UniProt O00408

cGMP-dependent 3',5'-cyclic phosphodiesterase (O00408)

cGMP-dependent 3',5'-cyclic phosphodiesterase (UniProt O00408), EC 3.1.4.17: 84 experimental structures and 1 predicted model on GenesisL1, 37 ligands bound, 286 pockets. Binding sites, druggability and experiment against…

UniProt: O00408
Protein: cGMP-dependent 3',5'-cyclic phosphodiesterase
EC: 3.1.4.17
Experimental structures: 84
Predicted models: 1
Ligands: 37
Pockets: 286 · 30 records with a druggable one

Structures

85 records of O00408 in the MolNFT archive: 84 experimental, 1 predicted.

Entry	Title	Method	Chains	Ligands	Pockets
1Z1L	The Crystal Structure of the Phosphodiesterase 2A Catalytic Domain	x-ray diffraction	A	ZN, MG, PO4	3 (best 0.76)
1Z1L	The crystal structure of the phosphodiesterase 2A catalytic domain	x-ray diffraction	A	—	—
3IBJ	X-ray structure of PDE2A	x-ray diffraction	A, B	—	—
3IBJ	X-ray structure of PDE2A	x-ray diffraction	A, B	—	—
3ITM	Catalytic domain of hPDE2A	x-ray diffraction	A, B, C, D	—	—
3ITM	Catalytic domain of HPDE2A	x-ray diffraction	A, B, C, D	—	—
3ITU	hPDE2A catalytic domain complexed with IBMX	x-ray diffraction	A, B, C, D	—	—
3ITU	HPDE2A catalytic domain complexed with ibmx	x-ray diffraction	A, B, C, D	—	—
4C1I	Selective Inhibitors of PDE2, PDE9, and PDE10: Modulators of Activity of the Central Nervous System	x-ray diffraction	A, B, C, D	—	—
4C1I	Selective inhibitors of PDE2, PDE9, and PDE10: modulators of activity of the central nervous system	x-ray diffraction	A, B, C, D	—	—
4D08	PDE2a catalytic domain in complex with a brain penetrant inhibitor	x-ray diffraction	A, B, C, D	—	—
4D08	PDE2A catalytic domain in complex with a brain penetrant inhibitor	x-ray diffraction	A, B, C, D	—	—
4D09	PDE2a catalytic domain in complex with a brain penetrant inhibitor	x-ray diffraction	A, B, C, D	—	—
4D09	PDE2A catalytic domain in complex with a brain penetrant inhibitor	x-ray diffraction	A, B, C, D	—	—
4HTX	Crystal structure of PDE2 catalytic domain in complex with BAY60-7550	x-ray diffraction	A, B, C, D	—	—
4HTX	Crystal structure of PDE2 catalytic domain in complex with BAY60-7550	x-ray diffraction	A, B, C, D	—	—
4HTZ	Crystal structure of PDE2 catalytic domain in space group P1	x-ray diffraction	A, B, C, D	—	—
4HTZ	Crystal structure of PDE2 catalytic domain in space group P1	x-ray diffraction	A, B, C, D	—	—
4JIB	Crystal structure of of PDE2-inhibitor complex	x-ray diffraction	A, B, C, D	—	—
4JIB	Crystal structure of of PDE2-inhibitor complex	x-ray diffraction	A, B, C, D	—	—
5TZ3	CRYSTAL STRUCTURE OF HUMAN PHOSPHODIESTERASE 2A IN COMPLEX with…	x-ray diffraction	A, B, C, D	7OM, ZN, MG	12 (best 0.85)
5TZ3	Crystal structure of human phosphodiesterase 2A in complex with [1,2…	x-ray diffraction	A, B, C, D	7OM, ZN, MG	—
5TZA	CRYSTAL STRUCTURE OF HUMAN PHOSPHODIESTERASE 2A WITH…	x-ray diffraction	A, B, C, D	7OG, ZN, MG	13 (best 0.82)
5TZA	Crystal structure of human phosphodiesterase 2A with 3-{5-methyl-[1,2…	x-ray diffraction	A, B, C, D	7OG, ZN, MG	—
5TZC	Crystal Structure of human PDE2a in complex with (5S)-1-[(3-bromo-4-fluorophenyl)carbonyl]-3,3-diflu…	x-ray diffraction	A, B, C, D	7OJ, ZN, MG	14 (best 0.83)
5TZC	Crystal structure of human PDE2A in complex with (5S)-1-[(3-bromo-4…	x-ray diffraction	A, B, C, D	7OJ, ZN, MG	—
5TZH	CRYSTAL STRUCTURE OF HUMAN PHOSPHODIESTERASE 2A IN COMPLEX WITH…	x-ray diffraction	A, B, C, D	7OP, ZN, MG	12 (best 0.85)
5TZH	Crystal structure of human phosphodiesterase 2A in complex with 3,3…	x-ray diffraction	A, B, C, D	7OP, ZN, MG	—
