6F8V
| Crystal structure of the PDE4D catalytic domain in complex with GEBR-18b | Descriptor: | 3-[3-(3-cyclopentyloxy-4-methoxy-phenyl)pyrazol-1-yl]-1-[(2~{R},6~{R})-2,6-dimethylmorpholin-4-yl]propan-1-one, MAGNESIUM ION, ZINC ION, ... | Authors: | Prosdocimi, T, Donini, S, Parisini, E. | Deposit date: | 2017-12-13 | Release date: | 2018-05-16 | Last modified: | 2024-01-17 | Method: | X-RAY DIFFRACTION (1.85 Å) | Cite: | Molecular Bases of PDE4D Inhibition by Memory-Enhancing GEBR Library Compounds. Biochemistry, 57, 2018
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6EZF
| PDE2 in complex with molecule 5 | Descriptor: | 6-[(2,4-dichlorophenyl)methyl]pyridazine-3-thiol, GLYCEROL, MAGNESIUM ION, ... | Authors: | Tresadern, G, Perez-Benito, L, Keraenen, H, van Vlijmen, H. | Deposit date: | 2017-11-15 | Release date: | 2018-04-04 | Last modified: | 2024-05-08 | Method: | X-RAY DIFFRACTION (1.5 Å) | Cite: | Predicting Binding Free Energies of PDE2 Inhibitors. The Difficulties of Protein Conformation. Sci Rep, 8, 2018
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6F8U
| Crystal structure of the PDE4D catalytic domain in complex with GEBR-20b | Descriptor: | 2-[(~{E})-[4-[bis(fluoranyl)methoxy]-3-cyclopentyloxy-phenyl]methylideneamino]oxy-1-[(2~{R},6~{R})-2,6-dimethylmorpholin-4-yl]ethanone, MAGNESIUM ION, ZINC ION, ... | Authors: | Prosdocimi, T, Donini, S, Parisini, E. | Deposit date: | 2017-12-13 | Release date: | 2018-05-16 | Last modified: | 2024-01-17 | Method: | X-RAY DIFFRACTION (2.1 Å) | Cite: | Molecular Bases of PDE4D Inhibition by Memory-Enhancing GEBR Library Compounds. Biochemistry, 57, 2018
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6FDI
| Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-226 | Descriptor: | 1,2-ETHANEDIOL, 1-[2-[4-[(4~{a}~{S},8~{a}~{R})-4-(3,4-dimethoxyphenyl)-1-oxidanylidene-4~{a},5,8,8~{a}-tetrahydrophthalazin-2-yl]piperi din-1-yl]-2-oxidanylidene-ethyl]-4,4-dimethyl-piperidine-2,6-dione, 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, ... | Authors: | Singh, A.K, Brown, D.G. | Deposit date: | 2017-12-24 | Release date: | 2019-04-10 | Last modified: | 2024-01-17 | Method: | X-RAY DIFFRACTION (1.9 Å) | Cite: | hPDE4D2 structure with inhibitor NPD-226 To be published
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6F8X
| Crystal structure of the PDE4D catalytic domain in complex with GEBR-26g | Descriptor: | 1,2-ETHANEDIOL, 2-[(5~{R})-3-(3-cyclopentyloxy-4-methoxy-phenyl)-4,5-dihydro-1,2-oxazol-5-yl]-~{N},~{N}-bis(2-hydroxyethyl)ethanamide, DIMETHYL SULFOXIDE, ... | Authors: | Prosdocimi, T, Donini, S, Parisini, E. | Deposit date: | 2017-12-13 | Release date: | 2018-05-16 | Last modified: | 2024-01-17 | Method: | X-RAY DIFFRACTION (1.95 Å) | Cite: | Molecular Bases of PDE4D Inhibition by Memory-Enhancing GEBR Library Compounds. Biochemistry, 57, 2018
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6FDW
