2Y5B
 
 | | Structure of USP21 in complex with linear diubiquitin-aldehyde | | Descriptor: | SULFATE ION, UBIQUITIN, UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 21, ... | | Authors: | Ye, Y, Akutsu, M, Reyes-Turcu, F, Enchev, R.I, Wilkinson, K.D, Komander, D. | | Deposit date: | 2011-01-12 | | Release date: | 2012-01-25 | | Last modified: | 2023-12-20 | | Method: | X-RAY DIFFRACTION (2.7 Å) | | Cite: | Polyubiquitin Binding and Cross-Reactivity in the Usp Domain Deubiquitinase Usp21.
Embo Rep., 12, 2011
|
|
6U9I
 | | Crystal structure of BvnE pinacolase from Penicillium brevicompactum | | Descriptor: | BvnE, DI(HYDROXYETHYL)ETHER, GLYCEROL | | Authors: | Ye, Y, Du, L, Zhang, X, Newmister, S.A, McCauley, M, Alegre-Requena, J.V, Zhang, W, Mu, S, Minami, A, Fraley, A.E, Adrover-Castellano, M.L, Carney, N, Shende, V.V, Oikawa, H, Kato, H, Tsukamoto, S, Paton, R.S, Williams, R.M, Sherman, D.H, Li, S. | | Deposit date: | 2019-09-09 | | Release date: | 2020-09-09 | | Last modified: | 2023-10-11 | | Method: | X-RAY DIFFRACTION (1.777 Å) | | Cite: | Fungal-derived brevianamide assembly by a stereoselective semipinacolase.
Nat Catal, 3, 2020
|
|
6LOL
 | | The crystal structure of full length IpaH9.8 | | Descriptor: | E3 ubiquitin-protein ligase ipaH9.8 | | Authors: | Ye, Y, Huang, H. | | Deposit date: | 2020-01-06 | | Release date: | 2020-12-23 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.75 Å) | | Cite: | Substrate-binding destabilizes the hydrophobic cluster to relieve the autoinhibition of bacterial ubiquitin ligase IpaH9.8.
Commun Biol, 3, 2020
|
|
5AYE
 | | Crystal structure of Ruminococcus albus beta-(1,4)-mannooligosaccharide phosphorylase (RaMP2) in complexes with phosphate and beta-(1,4)-mannobiose | | Descriptor: | Beta-1,4-mannooligosaccharide phosphorylase, PHOSPHATE ION, beta-D-mannopyranose-(1-4)-beta-D-mannopyranose | | Authors: | Ye, Y, Saburi, W, Kato, K, Yao, M. | | Deposit date: | 2015-08-13 | | Release date: | 2016-03-23 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Structural insights into the difference in substrate recognition of two mannoside phosphorylases from two GH130 subfamilies.
Febs Lett., 590, 2016
|
|
5AYD
 | | Crystal structure of Ruminococcus albus beta-(1,4)-mannooligosaccharide phosphorylase (RaMP2) in complexes with phosphate | | Descriptor: | Beta-1,4-mannooligosaccharide phosphorylase, PHOSPHATE ION | | Authors: | Ye, Y, Saburi, W, Kato, K, Yao, M. | | Deposit date: | 2015-08-13 | | Release date: | 2016-03-23 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Structural insights into the difference in substrate recognition of two mannoside phosphorylases from two GH130 subfamilies.
Febs Lett., 590, 2016
|
|
5AYC
 | | Crystal structure of Ruminococcus albus 4-O-beta-D-mannosyl-D-glucose phosphorylase (RaMP1) in complexes with sulfate and 4-O-beta-D-mannosyl-D-glucose | | Descriptor: | 4-O-beta-D-mannosyl-D-glucose phosphorylase, SULFATE ION, beta-D-mannopyranose-(1-4)-beta-D-glucopyranose | | Authors: | Ye, Y, Saburi, W, Kato, K, Yao, M. | | Deposit date: | 2015-08-13 | | Release date: | 2016-03-23 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Structural insights into the difference in substrate recognition of two mannoside phosphorylases from two GH130 subfamilies.
Febs Lett., 590, 2016
|
|
5AY9
 | |
8YIN
 | | Cryo-EM structure of Saccharomyces cerevisiae bc1 complex in YF23694-bound state | | Descriptor: | (1R)-2-(phosphonooxy)-1-[(tridecanoyloxy)methyl]ethyl pentadecanoate, (1R)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(heptanoyloxy)methyl]ethyl octadecanoate, (2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl octadecanoate, ... | | Authors: | Ye, Y, Li, Z.W, Yang, G.F. | | Deposit date: | 2024-02-29 | | Release date: | 2024-12-25 | | Method: | ELECTRON MICROSCOPY (2.74 Å) | | Cite: | Cryo-EM Structures Reveal the Unique Binding Modes of Metyltetraprole in Yeast and Porcine Cytochrome bc 1 Complex Enabling Rational Design of Inhibitors.
