3J67
 
 | | Structural mechanism of the dynein powerstroke (post-powerstroke state) | | Descriptor: | Dynein motor domain | | Authors: | Lin, J, Okada, K, Raytchev, M, Smith, M.C, Nicastro, D. | | Deposit date: | 2013-12-22 | | Release date: | 2014-04-23 | | Last modified: | 2024-02-21 | | Method: | ELECTRON MICROSCOPY (34 Å) | | Cite: | Structural mechanism of the dynein power stroke.
Nat.Cell Biol., 16, 2014
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1BKG
 | | ASPARTATE AMINOTRANSFERASE FROM THERMUS THERMOPHILUS WITH MALEATE | | Descriptor: | 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE, ASPARTATE AMINOTRANSFERASE, MALEIC ACID | | Authors: | Nakai, T, Okada, K, Kuramitsu, S, Hirotsu, K, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 1998-07-07 | | Release date: | 1999-07-22 | | Last modified: | 2023-08-02 | | Method: | X-RAY DIFFRACTION (2.6 Å) | | Cite: | Structure of Thermus thermophilus HB8 aspartate aminotransferase and its complex with maleate.
Biochemistry, 38, 1999
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1G7X
 | | ASPARTATE AMINOTRANSFERASE ACTIVE SITE MUTANT N194A/R292L/R386L | | Descriptor: | ASPARTATE AMINOTRANSFERASE, PYRIDOXAL-5'-PHOSPHATE | | Authors: | Mizuguchi, H, Hayashi, H, Okada, K, Miyahara, I, Hirotsu, K, Kagamiyama, H. | | Deposit date: | 2000-11-15 | | Release date: | 2000-11-29 | | Last modified: | 2023-08-09 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Strain is more important than electrostatic interaction in controlling the pKa of the catalytic group in aspartate aminotransferase.
Biochemistry, 40, 2001
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1G4V
 | | ASPARTATE AMINOTRANSFERASE ACTIVE SITE MUTANT N194A/Y225F | | Descriptor: | ASPARTATE AMINOTRANSFERASE, PYRIDOXAL-5'-PHOSPHATE | | Authors: | Mizuguchi, H, Hayashi, H, Okada, K, Miyahara, I, Hirotsu, K, Kagamiyama, H. | | Deposit date: | 2000-10-28 | | Release date: | 2000-11-22 | | Last modified: | 2021-10-27 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Strain is more important than electrostatic interaction in controlling the pKa of the catalytic group in aspartate aminotransferase.
Biochemistry, 40, 2001
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1G7W
 | | ASPARTATE AMINOTRANSFERASE ACTIVE SITE MUTANT N194A/R386L | | Descriptor: | ASPARTATE AMINOTRANSFERASE, PYRIDOXAL-5'-PHOSPHATE | | Authors: | Mizuguchi, H, Hayashi, H, Okada, K, Miyahara, I, Hirotsu, K, Kagamiyama, H. | | Deposit date: | 2000-11-15 | | Release date: | 2000-11-29 | | Last modified: | 2021-10-27 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Strain is more important than electrostatic interaction in controlling the pKa of the catalytic group in aspartate aminotransferase.
Biochemistry, 40, 2001
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6ANL
 | | Structure-based Design, Synthesis, and Biological Evaluation of Imidazo[1,2-b]pyridazine-based p38 MAP Kinase Inhibitors | | Descriptor: | Mitogen-activated protein kinase 14, TAK-715 | | Authors: | Snell, G.P, Okada, K, Bragstad, K, Sang, B.-C. | | Deposit date: | 2017-08-14 | | Release date: | 2018-01-17 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Structure-based design, synthesis, and biological evaluation of imidazo[1,2-b]pyridazine-based p38 MAP kinase inhibitors.
