5I13
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![BU of 5i13 by Molmil](/molmil-images/mine/5i13) | Endonuclease inhibitor 2 bound to influenza strain H1N1 polymerase acidic subunit N-terminal region at pH 7.0 | Descriptor: | 4-{(E)-[2-(4-chlorophenyl)hydrazinylidene]methyl}benzene-1,2,3-triol, MANGANESE (II) ION, Polymerase acidic protein, ... | Authors: | Fudo, S, Yamamoto, N, Nukaga, M, Odagiri, T, Tashiro, M, Hoshino, T. | Deposit date: | 2016-02-05 | Release date: | 2016-02-17 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.151 Å) | Cite: | Two Distinctive Binding Modes of Endonuclease Inhibitors to the N-Terminal Region of Influenza Virus Polymerase Acidic Subunit Biochemistry, 55, 2016
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6LN3
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![BU of 6ln3 by Molmil](/molmil-images/mine/6ln3) | Crystal structure of adenylate kinase from an extremophilic archaeon Aeropyrum pernix with ATP and AMP | Descriptor: | 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, ADENOSINE MONOPHOSPHATE, ADENOSINE-5'-TRIPHOSPHATE, ... | Authors: | Shibanuma, Y, Nemoto, N, Yamamoto, N, Sampei, G, Kawai, G. | Deposit date: | 2019-12-28 | Release date: | 2020-04-22 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Crystal structure of adenylate kinase from an extremophilic archaeon Aeropyrum pernix with ATP and AMP. J.Biochem., 168, 2020
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4YYL
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![BU of 4yyl by Molmil](/molmil-images/mine/4yyl) | Phenolic acid derivative bound to influenza strain H1N1 polymerase subunit PA endonuclease | Descriptor: | 2-(4-fluorophenoxy)-1-(2,3,4-trihydroxyphenyl)ethanone, MANGANESE (II) ION, Polymerase acidic protein, ... | Authors: | Fudo, S, Yamamoto, N, Nukaga, M, Odagiri, T, Tashiro, M, Neya, S, Hoshino, T. | Deposit date: | 2015-03-24 | Release date: | 2015-04-29 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.905 Å) | Cite: | Structural and computational study on inhibitory compounds for endonuclease activity of influenza virus polymerase Bioorg.Med.Chem., 23, 2015
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4ZQQ
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![BU of 4zqq by Molmil](/molmil-images/mine/4zqq) | Apo form of influenza strain H1N1 polymerase acidic subunit N-terminal region | Descriptor: | MANGANESE (II) ION, Polymerase acidic protein,Polymerase acidic protein, SULFATE ION | Authors: | Fudo, S, Yamamoto, N, Nukaga, M, Odagiri, T, Tashiro, M, Neya, S, Hoshino, T. | Deposit date: | 2015-05-11 | Release date: | 2015-06-03 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.8 Å) | Cite: | Two Distinctive Binding Modes of Endonuclease Inhibitors to the N-Terminal Region of Influenza Virus Polymerase Acidic Subunit. Biochemistry, 55, 2016
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4ZI0
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![BU of 4zi0 by Molmil](/molmil-images/mine/4zi0) | Endonuclease inhibitor bound to influenza strain H1N1 polymerase acidic subunit N-terminal region without a chelation to the metal ions in the active site | Descriptor: | 4-{(E)-[2-(4-chlorophenyl)hydrazinylidene]methyl}benzene-1,2,3-triol, MANGANESE (II) ION, Polymerase acidic protein, ... | Authors: | Fudo, S, Yamamoto, N, Nukaga, M, Odagiri, T, Tashiro, M, Neya, S, Hoshino, T. | Deposit date: | 2015-04-27 | Release date: | 2015-05-13 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.802 Å) | Cite: | Two Distinctive Binding Modes of Endonuclease Inhibitors to the N-Terminal Region of Influenza Virus Polymerase Acidic Subunit Biochemistry, 55, 2016
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4ZHZ
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![BU of 4zhz by Molmil](/molmil-images/mine/4zhz) | Endonuclease inhibitor bound to influenza strain H1N1 polymerase acidic subunit N-terminal region with expelling one of the metal ions in the active site | Descriptor: | 5-(2-chlorobenzyl)-2-hydroxy-3-nitrobenzaldehyde, MANGANESE (II) ION, Polymerase acidic protein, ... | Authors: | Fudo, S, Yamamoto, N, Nukaga, M, Odagiri, T, Tashiro, M, Neya, S, Hoshino, T. | Deposit date: | 2015-04-27 | Release date: | 2015-05-13 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.5 Å) | Cite: | Two Distinctive Binding Modes of Endonuclease Inhibitors to the N-Terminal Region of Influenza Virus Polymerase Acidic Subunit Biochemistry, 55, 2016
