7WMC
| Crystal structure of macrocyclic peptide 1 bound to human Nicotinamide N-methyltransferase | Descriptor: | Nicotinamide N-methyltransferase, Peptide1 | Authors: | Yoshida, S, Uehara, S, Kondo, N, Takahashi, Y, Yamamoto, S, Kameda, A, Kawagoe, S, Inoue, N, Yamada, M, Yoshimura, N, Tachibana, Y. | Deposit date: | 2022-01-14 | Release date: | 2022-08-31 | Last modified: | 2023-11-15 | Method: | X-RAY DIFFRACTION (2.55 Å) | Cite: | Peptide-to-Small Molecule: A Pharmacophore-Guided Small Molecule Lead Generation Strategy from High-Affinity Macrocyclic Peptides. J.Med.Chem., 65, 2022
|
|
7WMT
| Crystal structure of small molecule 13 bound to human Nicotinamide N-methyltransferase | Descriptor: | Nicotinamide N-methyltransferase, [(2~{R},4~{S})-4-[2-(aminomethyl)imidazol-1-yl]-2-[1-[(4-chlorophenyl)methyl]-5-methyl-indol-2-yl]pyrrolidin-1-yl]-(1~{H}-pyrrolo[2,3-b]pyridin-5-yl)methanone | Authors: | Yoshida, S, Uehara, S, Kondo, N, Takahashi, Y, Yamamoto, S, Kameda, A, Kawagoe, S, Inoue, N, Yamada, M, Yoshimura, N, Tachibana, Y. | Deposit date: | 2022-01-17 | Release date: | 2022-08-31 | Last modified: | 2024-05-29 | Method: | X-RAY DIFFRACTION (1.77 Å) | Cite: | Peptide-to-Small Molecule: A Pharmacophore-Guided Small Molecule Lead Generation Strategy from High-Affinity Macrocyclic Peptides. J.Med.Chem., 65, 2022
|
|
8J3S
| Complex structure of human cytomegalovirus protease and a macrocyclic peptide ligand | Descriptor: | Assemblin, PHE-ILE-THR-GLY-HIS-TYR-TRP-VAL-ARG-PHE-LEU-PRO-CYS-GLY | Authors: | Yoshida, S, Sako, Y, Nikaido, E, Ueda, T, Kozono, I, Ichihashi, Y, Nakahashi, A, Onishi, M, Yamatsu, Y, Kato, T, Nishikawa, J, Tachibana, Y. | Deposit date: | 2023-04-18 | Release date: | 2023-11-08 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (3.09 Å) | Cite: | Peptide-to-Small Molecule: Discovery of Non-Covalent, Active-Site Inhibitors of beta-Herpesvirus Proteases. Acs Med.Chem.Lett., 14, 2023
|
|
8J3T
| Complex structure of human cytomegalovirus protease and a non-covalent small-molecule ligand | Descriptor: | (4R)-1-[1-[(S)-[1-cyclopentyl-3-(2-methylphenyl)pyrazol-4-yl]-(4-methylphenyl)methyl]-2-oxidanylidene-pyridin-3-yl]-3-methyl-2-oxidanylidene-N-(3-oxidanylidene-2-azabicyclo[2.2.2]octan-4-yl)imidazolidine-4-carboxamide, Assemblin | Authors: | Yoshida, S, Sako, Y, Nikaido, E, Ueda, T, Kozono, I, Ichihashi, Y, Nakahashi, A, Onishi, M, Yamatsu, Y, Kato, T, Nishikawa, J, Tachibana, Y. | Deposit date: | 2023-04-18 | Release date: | 2023-11-08 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.9 Å) | Cite: | Peptide-to-Small Molecule: Discovery of Non-Covalent, Active-Site Inhibitors of beta-Herpesvirus Proteases. Acs Med.Chem.Lett., 14, 2023
|
|
3KDO
| Crystal structure of Type III Rubisco SP6 mutant complexed with 2-CABP | Descriptor: | 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE, MAGNESIUM ION, Ribulose bisphosphate carboxylase | Authors: | Nishitani, Y, Fujihashi, M, Doi, T, Yoshida, S, Atomi, H, Imanaka, T, Miki, K. | Deposit date: | 2009-10-23 | Release date: | 2010-10-06 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2.36 Å) | Cite: | Structure-based catalytic optimization of a type III Rubisco from a hyperthermophile J.Biol.Chem., 285, 2010
