8H28
 
 | | Crystal structure of the K87V mutant of cytochrome c' from Shewanella benthica DB6705 | | 分子名称: | Class II cytochrome c, HEME C | | 著者 | Fujii, S, Sakaguchi, R, Oki, H, Kawahara, K, Ohkubo, T, Fujiyoshi, S, Sambongi, Y. | | 登録日 | 2022-10-05 | | 公開日 | 2023-10-11 | | 最終更新日 | 2024-04-24 | | 実験手法 | X-RAY DIFFRACTION (2.06 Å) | | 主引用文献 | Contribution of a surface salt bridge to the protein stability of deep-sea Shewanella benthica cytochrome c'.
J.Struct.Biol., 215, 2023
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6A3K
 | | Crystal structure of cytochrome c' from Shewanella benthica DB6705 | | 分子名称: | Cytochrome c, HEME C, PENTAETHYLENE GLYCOL | | 著者 | Suka, A, Oki, H, Kato, Y, Kawahara, K, Ohkubo, T, Maruno, T, Kobayashi, Y, Fujii, S, Wakai, S, Sambongi, Y. | | 登録日 | 2018-06-15 | | 公開日 | 2019-06-12 | | 最終更新日 | 2019-10-02 | | 実験手法 | X-RAY DIFFRACTION (1.71 Å) | | 主引用文献 | Stability of cytochromes c' from psychrophilic and piezophilic Shewanella species: implications for complex multiple adaptation to low temperature and high hydrostatic pressure.
Extremophiles, 23, 2019
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5T4S
 | | Novel Approach of Fragment-Based Lead Discovery applied to Renin Inhibitors | | 分子名称: | 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE, 2-acetamido-2-deoxy-beta-D-glucopyranose, 6-chloro-N-[(furan-2-yl)methyl]pyrazin-2-amine, ... | | 著者 | Snell, G.P, Behnke, C.A, Okada, K, Oki, H, Sang, B.C, Lane, W. | | 登録日 | 2016-08-30 | | 公開日 | 2016-10-26 | | 最終更新日 | 2020-07-29 | | 実験手法 | X-RAY DIFFRACTION (2.64 Å) | | 主引用文献 | Novel approach of fragment-based lead discovery applied to renin inhibitors.
Bioorg.Med.Chem., 24, 2016
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5H03
 | | Crystal structure of an ADP-ribosylating toxin BECa from C. perfringens | | 分子名称: | Binary enterotoxin of Clostridium perfringens component a | | 著者 | Kawahara, K, Yonogi, S, Munetomo, R, Oki, H, Yoshida, T, Ohkubo, T, Kumeda, Y, Matsuda, S, Kodama, T, Iida, T, Nakamura, S. | | 登録日 | 2016-10-03 | | 公開日 | 2016-11-02 | | 最終更新日 | 2023-11-08 | | 実験手法 | X-RAY DIFFRACTION (1.89 Å) | | 主引用文献 | Crystal structure of the ADP-ribosylating component of BEC, the binary enterotoxin of Clostridium perfringens.
Biochem.Biophys.Res.Commun., 480, 2016
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5H04
 | | Crystal structure of an ADP-ribosylating toxin BECa of a novel binary enterotoxin of C. perfringens with NADH | | 分子名称: | 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE, Binary enterotoxin of Clostridium perfringens component a | | 著者 | Kawahara, K, Yonogi, S, Munetomo, R, Oki, H, Yoshida, T, Ohkubo, T, Kumeda, Y, Matsuda, S, Kodama, T, Iida, T, Nakamura, S. | | 登録日 | 2016-10-03 | | 公開日 | 2016-11-02 | | 最終更新日 | 2023-11-08 | | 実験手法 | X-RAY DIFFRACTION (1.825 Å) | | 主引用文献 | Crystal structure of the ADP-ribosylating component of BEC, the binary enterotoxin of Clostridium perfringens.
Biochem.Biophys.Res.Commun., 480, 2016
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6KXX
 | | Human PPAR alpha ligand binding domain in complex with a synthetic agonist (compound A) | | 分子名称: | 1-(4-chlorophenyl)-6-methyl-3-propan-2-yl-pyrazolo[3,4-b]pyridine-4-carboxylic acid, PGC1alpha, Peroxisome proliferator-activated receptor alpha | | 著者 | Yoshida, T, Tachibana, K, Oki, H, Doi, M, Fukuda, S, Yuzuriha, T, Tabata, R, Ishimoto, K, Kawahara, K, Ohkubo, T, Miyachi, H, Doi, T. | | 登録日 | 2019-09-14 | | 公開日 | 2020-05-20 | | 最終更新日 | 2024-03-27 | | 実験手法 | X-RAY DIFFRACTION (1.95 Å) | | 主引用文献 | Structural Basis for PPAR alpha Activation by 1H-pyrazolo-[3,4-b]pyridine Derivatives.
