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7X7O
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BU of 7x7o by Molmil
SARS-CoV-2 spike RBD in complex with neutralizing antibody UT28K
Descriptor: Spike protein S1, UT28K Fab, heavy chain, ...
Authors:Ozawa, T, Tani, H, Anraku, Y, Kita, S, Igarashi, E, Saga, Y, Inasaki, N, Kawasuji, H, Yamada, H, Sasaki, S, Somekawa, M, Sasaki, J, Hayakawa, Y, Yamamoto, Y, Morinaga, Y, Kurosawa, N, Isobe, M, Fukuhara, H, Maenaka, K, Hashiguchi, T, Kishi, H, Kitajima, I, Saito, S, Niimi, H.
Deposit date:2022-03-10
Release date:2022-05-25
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (3.75 Å)
Cite:Novel super-neutralizing antibody UT28K is capable of protecting against infection from a wide variety of SARS-CoV-2 variants.
Mabs, 14, 2022
2DIE
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BU of 2die by Molmil
Alkaline alpha-amylase AmyK from Bacillus sp. KSM-1378
Descriptor: CALCIUM ION, SODIUM ION, amylase
Authors:Shirai, T, Igarashi, K, Ozawa, T, Hagihara, H, Kobayashi, T, Ozaki, K, Ito, S.
Deposit date:2006-03-29
Release date:2007-02-13
Last modified:2023-10-25
Method:X-RAY DIFFRACTION (2.1 Å)
Cite:Ancestral sequence evolutionary trace and crystal structure analyses of alkaline alpha-amylase from Bacillus sp. KSM-1378 to clarify the alkaline adaptation process of proteins
Proteins, 66, 2007
1IUA
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BU of 1iua by Molmil
Ultra-high resolution structure of HiPIP from Thermochromatium tepidum
Descriptor: High-potential iron-sulfur protein, IRON/SULFUR CLUSTER, SULFATE ION
Authors:Liu, L, Nogi, T, Kobayashi, M, Nozawa, T, Miki, K.
Deposit date:2002-03-01
Release date:2002-03-20
Last modified:2023-12-27
Method:X-RAY DIFFRACTION (0.8 Å)
Cite:Ultrahigh-resolution structure of high-potential iron-sulfur protein from Thermochromatium tepidum.
Acta Crystallogr.,Sect.D, 58, 2002
1EYT
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BU of 1eyt by Molmil
CRYSTAL STRUCTURE OF HIGH-POTENTIAL IRON-SULFUR PROTEIN FROM THERMOCHROMATIUM TEPIDUM
Descriptor: HIGH-POTENTIAL IRON-SULFUR PROTEIN, IRON/SULFUR CLUSTER
Authors:Nogi, T, Fathir, I, Kobayashi, M, Nozawa, T, Miki, K.
Deposit date:2000-05-08
Release date:2000-12-13
Last modified:2024-02-07
Method:X-RAY DIFFRACTION (1.5 Å)
Cite:Crystal structures of photosynthetic reaction center and high-potential iron-sulfur protein from Thermochromatium tepidum: thermostability and electron transfer.
Proc.Natl.Acad.Sci.USA, 97, 2000
1EYS
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BU of 1eys by Molmil
CRYSTAL STRUCTURE OF PHOTOSYNTHETIC REACTION CENTER FROM A THERMOPHILIC BACTERIUM, THERMOCHROMATIUM TEPIDUM
Descriptor: 2-O-octyl-beta-D-glucopyranose, BACTERIOCHLOROPHYLL A, BACTERIOPHEOPHYTIN A, ...
Authors:Nogi, T, Fathir, I, Kobayashi, M, Nozawa, T, Miki, K.
Deposit date:2000-05-08
Release date:2000-12-13
Last modified:2020-07-29
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:Crystal structures of photosynthetic reaction center and high-potential iron-sulfur protein from Thermochromatium tepidum: thermostability and electron transfer.
Proc.Natl.Acad.Sci.USA, 97, 2000
1WRG
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BU of 1wrg by Molmil
Light-Harvesting Complex 1 Beta Subunit from Wild-Type Rhodospirillum rubrum
Descriptor: Light-harvesting protein B-880, beta chain
Authors:Wang, Z.-Y, Gokan, K, Kobayashi, M, Nozawa, T.
Deposit date:2004-10-15
Release date:2005-03-15
Last modified:2024-05-29
Method:SOLUTION NMR
Cite:Solution Structures of the Core Light-harvesting alpha and beta Polypeptides from Rhodospirillum rubrum: Implications for the Pigment-Protein and Protein-Protein Interactions
J.Mol.Biol., 347, 2005
1XRD
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BU of 1xrd by Molmil
Light-Harvesting Complex 1 Alfa Subunit from Wild-Type Rhodospirillum rubrum
Descriptor: Light-harvesting protein B-880, alpha chain
Authors:Wang, Z.-Y, Gokan, K, Kobayashi, M, Nozawa, T.
