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3AJI
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BU of 3aji by Molmil
Structure of Gankyrin-S6ATPase photo-cross-linked site-specifically, and incoporated by genetic code expansion
Descriptor: 26S proteasome non-ATPase regulatory subunit 10, Proteasome (Prosome, macropain) 26S subunit, ...
Authors:Sato, S, Mimasu, S, Sato, A, Hino, N, Sakamoto, K, Umehara, T, Yokoyama, S, RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Deposit date:2010-06-07
Release date:2010-12-22
Last modified:2023-11-15
Method:X-RAY DIFFRACTION (2.05 Å)
Cite:Crystallographic study of a site-specifically cross-linked protein complex with a genetically incorporated photoreactive amino acid
Biochemistry, 50, 2011
7D69
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BU of 7d69 by Molmil
Cryo-EM structure of the nucleosome containing Giardia histones
Descriptor: 601L DNA (145-MER), Histone H2A, Histone H2B, ...
Authors:Sato, S, Takizawa, Y, Kurumizaka, H.
Deposit date:2020-09-29
Release date:2021-09-08
Last modified:2022-03-23
Method:ELECTRON MICROSCOPY (3.57 Å)
Cite:Cryo-EM structure of the nucleosome core particle containing Giardia lamblia histones.
Nucleic Acids Res., 49, 2021
1SS1
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BU of 1ss1 by Molmil
STAPHYLOCOCCAL PROTEIN A, B-DOMAIN, Y15W MUTANT, NMR, 25 STRUCTURES
Descriptor: Immunoglobulin G binding protein A
Authors:Sato, S, Religa, T.L, Daggett, V, Fersht, A.R.
Deposit date:2004-03-23
Release date:2004-04-06
Last modified:2021-10-27
Method:SOLUTION NMR
Cite:From The Cover: Testing protein-folding simulations by experiment: B domain of protein A.
Proc.Natl.Acad.Sci.USA, 101, 2004
3AMF
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BU of 3amf by Molmil
E13R mutant of FMN-binding protein from Desulfovibrio vulgaris (Miyazaki F)
Descriptor: CHLORIDE ION, FLAVIN MONONUCLEOTIDE, FMN-binding protein
Authors:Sato, S, Nakanishi, T, Inoue, H, Kitamura, M.
Deposit date:2010-08-19
Release date:2011-10-05
Last modified:2023-11-01
Method:X-RAY DIFFRACTION (1.6 Å)
Cite:Crystal structure of E13R mutant of FMN-binding protein from Desulfovibrio vulgaris (Miyazaki F)
To be Published
3AWH
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BU of 3awh by Molmil
E13K mutant of FMN-binding protein from Desulfovibrio vulgaris (Miyazaki F)
Descriptor: CHLORIDE ION, FLAVIN MONONUCLEOTIDE, FMN-binding protein
Authors:Sato, S, Nakanishi, T, Inoue, H, Kitamura, M.
Deposit date:2011-03-22
Release date:2012-04-18
Last modified:2023-11-01
Method:X-RAY DIFFRACTION (1.6 Å)
Cite:Crystal structure of E13K mutant of FMN-binding protein from Desulfovibrio vulgaris (Miyazaki F)
To be Published
5ZDM
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BU of 5zdm by Molmil
The ligand-free structure of FomD
Descriptor: CALCIUM ION, FomD, GLYCEROL
Authors:Sato, S, Miyanaga, A, Kudo, F, Eguchi, T.
Deposit date:2018-02-23
Release date:2018-07-25
Last modified:2023-11-22
Method:X-RAY DIFFRACTION (1.38 Å)
Cite:Biochemical and Structural Analysis of FomD That Catalyzes the Hydrolysis of Cytidylyl ( S)-2-Hydroxypropylphosphonate in Fosfomycin Biosynthesis.
Biochemistry, 57, 2018
5ZDN
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BU of 5zdn by Molmil
The complex structure of FomD with CDP
Descriptor: CYTIDINE-5'-DIPHOSPHATE, FomD, GLYCEROL, ...
Authors:Sato, S, Miyanaga, A, Kudo, F, Eguchi, T.
