8H28
| Crystal structure of the K87V mutant of cytochrome c' from Shewanella benthica DB6705 | Descriptor: | Class II cytochrome c, HEME C | Authors: | Fujii, S, Sakaguchi, R, Oki, H, Kawahara, K, Ohkubo, T, Fujiyoshi, S, Sambongi, Y. | Deposit date: | 2022-10-05 | Release date: | 2023-10-11 | Last modified: | 2024-04-24 | Method: | X-RAY DIFFRACTION (2.06 Å) | Cite: | Contribution of a surface salt bridge to the protein stability of deep-sea Shewanella benthica cytochrome c'. J.Struct.Biol., 215, 2023
|
|
5H03
| Crystal structure of an ADP-ribosylating toxin BECa from C. perfringens | Descriptor: | Binary enterotoxin of Clostridium perfringens component a | Authors: | Kawahara, K, Yonogi, S, Munetomo, R, Oki, H, Yoshida, T, Ohkubo, T, Kumeda, Y, Matsuda, S, Kodama, T, Iida, T, Nakamura, S. | Deposit date: | 2016-10-03 | Release date: | 2016-11-02 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.89 Å) | Cite: | Crystal structure of the ADP-ribosylating component of BEC, the binary enterotoxin of Clostridium perfringens. Biochem.Biophys.Res.Commun., 480, 2016
|
|
5H04
| Crystal structure of an ADP-ribosylating toxin BECa of a novel binary enterotoxin of C. perfringens with NADH | Descriptor: | 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE, Binary enterotoxin of Clostridium perfringens component a | Authors: | Kawahara, K, Yonogi, S, Munetomo, R, Oki, H, Yoshida, T, Ohkubo, T, Kumeda, Y, Matsuda, S, Kodama, T, Iida, T, Nakamura, S. | Deposit date: | 2016-10-03 | Release date: | 2016-11-02 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.825 Å) | Cite: | Crystal structure of the ADP-ribosylating component of BEC, the binary enterotoxin of Clostridium perfringens. Biochem.Biophys.Res.Commun., 480, 2016
|
|
5T4S
| Novel Approach of Fragment-Based Lead Discovery applied to Renin Inhibitors | Descriptor: | 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, ... | Authors: | Snell, G.P, Behnke, C.A, Okada, K, Oki, H, Sang, B.C, Lane, W. | Deposit date: | 2016-08-30 | Release date: | 2016-10-26 | Last modified: | 2020-07-29 | Method: | X-RAY DIFFRACTION (2.64 Å) | Cite: | Novel approach of fragment-based lead discovery applied to renin inhibitors. Bioorg.Med.Chem., 24, 2016
|
|
6KXX
| Human PPAR alpha ligand binding domain in complex with a synthetic agonist (compound A) | Descriptor: | 1-(4-chlorophenyl)-6-methyl-3-propan-2-yl-pyrazolo[3,4-b]pyridine-4-carboxylic acid, PGC1alpha, Peroxisome proliferator-activated receptor alpha | Authors: | Yoshida, T, Tachibana, K, Oki, H, Doi, M, Fukuda, S, Yuzuriha, T, Tabata, R, Ishimoto, K, Kawahara, K, Ohkubo, T, Miyachi, H, Doi, T. | Deposit date: | 2019-09-14 | Release date: | 2020-05-20 | Last modified: | 2024-03-27 | Method: | X-RAY DIFFRACTION (1.95 Å) | Cite: | Structural Basis for PPAR alpha Activation by 1H-pyrazolo-[3,4-b]pyridine Derivatives. Sci Rep, 10, 2020
|
|
6KXY
| Human PPAR alpha ligand binding domain in complex with a synthetic agonist (compound B) | Descriptor: | 6-ethyl-1-(4-fluorophenyl)-3-pentan-3-yl-pyrazolo[3,4-b]pyridine-4-carboxylic acid, PGC1alpha, Peroxisome proliferator-activated receptor alpha | Authors: | Yoshida, T, Tachibana, K, Oki, H, Doi, M, Fukuda, S, Yuzuriha, T, Tabata, R, Ishimoto, K, Kawahara, K, Ohkubo, T, Miyachi, H, Doi, T. | Deposit date: | 2019-09-14 | Release date: | 2020-05-20 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Structural Basis for PPAR alpha Activation by 1H-pyrazolo-[3,4-b]pyridine Derivatives. Sci Rep, 10, 2020
|
|
3VHK