|
|
3KDN
| Crystal structure of Type III Rubisco SP4 mutant complexed with 2-CABP | Descriptor: | 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE, MAGNESIUM ION, Ribulose bisphosphate carboxylase | Authors: | Nishitani, Y, Fujihashi, M, Doi, T, Yoshida, S, Atomi, H, Imanaka, T, Miki, K. | Deposit date: | 2009-10-23 | Release date: | 2010-10-06 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2.09 Å) | Cite: | Structure-based catalytic optimization of a type III Rubisco from a hyperthermophile J.Biol.Chem., 285, 2010
|
|
1NPM
| NEUROPSIN, A SERINE PROTEASE EXPRESSED IN THE LIMBIC SYSTEM OF MOUSE BRAIN | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, NEUROPSIN | Authors: | Kishi, T, Kato, M, Shimizu, T, Kato, K, Matsumoto, K, Yoshida, S, Shiosaka, S, Hakoshima, T. | Deposit date: | 1998-01-07 | Release date: | 1999-03-23 | Last modified: | 2023-08-09 | Method: | X-RAY DIFFRACTION (2.1 Å) | Cite: | Crystal structure of neuropsin, a hippocampal protease involved in kindling epileptogenesis. J.Biol.Chem., 274, 1999
|
|
5YGY
| Crystal Structure of BACE1 in complex with (S)-N-(3-(2-amino-6-(fluoromethyl)-4 -methyl-4H-1,3-oxazin-4-yl)-4-fluorophenyl)-5-cyanopicolinamide | Descriptor: | Beta-secretase 1, GLYCEROL, IODIDE ION, ... | Authors: | Fuchino, K, Mitsuoka, Y, Masui, M, Kurose, N, Yoshida, S, Komano, K, Yamamoto, T, Ogawa, M, Unemura, C, Hosono, M, Ito, H, Sakaguchi, G, Ando, S, Ohnishi, S, Kido, Y, Fukushima, T, Miyajima, H, Hiroyama, S, Koyabu, K, Dhuyvetter, D, Borghys, H, Gijsen, H, Yamano, Y, Iso, Y, Kusakabe, K. | Deposit date: | 2017-09-27 | Release date: | 2018-05-23 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2.3 Å) | Cite: | Rational Design of Novel 1,3-Oxazine Based beta-Secretase (BACE1) Inhibitors: Incorporation of a Double Bond To Reduce P-gp Efflux Leading to Robust A beta Reduction in the Brain J. Med. Chem., 61, 2018
|
|
7D5U
| BACE2 xaperone complex with N-{3-[(9S)-7-amino-2,2-difluoro-9-(prop-1-yn-1-yl)-6-oxa-8-azaspiro[3.5]non-7-en-9-yl]-4-fluorophenyl}-5-cyanopyridine-2-carboxamide | Descriptor: | Beta-secretase 2, N-[3-[(9S)-7-azanyl-2,2-bis(fluoranyl)-9-prop-1-ynyl-6-oxa-8-azaspiro[3.5]non-7-en-9-yl]-4-fluoranyl-phenyl]-5-cyano-pyridine-2-carboxamide, xaperone | Authors: | Fujimoto, K, Yoshida, S, Tadano, G, Asada, N, Fuchino, K, Suzuki, S, Matsuoka, E, Yamamoto, T, Yamamoto, S, Ando, S, Kanegawa, N, Tonomura, Y, Ito, H, Moechars, D, Rombouts, F.J.R, Gijsen, H.J.M, Kusakabe, K.I. | Deposit date: | 2020-09-28 | Release date: | 2021-03-31 | Last modified: | 2021-04-07 | Method: | X-RAY DIFFRACTION (2.04 Å) | Cite: | Structure-Based Approaches to Improving Selectivity through Utilizing Explicit Water Molecules: Discovery of Selective beta-Secretase (BACE1) Inhibitors over BACE2. J.Med.Chem., 64, 2021
|
|
7D5A