5TZW	CRYSTAL STRUCTURE OF HUMAN PHOSPHODIESTERASE 2A IN COMPLEX WITH…	x-ray diffraction	A, B, C, D	7P4, ZN, MG	—
5TZW	Crystal structure of human phosphodiesterase 2A in complex with 1-[(3…	x-ray diffraction	A, B, C, D	7P4, ZN, MG	—
5TZX	CRYSTAL STRUCTURE OF HUMAN PHOSPHODIESTERASE 2A IN COMPLEX WITH…	x-ray diffraction	A, B, C, D	7OY, ZN, MG	13 (best 0.83)
5TZX	Crystal structure of human phosphodiesterase 2A in complex with 1-[(3…	x-ray diffraction	A, B, C, D	7OY, ZN, MG	—
5TZZ	CRYSTAL STRUCTURE OF HUMAN PHOSPHODIESTERASE 2A IN COMPLEX WITH…	x-ray diffraction	A, B, C, D	7OJ, ZN, MG	13 (best 0.83)
5TZZ	Crystal structure of human phosphodiesterase 2A in complex with 1-[(3…	x-ray diffraction	A, B, C, D	7OJ, ZN, MG	—
5U00	CRYSTAL STRUCTURE OF HUMAN PHOSPHODIESTERASE 2A IN COMPLEX WITH…	x-ray diffraction	A, B, C, D	7OV, ZN, MG	14 (best 0.82)
5U00	Crystal structure of human phosphodiesterase 2A in complex with 3,3…	x-ray diffraction	A, B, C, D	7OV, ZN, MG	—
5U7D	PDE2 catalytic domain complexed with inhibitors	x-ray diffraction	A, B, C	19F, ZN, MG	—
5U7D	PDE2 catalytic domain complexed with inhibitors	x-ray diffraction	A, B, C	19F, ZN, MG	—
5U7I	PDE2 catalytic domain complexed with inhibitors	x-ray diffraction	A, B, C, D	7XS, ZN, MG	12 (best 0.83)
5U7I	PDE2 catalytic domain complexed with inhibitors	x-ray diffraction	A, B, C, D	7XS, ZN, MG	—
5U7J	PDE2 catalytic domain complexed with inhibitors	x-ray diffraction	A, B, C, D	7XV, ZN, MG	15 (best 0.82)
5U7J	PDE2 catalytic domain complexed with inhibitors	x-ray diffraction	A, B, C, D	7XV, ZN, MG	—
5U7K	PDE2 catalytic domain complexed with inhibitors	x-ray diffraction	A, B, C, D	ZN, MG, 7Y1, CL	13 (best 0.84)
5U7K	PDE2 catalytic domain complexed with inhibitors	x-ray diffraction	A, B, C, D	ZN, MG, 7Y1, CL	—
5U7L	PDE2 catalytic domain complexed with inhibitors	x-ray diffraction	A, B, C	7Y4, ZN, MG	8 (best 0.76)
5U7L	PDE2 catalytic domain complexed with inhibitors	x-ray diffraction	A, B, C	7Y4, ZN, MG	—
5VP0	Discovery of Clinical Candidate N-{(1S)-1-[3-Fluoro-4-(trifluoromethoxy)phenyl]-2-methoxyethyl}-7-me…	x-ray diffraction	A, B, C	ZN, MG, 9GJ	7 (best 0.76)
5VP0	Discovery of clinical candidate N-{(1S)-1-[3-fluoro-4…	x-ray diffraction	A, B, C	ZN, MG, 9GJ	—
5VP1	Discovery of Clinical Candidate N-{(1S)-1-[3-Fluoro-4-(trifluoromethoxy)phenyl]-2-methoxyethyl}-7-me…	x-ray diffraction	A, B, C	ZN, MG, 9GA	7 (best 0.78)
5VP1	Discovery of clinical candidate N-{(1S)-1-[3-fluoro-4…	x-ray diffraction	A, B, C	ZN, MG, 9GA	—
5XKM	Crystal structure of human phosphodiesterase 2A in complex with…	x-ray diffraction	A, B, C, D, E, F	MG, ZN, 87R	20 (best 0.84)
5XKM	Crystal structure of human phosphodiesterase 2A in complex with 6…	x-ray diffraction	A, B, C, D, E, F	MG, ZN, 87R	—
6B96	Crystal Structure of PDE2 in complex with compound 16	x-ray diffraction	A, B	ZN, MG, CZV	4 (best 0.81)
6B96	Crystal structure of PDE2 in complex with compound 16	x-ray diffraction	A, B	ZN, MG, CZV	—
6B97	Crystal structure of PDE2 in complex with complex 9	x-ray diffraction	A, B	ZN, MG, CZY	5 (best 0.78)
6B97	Crystal structure of PDE2 in complex with complex 9	x-ray diffraction	A, B	ZN, MG, CZY	—
6B98	PDE2 in complex with compound 1	x-ray diffraction	A, B	ZN, MG, D07	3 (best 0.77)
6B98	PDE2 in complex with compound 1	x-ray diffraction	A, B	ZN, MG, D07	—
6BLF	PDE2 complexed with 2-[6-fluoro-8-methylsulfonyl-9-[(1R)-1-[4-(trifluoromethyl)phenyl]ethyl]-1,2,3,4…	x-ray diffraction	A, B	DY1, ZN, MG	5 (best 0.76)
6BLF	PDE2 complexed with 2-[6-fluoro-8-methylsulfonyl-9-[(1R)-1-[4…	x-ray diffraction	A, B	DY1, ZN, MG	—