Deposit date:2004-10-14
Release date:2005-03-15
Last modified:2024-05-29
Method:SOLUTION NMR
Cite:Solution Structures of the Core Light-harvesting alpha and beta Polypeptides from Rhodospirillum rubrum: Implications for the Pigment-Protein and Protein-Protein Interactions
J.Mol.Biol., 347, 2005
8K5H
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BU of 8k5h by Molmil
Structure of the SARS-CoV-2 BA.1 spike with UT28-RD
Descriptor: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein, ...
Authors:Chen, L, Kita, S, Anraku, Y, Maenaka, K.
Deposit date:2023-07-21
Release date:2023-12-27
Last modified:2024-07-10
Method:ELECTRON MICROSCOPY (3.22 Å)
Cite:Rational in silico design identifies two mutations that restore UT28K SARS-CoV-2 monoclonal antibody activity against Omicron BA.1.
Structure, 32, 2024
8K5G
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BU of 8k5g by Molmil
Structure of the SARS-CoV-2 BA.1 RBD with UT28-RD
Descriptor: Spike protein S1, UT28K-RD Fab Heavy chain, UT28K-RD Fab Light chain
Authors:Chen, L, Kita, S, Anraku, Y, Maenaka, K.
Deposit date:2023-07-21
Release date:2023-12-27
Last modified:2024-07-10
Method:ELECTRON MICROSCOPY (3.41 Å)
Cite:Rational in silico design identifies two mutations that restore UT28K SARS-CoV-2 monoclonal antibody activity against Omicron BA.1.
Structure, 32, 2024
2ZM4
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BU of 2zm4 by Molmil
Crystal structure of imidazo quinoxaline 1 bound to the kinase domain of human LCK, activated form (auto-phosphorylated on TYR394)
Descriptor: DIMETHYL SULFOXIDE, N-(2-chloro-6-methylphenyl)-8-[(3S)-3-methylpiperazin-1-yl]imidazo[1,5-a]quinoxalin-4-amine, Proto-oncogene tyrosine-protein kinase LCK, ...
Authors:Tsuji, E.
Deposit date:2008-04-11
Release date:2008-10-14
Last modified:2023-11-15
Method:X-RAY DIFFRACTION (2.7 Å)
Cite:The importance of CH/pi hydrogen bonds in rational drug design: An ab initio fragment molecular orbital study to leukocyte-specific protein tyrosine (LCK) kinase
Bioorg.Med.Chem., 16, 2008
2ZYB
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BU of 2zyb by Molmil
Crystal structure of phenylimidazo pyrazin 2 bound to the kinase domain of human LCK, (auto-phosphorylated on TYR394)
Descriptor: N-(2,6-dimethylphenyl)-5-phenylimidazo[1,5-a]pyrazin-8-amine, Proto-oncogene tyrosine-protein kinase LCK, SULFATE ION
Authors:Tsuji, E.
Deposit date:2009-01-19
Release date:2009-02-03
Last modified:2023-11-15
Method:X-RAY DIFFRACTION (2.55 Å)
Cite:The importance of CH/pi hydrogen bonds in rational drug design: An ab initio fragment molecular orbital study to leukocyte-specific protein tyrosine (LCK) kinase
Bioorg.Med.Chem., 16, 2008
2ZM1
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BU of 2zm1 by Molmil
Crystal structure of imidazo pyrazin 1 bound to the kinase domain of human LCK, (auto-phosphorylated on TYR394)
Descriptor: DIMETHYL SULFOXIDE, N-(2-chlorophenyl)-5-phenylimidazo[1,5-a]pyrazin-8-amine, Proto-oncogene tyrosine-protein kinase LCK, ...
Authors:Tsuji, E.
Deposit date:2008-04-10
Release date:2008-10-14
Last modified:2023-11-15
Method:X-RAY DIFFRACTION (2.1 Å)
Cite:The importance of CH/pi hydrogen bonds in rational drug design: An ab initio fragment molecular orbital study to leukocyte-specific protein tyrosine (LCK) kinase
Bioorg.Med.Chem., 16, 2008
6IQN
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BU of 6iqn by Molmil
Crystal structure of TrkA kinase with ligand
Descriptor: 4-[[4-azanyl-3-(4-cyclohexylpiperazin-1-yl)-9,10-bis(oxidanylidene)anthracen-1-yl]amino]benzoic acid, High affinity nerve growth factor receptor
Authors:Noritaka, F.
