5ZEQ
 
 | | Carboxypeptidase B in complex with DD28 | | Descriptor: | (2~{S})-2-[(6-azanyl-5-chloranyl-pyridin-3-yl)methyl]-3-selanyl-propanoic acid, CACODYLATE ION, Carboxypeptidase B, ... | | Authors: | Itoh, T, Yoshimoto, N, Yamamoto, K. | | Deposit date: | 2018-02-27 | | Release date: | 2018-06-20 | | Last modified: | 2024-10-09 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Structural basis for the selective inhibition of activated thrombin-activatable fibrinolysis inhibitor (TAFIa) by a selenium-containing inhibitor with chloro-aminopyridine as a basic group
Bioorg. Med. Chem. Lett., 28, 2018
|
|
3VYJ
 | | Crystal structure of C-type lectin domain of murine dendritic cell inhibitory receptor 2 (apo form) | | Descriptor: | C-type lectin domain family 4, member a4, SULFATE ION | | Authors: | Nagae, M, Yamanaka, K, Hanashima, S, Ikeda, A, Satoh, T, Matsumoto, N, Yamamoto, K, Yamaguchi, Y. | | Deposit date: | 2012-09-26 | | Release date: | 2013-10-02 | | Last modified: | 2024-11-06 | | Method: | X-RAY DIFFRACTION (2.15 Å) | | Cite: | Recognition of Bisecting N-Acetylglucosamine: STRUCTURAL BASIS FOR ASYMMETRIC INTERACTION WITH THE MOUSE LECTIN DENDRITIC CELL INHIBITORY RECEPTOR 2
J.Biol.Chem., 288, 2013
|
|
3VYK
 | | Crystal structure of C-type lectin domain of murine dendritic cell inhibitory receptor 2 in complex with N-glycan | | Descriptor: | 1,2-ETHANEDIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)][2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]methyl alpha-D-mannopyranoside, C-type lectin domain family 4, ... | | Authors: | Nagae, M, Yamanaka, K, Hanashima, S, Ikeda, A, Satoh, T, Matsumoto, N, Yamamoto, K, Yamaguchi, Y. | | Deposit date: | 2012-09-26 | | Release date: | 2013-10-02 | | Last modified: | 2020-07-29 | | Method: | X-RAY DIFFRACTION (1.5 Å) | | Cite: | Recognition of Bisecting N-Acetylglucosamine: STRUCTURAL BASIS FOR ASYMMETRIC INTERACTION WITH THE MOUSE LECTIN DENDRITIC CELL INHIBITORY RECEPTOR 2
J.Biol.Chem., 288, 2013
|
|
3AY8
 | | Glutathione S-transferase unclassified 2 from Bombyx mori | | Descriptor: | GLYCEROL, Glutathione S-transferase | | Authors: | Kakuta, Y, Usuda, K, Nakashima, T, Kimura, M, Aso, Y, Yamamoto, K. | | Deposit date: | 2011-05-02 | | Release date: | 2011-09-07 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Crystallographic survey of active sites of an unclassified glutathione transferase from Bombyx mori
Biochim.Biophys.Acta, 1810, 2011
|
|
5AJ0
 | | Cryo electron microscopy of actively translating human polysomes (POST state). | | Descriptor: | 18S ribosomal RNA, 28S ribosomal RNA, 40S ribosomal protein S10, ... | | Authors: | Behrmann, E, Loerke, J, Budkevich, T.V, Yamamoto, K, Schmidt, A, Penczek, P.A, Vos, M.R, Burger, J, Mielke, T, Scheerer, P, Spahn, C.M.T. | | Deposit date: | 2015-02-19 | | Release date: | 2015-05-20 | | Last modified: | 2019-12-18 | | Method: | ELECTRON MICROSCOPY (3.5 Å) | | Cite: | Structural Snapshots of Actively Translating Human Ribosomes