25 records more on the page itself.

Ligands

MG · Magnesium ion · in 65 records
ZN · Zinc ion · in 65 records
7OJ · (3-bromo-4-fluorophenyl)[(5S)-3,3-difluoro-5-(5-methyl[1,2,4]triazolo[1,5-a]pyrimidin-7-yl)piperidin-1-yl]methanone · in 4 records
19F · 2-(3,4-dimethoxybenzyl)-7-[(2R,3R)-2-hydroxy-6-phenylhexan-3-yl]-5-methylimidazo[5,1-f][1,2,4]triazin-4(3H)-one · in 2 records
7OG · [(3S)-3-(5-methyl[1,2,4]triazolo[1,5-a]pyrimidin-7-yl) piperidin-1-yl](naphthalen-2-yl)methanone · in 2 records
7OM · (3~{R})-1-(5-methyl-[1,2,4]triazolo[1,5-a]pyrimidin-7-yl)-~{N}-naphthalen-2-yl-piperidine-3-carboxamide · in 2 records
7OP · [(5S)-3,3-difluoro-5-(5-methyl[1,2,4]triazolo[1,5-a]pyrimidin-7-yl)piperidin-1-yl](4-fluorophenyl) methanone · in 2 records
7OV · [(5S)-3,3-difluoro-5-(5-methyl[1,2,4]triazolo[1,5-a]pyrimidin-7-yl)piperidin-1-yl](4-fluoro-3-iodophenyl)methanone · in 2 records
7OY · (3-chloro-4-fluorophenyl)[(5S)-3,3-difluoro-5-(5-methyl[1,2,4]triazolo[1,5-a]pyrimidin-7-yl)piperidin-1-yl]methanone · in 2 records
7P4 · [(5S)-3,3-difluoro-5-(5-methyl[1,2,4]triazolo[1,5-a]pyrimidin-7-yl)piperidin-1-yl](3,4-difluorophenyl)methanone · in 2 records
7XS · 4-[3-(4-methoxyphenoxy)azetidin-1-yl]-1-methyl-3-(2-methylpropyl)-1H-pyrazolo[3,4-d]pyrimidine · in 2 records
7XV · 5-[2-(2-methoxyphenyl)ethoxy]-3-(2-methylpropyl)[1,2, 4]triazolo[4,3-a]pyrazine · in 2 records
7Y1 · 3-[5-(4-ethylphenyl)-1-methyl-1H-pyrazol-4-yl]-5-propoxy[1,2,4]triazolo[4,3-a]pyrazine · in 2 records
7Y4 · (3R)-1-{3-[5-(4-ethylphenyl)-1-methyl-1H-pyrazol-4-yl]-1-methyl-1H-pyrazolo[3,4-d]pyrimidin-4-yl}-N,N-dimethylpyrrolidin-3-amine · in 2 records
87R · 6-methyl-N-[(1R)-1-[4-(trifluoromethyloxy) phenyl]propyl]pyrazolo[1,5-a]pyrimidine-3-carboxamide · in 2 records
9GA · N-{(1S)-2-hydroxy-2-methyl-1-[4-(trifluoromethoxy) phenyl]propyl}-6-methyl-5-(3-methyl-1H-1,2,4-triazol-1-yl)pyrazolo[1,5-a]pyrimidine-3-carboxamide · in 2 records
9GJ · N-{(1S)-1-[3-fluoro-4-(trifluoromethoxy)phenyl]-2-methoxyethyl}-7-methoxy-2-oxo-2,3-dihydropyrido[2,3-b]pyrazine-4(1H)-carboxamide · in 2 records
C6Z · 6-[(2,4-dichlorophenyl)methyl]pyridazine-3-thiol · in 2 records
CL · Chloride ion · in 2 records
