8UFI
| Cryo-EM structure of bovine phosphodiesterase 6 | Descriptor: | CYCLIC GUANOSINE MONOPHOSPHATE, MAGNESIUM ION, Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit gamma, ... | Authors: | Aplin, C, Cerione, R.A. | Deposit date: | 2023-10-04 | Release date: | 2024-01-17 | Last modified: | 2024-02-07 | Method: | ELECTRON MICROSCOPY (3.1 Å) | Cite: | Probing the mechanism by which the retinal G protein transducin activates its biological effector PDE6. J.Biol.Chem., 300, 2023
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8ULG
| Cryo-EM structure of bovine phosphodiesterase 6 bound to IBMX | Descriptor: | 3-ISOBUTYL-1-METHYLXANTHINE, CYCLIC GUANOSINE MONOPHOSPHATE, MAGNESIUM ION, ... | Authors: | Aplin, C, Cerione, R.A. | Deposit date: | 2023-10-16 | Release date: | 2024-01-17 | Last modified: | 2024-02-07 | Method: | ELECTRON MICROSCOPY (3.2 Å) | Cite: | Probing the mechanism by which the retinal G protein transducin activates its biological effector PDE6. J.Biol.Chem., 300, 2023
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8UGB
| Cryo-EM structure of bovine phosphodiesterase 6 bound to udenafil | Descriptor: | CYCLIC GUANOSINE MONOPHOSPHATE, MAGNESIUM ION, Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit gamma, ... | Authors: | Aplin, C, Cerione, R.A. | Deposit date: | 2023-10-05 | Release date: | 2024-01-17 | Last modified: | 2024-02-07 | Method: | ELECTRON MICROSCOPY (3 Å) | Cite: | Probing the mechanism by which the retinal G protein transducin activates its biological effector PDE6. J.Biol.Chem., 300, 2023
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8UGS
| Cryo-EM structure of bovine phosphodiesterase 6 bound to cGMP | Descriptor: | CYCLIC GUANOSINE MONOPHOSPHATE, MAGNESIUM ION, Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit gamma, ... | Authors: | Aplin, C, Cerione, R.A. | Deposit date: | 2023-10-06 | Release date: | 2024-01-17 | Last modified: | 2024-02-07 | Method: | ELECTRON MICROSCOPY (3.2 Å) | Cite: | Probing the mechanism by which the retinal G protein transducin activates its biological effector PDE6. J.Biol.Chem., 300, 2023
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5LAQ
| Crystal structure of human phosphodiesterase 4B catalytic domain with inhibitor NPD-001 | Descriptor: | (4~{a}~{S},8~{a}~{R})-2-cycloheptyl-4-[4-methoxy-3-[4-[4-(1~{H}-1,2,3,4-tetrazol-5-yl)phenoxy]butoxy]phenyl]-4~{a},5,8,8~{a}-tetrahydrophthalazin-1-one, ACETATE ION, MAGNESIUM ION, ... | Authors: | Singh, A.K, Brown, D.G. | Deposit date: | 2016-06-14 | Release date: | 2018-03-14 | Last modified: | 2024-01-10 | Method: | X-RAY DIFFRACTION (2.4 Å) | Cite: | Targeting a Subpocket in Trypanosoma brucei Phosphodiesterase B1 (TbrPDEB1) Enables the Structure-Based Discovery of Selective Inhibitors with Trypanocidal Activity. J. Med. Chem., 61, 2018
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6MZB
| Cryo-EM structure of phosphodiesterase 6 | Descriptor: | GUANOSINE-3',5'-MONOPHOSPHATE, MAGNESIUM ION, Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit gamma, ... | Authors: | Gulati, S, Palczewski, K. | Deposit date: | 2018-11-04 | Release date: | 2019-03-06 | Last modified: | 2021-05-19 | Method: | ELECTRON MICROSCOPY (3.4 Å) | Cite: | Cryo-EM structure of phosphodiesterase 6 reveals insights into the allosteric regulation of type I phosphodiesterases. Sci Adv, 5, 2019
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7XBB
| Crystal structure of PDE4D catalytic domain complexed with compound 23a | Descriptor: | (2~{R},4~{S})-6-ethyl-2-[(2~{E})-2-hydroxyiminoethyl]-2,8-dimethyl-4-(2-methylprop-1-enyl)-3,4-dihydropyrano[3,2-c][1,8]naphthyridin-5-one, Isoform 3 of cAMP-specific 3',5'-cyclic phosphodiesterase 4D, MAGNESIUM ION, ... | Authors: | Huang, Y.-Y, Luo, H.-B. | Deposit date: | 2022-03-21 | Release date: | 2022-07-06 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.100009 Å) | Cite: | Structure-based optimization of Toddacoumalone as highly potent and selective PDE4 inhibitors with anti-inflammatory effects. Biochem Pharmacol, 202, 2022
