Loading
PDBj
MenuPDBj@FacebookPDBj@TwitterPDBj@YouTubewwPDB FoundationwwPDB
RCSB PDBPDBeBMRBAdv. SearchSearch help
Search by PDB author
4IJ6
DownloadVisualize
BU of 4ij6 by Molmil
Crystal Structure of a Novel-type Phosphoserine Phosphatase Mutant (H9A) from Hydrogenobacter thermophilus TK-6 in Complex with L-phosphoserine
Descriptor: 1,2-ETHANEDIOL, CHLORIDE ION, PHOSPHOSERINE, ...
Authors:Chiba, Y, Horita, S, Ohtsuka, J, Arai, H, Nagata, K, Igarashi, Y, Tanokura, M, Ishii, M.
Deposit date:2012-12-21
Release date:2013-03-20
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Structural units important for activity of a novel-type phosphoserine phosphatase from Hydrogenobacter thermophilus TK-6 revealed by crystal structure analysis
J.Biol.Chem., 288, 2013
4IJ5
DownloadVisualize
BU of 4ij5 by Molmil
Crystal Structure of a Novel-type Phosphoserine Phosphatase from Hydrogenobacter thermophilus TK-6
Descriptor: 1,2-ETHANEDIOL, CHLORIDE ION, Phosphoserine phosphatase 1
Authors:Chiba, Y, Horita, S, Ohtsuka, J, Arai, H, Nagata, K, Igarashi, Y, Tanokura, M, Ishii, M.
Deposit date:2012-12-21
Release date:2013-03-20
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (1.5 Å)
Cite:Structural units important for activity of a novel-type phosphoserine phosphatase from Hydrogenobacter thermophilus TK-6 revealed by crystal structure analysis
J.Biol.Chem., 288, 2013
6K31
DownloadVisualize
BU of 6k31 by Molmil
Crystal structure of pyrophosphate-dependent phosphoenolpyruvate carboxykinase (PPi-PEPCK)
Descriptor: AiPEPCK, COBALT (II) ION
Authors:Chiba, Y, Miyakawa, T, Tanokura, M.
Deposit date:2019-05-15
Release date:2019-11-06
Last modified:2020-01-01
Method:X-RAY DIFFRACTION (2.6 Å)
Cite:Structural comparisons of phosphoenolpyruvate carboxykinases reveal the evolutionary trajectories of these phosphodiester energy conversion enzymes.
J.Biol.Chem., 294, 2019
3VQU
DownloadVisualize
BU of 3vqu by Molmil
CRYSTAL STRUCTURE OF HUMAN MPS1 CATALYTIC DOMAIN IN COMPLEX WITH 4-[(4-amino-5-cyano-6-ethoxypyridin-2- yl)amino]benzamide
Descriptor: 4-[(4-amino-5-cyano-6-ethoxypyridin-2-yl)amino]benzamide, Dual specificity protein kinase TTK, IODIDE ION
Authors:Kusakabe, K, Ide, N, Daigo, Y, Itoh, T, Higashino, K, Okano, Y, Tadano, G, Tachibana, Y, Sato, Y, Inoue, M, Wada, T, Iguchi, M, Kanazawa, T, Ishioka, Y, Dohi, K, Tagashira, S, Kido, Y, Sakamoto, S, Yasuo, K, Maeda, M, Yamamoto, T, Higaki, M, Endoh, T, Ueda, K, Shiota, T, Murai, H, Nakamura, Y.
Deposit date:2012-03-30
Release date:2012-06-27
Last modified:2024-03-20
Method:X-RAY DIFFRACTION (2.4 Å)
Cite:Diaminopyridine-based potent and selective mps1 kinase inhibitors binding to an unusual flipped-Peptide conformation.
Acs Med.Chem.Lett., 3, 2012
3W1F
DownloadVisualize
BU of 3w1f by Molmil
Crystal structure of Human MPS1 catalytic domain in complex with 5-(5-ethoxy-6-(1-methyl-1H-pyrazol-4-yl)-1H-indazol-3-yl)-2-methylbenzenesulfonamide
Descriptor: 5-[5-ethoxy-6-(1-methyl-1H-pyrazol-4-yl)-1H-indazol-3-yl]-2-methylbenzenesulfonamide, Dual specificity protein kinase TTK
Authors:Kusakabe, K, Ide, N, Daigo, Y, Tachibana, Y, Itoh, T, Yamamoto, T, Hashizume, H, Hato, Y, Higashino, K, Okano, Y, Sato, Y, Inoue, M, Iguchi, M, Kanazawa, T, Ishioka, Y, Dohi, K, Kido, Y, Sakamoto, S, Yasuo, K, Maeda, M, Higaki, M, Ueda, K, Yoshizawa, H, Baba, Y, Shiota, T, Murai, H, Nakamura, Y.