J.Am.Chem.Soc., 146, 2024
|
|
8YHQ
 | | Cryo-EM structure of Saccharomyces cerevisiae bc1 complex in pyraclostrobin-bound state | | Descriptor: | (1R)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate, (1R)-2-(phosphonooxy)-1-[(tridecanoyloxy)methyl]ethyl pentadecanoate, (1R)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(heptanoyloxy)methyl]ethyl octadecanoate, ... | | Authors: | Ye, Y, Li, Z.W, Yang, G.F. | | Deposit date: | 2024-02-28 | | Release date: | 2024-12-25 | | Method: | ELECTRON MICROSCOPY (2.42 Å) | | Cite: | Cryo-EM Structures Reveal the Unique Binding Modes of Metyltetraprole in Yeast and Porcine Cytochrome bc 1 Complex Enabling Rational Design of Inhibitors.
J.Am.Chem.Soc., 146, 2024
|
|
8ZMT
 | | Cryo-EM structure of Saccharomyces cerevisiae bc1 complex in Metyltetraprole-bound state | | Descriptor: | (1R)-2-(phosphonooxy)-1-[(tridecanoyloxy)methyl]ethyl pentadecanoate, (1R)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(heptanoyloxy)methyl]ethyl octadecanoate, (2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl octadecanoate, ... | | Authors: | Ye, Y, Li, Z.W, Yang, G.F. | | Deposit date: | 2024-05-23 | | Release date: | 2024-12-25 | | Method: | ELECTRON MICROSCOPY (2.52 Å) | | Cite: | Cryo-EM Structures Reveal the Unique Binding Modes of Metyltetraprole in Yeast and Porcine Cytochrome bc 1 Complex Enabling Rational Design of Inhibitors.
J.Am.Chem.Soc., 146, 2024
|
|
6LOJ
 | | The complex structure of IpaH9.8-LRR and hGBP1 | | Descriptor: | GUANOSINE-5'-DIPHOSPHATE, Guanylate-binding protein 1, Invasion plasmid antigen | | Authors: | Ye, Y, Huang, H. | | Deposit date: | 2020-01-06 | | Release date: | 2020-12-23 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (3.72 Å) | | Cite: | Substrate-binding destabilizes the hydrophobic cluster to relieve the autoinhibition of bacterial ubiquitin ligase IpaH9.8.
Commun Biol, 3, 2020
|
|
8YIO
 | | Cryo-EM structure of Saccharomyces cerevisiae bc1 complex in azoxystrobin-bound state | | Descriptor: | (1R)-2-(phosphonooxy)-1-[(tridecanoyloxy)methyl]ethyl pentadecanoate, (1R)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(heptanoyloxy)methyl]ethyl octadecanoate, (2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl octadecanoate, ... | | Authors: | Ye, Y, Li, Z.W, Yang, G.F. | | Deposit date: | 2024-02-29 | | Release date: | 2025-03-05 | | Method: | ELECTRON MICROSCOPY (2.35 Å) | | Cite: | Cryo-EM structure of Saccharomyces cerevisiae bc1 complex in azoxystrobin-bound state
To Be Published
|
|
8YIL
 | | Cryo-EM structure of Saccharomyces cerevisiae bc1 complex in YF24228-bound state | | Descriptor: | (1R)-2-(phosphonooxy)-1-[(tridecanoyloxy)methyl]ethyl pentadecanoate, (1R)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(heptanoyloxy)methyl]ethyl octadecanoate, (2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl octadecanoate, ... | | Authors: | Ye, Y, Li, Z.W, Yang, G.F. | | Deposit date: | 2024-02-29 | | Release date: | 2025-03-05 | | Method: | ELECTRON MICROSCOPY (2.58 Å) | | Cite: | Cryo-EM structure of Saccharomyces cerevisiae bc1 complex in YF24228-bound state
To Be Published
|
|
3L8B
 | | Crystal structure of a replicative DNA polymerase bound to the oxidized guanine lesion guanidinohydantoin | | Descriptor: | DNA (5'-D(*AP*C*TP*(G35)P*TP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3'), DNA (5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*A)-3'), DNA polymerase, ... | | Authors: | Aller, P, Ye, Y, Wallace, S.S, Burrows, C.J, Doublie, S. | | Deposit date: | 2009-12-30 | | Release date: | 2010-03-09 | | Last modified: | 2023-09-06 | | Method: | X-RAY DIFFRACTION (2.15 Å) | | Cite: | Crystal structure of a replicative DNA polymerase bound to the oxidized guanine lesion guanidinohydantoin.