Deposit date:2018-02-23
Release date:2018-07-25
Last modified:2023-11-22
Method:X-RAY DIFFRACTION (2.02 Å)
Cite:Biochemical and Structural Analysis of FomD That Catalyzes the Hydrolysis of Cytidylyl ( S)-2-Hydroxypropylphosphonate in Fosfomycin Biosynthesis.
Biochemistry, 57, 2018
5H6R
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BU of 5h6r by Molmil
Crystal structure of LSD1-CoREST in complex with peptide 13
Descriptor: FLAVIN-ADENINE DINUCLEOTIDE, GLYCEROL, Lysine-specific histone demethylase 1A, ...
Authors:Kkuchi, M, Amano, Y, Sato, S, Yokoyama, S, Umezawa, N, Higuchi, T, Umehara, T.
Deposit date:2016-11-14
Release date:2017-04-12
Last modified:2023-11-15
Method:X-RAY DIFFRACTION (2.6 Å)
Cite:Development and crystallographic evaluation of histone H3 peptide with N-terminal serine substitution as a potent inhibitor of lysine-specific demethylase 1.
Bioorg. Med. Chem., 25, 2017
5H6Q
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BU of 5h6q by Molmil
Crystal structure of LSD1-CoREST in complex with peptide 11
Descriptor: FLAVIN-ADENINE DINUCLEOTIDE, GLYCEROL, Lysine-specific histone demethylase 1A, ...
Authors:Kikuchi, M, Amano, Y, Sato, S, Yokoyama, S, Umezawa, N, Higuchi, T, Umehara, T.
Deposit date:2016-11-14
Release date:2017-04-12
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (2.53 Å)
Cite:Development and crystallographic evaluation of histone H3 peptide with N-terminal serine substitution as a potent inhibitor of lysine-specific demethylase 1.
Bioorg. Med. Chem., 25, 2017
7XUB
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BU of 7xub by Molmil
Structure of G9a in complex with compound 10d
Descriptor: 1,2-ETHANEDIOL, 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, Histone-lysine N-methyltransferase EHMT2, ...
Authors:Niwa, H, Shirai, F, Sato, S, Nishigaya, Y, Umehara, T.
Deposit date:2022-05-18
Release date:2023-03-29
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2 Å)
Cite:Discovery of Novel Substrate-Competitive Lysine Methyltransferase G9a Inhibitors as Anticancer Agents.
J.Med.Chem., 66, 2023
7XUD
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BU of 7xud by Molmil
Structure of G9a in complex with compound 26a
Descriptor: 1,2-ETHANEDIOL, 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, CHLORIDE ION, ...
Authors:Niwa, H, Shirai, F, Sato, S, Nishigaya, Y, Umehara, T.
Deposit date:2022-05-18
Release date:2023-03-29
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (1.45 Å)
Cite:Discovery of Novel Substrate-Competitive Lysine Methyltransferase G9a Inhibitors as Anticancer Agents.
J.Med.Chem., 66, 2023
7XUC
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BU of 7xuc by Molmil
Structure of G9a in complex with compound 11a
Descriptor: 1,2-ETHANEDIOL, 3,6,6-trimethyl-4-oxidanylidene-~{N}-[(2~{S})-1-oxidanylidene-1-phenylazanyl-hexan-2-yl]-5,7-dihydro-1~{H}-indole-2-carboxamide, CHLORIDE ION, ...
Authors:Niwa, H, Shirai, F, Sato, S, Nishigaya, Y, Umehara, T.
Deposit date:2022-05-18
Release date:2023-03-29
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (1.67 Å)
Cite:Discovery of Novel Substrate-Competitive Lysine Methyltransferase G9a Inhibitors as Anticancer Agents.
J.Med.Chem., 66, 2023
7XUA
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BU of 7xua by Molmil
Structure of G9a in complex with compound 10a
Descriptor: 1,2-ETHANEDIOL, 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, Histone-lysine N-methyltransferase EHMT2, ...
Authors:Niwa, H, Shirai, F, Sato, S, Nishigaya, Y, Umehara, T.
Deposit date:2022-05-18
Release date:2023-03-29
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (1.87 Å)
Cite:Discovery of Novel Substrate-Competitive Lysine Methyltransferase G9a Inhibitors as Anticancer Agents.