Deposit date:2012-11-14
Release date:2013-06-26
Last modified:2024-03-20
Method:X-RAY DIFFRACTION (2.7 Å)
Cite:Indazole-based potent and cell-active Mps1 kinase inhibitors: rational design from pan-kinase inhibitor anthrapyrazolone (SP600125)
J.Med.Chem., 56, 2013
8J3S
DownloadVisualize
BU of 8j3s by Molmil
Complex structure of human cytomegalovirus protease and a macrocyclic peptide ligand
Descriptor: Assemblin, PHE-ILE-THR-GLY-HIS-TYR-TRP-VAL-ARG-PHE-LEU-PRO-CYS-GLY
Authors:Yoshida, S, Sako, Y, Nikaido, E, Ueda, T, Kozono, I, Ichihashi, Y, Nakahashi, A, Onishi, M, Yamatsu, Y, Kato, T, Nishikawa, J, Tachibana, Y.
Deposit date:2023-04-18
Release date:2023-11-08
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (3.09 Å)
Cite:Peptide-to-Small Molecule: Discovery of Non-Covalent, Active-Site Inhibitors of beta-Herpesvirus Proteases.
Acs Med.Chem.Lett., 14, 2023
8J3T
DownloadVisualize
BU of 8j3t by Molmil
Complex structure of human cytomegalovirus protease and a non-covalent small-molecule ligand
Descriptor: (4R)-1-[1-[(S)-[1-cyclopentyl-3-(2-methylphenyl)pyrazol-4-yl]-(4-methylphenyl)methyl]-2-oxidanylidene-pyridin-3-yl]-3-methyl-2-oxidanylidene-N-(3-oxidanylidene-2-azabicyclo[2.2.2]octan-4-yl)imidazolidine-4-carboxamide, Assemblin
Authors:Yoshida, S, Sako, Y, Nikaido, E, Ueda, T, Kozono, I, Ichihashi, Y, Nakahashi, A, Onishi, M, Yamatsu, Y, Kato, T, Nishikawa, J, Tachibana, Y.
Deposit date:2023-04-18
Release date:2023-11-08
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.9 Å)
Cite:Peptide-to-Small Molecule: Discovery of Non-Covalent, Active-Site Inhibitors of beta-Herpesvirus Proteases.
Acs Med.Chem.Lett., 14, 2023
7VU6
DownloadVisualize
BU of 7vu6 by Molmil
The crystal structure of SARS-CoV-2 3CL protease in complex with compound 3
Descriptor: 3C-like proteinase, 6-[(6-chloranyl-2-methyl-indazol-5-yl)amino]-3-[(1-methyl-1,2,4-triazol-3-yl)methyl]-1-[[2,4,5-tris(fluoranyl)phenyl]methyl]-1,3,5-triazine-2,4-dione
Authors:Yamamoto, S, Yamane, J, Tachibana, Y.
Deposit date:2021-11-01
Release date:2022-04-06
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (1.8 Å)
Cite:Discovery of S-217622, a Noncovalent Oral SARS-CoV-2 3CL Protease Inhibitor Clinical Candidate for Treating COVID-19.
J.Med.Chem., 65, 2022
7VTH
DownloadVisualize
BU of 7vth by Molmil
The crystal structure of SARS-CoV-2 3CL protease in complex with compound 1
Descriptor: 2-[4-[[4-[bis(fluoranyl)methoxy]-2-methyl-phenyl]amino]-2,6-bis(oxidanylidene)-3-[[3,4,5-tris(fluoranyl)phenyl]methyl]-1,3,5-triazin-1-yl]-N-methyl-ethanamide, 3C-like proteinase
Authors:Yamamoto, S, Tachibana, Y.
Deposit date:2021-10-29
Release date:2022-04-06
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2 Å)
Cite:Discovery of S-217622, a Noncovalent Oral SARS-CoV-2 3CL Protease Inhibitor Clinical Candidate for Treating COVID-19.
J.Med.Chem., 65, 2022
7WCQ
DownloadVisualize
BU of 7wcq by Molmil
Crystal structure of HIV-1 protease in complex with lactam derivative 1
Descriptor: (3R,4R)-3-[(4-fluorophenyl)methyl]-1-[(4-methoxyphenyl)methyl]-3-(4-methylsulfonylphenyl)-4-oxidanyl-pyrrolidin-2-one, Protease
Authors:Kojima, E, Iimuro, A, Nakajima, M, Kinuta, H, Asada, N, Sako, Y, Nakata, Z, Uemura, K, Arita, S, Miki, S, Wakasa-Morimoto, C, Tachibana, Y, Fumoto, M.
Deposit date:2021-12-20
Release date:2022-11-02
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.011 Å)
Cite:Pocket-to-Lead: Structure-Based De Novo Design of Novel Non-peptidic HIV-1 Protease Inhibitors Using the Ligand Binding Pocket as a Template.