Cell(Cambridge,Mass.), 161, 2015
|
|
5AZV
 | | Crystal structure of hPPARgamma ligand binding domain complexed with 17-oxoDHA | | Descriptor: | (4~{Z},7~{Z},10~{Z},13~{Z},19~{Z})-17-oxidanylidenedocosa-4,7,10,13,19-pentaenoic acid, Peroxisome proliferator-activated receptor gamma | | Authors: | Egawa, D, Itoh, T, Yamamoto, K. | | Deposit date: | 2015-10-23 | | Release date: | 2016-07-06 | | Last modified: | 2024-10-23 | | Method: | X-RAY DIFFRACTION (2.7 Å) | | Cite: | 17-OxoDHA Is a PPAR alpha/gamma Dual Covalent Modifier and Agonist
Acs Chem.Biol., 2016
|
|
5AZT
 | | Ternary complex of hPPARalpha ligand binding domain, 17-oxoDHA and a SRC1 peptide | | Descriptor: | (4~{Z},7~{Z},10~{Z},13~{Z},19~{Z})-17-oxidanylidenedocosa-4,7,10,13,19-pentaenoic acid, 15-meric peptide from Nuclear receptor coactivator 1, Peroxisome proliferator-activated receptor alpha | | Authors: | Egawa, D, Itoh, T, Yamamoto, K. | | Deposit date: | 2015-10-23 | | Release date: | 2016-07-06 | | Last modified: | 2024-10-30 | | Method: | X-RAY DIFFRACTION (3.45 Å) | | Cite: | 17-OxoDHA Is a PPAR alpha/gamma Dual Covalent Modifier and Agonist
Acs Chem.Biol., 2016
|
|
5AWK
 | | Crystal structure of VDR-LBD/partial agonist complex: 22S-ethyl analogue | | Descriptor: | (1R,3R)-5-[(2E)-2-[(1R,3aS,7aR)-1-[(2R,3S)-3-ethyl-5-oxidanyl-pentan-2-yl]-7a-methyl-2,3,3a,5,6,7-hexahydro-1H-inden-4-ylidene]ethylidene]-2-methylidene-cyclohexane-1,3-diol, Mediator of RNA polymerase II transcription subunit 1, Vitamin D3 receptor,Vitamin D3 receptor | | Authors: | Anami, Y, Itoh, T, Yamamoto, K. | | Deposit date: | 2015-07-04 | | Release date: | 2015-11-18 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (2.9 Å) | | Cite: | Fine tuning of agonistic/antagonistic activity for vitamin D receptor by 22-alkyl chain length of ligands: 22S-Hexyl compound unexpectedly restored agonistic activity.
Bioorg.Med.Chem., 23, 2015
|
|
5AWJ
 | | Crystal structure of VDR-LBD/partial agonist complex: 22S-hexyl analogue | | Descriptor: | (1R,3R)-5-[(2E)-2-[(1R,3aS,7aR)-1-[(2R,3S)-3-(2-hydroxyethyl)nonan-2-yl]-7a-methyl-2,3,3a,5,6,7-hexahydro-1H-inden-4-ylidene]ethylidene]-2-methylidene-cyclohexane-1,3-diol, Mediator of RNA polymerase II transcription subunit 1, Vitamin D3 receptor,Vitamin D3 receptor | | Authors: | Anami, Y, Itoh, T, Inaba, Y, Nakabayashi, M, Ikura, T, Ito, N, Yamamoto, K. | | Deposit date: | 2015-07-04 | | Release date: | 2015-11-18 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Fine tuning of agonistic/antagonistic activity for vitamin D receptor by 22-alkyl chain length of ligands: 22S-Hexyl compound unexpectedly restored agonistic activity.