Sci Rep, 10, 2020
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6KXY
 | | Human PPAR alpha ligand binding domain in complex with a synthetic agonist (compound B) | | 分子名称: | 6-ethyl-1-(4-fluorophenyl)-3-pentan-3-yl-pyrazolo[3,4-b]pyridine-4-carboxylic acid, PGC1alpha, Peroxisome proliferator-activated receptor alpha | | 著者 | Yoshida, T, Tachibana, K, Oki, H, Doi, M, Fukuda, S, Yuzuriha, T, Tabata, R, Ishimoto, K, Kawahara, K, Ohkubo, T, Miyachi, H, Doi, T. | | 登録日 | 2019-09-14 | | 公開日 | 2020-05-20 | | 最終更新日 | 2023-11-22 | | 実験手法 | X-RAY DIFFRACTION (2 Å) | | 主引用文献 | Structural Basis for PPAR alpha Activation by 1H-pyrazolo-[3,4-b]pyridine Derivatives.
Sci Rep, 10, 2020
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3VHK
 | | Crystal structure of the VEGFR2 kinase domain in complex with a back pocket binder | | 分子名称: | 1,2-ETHANEDIOL, Vascular endothelial growth factor receptor 2, {3-[(5-methyl-2-phenyl-1,3-oxazol-4-yl)methoxy]phenyl}methanol | | 著者 | Iwata, H, Oki, H, Okada, K, Takagi, T, Tawada, M, Miyazaki, Y, Imamura, S, Hori, A, Hixon, M.S, Kimura, H, Miki, H. | | 登録日 | 2011-08-25 | | 公開日 | 2012-09-05 | | 最終更新日 | 2024-03-20 | | 実験手法 | X-RAY DIFFRACTION (2.49 Å) | | 主引用文献 | A Back-to-Front Fragment-Based Drug Design Search Strategy Targeting the DFG-Out Pocket of Protein Tyrosine Kinases.
ACS MED.CHEM.LETT., 3, 2012
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3VID
 | | Crystal structure of human VEGFR2 kinase domain with Compound A. | | 分子名称: | 4,5,6,11-tetrahydro-1H-pyrazolo[4',3':6,7]cyclohepta[1,2-b]indole, Vascular endothelial growth factor receptor 2 | | 著者 | Iwata, H, Oki, H, Okada, K, Takagi, T, Tawada, M, Miyazaki, Y, Imamura, S, Hori, A, Hixon, M.S, Kimura, H, Miki, H. | | 登録日 | 2011-09-29 | | 公開日 | 2012-08-15 | | 最終更新日 | 2024-03-20 | | 実験手法 | X-RAY DIFFRACTION (2.3 Å) | | 主引用文献 | A Back-to-Front Fragment-Based Drug Design Search Strategy Targeting the DFG-Out Pocket of Protein Tyrosine Kinases.
ACS MED.CHEM.LETT., 3, 2012
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3VW8
 | | Crystal structure of human c-Met kinase domain with its inhibitor | | 分子名称: | CHLORIDE ION, Hepatocyte growth factor receptor, N-({4-[(6,7-dimethoxyquinolin-4-yl)oxy]phenyl}carbamothioyl)-2-phenylacetamide | | 著者 | Matsumoto, S, Miyamoto, N, Hirayama, T, Oki, H, Okada, K, Tawada, M, Iwata, H, Miki, H, Nakamura, K, Hori, A, Imamura, S. | | 登録日 | 2012-08-08 | | 公開日 | 2013-08-14 | | 最終更新日 | 2024-05-29 | | 実験手法 | X-RAY DIFFRACTION (2.1 Å) | | 主引用文献 | Structure-based design, synthesis, and evaluation of imidazo[1,2-b]pyridazine and imidazo[1,2-a]pyridine derivatives as novel dual c-Met and VEGFR2 kinase inhibitors.