J.Med.Chem., 65, 2022
7WBS
DownloadVisualize
BU of 7wbs by Molmil
Crystal structure of HIV-1 protease in complex with lactam derivative 2
Descriptor: (3~{R},4~{R})-1-[(4-methoxyphenyl)methyl]-3-(3-methylbutyl)-3-[4-methylsulfonyl-2-[(2~{S})-1-oxidanylpropan-2-yl]oxy-phenyl]-4-oxidanyl-pyrrolidin-2-one, GLYCEROL, Protease
Authors:Kojima, E, Iimuro, A, Nakajima, M, Kinuta, H, Asada, N, Sako, Y, Nakata, Z, Uemura, K, Arita, S, Miki, S, Wakabayashi-Morimoto, C, Tachibana, Y, Fumoto, M.
Deposit date:2021-12-17
Release date:2022-11-02
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (1.85 Å)
Cite:Pocket-to-Lead: Structure-Based De Novo Design of Novel Non-peptidic HIV-1 Protease Inhibitors Using the Ligand Binding Pocket as a Template.
J.Med.Chem., 65, 2022
7WMC
DownloadVisualize
BU of 7wmc by Molmil
Crystal structure of macrocyclic peptide 1 bound to human Nicotinamide N-methyltransferase
Descriptor: Nicotinamide N-methyltransferase, Peptide1
Authors:Yoshida, S, Uehara, S, Kondo, N, Takahashi, Y, Yamamoto, S, Kameda, A, Kawagoe, S, Inoue, N, Yamada, M, Yoshimura, N, Tachibana, Y.
Deposit date:2022-01-14
Release date:2022-08-31
Last modified:2023-11-15
Method:X-RAY DIFFRACTION (2.55 Å)
Cite:Peptide-to-Small Molecule: A Pharmacophore-Guided Small Molecule Lead Generation Strategy from High-Affinity Macrocyclic Peptides.
J.Med.Chem., 65, 2022
7WMT
DownloadVisualize
BU of 7wmt by Molmil
Crystal structure of small molecule 13 bound to human Nicotinamide N-methyltransferase
Descriptor: Nicotinamide N-methyltransferase, [(2~{R},4~{S})-4-[2-(aminomethyl)imidazol-1-yl]-2-[1-[(4-chlorophenyl)methyl]-5-methyl-indol-2-yl]pyrrolidin-1-yl]-(1~{H}-pyrrolo[2,3-b]pyridin-5-yl)methanone
Authors:Yoshida, S, Uehara, S, Kondo, N, Takahashi, Y, Yamamoto, S, Kameda, A, Kawagoe, S, Inoue, N, Yamada, M, Yoshimura, N, Tachibana, Y.
Deposit date:2022-01-17
Release date:2022-08-31
Last modified:2024-05-29
Method:X-RAY DIFFRACTION (1.77 Å)
Cite:Peptide-to-Small Molecule: A Pharmacophore-Guided Small Molecule Lead Generation Strategy from High-Affinity Macrocyclic Peptides.
J.Med.Chem., 65, 2022
6IIW
DownloadVisualize
BU of 6iiw by Molmil
Crystal structure of human UHRF1 PHD finger in complex with PAF15
Descriptor: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, E3 ubiquitin-protein ligase UHRF1, PCNA-associated factor, ...
Authors:Arita, K, Kori, S.
Deposit date:2018-10-07
Release date:2019-10-09
Last modified:2023-11-22
Method:X-RAY DIFFRACTION (1.699 Å)
Cite:Two distinct modes of DNMT1 recruitment ensure stable maintenance DNA methylation.
Nat Commun, 11, 2020
6LUB
DownloadVisualize
BU of 6lub by Molmil
Crystal Structure of EGFR(L858R/T790M/C797S) in complex with CH7233163
Descriptor: Epidermal growth factor receptor, N-[2-(1-cyclopropylsulfonylpyrazol-4-yl)pyrimidin-4-yl]-7-(4-methylpiperazin-1-yl)-5-propan-2-yl-9-[2,2,2-tris(fluoranyl)ethoxy]pyrido[4,3-b]indol-3-amine
Authors:Kawauchi, H, Fukami, T.A, Sato, S, Endo, M, Torizawa, T, Kashima, K, Chiba, T, Sakamoto, H.
Deposit date:2020-01-27
Release date:2020-10-07
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.315 Å)
Cite:CH7233163 Overcomes Osimertinib-Resistant EGFR-Del19/T790M/C797S Mutation.