| Crystal structure of T. brucei PDE-B1 catalytic domain with inhibitor NPD-356 | Descriptor: | (4aS,8aR)-2-(1-{2-aminothieno[2,3-d]pyrimidin-4-yl}piperidin-4-yl)-4-(3,4- dimethoxyphenyl)-1,2,4a,5,8,8a-hexahydrophthalazin-1-one, GLYCEROL, GUANIDINE, ... | Authors: | Singh, A.K, Brown, D.G. | Deposit date: | 2017-12-27 | Release date: | 2019-04-10 | Last modified: | 2024-01-17 | Method: | X-RAY DIFFRACTION (1.96 Å) | Cite: | TbrPDEB1 structure with inhibitor NPD-356 To be published
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6FE3
| Crystal structure of T. brucei PDE-B1 catalytic domain with inhibitor NPD-1439 | Descriptor: | 1-(2-{4-[(4aS,8aR)-4-[3,4-bis(difluoromethoxy)phenyl]-1-oxo-1,2,4a,5,8,8a-hexahydrophthalazin-2-yl]piperidin-1-yl}-2-oxoethyl)-4,4-dimethylpiperidine-2,6-dione, FORMIC ACID, GLYCEROL, ... | Authors: | Singh, A.K, Brown, D.G. | Deposit date: | 2017-12-28 | Release date: | 2019-04-10 | Last modified: | 2024-05-01 | Method: | X-RAY DIFFRACTION (1.62 Å) | Cite: | TbrPDEB1 structure with inhibitor NPD-1439 To be published
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6FDC
| Crystal structure of the PDE4D catalytic domain in complex with GEBR-32a | Descriptor: | (2~{R})-1-[3-[4-[bis(fluoranyl)methoxy]-3-cyclopentyloxy-phenyl]pyrazol-1-yl]-3-morpholin-4-yl-propan-2-ol, (2~{S})-1-[5-[4-[bis(fluoranyl)methoxy]-3-cyclopentyloxy-phenyl]pyrazol-1-yl]-3-morpholin-4-yl-propan-2-ol, 1,2-ETHANEDIOL, ... | Authors: | Prosdocimi, T, Donini, S, Parisini, E. | Deposit date: | 2017-12-22 | Release date: | 2018-05-16 | Last modified: | 2024-05-08 | Method: | X-RAY DIFFRACTION (1.45 Å) | Cite: | Molecular Bases of PDE4D Inhibition by Memory-Enhancing GEBR Library Compounds. Biochemistry, 57, 2018
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6F8R
| Crystal structure of the PDE4D catalytic domain in complex with GEBR-54 | Descriptor: | (2~{S})-1-[3-(3-cyclopentyloxy-4-methoxy-phenyl)pyrazol-1-yl]-3-morpholin-4-yl-propan-2-ol, 1,2-ETHANEDIOL, MAGNESIUM ION, ... | Authors: | Prosdocimi, T, Donini, S, Parisini, E. | Deposit date: | 2017-12-13 | Release date: | 2018-05-16 | Last modified: | 2024-01-17 | Method: | X-RAY DIFFRACTION (1.826 Å) | Cite: | Molecular Bases of PDE4D Inhibition by Memory-Enhancing GEBR Library Compounds. Biochemistry, 57, 2018
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6FDS
| Crystal structure of T. brucei PDE-B1 catalytic domain with inhibitor NPD-226 | Descriptor: | 1-[2-[4-[(4~{a}~{S},8~{a}~{R})-4-(3,4-dimethoxyphenyl)-1-oxidanylidene-4~{a},5,8,8~{a}-tetrahydrophthalazin-2-yl]piperi din-1-yl]-2-oxidanylidene-ethyl]-4,4-dimethyl-piperidine-2,6-dione, GLYCEROL, GUANIDINE, ... | Authors: | Singh, A.K, Brown, D.G. | Deposit date: | 2017-12-26 | Release date: | 2019-04-10 | Last modified: | 2024-01-17 | Method: | X-RAY DIFFRACTION (2.2 Å) | Cite: | TbrPDEB1 structure with inhibitor NPD-226 To be published
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6FE7
| Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-356 | Descriptor: | (4aS,8aR)-2-(1-{2-aminothieno[2,3-d]pyrimidin-4-yl}piperidin-4-yl)-4-(3,4- dimethoxyphenyl)-1,2,4a,5,8,8a-hexahydrophthalazin-1-one, 1,2-ETHANEDIOL, 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, ... | Authors: | Singh, A.K, Brown, D.G. | Deposit date: | 2017-12-29 | Release date: | 2019-04-10 | Last modified: | 2024-05-08 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | hPDE4D2 structure with inhibitor NPD-356 To be published