| Crystal structure of the VEGFR2 kinase domain in complex with a back pocket binder | Descriptor: | 1,2-ETHANEDIOL, Vascular endothelial growth factor receptor 2, {3-[(5-methyl-2-phenyl-1,3-oxazol-4-yl)methoxy]phenyl}methanol | Authors: | Iwata, H, Oki, H, Okada, K, Takagi, T, Tawada, M, Miyazaki, Y, Imamura, S, Hori, A, Hixon, M.S, Kimura, H, Miki, H. | Deposit date: | 2011-08-25 | Release date: | 2012-09-05 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (2.49 Å) | Cite: | 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
|
|
3VID
| Crystal structure of human VEGFR2 kinase domain with Compound A. | Descriptor: | 4,5,6,11-tetrahydro-1H-pyrazolo[4',3':6,7]cyclohepta[1,2-b]indole, Vascular endothelial growth factor receptor 2 | Authors: | Iwata, H, Oki, H, Okada, K, Takagi, T, Tawada, M, Miyazaki, Y, Imamura, S, Hori, A, Hixon, M.S, Kimura, H, Miki, H. | Deposit date: | 2011-09-29 | Release date: | 2012-08-15 | Last modified: | 2024-03-20 | Method: | X-RAY DIFFRACTION (2.3 Å) | Cite: | 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
|
|
5B6Q
| Crystal structure of monomeric cytochrome c5 from Shewanella violacea | Descriptor: | HEME C, IMIDAZOLE, Soluble cytochrome cA | Authors: | Masanari, M, Fujii, S, Kawahara, K, Oki, H, Tsujino, H, Maruno, T, Kobayashi, Y, Ohkubo, T, Nishiyama, M, Harada, Y, Wakai, S, Sambongi, Y. | Deposit date: | 2016-06-01 | Release date: | 2016-10-19 | Last modified: | 2019-10-02 | Method: | X-RAY DIFFRACTION (1.78 Å) | Cite: | Comparative study on stabilization mechanism of monomeric cytochrome c5 from deep-sea piezophilic Shewanella violacea Biosci.Biotechnol.Biochem., 2016
|
|
5B3I
| Homo-dimeric structure of cytochrome c' from Thermophilic Hydrogenophilus thermoluteolus | Descriptor: | Cytochrome c prime, HEME C | Authors: | Fujii, S, Oki, H, Kawahara, K, Yamane, D, Yamanaka, M, Maruno, T, Kobayashi, Y, Masanari, M, Wakai, S, Nishihara, H, Ohkubo, T, Sambongi, Y. | Deposit date: | 2016-02-29 | Release date: | 2017-03-01 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.89 Å) | Cite: | Structural and functional insights into thermally stable cytochrome c' from a thermophile Protein Sci., 26, 2017
|
|
3VW8
| Crystal structure of human c-Met kinase domain with its inhibitor | Descriptor: | CHLORIDE ION, Hepatocyte growth factor receptor, N-({4-[(6,7-dimethoxyquinolin-4-yl)oxy]phenyl}carbamothioyl)-2-phenylacetamide | Authors: | Matsumoto, S, Miyamoto, N, Hirayama, T, Oki, H, Okada, K, Tawada, M, Iwata, H, Miki, H, Nakamura, K, Hori, A, Imamura, S. | Deposit date: | 2012-08-08 | Release date: | 2013-08-14 | Last modified: | 2022-08-24 | Method: | X-RAY DIFFRACTION (2.1 Å) | Cite: | 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
|
|
6KQ1
| Crystal structure of cytochrome c551 from Pseudomonas sp. strain MT-1. | Descriptor: | Cytochrome C biogenesis protein CcsA, HEME C, ZINC ION | Authors: | Fujii, S, Oki, H, Kawahara, K, Ohkubo, T, Masanari-Fujii, M, Wakai, S, Sambongi, Y. | Deposit date: | 2019-08-16 | Release date: | 2020-08-19 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (1.57 Å) | Cite: | Structural insights into high stability of cytochrome c551 from a deep-sea piezo-tolerant bacterium, Pseudomonas sp. strain MT-1 To Be Published
|
|
7EAD
| Crystal structure of beta-sheet cytochrome c prime from Thermus thermophilus. | Descriptor: | Cytochrome_P460 domain-containing protein, HEME C | Authors: | Yoshimi, T, Fujii, S, Oki, H, Igawa, T, Adams, R.H, Ueda, K, Kawahara, K, Ohkubo, T, Hough, A.M, Sambongi, Y. | Deposit date: | 2021-03-07 | Release date: | 2022-03-09 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (1.74 Å) | Cite: | Crystal structure of thermally stable homodimeric cytochrome c'-beta from Thermus thermophilus. Acta Crystallogr.,Sect.F, 78, 2022
|
|
6LOS