Deposit date:2018-11-08
Release date:2020-01-22
Last modified:2023-11-22
Method:X-RAY DIFFRACTION (2.54 Å)
Cite:An isoform-selective inhibitor of tropomyosin receptor kinase A behaves as molecular glue.
Bioorg.Med.Chem.Lett., 30, 2020
5H3Q
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BU of 5h3q by Molmil
Crystal Structure of TrkA kinase with ligand
Descriptor: 1-[(3S,4R)-4-[3,4-bis(fluoranyl)phenyl]-1-(2-methoxyethyl)pyrrolidin-3-yl]-3-(5-ethoxy-4-methyl-2-phenyl-pyrazol-3-yl)urea, 2,3-DIHYDROXY-1,4-DITHIOBUTANE, High affinity nerve growth factor receptor, ...
Authors:Noritaka, F.
Deposit date:2016-10-26
Release date:2017-02-22
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (2.1 Å)
Cite:The juxtamembrane region of TrkA kinase is critical for inhibitor selectivity
Bioorg. Med. Chem. Lett., 27, 2017
3A7E
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BU of 3a7e by Molmil
Crystal structure of human COMT complexed with SAM and 3,5-dinitrocatechol
Descriptor: 3,5-DINITROCATECHOL, Catechol O-methyltransferase, MAGNESIUM ION, ...
Authors:Tsuji, E.
Deposit date:2009-09-26
Release date:2010-09-15
Last modified:2023-11-01
Method:X-RAY DIFFRACTION (2.8 Å)
Cite:Hit to Lead: Comprehensive Strategy of de novo Scaffold Generation by FBDD. Part 1: In silico Fragments Linking and Verification of Spatial Proximity using Inter Ligand NOE Approachs
To be Published
7XVY
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BU of 7xvy by Molmil
Human Estrogen Receptor beta Ligand-binding Domain in Complex with S-DPN
Descriptor: (2~{S})-2,3-bis(4-hydroxyphenyl)propanenitrile, Estrogen receptor beta, Nuclear receptor coactivator 1
Authors:Furuya, N, Handa, C.
Deposit date:2022-05-25
Release date:2022-07-20
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (1.544 Å)
Cite:Evaluating the correlation of binding affinities between isothermal titration calorimetry and fragment molecular orbital method of estrogen receptor beta with diarylpropionitrile (DPN) or DPN derivatives.
J.Steroid Biochem.Mol.Biol., 222, 2022
7XWR
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BU of 7xwr by Molmil
Human Estrogen Receptor beta Ligand-binding Domain in Complex with (S)-2-(2-chloro-4-hydroxyphenyl)-3-(4-hydroxyphenyl)propanenitrile
Descriptor: (2~{S})-2-(2-chloranyl-4-oxidanyl-phenyl)-3-(4-hydroxyphenyl)propanenitrile, Estrogen receptor beta, SRC peptide
Authors:Furuya, N, Handa, C.
Deposit date:2022-05-27
Release date:2022-07-20
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.164 Å)
Cite:Evaluating the correlation of binding affinities between isothermal titration calorimetry and fragment molecular orbital method of estrogen receptor beta with diarylpropionitrile (DPN) or DPN derivatives.
J.Steroid Biochem.Mol.Biol., 222, 2022
7XWQ
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BU of 7xwq by Molmil
Human Estrogen Receptor beta Ligand-binding Domain in Complex with (R)-2-(2-chloro-4-hydroxyphenyl)-3-(4-hydroxyphenyl)propanenitrile
Descriptor: (2~{R})-2-(2-chloranyl-4-oxidanyl-phenyl)-3-(4-hydroxyphenyl)propanenitrile, Estrogen receptor beta, SRC peptide
Authors:Furuya, N, Handa, C.
Deposit date:2022-05-27
Release date:2022-07-20
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (1.89 Å)
Cite:Evaluating the correlation of binding affinities between isothermal titration calorimetry and fragment molecular orbital method of estrogen receptor beta with diarylpropionitrile (DPN) or DPN derivatives.
J.Steroid Biochem.Mol.Biol., 222, 2022
7XWP
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BU of 7xwp by Molmil
Human Estrogen Receptor beta Ligand-binding Domain in Complex with (S)-3-(2-chloro-4-hydroxyphenyl)-2-(4-hydroxyphenyl)propanenitrile
Descriptor: (2~{S})-3-(2-chloranyl-4-oxidanyl-phenyl)-2-(4-hydroxyphenyl)propanenitrile, Estrogen receptor beta, SRC peptide
Authors:Furuya, N, Handa, C.
Deposit date:2022-05-27
Release date:2022-07-20
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (1.919 Å)
Cite:Evaluating the correlation of binding affinities between isothermal titration calorimetry and fragment molecular orbital method of estrogen receptor beta with diarylpropionitrile (DPN) or DPN derivatives.