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6FET
| Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-1439 | Descriptor: | 1,2-ETHANEDIOL, 1-(2-{4-[(4aS,8aR)-4-[3,4-bis(difluoromethoxy)phenyl]-1-oxo-1,2,4a,5,8,8a-hexahydrophthalazin-2-yl]piperidin-1-yl}-2-oxoethyl)-4,4-dimethylpiperidine-2,6-dione, 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, ... | Authors: | Singh, A.K, Brown, D.G. | Deposit date: | 2018-01-03 | Release date: | 2019-04-24 | Last modified: | 2024-05-08 | Method: | X-RAY DIFFRACTION (1.88 Å) | Cite: | hPDE4D2 structure with inhibitor NPD-1439 To be published
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6FTM
| Crystal structure of T. brucei PDE-B1 catalytic domain with inhibitor NPD-048 | Descriptor: | 1,2-ETHANEDIOL, 3-{5-[(4aR,8aS)-3-cycloheptyl-4-oxo-3,4,4a,5,8,8a-hexahydrophthalazin-1-yl]-2-methoxyphenyl}prop-2-ynamide, FORMIC ACID, ... | Authors: | Singh, A.K, Brown, D.G. | Deposit date: | 2018-02-22 | Release date: | 2019-03-20 | Last modified: | 2024-01-17 | Method: | X-RAY DIFFRACTION (2.1 Å) | Cite: | Crystal structure of T. brucei PDE-B1 catalytic domain with inhibitor NPD-048 To be published
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6FRD
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6FW3
| Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-007 | Descriptor: | 1,2-ETHANEDIOL, 1-(2-{4-[(4aS,8aR)-4-(3,4-dimethoxyphenyl)-1-oxo-1,2,4a,5,8,8a-hexahydrophthalazin-2-yl]piperidin-1-yl}-2-oxoethyl)pyrrolidine-2,5-dione, 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, ... | Authors: | Singh, A.K, Brown, D.G. | Deposit date: | 2018-03-05 | Release date: | 2019-03-20 | Last modified: | 2024-01-17 | Method: | X-RAY DIFFRACTION (1.78 Å) | Cite: | hPDE4D2 structure with inhibitor NPD-007 To be published
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6FV9
| Crystal structure of T. brucei PDE-B1 catalytic domain with inhibitor NPD-007 | Descriptor: | 1-(2-{4-[(4aS,8aR)-4-(3,4-dimethoxyphenyl)-1-oxo-1,2,4a,5,8,8a-hexahydrophthalazin-2-yl]piperidin-1-yl}-2-oxoethyl)pyrrolidine-2,5-dione, GLYCEROL, MAGNESIUM ION, ... | Authors: | Singh, A.K, Brown, D.G. | Deposit date: | 2018-03-01 | Release date: | 2019-03-20 | Last modified: | 2024-01-17 | Method: | X-RAY DIFFRACTION (2.48 Å) | Cite: | TbrPDEB1 structure with inhibitor NPD-007 To be published
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5OHJ
| Human phosphodiesterase 4B catalytic domain in complex with a pyrrolidinyl inhibitor. | Descriptor: | MAGNESIUM ION, ZINC ION, [(1~{S})-2-[3,5-bis(chloranyl)-1-oxidanyl-pyridin-1-ium-4-yl]-1-[4-[bis(fluoranyl)methoxy]-3-(cyclopropylmethoxy)phenyl]ethyl] (2~{S})-1-[3-(dimethylcarbamoyl)phenyl]sulfonylpyrrolidine-2-carboxylate, ... | Authors: | Rizzi, A, Carzaniga, L, Armani, E. | Deposit date: | 2017-07-17 | Release date: | 2017-12-13 | Last modified: | 2024-05-01 | Method: | X-RAY DIFFRACTION (1.6 Å) | Cite: | Discovery and Optimization of Thiazolidinyl and Pyrrolidinyl Derivatives as Inhaled PDE4 Inhibitors for Respiratory Diseases. J. Med. Chem., 60, 2017
