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5I13
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BU of 5i13 by Molmil
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
4YYL
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BU of 4yyl by Molmil
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
4ZQQ
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BU of 4zqq by Molmil
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
4ZI0
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BU of 4zi0 by Molmil
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
4ZHZ
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BU of 4zhz by Molmil
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
6LN3
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BU of 6ln3 by Molmil
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
5FDD
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BU of 5fdd by Molmil
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
5FDG
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BU of 5fdg by Molmil
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
7DEL
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BU of 7del by Molmil
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
2D19
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BU of 2d19 by Molmil
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:2022-03-09
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
2D17
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BU of 2d17 by Molmil
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:2022-03-09
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
2D1A
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BU of 2d1a by Molmil
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:2022-03-09
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
2D18
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BU of 2d18 by Molmil
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:2022-03-09
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
2D1B
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BU of 2d1b by Molmil
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:2022-03-09
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
3KKQ
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BU of 3kkq by Molmil
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
3KKM
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BU of 3kkm by Molmil
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
3KKP
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BU of 3kkp by Molmil
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
3KKN
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BU of 3kkn by Molmil
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
3KKO
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BU of 3kko by Molmil
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
8JYG
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BU of 8jyg by Molmil
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
7C7O
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BU of 7c7o by Molmil
Crystal structure of E.coli DNA gyrase B in complex with 6-fluoro-8-(methylamino)-2-oxo-1,2-dihydroquinoline derivative
Descriptor: 4-[[4-(3-azanylpropylamino)-6-fluoranyl-8-(methylamino)-2-oxidanylidene-1~{H}-quinolin-3-yl]carbonylamino]benzoic acid, DNA gyrase subunit B
Authors:Kamitani, M, Mima, M, Takeuchi, T, Ushiyama, F.
Deposit date:2020-05-26
Release date:2020-10-14
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Lead optimization of 8-(methylamino)-2-oxo-1,2-dihydroquinolines as bacterial type II topoisomerase inhibitors.
Bioorg.Med.Chem., 28, 2020
7C7N
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BU of 7c7n by Molmil
Crystal structure of E.coli DNA gyrase B in complex with 6-fluoro-8-(methylamino)-2-oxo-1,2-dihydroquinoline derivative
Descriptor: 4-[[6-fluoranyl-8-(methylamino)-2-oxidanylidene-1~{H}-quinolin-3-yl]carbonylamino]benzoic acid, DNA gyrase subunit B
Authors:Mima, M, Ushiyama, F.
Deposit date:2020-05-26
Release date:2020-10-14
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.3 Å)
Cite:Lead optimization of 8-(methylamino)-2-oxo-1,2-dihydroquinolines as bacterial type II topoisomerase inhibitors.
Bioorg.Med.Chem., 28, 2020
7CID
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BU of 7cid by Molmil
Crystal structure of P.aeruginosa LpxC in complex with inhibitor
Descriptor: 1-[3-(4-chlorophenyl)propyl]imidazole, DIMETHYL SULFOXIDE, UDP-3-O-acyl-N-acetylglucosamine deacetylase, ...
Authors:Baker, L.M, Mima, M, Surgenor, A, Robertson, A.
Deposit date:2020-07-07
Release date:2020-12-02
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.49 Å)
Cite:Fragment-Based Discovery of Novel Non-Hydroxamate LpxC Inhibitors with Antibacterial Activity.
J.Med.Chem., 63, 2020
7CI4
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BU of 7ci4 by Molmil
Crystal structure of P.aeruginosa LpxC in complex with inhibitor
Descriptor: (2R)-2-azanyl-4-methylsulfonyl-N-[3-(trifluoromethyloxy)phenyl]butanamide, CHLORIDE ION, MAGNESIUM ION, ...
Authors:Mima, M, Baker, L.M, Surgenor, A, Robertson, A.
Deposit date:2020-07-07
Release date:2020-12-02
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2 Å)
Cite:Fragment-Based Discovery of Novel Non-Hydroxamate LpxC Inhibitors with Antibacterial Activity.
J.Med.Chem., 63, 2020
7CIC
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BU of 7cic by Molmil
Crystal structure of P.aeruginosa LpxC in complex with inhibitor
Descriptor: 2-azanyl-N-[3-(trifluoromethyloxy)phenyl]ethanamide, UDP-3-O-acyl-N-acetylglucosamine deacetylase, ZINC ION
Authors:Baker, L.M, Mima, M, Surgenor, A, Robertson, A.
Deposit date:2020-07-07
Release date:2020-12-02
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (1.78 Å)
Cite:Fragment-Based Discovery of Novel Non-Hydroxamate LpxC Inhibitors with Antibacterial Activity.
J.Med.Chem., 63, 2020

 

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