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7XAA
| Crystal structure of PDE4D catalytic domain complexed with compound 21d | Descriptor: | 8-methoxy-2,2-dimethyl-7-(3-methylbut-2-enyl)-9-oxidanyl-5-(pyridin-4-ylmethoxy)pyrano[3,2-b]xanthen-6-one, Isoform 3 of cAMP-specific 3',5'-cyclic phosphodiesterase 4D, MAGNESIUM ION, ... | Authors: | Huang, Y.-Y, He, X, Luo, H.-B. | Deposit date: | 2022-03-17 | Release date: | 2023-02-22 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.100414 Å) | Cite: | Discovery of novel PDE4 inhibitors targeting the M-pocket from natural mangostanin with improved safety for the treatment of Inflammatory Bowel Diseases. Eur.J.Med.Chem., 242, 2022
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7XAB
| Crystal structure of PDE4D catalytic domain complexed with compound 22d | Descriptor: | 9-(cyclopropylmethoxy)-8-methoxy-2,2-dimethyl-7-(3-methylbut-2-enyl)-5-(pyridin-4-ylmethoxy)pyrano[3,2-b]xanthen-6-one, Isoform 3 of cAMP-specific 3',5'-cyclic phosphodiesterase 4D, MAGNESIUM ION, ... | Authors: | Huang, Y.-Y, He, X, Luo, H.-B. | Deposit date: | 2022-03-17 | Release date: | 2023-02-22 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.00067449 Å) | Cite: | Discovery of novel PDE4 inhibitors targeting the M-pocket from natural mangostanin with improved safety for the treatment of Inflammatory Bowel Diseases. Eur.J.Med.Chem., 242, 2022
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3JAB
| Domain organization and conformational plasticity of the G protein effector, PDE6 | Descriptor: | 3-ISOBUTYL-1-METHYLXANTHINE, GafA domain of cone phosphodiesterase 6C, GafB domain of phosphodiesterase 2A, ... | Authors: | Zhang, Z, He, F, Constantine, R, Baker, M.L, Baehr, W, Schmid, M.F, Wensel, T.G, Agosto, M.A. | Deposit date: | 2015-05-26 | Release date: | 2015-06-10 | Last modified: | 2018-07-18 | Method: | ELECTRON MICROSCOPY (11 Å) | Cite: | Domain Organization and Conformational Plasticity of the G Protein Effector, PDE6. J.Biol.Chem., 290, 2015
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7EG4
| Cryo-EM structure of nauclefine-induced PDE3A-SLFN12 complex | Descriptor: | MAGNESIUM ION, Parvine, Schlafen family member 12, ... | Authors: | Liu, N, Chen, J, Wang, X.D, Wang, H.W. | Deposit date: | 2021-03-24 | Release date: | 2021-09-29 | Last modified: | 2022-05-25 | Method: | ELECTRON MICROSCOPY (3.2 Å) | Cite: | Structure of PDE3A-SLFN12 complex and structure-based design for a potent apoptosis inducer of tumor cells. Nat Commun, 12, 2021
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7EG0
| Cryo-EM structure of anagrelide-induced PDE3A-SLFN12 complex | Descriptor: | 6,7-bis(chloranyl)-3,5-dihydro-1H-imidazo[2,1-b]quinazolin-2-one, MAGNESIUM ION, Schlafen family member 12, ... | Authors: | Liu, N, Chen, J, Wang, X.D, Wang, H.W. | Deposit date: | 2021-03-23 | Release date: | 2021-09-29 | Last modified: | 2022-05-25 | Method: | ELECTRON MICROSCOPY (3.4 Å) | Cite: | Structure of PDE3A-SLFN12 complex and structure-based design for a potent apoptosis inducer of tumor cells. Nat Commun, 12, 2021
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7EG1
| Cryo-EM structure of DNMDP-induced PDE3A-SLFN12 complex | Descriptor: | (4~{R})-3-[4-(diethylamino)-3-[oxidanyl(oxidanylidene)-$l^{4}-azanyl]phenyl]-4-methyl-4,5-dihydro-1~{H}-pyridazin-6-one, MAGNESIUM ION, Schlafen family member 12, ... | Authors: | Liu, N, Chen, J, Wang, X.D, Wang, H.W. | Deposit date: | 2021-03-23 | Release date: | 2021-11-03 | Last modified: | 2022-05-25 | Method: | ELECTRON MICROSCOPY (3.2 Å) | Cite: | Structure of PDE3A-SLFN12 complex and structure-based design for a potent apoptosis inducer of tumor cells. Nat Commun, 12, 2021
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7F2M