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6X88
| PDE6 chicken GAF domain | Descriptor: | Cone cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha' | Authors: | Ke, H. | Deposit date: | 2020-06-01 | Release date: | 2020-11-04 | Method: | X-RAY DIFFRACTION (3.1997447 Å) | Cite: | Structural Analysis of the Regulatory GAF Domains of cGMP Phosphodiesterase Elucidates the Allosteric Communication Pathway. J.Mol.Biol., 432, 2020
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8OEG
| PDE4B bound to MAPI compound 92a | Descriptor: | MAGNESIUM ION, ZINC ION, [(1~{S})-2-[3,5-bis(chloranyl)-1-oxidanyl-pyridin-4-yl]-1-(3,4-dimethoxyphenyl)ethyl] 5-[[[(1~{R})-2-[[(3~{R})-1-azabicyclo[2.2.2]octan-3-yl]oxy]-2-oxidanylidene-1-phenyl-ethyl]amino]methyl]thiophene-2-carboxylate, ... | Authors: | Rizzi, A, Armani, E. | Deposit date: | 2023-03-10 | Release date: | 2023-04-26 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.89 Å) | Cite: | Optimization of M 3 Antagonist-PDE4 Inhibitor (MAPI) Dual Pharmacology Molecules for the Treatment of COPD. J.Med.Chem., 66, 2023
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3BJC
| Crystal structure of the PDE5A catalytic domain in complex with a novel inhibitor | Descriptor: | 5-ethoxy-4-(1-methyl-7-oxo-3-propyl-6,7-dihydro-1H-pyrazolo[4,3-d]pyrimidin-5-yl)thiophene-2-sulfonamide, MAGNESIUM ION, ZINC ION, ... | Authors: | Chen, G, Wang, H, Howard, R, Cai, J, Wan, Y, Ke, H. | Deposit date: | 2007-12-03 | Release date: | 2008-04-29 | Last modified: | 2024-04-03 | Method: | X-RAY DIFFRACTION (2 Å) | Cite: | An insight into the pharmacophores of phosphodiesterase-5 inhibitors from synthetic and crystal structural studies BIOCHEM.PHARM., 75, 2008
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4WZI
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4X0F
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7LRD
| Cryo-EM of the SLFN12-PDE3A complex: Consensus subset model | Descriptor: | (4~{R})-3-[4-(diethylamino)-3-[oxidanyl(oxidanylidene)-$l^{4}-azanyl]phenyl]-4-methyl-4,5-dihydro-1~{H}-pyridazin-6-one, MAGNESIUM ION, MANGANESE (II) ION, ... | Authors: | Fuller, J.R, Garvie, C.W, Lemke, C.T. | Deposit date: | 2021-02-16 | Release date: | 2021-06-09 | Last modified: | 2024-03-06 | Method: | ELECTRON MICROSCOPY (3.22 Å) | Cite: | Structure of PDE3A-SLFN12 complex reveals requirements for activation of SLFN12 RNase. Nat Commun, 12, 2021
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7LRC
| Cryo-EM of the SLFN12-PDE3A complex: PDE3A body refinement | Descriptor: | (4~{R})-3-[4-(diethylamino)-3-[oxidanyl(oxidanylidene)-$l^{4}-azanyl]phenyl]-4-methyl-4,5-dihydro-1~{H}-pyridazin-6-one, MAGNESIUM ION, MANGANESE (II) ION, ... | Authors: | Fuller, J.R, Garvie, C.W, Lemke, C.T. | Deposit date: | 2021-02-16 | Release date: | 2021-06-09 | Last modified: | 2024-03-06 | Method: | ELECTRON MICROSCOPY (2.97 Å) | Cite: | Structure of PDE3A-SLFN12 complex reveals requirements for activation of SLFN12 RNase. Nat Commun, 12, 2021
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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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