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5FDG
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![BU of 5fdg by Molmil](/molmil-images/mine/5fdg) | Endonuclease inhibitor 3 bound to influenza strain H1N1 polymerase acidic subunit N-terminal region at pH 7.0 | Descriptor: | (2Z)-4-[1-benzyl-4-(4-chlorobenzyl)piperidin-4-yl]-2-hydroxy-4-oxobut-2-enoic acid, MANGANESE (II) ION, Polymerase acidic protein, ... | Authors: | Fudo, S, Yamamoto, N, Nukaga, M, Odagiri, T, Tashiro, M, Hoshino, T. | Deposit date: | 2015-12-16 | Release date: | 2015-12-30 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.1 Å) | Cite: | Two Distinctive Binding Modes of Endonuclease Inhibitors to the N-Terminal Region of Influenza Virus Polymerase Acidic Subunit Biochemistry, 55, 2016
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5FDD
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![BU of 5fdd by Molmil](/molmil-images/mine/5fdd) | Endonuclease inhibitor 1 bound to influenza strain H1N1 polymerase acidic subunit N-terminal region at pH 7.0 | Descriptor: | 5-(2-chlorobenzyl)-2-hydroxy-3-nitrobenzaldehyde, MANGANESE (II) ION, Polymerase acidic protein,Polymerase acidic protein, ... | Authors: | Fudo, S, Yamamoto, N, Nukaga, M, Odagiri, T, Tashiro, M, Hoshino, T. | Deposit date: | 2015-12-16 | Release date: | 2015-12-30 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (2.506 Å) | Cite: | Two Distinctive Binding Modes of Endonuclease Inhibitors to the N-Terminal Region of Influenza Virus Polymerase Acidic Subunit Biochemistry, 55, 2016
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7DEL
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![BU of 7del by Molmil](/molmil-images/mine/7del) | Crystal structure of P.aeruginosa LpxC in complex with inhibitor | Descriptor: | 3-[4-[2-[3-[[2-[(1~{S})-1-oxidanylethyl]imidazol-1-yl]methyl]-1,2-oxazol-5-yl]ethynyl]phenyl]propan-1-ol, UDP-3-O-acyl-N-acetylglucosamine deacetylase, ZINC ION | Authors: | Mima, M, Ushiyama, F, Tanaka-Yamamoto, N. | Deposit date: | 2020-11-04 | Release date: | 2021-01-13 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.15 Å) | Cite: | Lead optimization of 2-hydroxymethyl imidazoles as non-hydroxamate LpxC inhibitors: Discovery of TP0586532. Bioorg.Med.Chem., 30, 2020
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2D19
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![BU of 2d19 by Molmil](/molmil-images/mine/2d19) | Solution RNA structure of loop region of the HIV-1 dimerization initiation site in the kissing-loop dimer | Descriptor: | 5'-R(*GP*CP*UP*GP*AP*AP*GP*UP*GP*CP*AP*CP*AP*CP*GP*GP*C)-3' | Authors: | Baba, S, Takahashi, K, Noguchi, S, Takaku, H, Koyanagi, Y, Yamamoto, N, Kawai, G. | Deposit date: | 2005-08-15 | Release date: | 2005-11-01 | Last modified: | 2024-05-29 | Method: | SOLUTION NMR | Cite: | Solution RNA structures of the HIV-1 dimerization initiation site in the kissing-loop and extended-duplex dimers. J.Biochem.(Tokyo), 138, 2005
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2D17
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![BU of 2d17 by Molmil](/molmil-images/mine/2d17) | Solution RNA structure of stem-bulge-stem region of the HIV-1 dimerization initiation site | Descriptor: | 5'-R(*CP*GP*GP*CP*AP*AP*GP*AP*GP*GP*CP*GP*AP*CP*CP*C)-3', 5'-R(*GP*GP*GP*UP*CP*GP*GP*CP*UP*UP*GP*CP*UP*G)-3' | Authors: | Baba, S, Takahashi, K, Noguchi, S, Takaku, H, Koyanagi, Y, Yamamoto, N, Kawai, G. | Deposit date: | 2005-08-15 | Release date: | 2005-11-01 | Last modified: | 2024-05-29 | Method: | SOLUTION NMR | Cite: | Solution RNA structures of the HIV-1 dimerization initiation site in the kissing-loop and extended-duplex dimers. J.Biochem.(Tokyo), 138, 2005
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2D18
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![BU of 2d18 by Molmil](/molmil-images/mine/2d18) | Solution RNA structure of loop region of the HIV-1 dimerization initiation site in the extended-duplex dimer | Descriptor: | 5'-R(*GP*CP*UP*GP*AP*AP*GP*UP*GP*CP*AP*CP*AP*CP*GP*GP*C)-3' | Authors: | Baba, S, Takahashi, K, Noguchi, S, Takaku, H, Koyanagi, Y, Yamamoto, N, Kawai, G. | Deposit date: | 2005-08-15 | Release date: | 2005-11-01 | Last modified: | 2024-05-29 | Method: | SOLUTION NMR | Cite: | Solution RNA structures of the HIV-1 dimerization initiation site in the kissing-loop and extended-duplex dimers. J.Biochem.(Tokyo), 138, 2005