| Crystal Structure of BACE1 in complex with N-{3-[(9S)-7-amino-2,2-difluoro-9-(prop-1-yn-1-yl)-6-oxa-8-azaspiro[3.5]non-7-en-9-yl]-4-fluorophenyl}-5-cyanopyridine-2-carboxamide | Descriptor: | Beta-secretase 1, GLYCEROL, IODIDE ION, ... | Authors: | Fujimoto, K, Yoshida, S, Tadano, G, Asada, N, Fuchino, K, Suzuki, S, Matsuoka, E, Yamamoto, T, Yamamoto, S, Ando, S, Kanegawa, N, Tonomura, Y, Ito, H, Moechars, D, Rombouts, F.J.R, Gijsen, H.J.M, Kusakabe, K.I. | Deposit date: | 2020-09-25 | Release date: | 2021-03-31 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.2 Å) | Cite: | Structure-Based Approaches to Improving Selectivity through Utilizing Explicit Water Molecules: Discovery of Selective beta-Secretase (BACE1) Inhibitors over BACE2. J.Med.Chem., 64, 2021
|
|
7D2V
| Crystal Structure of BACE1 in complex with N-{3-[(5R)-3-amino-2,5-dimethyl-1,1-dioxo-5,6-dihydro-2H-1lambda6,2,4-thiadiazin-5-yl]-4-fluorophenyl}-5-fluoropyridine-2-carboxamide | Descriptor: | Beta-secretase 1, GLYCEROL, IODIDE ION, ... | Authors: | Fujimoto, K, Yoshida, S, Tadano, G, Asada, N, Fuchino, K, Suzuki, S, Matsuoka, E, Yamamoto, T, Yamamoto, S, Ando, S, Kanegawa, N, Tonomura, Y, Ito, H, Moechars, D, Rombouts, F.J.R, Gijsen, H.J.M, Kusakabe, K.I. | Deposit date: | 2020-09-17 | Release date: | 2021-03-31 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.1 Å) | Cite: | Structure-Based Approaches to Improving Selectivity through Utilizing Explicit Water Molecules: Discovery of Selective beta-Secretase (BACE1) Inhibitors over BACE2. J.Med.Chem., 64, 2021
|
|
7D5B
| BACE2 xaperone complex with N-{3-[(5R)-3-amino-2,5-dimethyl-1,1-dioxo-5,6-dihydro-2H-1lambda6,2,4-thiadiazin-5-yl]-4-fluorophenyl}-5-fluoropyridine-2-carboxamide | Descriptor: | 1,2-ETHANEDIOL, Beta-secretase 2, CHLORIDE ION, ... | Authors: | Fujimoto, K, Yoshida, S, Tadano, G, Asada, N, Fuchino, K, Suzuki, S, Matsuoka, E, Yamamoto, T, Yamamoto, S, Ando, S, Kanegawa, N, Tonomura, Y, Ito, H, Moechars, D, Rombouts, F.J.R, Gijsen, H.J.M, Kusakabe, K.I. | Deposit date: | 2020-09-25 | Release date: | 2021-03-31 | Last modified: | 2021-04-07 | Method: | X-RAY DIFFRACTION (1.31 Å) | Cite: | Structure-Based Approaches to Improving Selectivity through Utilizing Explicit Water Molecules: Discovery of Selective beta-Secretase (BACE1) Inhibitors over BACE2. J.Med.Chem., 64, 2021
|
|
7D2X
| Crystal Structure of BACE1 in complex with N-{3-[(4R)-2-amino-4-(prop-1-yn-1-yl)-5,6-dihydro-4H-1,3-oxazin-4-yl]-4-fluorophenyl}-5-cyanopyridine-2-carboxamide | Descriptor: | Beta-secretase 1, GLYCEROL, IODIDE ION, ... | Authors: | Fujimoto, K, Yoshida, S, Tadano, G, Asada, N, Fuchino, K, Suzuki, S, Matsuoka, E, Yamamoto, T, Yamamoto, S, Ando, S, Kanegawa, N, Tonomura, Y, Ito, H, Moechars, D, Rombouts, F.J.R, Gijsen, H.J.M, Kusakabe, K.I. | Deposit date: | 2020-09-17 | Release date: | 2021-03-31 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.45 Å) | Cite: | Structure-Based Approaches to Improving Selectivity through Utilizing Explicit Water Molecules: Discovery of Selective beta-Secretase (BACE1) Inhibitors over BACE2. J.Med.Chem., 64, 2021
|
|
6JT3