J.Med.Chem., 66, 2023
5CPG
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BU of 5cpg by Molmil
R-Hydratase PhaJ1 from Pseudomonas aeruginosa in the unliganded form
Descriptor: (R)-specific enoyl-CoA hydratase, GLYCEROL
Authors:Tsuge, T, Sato, S, Hiroe, A, Ishizuka, K, Kanazawa, H, Kanagarajan, S, Shiro, Y, Hisano, T.
Deposit date:2015-07-21
Release date:2015-10-07
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (1.694 Å)
Cite:Contribution of the Distal Pocket Residue to the Acyl-Chain-Length Specificity of (R)-Specific Enoyl-Coenzyme A Hydratases from Pseudomonas spp.
Appl.Environ.Microbiol., 81, 2015
7VQT
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BU of 7vqt by Molmil
Crystal structure of LSD1 in complex with compound 5
Descriptor: 3-[3,5-bis(fluoranyl)-2-[(2-fluoranylpyridin-4-yl)methoxy]phenyl]propanal, FLAVIN-ADENINE DINUCLEOTIDE, GLYCEROL, ...
Authors:Niwa, H, Koda, Y, Sato, S, Yamamoto, H, Koyama, H, Umehara, T.
Deposit date:2021-10-20
Release date:2022-06-01
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.91 Å)
Cite:Design and Synthesis of Tranylcypromine-Derived LSD1 Inhibitors with Improved hERG and Microsomal Stability Profiles.
Acs Med.Chem.Lett., 13, 2022
7VQS
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BU of 7vqs by Molmil
Crystal structure of LSD1 in complex with compound 4
Descriptor: 3-[3,5-bis(fluoranyl)-2-[(2-fluoranylpyridin-3-yl)methoxy]phenyl]propanal, FLAVIN-ADENINE DINUCLEOTIDE, GLYCEROL, ...
Authors:Niwa, H, Koda, Y, Sato, S, Yamamoto, H, Koyama, H, Umehara, T.
Deposit date:2021-10-20
Release date:2022-06-01
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.94 Å)
Cite:Design and Synthesis of Tranylcypromine-Derived LSD1 Inhibitors with Improved hERG and Microsomal Stability Profiles.
Acs Med.Chem.Lett., 13, 2022
7VQU
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BU of 7vqu by Molmil
Crystal structure of LSD1 in complex with compound S1427
Descriptor: 3-[3,5-bis(fluoranyl)-2-[(2-fluoranylpyridin-3-yl)methoxy]phenyl]propanal, FLAVIN-ADENINE DINUCLEOTIDE, GLYCEROL, ...
Authors:Niwa, H, Koda, Y, Sato, S, Yamamoto, H, Koyama, H, Umehara, T.
Deposit date:2021-10-20
Release date:2022-06-01
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.94 Å)
Cite:Design and Synthesis of Tranylcypromine-Derived LSD1 Inhibitors with Improved hERG and Microsomal Stability Profiles.
Acs Med.Chem.Lett., 13, 2022
7YF6
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BU of 7yf6 by Molmil
Crystal structure of HIV-1 protease in complex with macrocyclic peptide
Descriptor: MAGNESIUM ION, Macrocyclic Peptide, Protease
Authors:Kusumoto, Y, Sato, S, Yamada, T, Kozono, I, Nakata, Z, Asada, N, Mitsuki, S, Wakasa-Morimoto, C, Tohru, M, Watanabe, A, Hayashi, K, Mikamiyama, H.
Deposit date:2022-07-07
Release date:2022-11-02
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.01 Å)
Cite:Highly Potent and Oral Macrocyclic Peptides as a HIV-1 Protease Inhibitor: mRNA Display-Derived Hit-to-Lead Optimization.
Acs Med.Chem.Lett., 13, 2022
7X73
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BU of 7x73 by Molmil
Structure of G9a in complex with RK-701
Descriptor: 1,2-ETHANEDIOL, 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, Histone-lysine N-methyltransferase EHMT2, ...
Authors:Niwa, H, Shirai, F, Sato, S, Nishigaya, Y, Shirouzu, M, Umehara, T.
Deposit date:2022-03-09
Release date:2022-12-21
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (1.49 Å)
Cite:A specific G9a inhibitor unveils BGLT3 lncRNA as a universal mediator of chemically induced fetal globin gene expression.