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2D1B
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![BU of 2d1b by Molmil](/molmil-images/mine/2d1b) | Solution RNA structure model of the HIV-1 dimerization initiation site in the kissing-loop dimer | Descriptor: | RNA | Authors: | Baba, S, Takahashi, K, Noguchi, S, Takaku, H, Koyanagi, Y, Yamamoto, N, Kawai, G. | Deposit date: | 2005-08-15 | Release date: | 2005-11-01 | Last modified: | 2024-05-29 | Method: | SOLUTION NMR | Cite: | Solution RNA structures of the HIV-1 dimerization initiation site in the kissing-loop and extended-duplex dimers. J.Biochem.(Tokyo), 138, 2005
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2D1A
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![BU of 2d1a by Molmil](/molmil-images/mine/2d1a) | Solution RNA structure model of the HIV-1 dimerization initiation site in the extended-duplex dimer | Descriptor: | RNA | Authors: | Baba, S, Takahashi, K, Noguchi, S, Takaku, H, Koyanagi, Y, Yamamoto, N, Kawai, G. | Deposit date: | 2005-08-15 | Release date: | 2005-11-01 | Last modified: | 2024-05-29 | Method: | SOLUTION NMR | Cite: | Solution RNA structures of the HIV-1 dimerization initiation site in the kissing-loop and extended-duplex dimers. J.Biochem.(Tokyo), 138, 2005
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6L01
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![BU of 6l01 by Molmil](/molmil-images/mine/6l01) | Crystal structure of E.coli DNA gyrase B in complex with 2-oxo-1,2-dihydroquinoline derivative | Descriptor: | 2-[3-[[8-(methylamino)-2-oxidanylidene-1~{H}-quinolin-3-yl]carbonylamino]phenyl]ethanoic acid, DNA gyrase subunit B | Authors: | Mima, M, Takeuchi, T, Ushiyama, F. | Deposit date: | 2019-09-25 | Release date: | 2020-05-06 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2.6 Å) | Cite: | Lead Identification of 8-(Methylamino)-2-oxo-1,2-dihydroquinoline Derivatives as DNA Gyrase Inhibitors: Hit-to-Lead Generation Involving Thermodynamic Evaluation. Acs Omega, 5, 2020
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6KZV
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![BU of 6kzv by Molmil](/molmil-images/mine/6kzv) | |
6KZZ
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![BU of 6kzz by Molmil](/molmil-images/mine/6kzz) | Crystal structure of E.coli DNA gyrase B in complex with 2-oxo-1,2-dihydroquinoline derivative | Descriptor: | 4-[[8-(methylamino)-2-oxidanylidene-1~{H}-quinolin-3-yl]carbonylamino]benzoic acid, DNA gyrase subunit B | Authors: | Mima, M, Takeuchi, T, Ushiyama, F. | Deposit date: | 2019-09-25 | Release date: | 2020-05-06 | Last modified: | 2023-11-22 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Lead Identification of 8-(Methylamino)-2-oxo-1,2-dihydroquinoline Derivatives as DNA Gyrase Inhibitors: Hit-to-Lead Generation Involving Thermodynamic Evaluation. Acs Omega, 5, 2020
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3KKQ
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![BU of 3kkq by Molmil](/molmil-images/mine/3kkq) | Crystal structure of M-Ras P40D in complex with GDP | Descriptor: | GUANOSINE-5'-DIPHOSPHATE, MAGNESIUM ION, Ras-related protein M-Ras | Authors: | Muraoka, S, Shima, F, Liao, J, Ijiri, Y, Matsumoto, K, Ye, M, Inoue, T, Kataoka, T. | Deposit date: | 2009-11-06 | Release date: | 2010-06-16 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (1.2 Å) | Cite: | Structural basis for conformational dynamics of GTP-bound Ras protein J.Biol.Chem., 285, 2010
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3KKO
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![BU of 3kko by Molmil](/molmil-images/mine/3kko) | Crystal structure of M-Ras P40D/D41E/L51R in complex with GppNHp | Descriptor: | MAGNESIUM ION, PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER, Ras-related protein M-Ras, ... | Authors: | Muraoka, S, Shima, F, Liao, J, Ijiri, Y, Matsumoto, K, Ye, M, Inoue, T, Kataoka, T. | Deposit date: | 2009-11-06 | Release date: | 2010-06-16 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (1.9 Å) | Cite: | Structural basis for conformational dynamics of GTP-bound Ras protein J.Biol.Chem., 285, 2010