J.Steroid Biochem.Mol.Biol., 222, 2022
7XVZ
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BU of 7xvz by Molmil
Human Estrogen Receptor beta Ligand-binding Domain in Complex with (R)-3-(2-chloro-4-hydroxyphenyl)-2-(4-hydroxyphenyl)propanenitrile
Descriptor: (2~{R})-3-(2-chloranyl-4-oxidanyl-phenyl)-2-(4-hydroxyphenyl)propanenitrile, Estrogen receptor beta, SRC peptide
Authors:Furuya, N, Handa, C.
Deposit date:2022-05-25
Release date:2022-07-20
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.08 Å)
Cite:Evaluating the correlation of binding affinities between isothermal titration calorimetry and fragment molecular orbital method of estrogen receptor beta with diarylpropionitrile (DPN) or DPN derivatives.
J.Steroid Biochem.Mol.Biol., 222, 2022
3ACJ
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BU of 3acj by Molmil
Crystal structure of imidazo pyrimidine derivative bound to the kinase domain of human LCK, (Auto-phosphorylated on TYR394)
Descriptor: 7-(3,4-dimethoxyphenyl)-5-(ethylsulfanyl)imidazo[1,2-c]pyrimidine, DIMETHYL SULFOXIDE, Proto-oncogene tyrosine-protein kinase LCK, ...
Authors:Tsuji, E.
Deposit date:2010-01-05
Release date:2010-06-30
Last modified:2023-11-15
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:Ab initio fragment molecular orbital study of ligand binding to leukocyte-specific protein tyrosine (LCK) kinase
To be Published
3ACK
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BU of 3ack by Molmil
Crystal structure of Pyrrolo pyrazine derivative bound to the kinase domain of human LCK, (auto-phosphorylated on TYR394)
Descriptor: 6-(5-methoxy-1-methyl-1H-indol-3-yl)-5H-pyrrolo[2,3-b]pyrazine, DIMETHYL SULFOXIDE, Proto-oncogene tyrosine-protein kinase LCK, ...
Authors:Tsuji, E.
Deposit date:2010-01-05
Release date:2010-06-30
Last modified:2023-11-15
Method:X-RAY DIFFRACTION (2.6 Å)
Cite:Ab initio fragment molecular orbital study of ligand binding to leukocyte-specific protein tyrosine (LCK) kinase
To be Published
3AD4
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BU of 3ad4 by Molmil
Crystal Structure of Methoxy Benzofuran Derivative bound to the Kinase domain of human LCK, (auto-phosphorylated on TYR394)
Descriptor: (4-chlorophenyl)(5-methoxy-1-benzofuran-2-yl)methanone, (4S)-2-METHYL-2,4-PENTANEDIOL, DIMETHYL SULFOXIDE, ...
Authors:Tsuji, E.
Deposit date:2010-01-14
Release date:2011-01-19
Last modified:2023-11-15
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:Ab initio fragment molecular orbital study of ligand binding to leukocyte-specific protein tyrosine (LCK) kinase
To be Published
3AD5
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BU of 3ad5 by Molmil
Crystal structure of Triazolone derivative bound to the kinase domain of human LCK, (auto-phosphorylated on TYR394)
Descriptor: (4S)-2-METHYL-2,4-PENTANEDIOL, 4-[4-(benzyloxy)phenyl]-5-{[2-(4-chlorophenyl)-2-oxoethyl]sulfanyl}-2,4-dihydro-3H-1,2,4-triazol-3-one, DIMETHYL SULFOXIDE, ...
Authors:Tsuji, E.
Deposit date:2010-01-14
Release date:2011-01-19
Last modified:2023-11-15
Method:X-RAY DIFFRACTION (2 Å)
Cite:Ab initio fragment molecular orbital study of ligand binding to leukocyte-specific protein tyrosine (LCK) kinase
To be Published
3AC1
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BU of 3ac1 by Molmil
Crystal structure of pyrazin derivative bound to the kinase domain of Human LCK, (Auto-phosphorylated on TYR394)
Descriptor: (4S)-2-METHYL-2,4-PENTANEDIOL, 5-{[(1R,2S)-2-aminocyclohexyl]amino}-3-[(3,5-dimethoxyphenyl)amino]pyrazine-2-carboxamide, DIMETHYL SULFOXIDE, ...
Authors:Tsuji, E.
Deposit date:2009-12-28
Release date:2010-06-30
Last modified:2023-11-15
Method:X-RAY DIFFRACTION (1.99 Å)
Cite:Ab initio fragment molecular orbital study of ligand binding to leukocyte-specific protein tyrosine (LCK) kinase
To be Published

 

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