CZV · 6-chloro-N-{1-[4-(trifluoromethyl)phenyl]cyclopropyl}-1H-pyrazolo[3,4-d]pyrimidin-4-amine · in 2 records
CZY · 6-chloro-1-methyl-N-{(1R)-1-[4-(trifluoromethyl) phenyl]ethyl}-1H-pyrazolo[3,4-d]pyrimidin-4-amine · in 2 records
D07 · 6-chloro-N,1-dimethyl-1H-pyrazolo[3,4-d]pyrimidin-4-amine · in 2 records
DY1 · [(1S)-6-fluoro-8-(methylsulfonyl)-9-{(1R)-1-[4-(trifluoromethyl)phenyl]ethyl}-2,3,4,9-tetrahydro-1H-carbazol-1-yl]acetic acid · in 2 records
EOG · 1-(2-chlorophenyl)-N,4-dimethyl[1,2,4]triazolo[4,3-a]quinoxaline-8-carboxamide · in 2 records
EOJ · 1-(2-chlorophenyl)-4-methyl-N-[(3s,5s,7s)-tricyclo[3.3.1.1~3,7~]decan-1-yl][1,2,4]triazolo[4,3-a]quinoxaline-8-carboxamide · in 2 records
EOS · 1-[2-chloro-5-(2-methylpropoxy)phenyl]-N,4-dimethyl[1, 2,4]triazolo[4,3-a]quinoxaline-8-carboxamide · in 2 records
EOY · 1-[2-chloro-5-(2-methylpropoxy)phenyl]-4-methyl-N-[(3S, 5S,7S)-tricyclo[3.3.1.1~3,7~]decan-1-yl][1,2, 4]triazolo[4,3-a]quinoxaline-8-carboxamide · in 2 records
EP7 · 1-(2-chloro-5-methoxyphenyl)-4-methyl-N-(2-methylpropyl)[1,2,4]triazolo[4,3-a]quinoxaline-8-carboxamide · in 2 records
EPV · 1-(5-tert-butoxy-2-chlorophenyl)-4-methyl-N-(2-methylpropyl)[1,2,4]triazolo[4,3-a]quinoxaline-8-carboxamide · in 2 records
FKG · 3-(hydroxymethyl)-6-methyl-1-{(1S)-1-[4-(trifluoromethyl)phenyl]ethyl}-1,5-dihydro-4H-pyrazolo[3,4-d]pyrimidin-4-one · in 2 records

Experiment against prediction

4C1I chain C against the predicted model O00408: TM-score 0.99, RMSD 0.53 Å
4C1I chain B against the predicted model O00408: TM-score 0.99, RMSD 0.60 Å
4C1I chain A against the predicted model O00408: TM-score 0.99, RMSD 0.69 Å
1Z1L chain A against the predicted model O00408: TM-score 0.97, RMSD 1.43 Å
1Z1L chain A against the predicted model O00408: TM-score 0.97, RMSD 1.43 Å
5U7I chain D against the predicted model O00408: TM-score 0.97, RMSD 1.31 Å
6B96 chain A against the predicted model O00408: TM-score 0.96, RMSD 1.45 Å
6B97 chain A against the predicted model O00408: TM-score 0.96, RMSD 1.45 Å
6CYB chain A against the predicted model O00408: TM-score 0.96, RMSD 1.45 Å
6CYC chain A against the predicted model O00408: TM-score 0.96, RMSD 1.49 Å

Elsewhere

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.