Bioorg. Med. Chem., 26, 2018
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5WJJ
 | | Structure-based Design, Synthesis, and Biological Evaluation of Imidazo[1,2-b]pyridazine-based p38 MAP Kinase Inhibitors | | Descriptor: | Mitogen-activated protein kinase 14, N-{4-[2-(4-fluoro-3-methylphenyl)imidazo[1,2-b]pyridazin-3-yl]pyridin-2-yl}-2-methyl-1-oxo-1lambda~5~-pyridine-4-carboxamide | | Authors: | Snell, G.P, Okada, K, Bragstad, K, Sang, B.-C. | | Deposit date: | 2017-07-23 | | Release date: | 2018-01-17 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (1.6 Å) | | Cite: | Structure-based design, synthesis, and biological evaluation of imidazo[1,2-b]pyridazine-based p38 MAP kinase inhibitors.
Bioorg. Med. Chem., 26, 2018
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1UL1
 | | Crystal structure of the human FEN1-PCNA complex | | Descriptor: | Flap endonuclease-1, MAGNESIUM ION, Proliferating cell nuclear antigen | | Authors: | Sakurai, S, Kitano, K, Yamaguchi, H, Hamada, K, Okada, K, Fukuda, K, Uchida, M, Ohtsuka, E, Morioka, H, Hakoshima, T. | | Deposit date: | 2003-09-05 | | Release date: | 2005-03-01 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (2.9 Å) | | Cite: | Structural basis for recruitment of human flap endonuclease 1 to PCNA
EMBO J., 24, 2005
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6JPL
 | | The X-ray structure of yeast tRNA methyltransferase Trm7-Trm734 in complex with S-adenosyl-L-methionine | | Descriptor: | 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, S-ADENOSYLMETHIONINE, SULFATE ION, ... | | Authors: | Hirata, A, Okada, K, Yoshii, K, Shiraisi, H, Saijo, S, Yonezawa, K, Shimizu, N, Hori, H. | | Deposit date: | 2019-03-27 | | Release date: | 2019-10-02 | | Last modified: | 2024-03-27 | | Method: | X-RAY DIFFRACTION (2.32 Å) | | Cite: | Structure of tRNA methyltransferase complex of Trm7 and Trm734 reveals a novel binding interface for tRNA recognition.
Nucleic Acids Res., 47, 2019
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6JP6
 | | The X-ray structure of yeast tRNA methyltransferase complex of Trm7 and Trm734 essential for 2'-O-methylation at the first position of anticodon in specific tRNAs | | Descriptor: | 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, SULFATE ION, tRNA (cytidine(34)/guanosine(34)-2'-O)-methyltransferase, ... | | Authors: | Hirata, A, Okada, K, Yoshii, K, Shiraisi, H, Saijo, S, Yonezawa, K, Sihimzu, N, Hori, H. | | Deposit date: | 2019-03-26 | | Release date: | 2019-10-02 | | Last modified: | 2024-03-27 | | Method: | X-RAY DIFFRACTION (2.699 Å) | | Cite: | Structure of tRNA methyltransferase complex of Trm7 and Trm734 reveals a novel binding interface for tRNA recognition.
Nucleic Acids Res., 47, 2019
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1WPL
 | | Crystal structure of the inhibitory form of rat GTP cyclohydrolase I/GFRP complex | | Descriptor: | 7,8-DIHYDROBIOPTERIN, GTP cyclohydrolase I, GTP cyclohydrolase I feedback regulatory protein, ... | | Authors: | Maita, N, Hatakeyama, K, Okada, K, Hakoshima, T. | | Deposit date: | 2004-09-08 | | Release date: | 2004-09-28 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2.8 Å) | | Cite: | Structural basis of biopterin-induced inhibition of GTP cyclohydrolase I by GFRP, its feedback regulatory protein
J.Biol.Chem., 279, 2004
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1IS8
 | | Crystal structure of rat GTPCHI/GFRP stimulatory complex plus Zn | | Descriptor: | GTP Cyclohydrolase I, GTP Cyclohydrolase I Feedback Regulatory Protein, PHENYLALANINE, ... | | Authors: | Maita, N, Okada, K, Hatakeyama, K, Hakoshima, T. | | Deposit date: | 2001-11-18 | | Release date: | 2002-02-20 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (2.7 Å) | | Cite: | Crystal structure of the stimulatory complex of GTP cyclohydrolase I and its feedback regulatory protein GFRP.
