Ligand clusters for UniProt code Q08499

Ligand clusters for Q08499: cAMP-specific 3',5'-cyclic phosphodiesterase 4D from Homo sapiens

		Top 6 (of 41) ligand clusters Cluster 1. 78 ligand types 286 ligands Cluster 2. 9 ligand types 186 ligands Cluster 3. 3 ligand types 7 ligands Cluster 4. 3 ligand types 4 ligands Cluster 5. 6 ligand types 23 ligands Cluster 6. 2 ligand types 51 ligands
Representative protein: 3iadA

Structures

PDB		Schematic diagram
3iadA
3sl5A
5lboA
4ogbA
3g4kA
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Cluster 1 contains 78 ligand types (of which only 20 are listed. Click for all)

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Ligand		Description
		1. Ligand: AMP × 2 Adenosine monophosphate PDB codes: 1ptw(A), 1tb7(A).
		2. Ligand: CMP × 1 Adenosine-3',5'-Cyclic-Monophosphate PDB code: 2pw3(A).
_Zn		3. Metal: _ZN × 95 PDB codes: 1mkd(A), 1oyn(A), 1ptw(A), 1q9m(A), 1tb7(A), 1tbb(A), 1xom(A), 1xon(A), 1xoq(A), 1xor(A), 1y2b(A), 1y2c(A), 1y2d(A), 1y2e(A), 1y2k(A), 1zkn(A), 2fm0(A), 2fm5(A), 2pw3(A), 2qyn(A), 3g4g(A), 3g4i(A), 3g4k(A), 3g4l(A), 3g58(A), 3iad(A), 3iak(A), 3k4s(A), 3sl3(A), 3sl4(A), 3sl5(A), 3sl6(A), 3sl8(A), 3v9b(A), 4ogb(A), 4w1o(A), 4wcu(A), 5k1i(A), 5k32(A), 5lbo(A), 5tkb(A), 5wh5(A), 5wh6(A), 5wqa(A), 6akr(A), 6boj(A), 6f6u(A), 6f8r(A), 6f8t(A), 6f8u(A), 6f8v(A), 6f8w(A), 6f8x(A), 6fdc(A), 6fdi(A), 6fe7(A), 6feb(A), 6fet(A), 6ft0(A), 6fta(A), 6ftw(A), 6fw3(A), 6hwo(A), 6iag(A), 6ibf(A), 6im6(A), 6imb(A), 6imd(A), 6imi(A), 6imo(A), 6imr(A), 6imt(A), 6ind(A), 6ink(A), 6inm(A), 6kjz(A), 6kk0(A), 6lrm(A), 6njh(A), 6nji(A), 6njj(A), 6rcw(A), 7cbq(A).
_Mg		4. Metal: _MG × 65 PDB codes: 1mkd(A), 1tb7(A), 1tbb(A), 1xom(A), 1xon(A), 1xoq(A), 1xor(A), 1y2b(A), 1y2c(A), 1y2d(A), 1y2e(A), 1y2k(A), 1zkn(A), 2fm0(A), 2fm5(A), 2qyn(A), 3g4g(A), 3g4i(A), 3g4k(A), 3g4l(A), 3g58(A), 3iad(A), 3iak(A), 3k4s(A), 4wcu(A), 5k1i(A), 5k32(A), 5lbo(A), 5tkb(A), 5wh5(A), 5wqa(A), 6boj(A), 6f6u(A), 6f8r(A), 6f8t(A), 6f8u(A), 6f8v(A), 6f8w(A), 6f8x(A), 6fdc(A), 6fdi(A), 6fe7(A), 6feb(A), 6fet(A), 6ft0(A), 6fta(A), 6ftw(A), 6fw3(A), 6hwo(A), 6iag(A), 6ibf(A), 6im6(A), 6imb(A), 6imd(A), 6imi(A), 6imo(A), 6imr(A), 6imt(A), 6ind(A), 6ink(A), 6inm(A), 6njh(A), 6nji(A), 6njj(A), 6rcw(A).
		5. Ligand: ROF × 2 roflumilast 3-(Cyclopropylmethoxy)-N-(3,5-Dichloropyridin-4-Yl)-4- (Difluoromethoxy)benzamide PDB codes: 1xoq(A), 3g4l(A).
		6. Ligand: A9L × 1 apremilast N-{2-[(1s)-1-(3-Ethoxy-4-Methoxyphenyl)-2- (Methylsulfonyl)ethyl]-1,3-Dioxo-2,3-Dihydro-1h- Isoindol-4-Yl}acetamide PDB code: 7cbq(A).
		7. Ligand: EV1 × 1 papaverine 1-(3,4-Dimethoxybenzyl)-6,7-Dimethoxyisoquinoline PDB code: 3iak(A).
		8. Ligand: IBM × 1 3-Isobutyl-1-Methylxanthine PDB code: 1zkn(A).
		9. Ligand: EDO × 16 1,2-Ethanediol PDB codes: 1tb7(A), 1xon(A), 1xoq(A), 1y2b(A), 1y2c(A), 1y2d(A), 1y2e(A), 1y2k(A),
		10. Ligand: DEE × 1 3,5-Dimethyl-1h-Pyrazole-4-Carboxylic acid ethyl ester PDB code: 1y2b(A).
		11. Ligand: ROL × 3 Rolipram PDB codes: 1oyn(A), 1q9m(A), 1tbb(A).
		12. Ligand: 3DE × 1 3,5-Dimethyl-1-Phenyl-1h-Pyrazole-4-Carboxylic acid ethyl ester PDB code: 1y2c(A).
		13. Ligand: 5DE × 1 1-(4-Aminophenyl)-3,5-Dimethyl-1h-Pyrazole-4-Carboxylic acid ethyl ester PDB code: 1y2e(A).
		14. Ligand: CIO × 1 Cilomilast PDB code: 1xom(A).
		15. Ligand: PIL × 1 3-(Cyclopentyloxy)-N-(3,5-Dichloropyridin-4-Yl)-4- Methoxybenzamide PDB code: 1xon(A).
		16. Ligand: 4DE × 1 1-(4-Methoxyphenyl)-3,5-Dimethyl-1h-Pyrazole-4- Carboxylic acid ethyl ester PDB code: 1y2d(A).
		17. Ligand: 7DE × 1 3,5-Dimethyl-1-(3-Nitrophenyl)-1h-Pyrazole-4-Carboxylic acid ethyl ester PDB code: 1y2k(A).
		18. Ligand: ZAR × 2 6-(4-Difluoromethoxy-3-Methoxy-Phenyl)-2h-Pyridazin-3- One PDB codes: 1mkd(A), 1xor(A).
		19. Ligand: M98 × 1 (S)-3-(2-(3-Cyclopropoxy-4-(Difluoromethoxy)phenyl)-2- (5-(1,1,1,3,3,3-Hexafluoro-2-Hydroxypropan- 2-Yl) thiazol-2-Yl)ethyl)pyridine 1-Oxide PDB code: 2fm0(A).
		20. Ligand: M99 × 1 (R)-3-(2-(3-Cyclopropoxy-4-(Difluoromethoxy)phenyl)-2- (5-(1,1,1,3,3,3-Hexafluoro-2-Hydroxypropan- 2-Yl) thiazol-2-Yl)ethyl)pyridine 1-Oxide PDB code: 2fm5(A).
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Cluster 2 contains 9 ligand types