Mol.Cancer Ther., 19, 2020
6LUD
DownloadVisualize
BU of 6lud by Molmil
Crystal Structure of EGFR(L858R/T790M/C797S) in complex with Osimertinib
Descriptor: Epidermal growth factor receptor, N-(2-{[2-(dimethylamino)ethyl](methyl)amino}-4-methoxy-5-{[4-(1-methyl-1H-indol-3-yl)pyrimidin-2-yl]amino}phenyl)prop-2-enamide
Authors:Kawauchi, H, Fukami, T.A, Sato, S, Endo, M, Torizawa, T, Kashima, K, Chiba, T, Sakamoto, H.
Deposit date:2020-01-27
Release date:2020-10-07
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.05 Å)
Cite:CH7233163 Overcomes Osimertinib-Resistant EGFR-Del19/T790M/C797S Mutation.
Mol.Cancer Ther., 19, 2020
2RQQ
DownloadVisualize
BU of 2rqq by Molmil
Structure of C-terminal region of Cdt1
Descriptor: DNA replication factor Cdt1
Authors:Jee, J.G, Mizuno, T, Kamada, K, Tochio, H, Hiroaki, H, Hanaoka, F, Shirakawa, M.
Deposit date:2009-10-14
Release date:2010-03-23
Last modified:2024-05-29
Method:SOLUTION NMR
Cite:Structure and mutagenesis studies of the C-terminal region of licensing factor Cdt1 enable the identification of key residues for binding to replicative helicase Mcm proteins
J.Biol.Chem., 285, 2010
7XI9
DownloadVisualize
BU of 7xi9 by Molmil
Cryo-EM structure of human DNMT1 (aa:351-1616) in complex with ubiquitinated H3 and hemimethylated DNA analog (CXXC-ordered form)
Descriptor: DNA (5'-D(*AP*CP*TP*TP*AP*(5CM)P*GP*GP*AP*AP*GP*G)-3'), DNA (5'-D(*CP*CP*TP*TP*CP*(C55)P*GP*TP*AP*AP*GP*T)-3'), DNA (cytosine-5)-methyltransferase 1, ...
Authors:Onoda, H, Kikuchi, A, Kori, S, Yoshimi, S, Yamagata, A, Arita, K.
Deposit date:2022-04-12
Release date:2022-11-30
Last modified:2024-07-03
Method:ELECTRON MICROSCOPY (2.52 Å)
Cite:Structural basis for activation of DNMT1.
Nat Commun, 13, 2022
7XIB
DownloadVisualize
BU of 7xib by Molmil
Cryo-EM structure of human DNMT1 (aa:351-1616) in complex with ubiquitinated H3 and hemimethylated DNA analog (CXXC-disordered form)
Descriptor: DNA (5'-D(*AP*CP*TP*TP*AP*(5CM)P*GP*GP*AP*AP*GP*G)-3'), DNA (5'-D(*CP*CP*TP*TP*CP*(C55)P*GP*TP*AP*AP*GP*T)-3'), DNA (cytosine-5)-methyltransferase 1, ...
Authors:Onoda, H, Kikuchi, A, Kori, S, Yoshimi, S, Yamagata, A, Arita, K.
Deposit date:2022-04-12
Release date:2022-11-30
Last modified:2024-07-03
Method:ELECTRON MICROSCOPY (2.23 Å)
Cite:Structural basis for activation of DNMT1.
Nat Commun, 13, 2022
7XGA
DownloadVisualize
BU of 7xga by Molmil
NMR strucutre of chimeric protein for model of PHD-Stella complex
Descriptor: Chimera of E3 ubiquitin-protein ligase UHRF1 and Developmental pluripotency-associated protein 3, ZINC ION
Authors:Kobayashi, N, Konuma, T, Arita, K.
Deposit date:2022-04-04
Release date:2022-12-07
Last modified:2024-05-15
Method:SOLUTION NMR
Cite:Structural basis for the unique multifaceted interaction of DPPA3 with the UHRF1 PHD finger.
Nucleic Acids Res., 50, 2022
5WR7
DownloadVisualize
BU of 5wr7 by Molmil
Crystal structure of Trk-A complexed with a selective inhibitor CH7057288
Descriptor: High affinity nerve growth factor receptor, N-tert-butyl-2-[2-[6,6-dimethyl-8-(methylsulfonylamino)-11-oxidanylidene-naphtho[2,3-b][1]benzofuran-3-yl]ethynyl]-6-methyl-pyridine-4-carboxamide
Authors:Tanaka, H, Blaesse, M, Augustin, M, Goesser, C.
Deposit date:2016-11-30
Release date:2017-12-06
Last modified:2018-12-19
Method:X-RAY DIFFRACTION (2.76 Å)
Cite:Selective TRK Inhibitor CH7057288 against TRK Fusion-Driven Cancer.
Mol. Cancer Ther., 17, 2018

225158

PDB entries from 2024-09-18

PDB statisticsPDBj update infoContact PDBjnumon