Bioorg.Med.Chem., 21, 2013
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5B6Q
 | | Crystal structure of monomeric cytochrome c5 from Shewanella violacea | | 分子名称: | HEME C, IMIDAZOLE, Soluble cytochrome cA | | 著者 | Masanari, M, Fujii, S, Kawahara, K, Oki, H, Tsujino, H, Maruno, T, Kobayashi, Y, Ohkubo, T, Nishiyama, M, Harada, Y, Wakai, S, Sambongi, Y. | | 登録日 | 2016-06-01 | | 公開日 | 2016-10-19 | | 最終更新日 | 2019-10-02 | | 実験手法 | X-RAY DIFFRACTION (1.78 Å) | | 主引用文献 | Comparative study on stabilization mechanism of monomeric cytochrome c5 from deep-sea piezophilic Shewanella violacea
Biosci.Biotechnol.Biochem., 2016
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5B3I
 | | Homo-dimeric structure of cytochrome c' from Thermophilic Hydrogenophilus thermoluteolus | | 分子名称: | Cytochrome c prime, HEME C | | 著者 | Fujii, S, Oki, H, Kawahara, K, Yamane, D, Yamanaka, M, Maruno, T, Kobayashi, Y, Masanari, M, Wakai, S, Nishihara, H, Ohkubo, T, Sambongi, Y. | | 登録日 | 2016-02-29 | | 公開日 | 2017-03-01 | | 最終更新日 | 2023-11-08 | | 実験手法 | X-RAY DIFFRACTION (1.89 Å) | | 主引用文献 | Structural and functional insights into thermally stable cytochrome c' from a thermophile
Protein Sci., 26, 2017
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6KQ1
 | | Crystal structure of cytochrome c551 from Pseudomonas sp. strain MT-1. | | 分子名称: | Cytochrome C biogenesis protein CcsA, HEME C, ZINC ION | | 著者 | Fujii, S, Oki, H, Kawahara, K, Ohkubo, T, Masanari-Fujii, M, Wakai, S, Sambongi, Y. | | 登録日 | 2019-08-16 | | 公開日 | 2020-08-19 | | 最終更新日 | 2023-11-22 | | 実験手法 | X-RAY DIFFRACTION (1.57 Å) | | 主引用文献 | Structural insights into high stability of cytochrome c551 from a deep-sea piezo-tolerant bacterium, Pseudomonas sp. strain MT-1
To Be Published
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6LOS
 | | Crystal structure of mouse PEDF in complex with heterotrimeric collagen model peptide. | | 分子名称: | Collagen model peptide, type I, alpha 1, ... | | 著者 | Kawahara, K, Maruno, T, Oki, H, Yoshida, T, Ohkubo, T, Koide, T, Kobayashi, Y. | | 登録日 | 2020-01-07 | | 公開日 | 2020-09-02 | | 最終更新日 | 2023-11-29 | | 実験手法 | X-RAY DIFFRACTION (2.476 Å) | | 主引用文献 | Spatiotemporal regulation of PEDF signaling by type I collagen remodeling.
Proc.Natl.Acad.Sci.USA, 117, 2020
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7EAD
 | | Crystal structure of beta-sheet cytochrome c prime from Thermus thermophilus. | | 分子名称: | Cytochrome_P460 domain-containing protein, HEME C | | 著者 | Yoshimi, T, Fujii, S, Oki, H, Igawa, T, Adams, R.H, Ueda, K, Kawahara, K, Ohkubo, T, Hough, A.M, Sambongi, Y. | | 登録日 | 2021-03-07 | | 公開日 | 2022-03-09 | | 最終更新日 | 2023-11-29 | | 実験手法 | X-RAY DIFFRACTION (1.74 Å) | | 主引用文献 | Crystal structure of thermally stable homodimeric cytochrome c'-beta from Thermus thermophilus.
Acta Crystallogr.,Sect.F, 78, 2022
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6A3L
 | | Crystal structure of cytochrome c' from Shewanella violacea DSS12 | | 分子名称: | Cytochrome c, HEME C | | 著者 | Suka, A, Oki, H, Kato, Y, Kawahara, K, Ohkubo, T, Maruno, T, Kobayashi, Y, Fujii, S, Wakai, S, Sambongi, Y. | | 登録日 | 2018-06-15 | | 公開日 | 2019-06-12 | | 最終更新日 | 2019-10-02 | | 実験手法 | X-RAY DIFFRACTION (2.14 Å) | | 主引用文献 | Stability of cytochromes c' from psychrophilic and piezophilic Shewanella species: implications for complex multiple adaptation to low temperature and high hydrostatic pressure.
Extremophiles, 23, 2019
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5VP1
 | | Discovery of Clinical Candidate N-{(1S)-1-[3-Fluoro-4-(trifluoromethoxy)phenyl]-2-methoxyethyl}-7-methoxy-2-oxo-2,3-dihydropyrido[2,3-b]pyrazine-4(1H)-carboxamide (TAK-915), A Highly Potent, Selective, and Brain-Penetrating Phosphodiesterase 2A Inhibitor for the Treatment of Cognitive Disorders | | 分子名称: | MAGNESIUM ION, N-{(1S)-2-hydroxy-2-methyl-1-[4-(trifluoromethoxy)phenyl]propyl}-6-methyl-5-(3-methyl-1H-1,2,4-triazol-1-yl)pyrazolo[1,5-a]pyrimidine-3-carboxamide, ZINC ION, ... | | 著者 | Hoffman, I.D. | | 登録日 | 2017-05-03 | | 公開日 | 2017-12-27 | | 最終更新日 | 2024-03-13 | | 実験手法 | X-RAY DIFFRACTION (1.86 Å) | | 主引用文献 | Discovery of a Novel Series of Pyrazolo[1,5-a]pyrimidine-Based Phosphodiesterase 2A Inhibitors Structurally Different from N-((1S)-1-(3-Fluoro-4-(trifluoromethoxy)phenyl)-2-methoxyethyl)-7-methoxy-2-oxo-2,3-dihydropyrido[2,3-b]pyrazine-4(1H)-carboxamide (TAK-915), for the Treatment of Cognitive Disorders.