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Ligand		Description
_Mg		1. Metal: _MG × 7 PDB codes: 5wh5(A), 6im6(A), 6imd(A), 6imi(A), 6imo(A), 6njh(A).
_Zn		2. Metal: _ZN × 2 PDB codes: 6boj(A), 6njj(A).
		3. Ligand: GOL × 1 glycerin Glycerol PDB code: 6f6u(A).
		4. Ligand: EDO × 163 1,2-Ethanediol PDB codes: 1tb7(A), 1tbb(A), 1xom(A), 1xon(A), 1xoq(A), 1y2b(A), 1y2c(A), 1y2d(A), 1y2e(A), 1y2k(A), 3g4k(A), 3g4l(A), 3g58(A), 3sl3(A), 3sl4(A), 3sl6(A), 3sl8(A), 4ogb(A), 5k32(A), 5lbo(A), 6fdi(A), 6fe7(A), 6fet(A), 6ft0(A), 6fta(A), 6ftw(A), 6fw3(A), 6hwo(A), 6iag(A), 6ibf(A), 6im6(A), 6imb(A), 6imd(A), 6imo(A), 6imr(A), 6imt(A), 6lrm(A), 6rcw(A), 7cbq(A),
		5. Ligand: PEG × 8 Di(hydroxyethyl)ether PDB codes: 3sl4(A), 4ogb(A), 6fdi(A), 6fe7(A), 6fet(A), 6fw3(A), 6hwo(A).
		6. Ligand: DTT × 2 2,3-Dihydroxy-1,4-Dithiobutane PDB codes: 5lbo(A), 6rcw(A).
		7. Ligand: BTB × 1 2-[Bis-(2-Hydroxy-Ethyl)-Amino]-2-Hydroxymethyl- Propane-1,3-Diol PDB code: 6njj(A).
		8. Ligand: PG4 × 1 Tetraethylene glycol PDB code: 6fe7(A).
_Ni		9. Metal: _NI × 1 PDB code: 6fet(A).