Nat Commun, 14, 2023
1X3K
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BU of 1x3k by Molmil
Crystal structure of a hemoglobin component (TA-V) from Tokunagayusurika akamusi
Descriptor: PROTOPORPHYRIN IX CONTAINING FE, hemoglobin component V
Authors:Kuwada, T, Hasegawa, T, Sato, S, Sato, I, Ishikawa, K, Takagi, T, Shishikura, F.
Deposit date:2005-05-09
Release date:2005-05-24
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (1.64 Å)
Cite:Crystal structures of two hemoglobin components from the midge larva Propsilocerus akamusi (Orthocladiinae, Diptera).
Gene, 398, 2007
1X46
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BU of 1x46 by Molmil
Crystal structure of a hemoglobin component (TA-VII) from Tokunagayusurika akamusi
Descriptor: PROTOPORPHYRIN IX CONTAINING FE, hemoglobin component VII
Authors:Kuwada, T, Hasegawa, T, Sato, S, Sato, I, Ishikawa, K, Takagi, T, Shishikura, F.
Deposit date:2005-05-14
Release date:2005-05-24
Last modified:2024-03-13
Method:X-RAY DIFFRACTION (1.5 Å)
Cite:Crystal structures of two hemoglobin components from the midge larva Propsilocerus akamusi (Orthocladiinae, Diptera).
Gene, 398, 2007
6KGK
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BU of 6kgk by Molmil
LSD1-CoREST-S2101 five-membered ring adduct model
Descriptor: 3-[3,5-bis(fluoranyl)-2-phenylmethoxy-phenyl]propanal, FLAVIN-ADENINE DINUCLEOTIDE, GLYCEROL, ...
Authors:Niwa, H, Sato, S, Sengoku, S, Umehara, T, Yokoyama, S.
Deposit date:2019-07-12
Release date:2020-03-25
Last modified:2024-03-27
Method:X-RAY DIFFRACTION (2.7 Å)
Cite:Development and Structural Evaluation of N-Alkylated trans-2-Phenylcyclopropylamine-Based LSD1 Inhibitors.
Chemmedchem, 15, 2020
6KGL
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BU of 6kgl by Molmil
LSD1-CoREST-S2101 N5 adduct model
Descriptor: 3-[3,5-bis(fluoranyl)-2-phenylmethoxy-phenyl]propanal, FLAVIN-ADENINE DINUCLEOTIDE, GLYCEROL, ...
Authors:Niwa, H, Sato, S, Sengoku, S, Umehara, T, Yokoyama, S.
Deposit date:2019-07-12
Release date:2020-03-25
Last modified:2024-03-27
Method:X-RAY DIFFRACTION (2.7 Å)
Cite:Development and Structural Evaluation of N-Alkylated trans-2-Phenylcyclopropylamine-Based LSD1 Inhibitors.
Chemmedchem, 15, 2020
7W3L
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BU of 7w3l by Molmil
Crystal structure of LSD1 in complex with cis-4-Br-2,5-F2-PCPA (S1024)
Descriptor: 3-[4-bromanyl-2,5-bis(fluoranyl)phenyl]propanal, FLAVIN-ADENINE DINUCLEOTIDE, GLYCEROL, ...
Authors:Niwa, H, Sato, S, Umehara, T.
Deposit date:2021-11-25
Release date:2022-09-14
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.51 Å)
Cite:Structure-Activity Relationship and In Silico Evaluation of cis- and trans-PCPA-Derived Inhibitors of LSD1 and LSD2
Acs Med.Chem.Lett., 13, 2022
7XE1
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BU of 7xe1 by Molmil
Crystal structure of LSD2 in complex with cis-4-Br-PCPA
Descriptor: 3-(4-bromophenyl)propanal, CITRATE ANION, DI(HYDROXYETHYL)ETHER, ...
Authors:Niwa, H, Sato, S, Umehara, T.
Deposit date:2022-03-29
Release date:2022-09-14
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.07 Å)
Cite:Structure-Activity Relationship and In Silico Evaluation of cis- and trans-PCPA-Derived Inhibitors of LSD1 and LSD2
Acs Med.Chem.Lett., 13, 2022

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