Biochemistry, 49, 2010
|
|
6GQJ
 | | Crystal structure of human c-KIT kinase domain in complex with AZD3229-analogue (compound 18) | | Descriptor: | 2-[4-(6,7-dimethoxyquinazolin-4-yl)oxy-2-methoxy-phenyl]-~{N}-(1-propan-2-ylpyrazol-4-yl)ethanamide, Mast/stem cell growth factor receptor Kit | | Authors: | Schimpl, M, Hardy, C.J, Ogg, D.J, Overman, R.C, Packer, M.J, Kettle, J.G, Anjum, R, Barry, E, Bhavsar, D, Brown, C, Campbell, A, Goldberg, K, Grondine, M, Guichard, S, Hunt, T, Jones, O, Li, X, Moleva, O, Pearson, S, Shao, W, Smith, A, Smith, J, Stead, D, Stokes, S, Tucker, M, Ye, Y. | | Deposit date: | 2018-06-07 | | Release date: | 2018-09-19 | | Last modified: | 2024-01-17 | | Method: | X-RAY DIFFRACTION (2.33 Å) | | Cite: | Discovery of N-(4-{[5-Fluoro-7-(2-methoxyethoxy)quinazolin-4-yl]amino}phenyl)-2-[4-(propan-2-yl)-1 H-1,2,3-triazol-1-yl]acetamide (AZD3229), a Potent Pan-KIT Mutant Inhibitor for the Treatment of Gastrointestinal Stromal Tumors.
J. Med. Chem., 61, 2018
|
|
6GQO
 | | Crystal structure of human KDR (VEGFR2) kinase domain in complex with AZD3229-analogue (compound 18) | | Descriptor: | 2-[4-(6,7-dimethoxyquinazolin-4-yl)oxy-2-methoxy-phenyl]-~{N}-(1-propan-2-ylpyrazol-4-yl)ethanamide, Vascular endothelial growth factor receptor 2 | | Authors: | Ogg, D.J, Schimpl, M, Hardy, C.J, Overman, R.C, Packer, M.J, Kettle, J.G, Anjum, R, Barry, E, Bhavsar, D, Brown, C, Campbell, A, Goldberg, K, Grondine, M, Guichard, S, Hunt, T, Jones, O, Li, X, Moleva, O, Pearson, S, Shao, W, Smith, A, Smith, J, Stead, D, Stokes, S, Tucker, M, Ye, Y. | | Deposit date: | 2018-06-07 | | Release date: | 2018-09-19 | | Last modified: | 2024-01-17 | | Method: | X-RAY DIFFRACTION (1.87 Å) | | Cite: | Discovery of N-(4-{[5-Fluoro-7-(2-methoxyethoxy)quinazolin-4-yl]amino}phenyl)-2-[4-(propan-2-yl)-1 H-1,2,3-triazol-1-yl]acetamide (AZD3229), a Potent Pan-KIT Mutant Inhibitor for the Treatment of Gastrointestinal Stromal Tumors.
J. Med. Chem., 61, 2018
|
|
6GQM
 | | Crystal structure of human c-KIT kinase domain in complex with a small molecule inhibitor, AZD3229 | | Descriptor: | CHLORIDE ION, Mast/stem cell growth factor receptor Kit, ~{N}-[4-[[5-fluoranyl-7-(2-methoxyethoxy)quinazolin-4-yl]amino]phenyl]-2-(4-propan-2-yl-1,2,3-triazol-1-yl)ethanamide | | Authors: | Schimpl, M, Hardy, C.J, Ogg, D.J, Overman, R.C, Packer, M.J, Kettle, J.G, Anjum, R, Barry, E, Bhavsar, D, Brown, C, Campbell, A, Goldberg, K, Grondine, M, Guichard, S, Hunt, T, Jones, O, Li, X, Moleva, O, Pearson, S, Shao, W, Smith, A, Smith, J, Stead, D, Stokes, S, Tucker, M, Ye, Y. | | Deposit date: | 2018-06-07 | | Release date: | 2018-09-19 | | Last modified: | 2024-05-15 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Discovery of N-(4-{[5-Fluoro-7-(2-methoxyethoxy)quinazolin-4-yl]amino}phenyl)-2-[4-(propan-2-yl)-1 H-1,2,3-triazol-1-yl]acetamide (AZD3229), a Potent Pan-KIT Mutant Inhibitor for the Treatment of Gastrointestinal Stromal Tumors.