Bioorg.Med.Chem., 23, 2015
|
|
5B5B
 | | Crystal structure of VDR-LBD complexed with 2-methylidene-26,27-diphenyl-19-nor-1,25-dihydroxyvitamin D3 | | Descriptor: | (1R,3R)-5-[(2E)-2-[(1R,3aS,7aR)-7a-methyl-1-[(2R)-6-oxidanyl-7-phenyl-6-(phenylmethyl)heptan-2-yl]-2,3,3a,5,6,7-hexahydro-1H-inden-4-ylidene]ethylidene]-2-methylidene-cyclohexane-1,3-diol, Mediator of RNA polymerase II transcription subunit 1, Vitamin D3 receptor | | Authors: | Kato, A, Itoh, T, Yamamoto, K. | | Deposit date: | 2016-05-02 | | Release date: | 2016-06-29 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Helix12-Stabilization Antagonist of Vitamin D Receptor
Bioconjug.Chem., 27, 2016
|
|
5B41
 | | Crystal structure of VDR-LBD complexed with 2-methylidene-19-nor-1a,25-dihydroxyvitamin D3 | | Descriptor: | (1R,3R)-5-(2-((1R,3aS,7aR,E)-1-((R)-6-hydroxy-6-methylheptan-2-yl)-7a-methyloctahydro-4H-inden-4-ylidene)ethylidene)-2- methylenecyclohexane-1,3-diol, Mediator of RNA polymerase II transcription subunit 1, Vitamin D3 receptor | | Authors: | Anami, Y, Itoh, T, Yamamoto, K. | | Deposit date: | 2016-03-23 | | Release date: | 2016-12-07 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.89 Å) | | Cite: | Apo- and Antagonist-Binding Structures of Vitamin D Receptor Ligand-Binding Domain Revealed by Hybrid Approach Combining Small-Angle X-ray Scattering and Molecular Dynamics
J.Med.Chem., 59, 2016
|
|
3AFR
 | | Crystal Structure of VDR-LBD/22S-Butyl-1a,24R-dihydroxyvitamin D3 complex | | Descriptor: | (1R,3S,5Z)-5-[(2E)-2-{(1R,3aS,7aR)-1-[(1R,2S,4R)-2-butyl-4-hydroxy-1,5-dimethylhexyl]-7a-methyloctahydro-4H-inden-4-yli dene}ethylidene]-4-methylidenecyclohexane-1,3-diol, 13-meric peptide from Mediator of RNA polymerase II transcription subunit 1, Vitamin D3 receptor | | Authors: | Inaba, Y, Nakabayashi, M, Itoh, T, Ikura, T, Ito, N, Yamamoto, K. | | Deposit date: | 2010-03-10 | | Release date: | 2010-03-31 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | 22S-Butyl-1alpha,24R-dihydroxyvitamin D(3): Recovery of vitamin D receptor agonistic activity
J.Steroid Biochem.Mol.Biol., 121, 2010
|
|
3AIH
 | | Human OS-9 MRH domain complexed with alpha3,alpha6-Man5 | | Descriptor: | Protein OS-9, alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose | | Authors: | Satoh, T, Chen, Y, Hu, D, Hanashima, S, Yamamoto, K, Yamaguchi, Y. | | Deposit date: | 2010-05-14 | | Release date: | 2010-12-22 | | Last modified: | 2024-10-23 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Structural Basis for Oligosaccharide Recognition of Misfolded Glycoproteins by OS-9 in ER-Associated Degradation
Mol.Cell, 40, 2010
|
|
3VRU
 | | VDR ligand binding domain in complex with 2-Methylidene-19,24-dinor-1alpha,25-dihydroxy vitaminD3 | | Descriptor: | (1R,3R,7E,17beta)-17-[(2R)-5-hydroxy-5-methylhexan-2-yl]-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol, 13-meric peptide from Mediator of RNA polymerase II transcription subunit 1, Vitamin D3 receptor | | Authors: | Yoshimoto, N, Inaba, Y, Itoh, T, Nakabayashi, M, Ito, N, Yamamoto, K. | | Deposit date: | 2012-04-14 | | Release date: | 2012-05-23 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Butyl pocket formation in the vitamin d receptor strongly affects the agonistic or antagonistic behavior of ligands