Proc.Natl.Acad.Sci.USA, 99, 2002
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1IS7
 | | Crystal structure of rat GTPCHI/GFRP stimulatory complex | | Descriptor: | GTP Cyclohydrolase I, GTP Cyclohydrolase I Feedback Regulatory Protein, PHENYLALANINE, ... | | Authors: | Maita, N, Okada, K, Hatakeyama, K, Hakoshima, T. | | Deposit date: | 2001-11-18 | | Release date: | 2002-02-20 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (2.8 Å) | | Cite: | Crystal structure of the stimulatory complex of GTP cyclohydrolase I and its feedback regulatory protein GFRP.
Proc.Natl.Acad.Sci.USA, 99, 2002
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7CMG
 | | The Structure of the periplasmic domain of PorM | | Descriptor: | Por secretion system protein porM/gldM | | Authors: | Sato, K, Okada, K, Nakayam, K, Imada, K. | | Deposit date: | 2020-07-27 | | Release date: | 2020-09-02 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (3.7 Å) | | Cite: | PorM, a core component of bacterial type IX secretion system, forms a dimer with a unique kinked-rod shape.
Biochem.Biophys.Res.Commun., 532, 2020
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3VHE
 | | Crystal structure of human VEGFR2 kinase domain with a novel pyrrolopyrimidine inhibitor. | | Descriptor: | 1-{2-fluoro-4-[(5-methyl-5H-pyrrolo[3,2-d]pyrimidin-4-yl)oxy]phenyl}-3-[3-(trifluoromethyl)phenyl]urea, Vascular endothelial growth factor receptor 2 | | Authors: | Oguro, Y, Miyamoto, N, Okada, K, Takagi, T, Iwata, H, Awazu, Y, Miki, H, Hori, A, Kamiyama, K, Imanura, S. | | Deposit date: | 2011-08-24 | | Release date: | 2011-11-02 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (1.55 Å) | | Cite: | Design, synthesis, and evaluation of 5-methyl-4-phenoxy-5H-pyrrolo[3,2-d]pyrimidine derivatives: novel VEGFR2 kinase inhibitors binding to inactive kinase conformation.
Bioorg.Med.Chem., 18, 2010
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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
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3VO3
 | | Crystal Structure of the Kinase domain of Human VEGFR2 with imidazo[1,2-b]pyridazine derivative | | Descriptor: | 1,2-ETHANEDIOL, N-[3-({2-[(cyclopropylcarbonyl)amino]imidazo[1,2-b]pyridazin-6-yl}oxy)phenyl]-1,3-dimethyl-1H-pyrazole-5-carboxamide, Vascular endothelial growth factor receptor 2 | | Authors: | Oki, H, Okada, K. | | Deposit date: | 2012-01-19 | | Release date: | 2013-03-06 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (1.52 Å) | | Cite: | Discovery of N-[5-({2-[(cyclopropylcarbonyl)amino]imidazo[1,2-b]pyridazin-6-yl}oxy)-2-methylphenyl]-1,3-dimethyl-1H-pyrazole-5-carboxamide (TAK-593), a highly potent VEGFR2 kinase inhibitor
Bioorg.Med.Chem., 21, 2013
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6M9L
 | | Structure-based Design, Synthesis, and Biological Evaluation of Imidazo[4,5-b]pyridine-2-one based p38 MAP Kinase Inhibitors by scaffold hopping - compound 10 | | Descriptor: | 3-benzyl-6-[(2,4-difluorophenyl)amino]-1,3-dihydro-2H-imidazo[4,5-b]pyridin-2-one, Mitogen-activated protein kinase 14 | | Authors: | Lane, W, Okada, K. | | Deposit date: | 2018-08-23 | | Release date: | 2019-04-17 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (2.45 Å) | | Cite: | Structure-Based Design, Synthesis, and Biological Evaluation of Imidazo[4,5-b]pyridin-2-one-Based p38 MAP Kinase Inhibitors: Part 1.