J. Med. Chem., 61, 2018
|
|
6GQK
 | | Crystal structure of human c-KIT kinase domain in complex with AZD3229-analogue (compound 23) | | Descriptor: | Mast/stem cell growth factor receptor Kit, ~{N}-[4-(6,7-dimethoxyquinazolin-4-yl)oxyphenyl]-2-(1-ethylpyrazol-4-yl)ethanamide | | Authors: | Schimpl, M, Hardy, C.J, Ogg, D.J, Overman, R.C, Packer, M.J, Kettle, J.G, Anjum, R, Barry, E, Bhavsar, D, Brown, C, Campbell, A, Goldberg, K, Grondine, M, Guichard, S, Hunt, T, Jones, O, Li, X, Moleva, O, Pearson, S, Shao, W, Smith, A, Smith, J, Stead, D, Stokes, S, Tucker, M, Ye, Y. | | Deposit date: | 2018-06-07 | | Release date: | 2018-09-19 | | Last modified: | 2024-05-15 | | Method: | X-RAY DIFFRACTION (2.31 Å) | | Cite: | Discovery of N-(4-{[5-Fluoro-7-(2-methoxyethoxy)quinazolin-4-yl]amino}phenyl)-2-[4-(propan-2-yl)-1 H-1,2,3-triazol-1-yl]acetamide (AZD3229), a Potent Pan-KIT Mutant Inhibitor for the Treatment of Gastrointestinal Stromal Tumors.
J. Med. Chem., 61, 2018
|
|
6GQL
 | | Crystal structure of human c-KIT kinase domain in complex with AZD3229-analogue (compound 35) | | Descriptor: | Mast/stem cell growth factor receptor Kit, ~{N}-[4-(6,7-dimethoxyquinazolin-4-yl)oxyphenyl]-2-(4-propan-2-yl-1,2,3-triazol-1-yl)ethanamide | | Authors: | Schimpl, M, Hardy, C.J, Ogg, D.J, Overman, R.C, Packer, M.J, Kettle, J.G, Anjum, R, Barry, E, Bhavsar, D, Brown, C, Campbell, A, Goldberg, K, Grondine, M, Guichard, S, Hunt, T, Jones, O, Li, X, Moleva, O, Pearson, S, Shao, W, Smith, A, Smith, J, Stead, D, Stokes, S, Tucker, M, Ye, Y. | | Deposit date: | 2018-06-07 | | Release date: | 2018-09-19 | | Last modified: | 2024-05-15 | | Method: | X-RAY DIFFRACTION (2.01 Å) | | Cite: | Discovery of N-(4-{[5-Fluoro-7-(2-methoxyethoxy)quinazolin-4-yl]amino}phenyl)-2-[4-(propan-2-yl)-1 H-1,2,3-triazol-1-yl]acetamide (AZD3229), a Potent Pan-KIT Mutant Inhibitor for the Treatment of Gastrointestinal Stromal Tumors.
J. Med. Chem., 61, 2018
|
|
6GQP
 | | Crystal structure of human KDR (VEGFR2) kinase domain in complex with AZD3229-analogue (compound 23) | | Descriptor: | Vascular endothelial growth factor receptor 2, ~{N}-[4-(6,7-dimethoxyquinazolin-4-yl)oxyphenyl]-2-(1-ethylpyrazol-4-yl)ethanamide | | Authors: | Hardy, C.J, Schimpl, M, Ogg, D.J, Overman, R.C, Packer, M.J, Kettle, J.G, Anjum, R, Barry, E, Bhavsar, D, Brown, C, Campbell, A, Goldberg, K, Grondine, M, Guichard, S, Hunt, T, Jones, O, Li, X, Moleva, O, Pearson, S, Shao, W, Smith, A, Smith, J, Stead, D, Stokes, S, Tucker, M, Ye, Y. | | Deposit date: | 2018-06-07 | | Release date: | 2018-09-19 | | Last modified: | 2024-01-17 | | Method: | X-RAY DIFFRACTION (2.09 Å) | | Cite: | Discovery of N-(4-{[5-Fluoro-7-(2-methoxyethoxy)quinazolin-4-yl]amino}phenyl)-2-[4-(propan-2-yl)-1 H-1,2,3-triazol-1-yl]acetamide (AZD3229), a Potent Pan-KIT Mutant Inhibitor for the Treatment of Gastrointestinal Stromal Tumors.