Chem. Pharm. Bull., 65, 2017
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4HBP
 | | Crystal Structure of FAAH in complex with inhibitor | | 分子名称: | 4-(3-phenyl-1,2,4-thiadiazol-5-yl)-N-(pyridin-3-yl)piperazine-1-carboxamide, Fatty-acid amide hydrolase 1 | | 著者 | Behnke, C, Skene, R.J. | | 登録日 | 2012-09-28 | | 公開日 | 2013-02-06 | | 最終更新日 | 2023-09-20 | | 実験手法 | X-RAY DIFFRACTION (2.91 Å) | | 主引用文献 | Synthesis, SAR study, and biological evaluation of a series of piperazine ureas as fatty acid amide hydrolase (FAAH) inhibitors.
Bioorg.Med.Chem., 21, 2013
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4DBN
 | | Crystal Structure of the Kinase domain of Human B-raf with a [1,3]thiazolo[5,4-b]pyridine derivative | | 分子名称: | 2-chloro-3-(1-cyanocyclopropyl)-N-[5-({2-[(cyclopropylcarbonyl)amino][1,3]thiazolo[5,4-b]pyridin-5-yl}oxy)-2-fluorophenyl]benzamide, Serine/threonine-protein kinase B-raf | | 著者 | Yano, J.K, Aertgeerts, K. | | 登録日 | 2012-01-16 | | 公開日 | 2012-04-11 | | 最終更新日 | 2024-02-28 | | 実験手法 | X-RAY DIFFRACTION (3.15 Å) | | 主引用文献 | Design and synthesis of novel DFG-out RAF/vascular endothelial growth factor receptor 2 (VEGFR2) inhibitors. 1. Exploration of [5,6]-fused bicyclic scaffolds.
J.Med.Chem., 55, 2012
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1XGO
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1XGN
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1XGM
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5AX6
 | | The crystal structure of CofB, the minor pilin subunit of CFA/III from human enterotoxigenic Escherichia coli. | | 分子名称: | ACETATE ION, CofB | | 著者 | Kawahara, K, Oki, K, Fukaksua, F, Maruno, T, Kobayashi, Y, Daisuke, M, Taniguchi, T, Honda, T, Iida, T, Nakamura, S, Ohkubo, T. | | 登録日 | 2015-07-16 | | 公開日 | 2016-03-09 | | 最終更新日 | 2020-02-26 | | 実験手法 | X-RAY DIFFRACTION (1.88 Å) | | 主引用文献 | Homo-trimeric Structure of the Type IVb Minor Pilin CofB Suggests Mechanism of CFA/III Pilus Assembly in Human Enterotoxigenic Escherichia coli
J.Mol.Biol., 428, 2016
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5VP0
 | | Discovery of Clinical Candidate N-{(1S)-1-[3-Fluoro-4-(trifluoromethoxy)phenyl]-2-methoxyethyl}-7-methoxy-2-oxo-2,3-dihydropyrido[2,3-b]pyrazine-4(1H)-carboxamide (TAK-915), A Highly Potent, Selective, and Brain-Penetrating Phosphodiesterase 2A Inhibitor for the Treatment of Cognitive Disorders | | 分子名称: | MAGNESIUM ION, N-{(1S)-1-[3-fluoro-4-(trifluoromethoxy)phenyl]-2-methoxyethyl}-7-methoxy-2-oxo-2,3-dihydropyrido[2,3-b]pyrazine-4(1H)-carboxamide, ZINC ION, ... | | 著者 | Hoffman, I.D. | | 登録日 | 2017-05-03 | | 公開日 | 2017-08-23 | | 最終更新日 | 2024-03-13 | | 実験手法 | X-RAY DIFFRACTION (2.2 Å) | | 主引用文献 | Discovery of Clinical Candidate N-((1S)-1-(3-Fluoro-4-(trifluoromethoxy)phenyl)-2-methoxyethyl)-7-methoxy-2-oxo-2,3-dihydropyrido[2,3-b]pyrazine-4(1H)-carboxamide (TAK-915): A Highly Potent, Selective, and Brain-Penetrating Phosphodiesterase 2A Inhibitor for the Treatment of Cognitive Disorders.
J. Med. Chem., 60, 2017
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1XGS
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