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3KKM
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![BU of 3kkm by Molmil](/molmil-images/mine/3kkm) | Crystal structure of H-Ras T35S in complex with GppNHp | Descriptor: | GTPase HRas, MAGNESIUM ION, PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER, ... | Authors: | Muraoka, S, Shima, F, Liao, J, Ijiri, Y, Matsumoto, K, Ye, M, Inoue, T, Kataoka, T. | Deposit date: | 2009-11-06 | Release date: | 2010-06-16 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (1.7 Å) | Cite: | Structural basis for conformational dynamics of GTP-bound Ras protein J.Biol.Chem., 285, 2010
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3KKP
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![BU of 3kkp by Molmil](/molmil-images/mine/3kkp) | Crystal structure of M-Ras P40D in complex with GppNHp | Descriptor: | MAGNESIUM ION, PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER, Ras-related protein M-Ras | Authors: | Muraoka, S, Shima, F, Liao, J, Ijiri, Y, Matsumoto, K, Ye, M, Inoue, T, Kataoka, T. | Deposit date: | 2009-11-06 | Release date: | 2010-06-16 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (1.35 Å) | Cite: | Structural basis for conformational dynamics of GTP-bound Ras protein J.Biol.Chem., 285, 2010
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3KKN
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![BU of 3kkn by Molmil](/molmil-images/mine/3kkn) | Crystal structure of H-Ras T35S in complex with GppNHp | Descriptor: | GTPase HRas, MAGNESIUM ION, PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER | Authors: | Muraoka, S, Shima, F, Liao, J, Ijiri, Y, Matsumoto, K, Ye, M, Inoue, T, Kataoka, T. | Deposit date: | 2009-11-06 | Release date: | 2010-06-16 | Last modified: | 2023-11-01 | Method: | X-RAY DIFFRACTION (2.09 Å) | Cite: | Structural basis for conformational dynamics of GTP-bound Ras protein J.Biol.Chem., 285, 2010
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8JYG
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![BU of 8jyg by Molmil](/molmil-images/mine/8jyg) | Crystal structure of Human HPSE1 in complex with inhibitor | Descriptor: | (5~{S},6~{R},7~{S},8~{S})-6,7,8-tris(oxidanyl)-2-[2-(3-phenoxyphenyl)ethyl]-5,6,7,8-tetrahydroimidazo[1,2-a]pyridine-5-carboxylic acid, 1,2-ETHANEDIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose, ... | Authors: | Mima, M, Fujimoto, N, Imai, Y. | Deposit date: | 2023-07-03 | Release date: | 2023-09-20 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Structure-based lead optimization to improve potency and selectivity of a novel tetrahydroimidazo[1,2-a]pyridine-5-carboxylic acid series of heparanase-1 inhibitor. Bioorg.Med.Chem., 93, 2023
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8K5W
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![BU of 8k5w by Molmil](/molmil-images/mine/8k5w) | Crystal structure of human proMMP-9 catalytic domain in complex with inhibitor | Descriptor: | 2-[[5-fluoranyl-7-(methylamino)-1H-indol-2-yl]carbonyl]-N-(2-pyrrol-1-ylethyl)-3,4-dihydro-1H-isoquinoline-7-carboxamide, CALCIUM ION, DIHYDROGENPHOSPHATE ION, ... | Authors: | Kamitani, M, Mima, M, Nishikawa-Shimono, R. | Deposit date: | 2023-07-24 | Release date: | 2023-12-06 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | Discovery of novel indole derivatives as potent and selective inhibitors of proMMP-9 activation. Bioorg.Med.Chem.Lett., 97, 2023
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8K5V
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![BU of 8k5v by Molmil](/molmil-images/mine/8k5v) | Crystal structure of human proMMP-9 catalytic domain in complex with inhibitor | Descriptor: | 6,7-dihydro-4H-[1,3]oxazolo[4,5-c]pyridin-5-yl-(7-ethyl-2H-indazol-3-yl)methanone, CALCIUM ION, DIHYDROGENPHOSPHATE ION, ... | Authors: | Kamitani, M, Mima, M, Nishikawa-Shimono, R. | Deposit date: | 2023-07-24 | Release date: | 2023-12-06 | Method: | X-RAY DIFFRACTION (1.7 Å) | Cite: | Discovery of novel indole derivatives as potent and selective inhibitors of proMMP-9 activation. Bioorg.Med.Chem.Lett., 97, 2023
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