J. Med. Chem., 61, 2018
|
|
6GQQ
 | | Crystal structure of human KDR (VEGFR2) kinase domain in complex with AZD3229-analogue (compound 35) | | Descriptor: | Vascular endothelial growth factor receptor 2, ~{N}-[4-(6,7-dimethoxyquinazolin-4-yl)oxyphenyl]-2-(4-propan-2-yl-1,2,3-triazol-1-yl)ethanamide | | Authors: | Schimpl, M, Hardy, C.J, Ogg, D.J, Overman, R.C, Packer, M.J, Kettle, J.G, Anjum, R, Barry, E, Bhavsar, D, Brown, C, Campbell, A, Goldberg, K, Grondine, M, Guichard, S, Hunt, T, Jones, O, Li, X, Moleva, O, Pearson, S, Shao, W, Smith, A, Smith, J, Stead, D, Stokes, S, Tucker, M, Ye, Y. | | Deposit date: | 2018-06-07 | | Release date: | 2018-09-19 | | Last modified: | 2024-01-17 | | Method: | X-RAY DIFFRACTION (1.52 Å) | | Cite: | Discovery of N-(4-{[5-Fluoro-7-(2-methoxyethoxy)quinazolin-4-yl]amino}phenyl)-2-[4-(propan-2-yl)-1 H-1,2,3-triazol-1-yl]acetamide (AZD3229), a Potent Pan-KIT Mutant Inhibitor for the Treatment of Gastrointestinal Stromal Tumors.
J. Med. Chem., 61, 2018
|
|
4AE4
 | | The UBAP1 subunit of ESCRT-I interacts with ubiquitin via a novel SOUBA domain | | Descriptor: | 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID, GLYCEROL, POTASSIUM ION, ... | | Authors: | Agromayor, M, Soler, N, Caballe, A, Kueck, T, Freund, S.M, Allen, M.D, Bycroft, M, Perisic, O, Ye, Y, McDonald, B, Scheel, H, Hofmann, K, Neil, S.J.D, Martin-Serrano, J, Williams, R.L. | | Deposit date: | 2012-01-06 | | Release date: | 2012-03-21 | | Last modified: | 2025-04-09 | | Method: | X-RAY DIFFRACTION (1.65 Å) | | Cite: | The UBAP1 subunit of ESCRT-I interacts with ubiquitin via a SOUBA domain.
Structure, 20, 2012
|
|
3PHX
 | | OTU Domain of Crimean Congo Hemorrhagic Fever Virus in complex with ISG15 | | Descriptor: | ACETIC ACID, ETHANAMINE, RNA-directed RNA polymerase L, ... | | Authors: | Akutsu, M, Ye, Y, Virdee, S, Komander, D. | | Deposit date: | 2010-11-04 | | Release date: | 2011-02-02 | | Last modified: | 2025-03-26 | | Method: | X-RAY DIFFRACTION (1.6 Å) | | Cite: | Molecular basis for ubiquitin and ISG15 cross-reactivity in viral ovarian tumor domains.
Proc.Natl.Acad.Sci.USA, 108, 2011
|
|
3PHU
 | | OTU Domain of Crimean Congo Hemorrhagic Fever Virus | | Descriptor: | GLYCEROL, RNA-directed RNA polymerase L | | Authors: | Akutsu, M, Ye, Y, Virdee, S, Komander, D. | | Deposit date: | 2010-11-04 | | Release date: | 2011-02-02 | | Last modified: | 2024-10-16 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Molecular basis for ubiquitin and ISG15 cross-reactivity in viral ovarian tumor domains.
Proc.Natl.Acad.Sci.USA, 108, 2011
|
|
3PHW
 | | OTU Domain of Crimean Congo Hemorrhagic Fever Virus in complex with Ubiquitin | | Descriptor: | ETHANAMINE, RNA-directed RNA polymerase L, Ubiquitin-40S ribosomal protein S27a | | Authors: | Akutsu, M, Ye, Y, Virdee, S, Komander, D. | | Deposit date: | 2010-11-04 | | Release date: | 2011-02-02 | | Last modified: | 2025-03-26 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Molecular basis for ubiquitin and ISG15 cross-reactivity in viral ovarian tumor domains.
Proc.Natl.Acad.Sci.USA, 108, 2011
|
|
