04
Method:X-RAY DIFFRACTION (1.849 Å)
Cite:Characterization of the molecular interactions between resveratrol derivatives and death-associated protein kinase 1.
Febs J., 290, 2023
8IP9
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BU of 8ip9 by Molmil
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
Last modified:2024-05-15
Method:ELECTRON MICROSCOPY (3 Å)
Cite:Boric acid intercepts 80S ribosome migration from AUG-stop by stabilizing eRF1.
Nat.Chem.Biol., 20, 2024
8IPA
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BU of 8ipa by Molmil
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
Last modified:2024-05-15
Method:ELECTRON MICROSCOPY (3.4 Å)
Cite:Boric acid intercepts 80S ribosome migration from AUG-stop by stabilizing eRF1.
Nat.Chem.Biol., 20, 2024
8IPB
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BU of 8ipb by Molmil
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
Last modified:2024-05-15
Method:ELECTRON MICROSCOPY (3.4 Å)
Cite:Boric acid intercepts 80S ribosome migration from AUG-stop by stabilizing eRF1.
Nat.Chem.Biol., 20, 2024
8IP8
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BU of 8ip8 by Molmil
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
Last modified:2024-05-15
Method:ELECTRON MICROSCOPY (2.9 Å)
Cite:Boric acid intercepts 80S ribosome migration from AUG-stop by stabilizing eRF1.
Nat.Chem.Biol., 20, 2024
4QRF
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BU of 4qrf by Molmil
Crystal structure of V30M mutant human transthyretin complexed with caffeic acid phenethyl ester
Descriptor: 2-phenylethyl (2E)-3-(3,4-dihydroxyphenyl)prop-2-enoate, Transthyretin
Authors:Yokoyama, T, Kosaka, Y, Mizuguchi, M.
Deposit date:2014-06-30
Release date:2014-11-26
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Inhibitory Activities of Propolis and Its Promising Component, Caffeic Acid Phenethyl Ester, against Amyloidogenesis of Human Transthyretin
J.Med.Chem., 57, 2014
8I74
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BU of 8i74 by Molmil
Crystal structure of decarboxylated osteocalcin at pH 8.5
Descriptor: Osteocalcin
Authors:Yokoyama, T, Nabeshima, Y, Obita, T, Mizuguchi, M.
Deposit date:2023-01-31
Release date:2024-01-31
Method:X-RAY DIFFRACTION (1.36 Å)
Cite:Crystal structures of decarboxylated osteocalcin and implications for the interaction with its receptor
To Be Published
8I75
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BU of 8i75 by Molmil
Crystal structure of decarboxylated osteocalcin at pH 2.0
Descriptor: Osteocalcin
Authors:Yokoyama, T, Nabeshima, Y, Obita, T, Mizuguchi, M.
Deposit date:2023-01-31
Release date:2024-01-31
Method:X-RAY DIFFRACTION (1.33 Å)
Cite:Crystal structures of decarboxylated osteocalcin and implications for the interaction with its receptor
To Be Published
8I76
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BU of 8i76 by Molmil
Crystal structure of decarboxylated osteocalcin at pH 2.0 without glycerol
Descriptor: Osteocalcin
Authors:Yokoyama, T, Nabeshima, Y, Obita, T, Mizuguchi, M.
Deposit date:2023-01-31
Release date:2024-01-31
Method:X-RAY DIFFRACTION (1.381 Å)
Cite:Crystal structures of decarboxylated osteocalcin and implications for the interaction with its receptor
To Be Published
6IP6
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BU of 6ip6 by Molmil
Cryo-EM structure of the CMV-stalled human 80S ribosome with HCV IRES (Structure iii)
Descriptor: 18S ribosomal RNA, 28S ribosomal RNA, 40S ribosomal protein S10, ...
Authors:Yokoyama, T, Shigematsu, H, Shirouzu, M, Imataka, H, Ito, T.
Deposit date:2018-11-02
Release date:2019-05-29
Last modified:2019-11-06
Method:ELECTRON MICROSCOPY (4.5 Å)
Cite:HCV IRES Captures an Actively Translating 80S Ribosome.
Mol.Cell, 74, 2019

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PDB entries from 2024-06-19

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