Ligand clusters for UniProt code O00408

Ligand clusters for O00408: cGMP-dependent 3',5'-cyclic phosphodiesterase from Homo sapiens

		Top 6 (of 8) ligand clusters Cluster 1. 41 ligand types 146 ligands Cluster 2. 2 ligand types 2 ligands Cluster 3. 1 ligand type 1 ligand Cluster 4. 1 ligand type 1 ligand Cluster 5. 1 ligand type 4 ligands Cluster 6. 1 ligand type 2 ligands
Representative protein: 3ibjA

Structures

PDB		Schematic diagram
3ibjA
5u7lA
6cydA
4c1iA
6c7fA
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Cluster 1 contains 41 ligand types (of which only 20 are listed. Click for all)

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Ligand		Description
_Zn		1. Metal: _ZN × 47 PDB codes: 1z1l(A), 3ibj(A), 3itm(A), 3itu(A), 4c1i(A), 4d08(A), 4d09(A), 4htx(A), 4htz(A), 4jib(A), 5tz3(A), 5tza(A), 5tzc(A), 5tzh(A), 5tzw(A), 5tzx(A), 5tzz(A), 5u00(A), 5u7d(A), 5u7i(A), 5u7j(A), 5u7k(A), 5u7l(A), 5vp0(A), 5vp1(A), 5xkm(A), 6b96(A), 6b97(A), 6b98(A), 6blf(A), 6c7d(A), 6c7e(A), 6c7f(A), 6c7g(A), 6c7i(A), 6c7j(A), 6cyb(A), 6cyc(A), 6cyd(A), 6ezf(A), 6znd(A), 6zqz(A).
_Mg		2. Metal: _MG × 46 PDB codes: 1z1l(A), 3ibj(A), 3itu(A), 4c1i(A), 4d08(A), 4d09(A), 4htx(A), 4htz(A), 4jib(A), 5tz3(A), 5tza(A), 5tzc(A), 5tzh(A), 5tzw(A), 5tzx(A), 5tzz(A), 5u00(A), 5u7d(A), 5u7i(A), 5u7j(A), 5u7k(A), 5u7l(A), 5vp0(A), 5vp1(A), 5xkm(A), 6b96(A), 6b97(A), 6b98(A), 6blf(A), 6c7d(A), 6c7e(A), 6c7f(A), 6c7g(A), 6c7i(A), 6c7j(A), 6cyb(A), 6cyc(A), 6cyd(A), 6ezf(A), 6znd(A), 6zqz(A).
		3. Ligand: PO4 × 1 Phosphate ion PDB code: 1z1l(A).
		4. Ligand: EDO × 8 1,2-Ethanediol PDB codes: 6cyb(A), 6cyc(A), 6cyd(A).
		5. Ligand: 19F × 2 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 PDB codes: 4htx(A), 5u7d(A).
		6. Ligand: 7OJ × 2 (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 PDB codes: 5tzc(A), 5tzz(A).
		7. Ligand: 7Y4 × 2 (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 PDB codes: 5u7l(A),
		8. Ligand: 87R × 2 6-Methyl-N-[(1r)-1-[4-(Trifluoromethyloxy) phenyl]propyl]pyrazolo[1,5-A]pyrimidine-3-Carboxamide PDB codes: 5xkm(A),
		9. Ligand: 9GA × 2 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 PDB codes: 5vp1(A),
		10. Ligand: 9GJ × 2 N-{(1s)-1-[3-Fluoro-4-(Trifluoromethoxy)phenyl]-2- Methoxyethyl}-7-Methoxy-2-Oxo-2,3- Dihydropyrido[2,3- B]pyrazine-4(1h)-Carboxamide PDB codes: 5vp0(A),
		11. Ligand: EOS × 2 1-[2-Chloro-5-(2-Methylpropoxy)phenyl]-N,4-Dimethyl[1, 2,4]triazolo[4,3-A]quinoxaline-8-Carboxamide PDB codes: 6c7f(A),
		12. Ligand: 1L6 × 1 1-(2-Hydroxyethyl)-3-(2-Methylbutan-2-Yl)-5-[4-(2- Methyl-1h-Imidazol-1-Yl)phenyl]-6,7- Dihydropyrazolo[4, 3-E][1,4]diazepin-8(1h)-One PDB code: 4jib(A).
		13. Ligand: 788 × 1 N-Benzyl-4-Methyl-1-Phenyl[1,2,4]triazolo[4,3- A]quinoxaline-8-Carboxamide PDB code: 4d09(A).
		14. Ligand: 7OG × 1 [(3s)-3-(5-Methyl[1,2,4]triazolo[1,5-A]pyrimidin-7-Yl) piperidin-1-Yl](naphthalen-2-Yl)methanone PDB code: 5tza(A).
		15. Ligand: 7OM × 1 (3~{r})-1-(5-Methyl-[1,2,4]triazolo[1,5-A]pyrimidin-7- Yl)-~{N}-Naphthalen-2-Yl-Piperidine-3- Carboxamide PDB code: 5tz3(A).
		16. Ligand: 7OP × 1 [(5s)-3,3-Difluoro-5-(5-Methyl[1,2,4]triazolo[1,5- A]pyrimidin-7-Yl)piperidin-1-Yl](4- Fluorophenyl) methanone PDB code: 5tzh(A).
		17. Ligand: 7OV × 1 [(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 PDB code: 5u00(A).
		18. Ligand: 7OY × 1 (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 PDB code: 5tzx(A).
		19. Ligand: 7P4 × 1 [(5s)-3,3-Difluoro-5-(5-Methyl[1,2,4]triazolo[1,5- A]pyrimidin-7-Yl)piperidin-1-Yl](3,4- Difluorophenyl) methanone PDB code: 5tzw(A).
		20. Ligand: 7XS × 1 4-[3-(4-Methoxyphenoxy)azetidin-1-Yl]-1-Methyl-3-(2- Methylpropyl)-1h-Pyrazolo[3,4-D]pyrimidine PDB code: 5u7i(A).
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Cluster 2 contains 2 ligand types

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Ligand		Description
		1. Ligand: GOL × 1 glycerin Glycerol PDB code: 6ezf(A).
		2. Ligand: EDO × 1 1,2-Ethanediol PDB code: 6cyd(A).

Cluster 3 contains 1 ligand type

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Ligand		Description
		1. Ligand: GOL × 1 glycerin Glycerol PDB code: 6ezf(A).

Cluster 4 contains 1 ligand type

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Ligand		Description
		1. Ligand: SO4 × 1 Sulfate ion PDB code: 6ezf(A).

Cluster 5 contains 1 ligand type

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Ligand		Description
		1. Ligand: EDO × 4 1,2-Ethanediol PDB codes: 6b96(A), 6b97(A), 6cyb(A), 6cyc(A).

Cluster 6 contains 1 ligand type

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Ligand		Description
		1. Ligand: EDO × 2 1,2-Ethanediol PDB codes: 6b97(A), 6cyc(A).