| Crystal Structure of BACE1 in complex with N-{3-[(4R,5R,6R)-2-amino-5-fluoro-4,6-dimethyl-5,6-dihydro-4H-1,3-thiazin-4-yl]-4-fluorophenyl}-5-(fluoromethoxy)pyrazine-2-carboxamide | Descriptor: | Beta-secretase 1, DIMETHYL SULFOXIDE, GLYCEROL, ... | Authors: | Tadano, G, Komano, K, Yoshida, S, Suzuki, S, Nakahara, K, Fuchino, K, Fujimoto, K, Matsuoka, E, Yamamoto, T, Asada, N, Ito, H, Sakaguchi, G, Kanegawa, N, Kido, Y, Ando, S, Fukushima, T, Teisman, A, Urmaliya, V, Dhuyvetter, D, Borghys, H, Bergh, A.V.D, Austin, N, Gijsen, H.J.M, Yamano, Y, Iso, Y, Kusakabe, K.I. | Deposit date: | 2019-04-08 | Release date: | 2019-10-30 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2.4 Å) | Cite: | Discovery of an Extremely Potent Thiazine-Based beta-Secretase Inhibitor with Reduced Cardiovascular and Liver Toxicity at a Low Projected Human Dose. J.Med.Chem., 62, 2019
|
|
3VM6
| Crystal structure of ribose-1,5-bisphosphate isomerase from Thermococcus kodakarensis KOD1 in complex with alpha-D-ribose-1,5-bisphosphate | Descriptor: | 1,5-di-O-phosphono-alpha-D-ribofuranose, CHLORIDE ION, DI(HYDROXYETHYL)ETHER, ... | Authors: | Nakamura, A, Fujihashi, M, Aono, R, Sato, T, Nishiba, Y, Yoshida, S, Yano, A, Atomi, H, Imanaka, T, Miki, K. | Deposit date: | 2011-12-08 | Release date: | 2012-04-25 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.85 Å) | Cite: | Dynamic, ligand-dependent conformational change triggers reaction of ribose-1,5-bisphosphate isomerase from Thermococcus kodakarensis KOD1 J.Biol.Chem., 287, 2012
|
|
3A11
| Crystal structure of ribose-1,5-bisphosphate isomerase from Thermococcus kodakaraensis KOD1 | Descriptor: | DI(HYDROXYETHYL)ETHER, MAGNESIUM ION, Translation initiation factor eIF-2B, ... | Authors: | Nakamura, A, Fujihashi, M, Nishiba, Y, Yoshida, S, Yano, A, Atomi, H, Imanaka, T, Miki, K. | Deposit date: | 2009-03-25 | Release date: | 2010-03-31 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (2.5 Å) | Cite: | Dynamic, ligand-dependent conformational change triggers reaction of ribose-1,5-bisphosphate isomerase from Thermococcus kodakarensis KOD1 J.Biol.Chem., 287, 2012
|
|
3A12
| Crystal structure of Type III Rubisco complexed with 2-CABP | Descriptor: | 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE, MAGNESIUM ION, Ribulose bisphosphate carboxylase | Authors: | Nishitani, Y, Fujihashi, M, Doi, T, Yoshida, S, Atomi, H, Imanaka, T, Miki, K. | Deposit date: | 2009-03-25 | Release date: | 2010-04-07 | Last modified: | 2023-11-15 | Method: | X-RAY DIFFRACTION (2.3 Å) | Cite: | Structure-based catalytic optimization of a type III Rubisco from a hyperthermophile J.Biol.Chem., 285, 2010
|
|
3A13
| Crystal structure of Type III Rubisco SP4 mutant complexed with 2-CABP and activated with Ca | Descriptor: | 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE, CALCIUM ION, MAGNESIUM ION, ... | Authors: | Nishitani, Y, Fujihashi, M, Doi, T, Yoshida, S, Atomi, H, Imanaka, T, Miki, K. | Deposit date: | 2009-03-25 | Release date: | 2010-04-07 | Last modified: | 2023-11-15 | Method: | X-RAY DIFFRACTION (2.34 Å) | Cite: | Structure-based optimization of a Type III Rubisco from a hyperthermophile To be Published
|
|
3A9C
| Crystal structure of ribose-1,5-bisphosphate isomerase from Thermococcus kodakaraensis KOD1 in complex with ribulose-1,5-bisphosphate | Descriptor: | DI(HYDROXYETHYL)ETHER, MAGNESIUM ION, RIBULOSE-1,5-DIPHOSPHATE, ... | Authors: | Nakamura, A, Fujihashi, M, Nishiba, Y, Yoshida, S, Yano, A, Atomi, H, Imanaka, T, Miki, K. | Deposit date: | 2009-10-22 | Release date: | 2010-11-03 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (2.6 Å) | Cite: | Dynamic, ligand-dependent conformational change triggers reaction of ribose-1,5-bisphosphate isomerase from Thermococcus kodakarensis KOD1 J.Biol.Chem., 287, 2012