| Crystal structure of mouse PEDF in complex with heterotrimeric collagen model peptide. | Descriptor: | Collagen model peptide, type I, alpha 1, ... | Authors: | Kawahara, K, Maruno, T, Oki, H, Yoshida, T, Ohkubo, T, Koide, T, Kobayashi, Y. | Deposit date: | 2020-01-07 | Release date: | 2020-09-02 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.476 Å) | Cite: | Spatiotemporal regulation of PEDF signaling by type I collagen remodeling. Proc.Natl.Acad.Sci.USA, 117, 2020
|
|
6A3L
| Crystal structure of cytochrome c' from Shewanella violacea DSS12 | Descriptor: | Cytochrome c, HEME C | Authors: | Suka, A, Oki, H, Kato, Y, Kawahara, K, Ohkubo, T, Maruno, T, Kobayashi, Y, Fujii, S, Wakai, S, Sambongi, Y. | Deposit date: | 2018-06-15 | Release date: | 2019-06-12 | Last modified: | 2019-10-02 | Method: | X-RAY DIFFRACTION (2.14 Å) | Cite: | 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
|
|
6A3K
| Crystal structure of cytochrome c' from Shewanella benthica DB6705 | Descriptor: | Cytochrome c, HEME C, PENTAETHYLENE GLYCOL | Authors: | Suka, A, Oki, H, Kato, Y, Kawahara, K, Ohkubo, T, Maruno, T, Kobayashi, Y, Fujii, S, Wakai, S, Sambongi, Y. | Deposit date: | 2018-06-15 | Release date: | 2019-06-12 | Last modified: | 2019-10-02 | Method: | X-RAY DIFFRACTION (1.71 Å) | Cite: | 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
|
|
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 | Descriptor: | 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, ... | Authors: | Hoffman, I.D. | Deposit date: | 2017-05-03 | Release date: | 2017-08-23 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (2.2 Å) | Cite: | 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
|
|
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 | Descriptor: | 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, ... | Authors: | Hoffman, I.D. | Deposit date: | 2017-05-03 | Release date: | 2017-12-27 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (1.86 Å) | Cite: | 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
|
|
1XGO
| |
1XGN
| |
1XGM
| |
4DBN
| Crystal Structure of the Kinase domain of Human B-raf with a [1,3]thiazolo[5,4-b]pyridine derivative | Descriptor: | 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 | Authors: | Yano, J.K, Aertgeerts, K. | Deposit date: | 2012-01-16 | Release date: | 2012-04-11 | Last modified: | 2024-02-28 | Method: | X-RAY DIFFRACTION (3.15 Å) | Cite: | 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
|
|
4HBP
| Crystal Structure of FAAH in complex with inhibitor | Descriptor: | 4-(3-phenyl-1,2,4-thiadiazol-5-yl)-N-(pyridin-3-yl)piperazine-1-carboxamide, Fatty-acid amide hydrolase 1 | Authors: | Behnke, C, Skene, R.J. | Deposit date: | 2012-09-28 | Release date: | 2013-02-06 | Last modified: | 2023-09-20 | Method: | X-RAY DIFFRACTION (2.91 Å) | Cite: | Synthesis, SAR study, and biological evaluation of a series of piperazine ureas as fatty acid amide hydrolase (FAAH) inhibitors. Bioorg.Med.Chem., 21, 2013
|
|
7CN0
| Cryo-EM structure of K+-bound hERG channel | Descriptor: | POTASSIUM ION, potassium channel 1 | Authors: | Asai, T, Adachi, N, Moriya, T, Kawasaki, M, Suzuki, K, Senda, T, Murata, T. | Deposit date: | 2020-07-29 | Release date: | 2021-01-20 | Last modified: | 2024-03-27 | Method: | ELECTRON MICROSCOPY (3.9 Å) | Cite: | Cryo-EM Structure of K + -Bound hERG Channel Complexed with the Blocker Astemizole. Structure, 29, 2021
|
|
7CN1
| Cryo-EM structure of K+-bound hERG channel in the presence of astemizole | Descriptor: | POTASSIUM ION, potassium channel | Authors: | Asai, T, Adachi, N, Moriya, T, Kawasaki, M, Suzuki, K, Senda, T, Murata, T. | Deposit date: | 2020-07-29 | Release date: | 2021-01-20 | Last modified: | 2024-03-27 | Method: | ELECTRON MICROSCOPY (3.7 Å) | Cite: | Cryo-EM Structure of K + -Bound hERG Channel Complexed with the Blocker Astemizole. Structure, 29, 2021
|
|