J.Med.Chem., 55, 2012
|
|
3VRW
 | | VDR ligand binding domain in complex with 22S-Butyl-2-methylidene-26,27-dimethyl-19,24-dinor-1alpha,25-dihydroxyvitamin D3 | | Descriptor: | (1R,3R,7E,17beta)-17-[(2R,3S)-3-butyl-5-ethyl-5-hydroxyheptan-2-yl]-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol, 13-meric peptide from Mediator of RNA polymerase II transcription subunit 1, Vitamin D3 receptor | | Authors: | Yoshimoto, N, Inaba, Y, Itoh, T, Nakabayashi, M, Ito, N, Yamamoto, K. | | Deposit date: | 2012-04-16 | | Release date: | 2012-05-23 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | Butyl pocket formation in the vitamin d receptor strongly affects the agonistic or antagonistic behavior of ligands
J.Med.Chem., 55, 2012
|
|
3VRV
 | | VDR ligand binding domain in complex with 2-Methylidene-26,27-dimethyl-19,24-dinor-1alpha,25-dihydroxyvitamin D3 | | Descriptor: | (1R,3R,7E,17beta)-17-[(2R)-5-ethyl-5-hydroxyheptan-2-yl]-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol, 13-meric peptide from Mediator of RNA polymerase II transcription subunit 1, Vitamin D3 receptor | | Authors: | Yoshimoto, N, Inaba, Y, Itoh, T, Nakabayashi, M, Ito, N, Yamamoto, K. | | Deposit date: | 2012-04-14 | | Release date: | 2012-05-23 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Butyl pocket formation in the vitamin d receptor strongly affects the agonistic or antagonistic behavior of ligands
J.Med.Chem., 55, 2012
|
|
3WC5
 | | Carboxypeptidase B in complex with DD9 | | Descriptor: | (2R)-7-amino-2-(selanylmethyl)heptanoic acid, CACODYLATE ION, Carboxypeptidase B, ... | | Authors: | Yoshimoto, N, Itoh, T, Inaba, Y, Yamamoto, K. | | Deposit date: | 2013-05-24 | | Release date: | 2013-10-02 | | Last modified: | 2024-11-06 | | Method: | X-RAY DIFFRACTION (1.7 Å) | | Cite: | Structural basis for inhibition of carboxypeptidase B by selenium-containing inhibitor: selenium coordinates to zinc in enzyme.
J.Med.Chem., 56, 2013
|
|
3WT5
 | | A mixed population of antagonist and agonist binding conformers in a single crystal explains partial agonism against vitamin D receptor: Active vitamin D analogues with 22R-alkyl group | | Descriptor: | (1R,3R,7E,17beta)-17-[(2R,3R)-3-butyl-6-hydroxy-6-methylheptan-2-yl]-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol, Mediator of RNA polymerase II transcription subunit 1, Vitamin D3 receptor | | Authors: | Anami, Y, Itoh, T, Yamamoto, K. | | Deposit date: | 2014-04-08 | | Release date: | 2014-06-11 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | A Mixed Population of Antagonist and Agonist Binding Conformers in a Single Crystal Explains Partial Agonism against Vitamin D Receptor: Active Vitamin D Analogues with 22R-Alkyl Group.
J.Med.Chem., 57, 2014
|
|
3WBQ
 | | Crystal structure of carbohydrate recognition domain of Blood Dendritic Cell Antigen-2 (BDCA2) lectin (crystal form-2) | | Descriptor: | C-type lectin domain family 4 member C | | Authors: | Nagae, M, Ikeda, A, Kitago, Y, Matsumoto, N, Yamamoto, K, Yamaguchi, Y. | | Deposit date: | 2013-05-20 | | Release date: | 2013-12-25 | | Last modified: | 2024-10-09 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Crystal structures of carbohydrate recognition domain of blood dendritic cell antigen-2 (BDCA2) reveal a common domain-swapped dimer.