|
|
4LGE
| Crystal structure of clAP1 BIR3 bound to T3261256 | Descriptor: | (4S,6aR,7aS)-5-{(2S)-2-cyclohexyl-2-[(N-methyl-L-alanyl)amino]acetyl}-N-[(4R)-3,4-dihydro-2H-chromen-4-yl]octahydro-1H-cyclopropa[4,5]pyrrolo[1,2-a]pyrazine-4-carboxamide, Baculoviral IAP repeat-containing protein 2, ZINC ION | Authors: | Dougan, D.R. | Deposit date: | 2013-06-27 | Release date: | 2013-08-28 | Last modified: | 2024-02-28 | Method: | X-RAY DIFFRACTION (1.55 Å) | Cite: | Design, stereoselective synthesis, and biological evaluation of novel tri-cyclic compounds as inhibitor of apoptosis proteins (IAP) antagonists. Bioorg.Med.Chem., 21, 2013
|
|
4LGU
| Crystal structure of clAP1 BIR3 bound to T3226692 | Descriptor: | (3S,8aR)-N-((R)-chroman-4-yl)-2-((S)-2-cyclohexyl-2-((S)-2-(methylamino)propanamido)acetyl)octahydropyrrolo[1,2-a]pyrazine-3-carboxamide, Baculoviral IAP repeat-containing protein 2, ZINC ION | Authors: | Dougan, D.R, Mol, C.D, Snell, G.P. | Deposit date: | 2013-06-28 | Release date: | 2013-08-28 | Last modified: | 2024-05-22 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Design, stereoselective synthesis, and biological evaluation of novel tri-cyclic compounds as inhibitor of apoptosis proteins (IAP) antagonists. Bioorg.Med.Chem., 21, 2013
|
|
4WUA
| Crystal structure of human SRPK1 complexed to an inhibitor SRPIN340 | Descriptor: | CITRIC ACID, N-[2-(1-piperidinyl)-5-(trifluoromethyl)phenyl]-4-pyridinecarboxamide, SRSF protein kinase 1, ... | Authors: | Hoshina, M, Ikura, T, Hosoya, T, Hagiwara, M, Ito, N. | Deposit date: | 2014-10-31 | Release date: | 2015-09-16 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Identification of a Dual Inhibitor of SRPK1 and CK2 That Attenuates Pathological Angiogenesis of Macular Degeneration in Mice Mol.Pharmacol., 88, 2015
|
|
4OJK
| Structure of the cGMP Dependent Protein Kinase II and Rab11b Complex | Descriptor: | GUANOSINE-5'-DIPHOSPHATE, Ras-related protein Rab-11B, cGMP-dependent protein kinase 2 | Authors: | Reger, A.S, Yang, M.P, Guo, E, Kim, C. | Deposit date: | 2014-01-21 | Release date: | 2014-08-06 | Last modified: | 2023-09-20 | Method: | X-RAY DIFFRACTION (2.657 Å) | Cite: | Crystal Structure of the cGMP-dependent Protein Kinase II Leucine Zipper and Rab11b Protein Complex Reveals Molecular Details of G-kinase-specific Interactions. J.Biol.Chem., 289, 2014
|
|
1MY6
| The 1.6 A Structure of Fe-Superoxide Dismutase from the thermophilic cyanobacterium Thermosynechococcus elongatus : Correlation of EPR and Structural Characteristics | Descriptor: | FE (III) ION, Iron (III) Superoxide Dismutase | Authors: | Yoshida, S.M, Cascio, D, Sawaya, M.R, Yeates, T.O, Kerfeld, C.A. | Deposit date: | 2002-10-03 | Release date: | 2003-07-29 | Last modified: | 2024-02-14 | Method: | X-RAY DIFFRACTION (1.6 Å) | Cite: | The 1.6 A resolution structure of Fe-superoxide dismutase from the thermophilic cyanobacterium Thermosynechococcus elongatus. J.BIOL.INORG.CHEM., 8, 2003
|
|
1LTH
| |