Chemmedchem, 14, 2019
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6M95
 | | Structure-based Design, Synthesis, and Biological Evaluation of Imidazo[4,5-b]pyridine-2-one based p38 MAP Kinase Inhibitors by scaffold hopping: compound 1 | | Descriptor: | (4-benzylpiperidin-1-yl)[2-methoxy-4-(methylsulfanyl)phenyl]methanone, Mitogen-activated protein kinase 14 | | Authors: | Lane, W, Okada, K. | | Deposit date: | 2018-08-22 | | Release date: | 2019-04-17 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Structure-Based Design, Synthesis, and Biological Evaluation of Imidazo[4,5-b]pyridin-2-one-Based p38 MAP Kinase Inhibitors: Part 1.
Chemmedchem, 14, 2019
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2ZW2
 | | Crystal Structure of Formylglycinamide Ribonucleotide Amidotransferase III from SULFOLOBUS TOKODAII (STPURS) | | Descriptor: | GLYCEROL, Putative uncharacterized protein STS178 | | Authors: | Suzuki, S, Tamura, S, Okada, K, Baba, S, Kumasaka, T, Nakagawa, N, Masui, R, Kuramitsu, S, Sampei, G, Kawai, G. | | Deposit date: | 2008-11-27 | | Release date: | 2009-11-17 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (1.55 Å) | | Cite: | Crystal Structure of Formylglycinamide Ribonucleotide Amidotransferase III from SULFOLOBUS TOKODAII (STPURS)
To be Published
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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
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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
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3VW6
 | | Crystal structure of human apoptosis signal-regulating kinase 1 (ASK1) with imidazopyridine inhibitor | | Descriptor: | 4-tert-butyl-N-[6-(1H-imidazol-1-yl)imidazo[1,2-a]pyridin-2-yl]benzamide, Mitogen-activated protein kinase kinase kinase 5 | | Authors: | Terao, Y, Suzuki, H, Yoshikawa, M, Yashiro, H, Takekawa, S, Fujitani, Y, Okada, K, Inoue, Y, Yamamoto, Y, Nakagawa, H, Yao, S, Kawamoto, T, Uchikawa, O. | | Deposit date: | 2012-08-06 | | Release date: | 2012-10-31 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | Design and biological evaluation of imidazo[1,2-a]pyridines as novel and potent ASK1 inhibitors.
Bioorg. Med. Chem. Lett., 22, 2012
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3AX6
 | | Crystal structure of N5-carboxyaminoimidazole ribonucleotide synthetase from Thermotoga maritima | | Descriptor: | ADENOSINE-5'-DIPHOSPHATE, Phosphoribosylaminoimidazole carboxylase, ATPase subunit | | Authors: | Miyazawa, R, Kanagawa, M, Baba, S, Nakagawa, N, Ebihara, A, Kuramitsu, S, Yokoyama, S, Kawai, G, Sampei, G, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2011-03-30 | | Release date: | 2012-04-25 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Crystal structures of N5-carboxyaminoimidazole ribonucleotide synthetase, PurK, from thermophilic bacteria
To be Published
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6OHD
 | | P38 in complex with T-3220137 | | Descriptor: | 3-(3-tert-butyl-2-oxo-2,3-dihydro-1H-imidazo[4,5-b]pyridin-6-yl)-4-methyl-N-(1,2-oxazol-3-yl)benzamide, Mitogen-activated protein kinase 14 | | Authors: | Lane, W, Saikatendu, K. | | Deposit date: | 2019-04-05 | | Release date: | 2019-11-20 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Structure-Based Design, Synthesis, and Biological Evaluation of Imidazo[4,5-b]Pyridin-2-one-Based p38 MAP Kinase Inhibitors: Part 2.
Chemmedchem, 14, 2019
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