| Crystal structure of PDE4D catalytic domain complexed with compound 18d | Descriptor: | (~{Z})-4-[9-[(4-fluorophenyl)methoxy]-8-methoxy-2,2-dimethyl-7-(3-methylbut-2-enyl)-6-oxidanylidene-pyrano[3,2-b]xanthen-5-yl]oxybut-2-enoic acid, Isoform 3 of cAMP-specific 3',5'-cyclic phosphodiesterase 4D, MAGNESIUM ION, ... | Authors: | Huang, Y.-Y, He, X, Luo, H.-B. | Deposit date: | 2021-06-11 | Release date: | 2021-10-20 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.20004153 Å) | Cite: | Mangostanin Derivatives as Novel and Orally Active Phosphodiesterase 4 Inhibitors for the Treatment of Idiopathic Pulmonary Fibrosis with Improved Safety. J.Med.Chem., 64, 2021
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7F2K
| Crystal structure of PDE4D catalytic domain complexed with compound 17a | Descriptor: | (~{E})-4-[8-methoxy-2,2-dimethyl-7-(3-methylbut-2-enyl)-9-oxidanyl-6-oxidanylidene-pyrano[3,2-b]xanthen-5-yl]oxybut-2-enoic acid, Isoform 3 of cAMP-specific 3',5'-cyclic phosphodiesterase 4D, MAGNESIUM ION, ... | Authors: | Huang, Y.-Y, He, X, Luo, H.-B. | Deposit date: | 2021-06-11 | Release date: | 2021-10-20 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.10001969 Å) | Cite: | Mangostanin Derivatives as Novel and Orally Active Phosphodiesterase 4 Inhibitors for the Treatment of Idiopathic Pulmonary Fibrosis with Improved Safety. J.Med.Chem., 64, 2021
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7F2L
| Crystal structure of PDE4D catalytic domain complexed with compound 18a | Descriptor: | (~{E})-4-[9-[(4-fluorophenyl)methoxy]-8-methoxy-2,2-dimethyl-7-(3-methylbut-2-enyl)-6-oxidanylidene-pyrano[3,2-b]xanthen-5-yl]oxybut-2-enoic acid, Isoform 3 of cAMP-specific 3',5'-cyclic phosphodiesterase 4D, MAGNESIUM ION, ... | Authors: | Huang, Y.-Y, He, X, Luo, H.-B. | Deposit date: | 2021-06-11 | Release date: | 2021-10-20 | Last modified: | 2023-11-29 | Method: | X-RAY DIFFRACTION (2.10111427 Å) | Cite: | Mangostanin Derivatives as Novel and Orally Active Phosphodiesterase 4 Inhibitors for the Treatment of Idiopathic Pulmonary Fibrosis with Improved Safety. J.Med.Chem., 64, 2021
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5WH6
| Crystal structure of PDE4D2 in complex with inhibitor (S_Zl-n-91) | Descriptor: | 1-[4-(difluoromethoxy)-3-{[(3S)-oxolan-3-yl]oxy}phenyl]-3-methylbutan-1-one, MAGNESIUM ION, ZINC ION, ... | Authors: | Ke, H, Wang, H. | Deposit date: | 2017-07-14 | Release date: | 2018-07-18 | Last modified: | 2024-03-13 | Method: | X-RAY DIFFRACTION (1.6 Å) | Cite: | Identification of a PDE4-Specific Pocket for the Design of Selective Inhibitors. Biochemistry, 57, 2018
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3G45
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3G4G
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3IBJ
| X-ray structure of PDE2A | Descriptor: | MAGNESIUM ION, ZINC ION, cGMP-dependent 3',5'-cyclic phosphodiesterase | Authors: | Pandit, J. | Deposit date: | 2009-07-16 | Release date: | 2009-10-27 | Last modified: | 2023-09-06 | Method: | X-RAY DIFFRACTION (3.02 Å) | Cite: | Mechanism for the allosteric regulation of phosphodiesterase 2A deduced from the X-ray structure of a near full-length construct. Proc.Natl.Acad.Sci.USA, 106, 2009
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3JBQ
| Domain Organization and Conformational Plasticity of the G Protein Effector, PDE6 | Descriptor: | GafA domain of cone phosphodiesterase 6C, GafB domain of phosphodiesterase 2A, IgG1-kappa 2E8 heavy chain, ... | Authors: | Zhang, Z, He, F, Constantine, R, Baker, M.L, Baehr, W, Schmid, M.F, Wensel, T.G, Agosto, M.A. | Deposit date: | 2015-09-17 | Release date: | 2015-09-30 | Last modified: | 2019-12-18 | Method: | ELECTRON MICROSCOPY (11 Å) | Cite: | Domain Organization and Conformational Plasticity of the G Protein Effector, PDE6. J.Biol.Chem., 290, 2015
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