Proteins, 82, 2014
|
|
3WTQ
 | | Crystal structure of VDR-LBD complexed with 22S-butyl-2-methylidene-19-nor-1a,25-dihydroxyvitamin D3 | | Descriptor: | (1R,3R,7E,17beta)-17-[(2R,3S)-3-butyl-6-hydroxy-6-methylheptan-2-yl]-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol, Mediator of RNA polymerase II transcription subunit 1, Vitamin D3 receptor | | Authors: | Nakabayashi, M, Inaba, Y, Itoh, T, Anami, Y, Ikura, T, Ito, N, Yamamoto, K. | | Deposit date: | 2014-04-15 | | Release date: | 2015-04-15 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Crystal structure of VDR-LBD complexed with 22S-butyl-2-methylidene-19-nor-1a,25-dihydroxyvitamin D3
To be Published
|
|
3WBP
 | | Crystal structure of carbohydrate recognition domain of Blood Dendritic Cell Antigen-2 (BDCA2) lectin (crystal form-1) | | Descriptor: | 1,2-ETHANEDIOL, C-type lectin domain family 4 member C | | Authors: | Nagae, M, Ikeda, A, Kitago, Y, Matsumoto, N, Yamamoto, K, Yamaguchi, Y. | | Deposit date: | 2013-05-20 | | Release date: | 2013-12-25 | | Last modified: | 2024-10-30 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Crystal structures of carbohydrate recognition domain of blood dendritic cell antigen-2 (BDCA2) reveal a common domain-swapped dimer.
Proteins, 82, 2014
|
|
3WT7
 | | Crystal structure of VDR-LBD complexed with 22R-Butyl-2-methylidene-26,27-dimethyl-19,24-dinor-1 ,25-dihydroxyvitamin D3 | | Descriptor: | (1R,3R,7E,17beta)-17-[(2R,3R)-3-butyl-5-ethyl-5-hydroxyheptan-2-yl]-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol, Mediator of RNA polymerase II transcription subunit 1, Vitamin D3 receptor | | Authors: | Anami, Y, Itoh, T, Yamamoto, K. | | Deposit date: | 2014-04-08 | | Release date: | 2014-06-11 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | A Mixed Population of Antagonist and Agonist Binding Conformers in a Single Crystal Explains Partial Agonism against Vitamin D Receptor: Active Vitamin D Analogues with 22R-Alkyl Group.
J.Med.Chem., 57, 2014
|
|
3WT6
 | | A mixed population of antagonist and agonist binding conformers in a single crystal explains partial agonism against vitamin D receptor: Active vitamin D analogues with 22R-alkyl group | | Descriptor: | (1R,3R,7E,17beta)-17-[(2R,3R)-3-butyl-6-hydroxy-6-methylheptan-2-yl]-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol, Mediator of RNA polymerase II transcription subunit 1, Vitamin D3 receptor | | Authors: | Anami, Y, Itoh, T, Yamamoto, K. | | Deposit date: | 2014-04-08 | | Release date: | 2014-06-11 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | A Mixed Population of Antagonist and Agonist Binding Conformers in a Single Crystal Explains Partial Agonism against Vitamin D Receptor: Active Vitamin D Analogues with 22R-Alkyl Group.
J.Med.Chem., 57, 2014
|
|
3WC6
 | | Carboxypeptidase B in complex with 2nd zinc | | Descriptor: | ACETATE ION, Carboxypeptidase B, ZINC ION | | Authors: | Yoshimoto, N, Itoh, T, Inaba, Y, Yamamoto, K. | | Deposit date: | 2013-05-24 | | Release date: | 2013-10-02 | | Last modified: | 2024-10-16 | | Method: | X-RAY DIFFRACTION (1.65 Å) | | Cite: | Structural basis for inhibition of carboxypeptidase B by selenium-containing inhibitor: selenium coordinates to zinc in enzyme.
J.Med.Chem., 56, 2013
|
|
3X1H
 | | hPPARgamma Ligand binding domain in complex with 5-oxo-tricosahexaenoic acid | | Descriptor: | (7E,11Z,14Z,17Z,20Z)-5-oxotricosa-7,11,14,17,20-pentaenoic acid, Peroxisome proliferator-activated receptor gamma | | Authors: | Egawa, D, Itoh, T, Yamamoto, K. | | Deposit date: | 2014-11-18 | | Release date: | 2015-04-08 | | Last modified: | 2024-11-06 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Characterization of covalent bond formation between PPAR gamma and oxo-fatty acids.
Bioconjug.Chem., 26, 2015
|
|