Cluster 3 contains 3 ligand types

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Ligand		Description
		1. Ligand: EDO × 3 1,2-Ethanediol PDB codes: 3sl4(A), 4ogb(A), 6fw3(A).
		2. Ligand: PEG × 3 Di(hydroxyethyl)ether PDB codes: 3sl3(A), 3sl8(A), 6hwo(A).
		3. Ligand: D5Z × 1 (4as,8ar)-2-[1-(2-Aminoquinazolin-4-Yl)piperidin-4-Yl]- 4-(3,4-Dimethoxyphenyl)-1,2,4a,5,8,8a- Hexahydrophthalazin-1-One PDB code: 6feb(A).

Cluster 4 contains 3 ligand types

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Ligand		Description
		1. Ligand: B3P × 2 2-[3-(2-Hydroxy-1,1-Dihydroxymethyl-Ethylamino)- Propylamino]-2-Hydroxymethyl-Propane-1,3-Diol PDB codes: 1tb7(A), 1xon(A).
		2. Ligand: EDO × 1 1,2-Ethanediol PDB code: 6fdi(A).
		3. Ligand: PEG × 1 Di(hydroxyethyl)ether PDB code: 6fe7(A).

Cluster 5 contains 6 ligand types

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Ligand		Description
		1. Ligand: DMS × 2 dimethyl sulfoxide Dimethyl sulfoxide PDB codes: 3sl4(A), 4ogb(A).
		2. Ligand: EDO × 1 1,2-Ethanediol PDB code: 1tb7(A).
		3. Ligand: EPE × 10 4-(2-Hydroxyethyl)-1-Piperazine ethanesulfonic acid PDB codes: 3iad(A), 6fe7(A), 6feb(A), 6fet(A), 6ft0(A), 6fta(A), 6ftw(A), 6fw3(A), 6hwo(A), 6ibf(A).
		4. Ligand: SO4 × 6 Sulfate ion PDB codes: 3g4i(A), 3g4k(A), 3g4l(A), 3g58(A), 5tkb(A), 6njj(A).
		5. Ligand: EDO × 3 1,2-Ethanediol PDB codes: 6im6(A), 6imd(A), 6lrm(A).
_Cl		6. Metal: _CL × 1 PDB code: 6boj(A).

Cluster 6 contains 2 ligand types

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Ligand		Description
		1. Ligand: EDO × 50 1,2-Ethanediol PDB codes: 1tb7(A), 1xom(A), 3g4k(A), 3sl3(A), 3sl4(A), 3sl5(A), 3sl6(A), 3sl8(A), 4ogb(A), 5lbo(A), 6fdi(A), 6fe7(A), 6fet(A), 6ft0(A), 6fta(A), 6ftw(A), 6fw3(A), 6hwo(A), 6iag(A), 6ibf(A), 6im6(A), 6imb(A), 6imd(A), 6imi(A), 6imo(A), 6imr(A), 6lrm(A), 6rcw(A), 7cbq(A).
		2. Ligand: DTT × 1 2,3-Dihydroxy-1,4-Dithiobutane PDB code: 5lbo(A).