Ligand clusters for UniProt code Q8IXJ6

Ligand clusters for Q8IXJ6: NAD-dependent protein deacetylase sirtuin-2 from Homo sapiens

		Top 6 (of 18) ligand clusters Cluster 1. 46 ligand types 75 ligands Cluster 2. 1 ligand type 1 ligand Cluster 3. 2 ligand types 2 ligands Cluster 4. 5 ligand types 7 ligands Cluster 5. 4 ligand types 4 ligands Cluster 6. 2 ligand types 4 ligands
Representative protein: 3zgoA

Structures

PDB		Schematic diagram
3zgoA
4r8mA
5marA
5g4cA
5d7qA
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Cluster 1 contains 46 ligand types (of which only 20 are listed. Click for all)

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Ligand		Description
		1. Ligand: NCA × 2 nicotinamide Nicotinamide PDB codes: 4rmj(A), 6l71(A).
		2. Ligand: DMS × 1 dimethyl sulfoxide Dimethyl sulfoxide PDB code: 5mar(A).
		3. Ligand: AR6 × 7 [(2r,3s,4r,5r)-5-(6-Aminopurin-9-Yl)-3,4- Dihydroxy-Oxolan-2-Yl]methyl [hydroxy-[[(2r,3s, 4r,5s)- 3,4,5-Trihydroxyoxolan-2-Yl]methoxy] phosphoryl] hydrogen phosphate PDB codes: 3zgv(A), 4rmj(A), 5d7o(A), 5d7p(A), 5d7q(A), 5mar(A), 6qcn(A).
		4. Ligand: OMR × 4 [(2s,3r,4r,5r)-5-[[[[(2r,3s,4r,5r)-5-(6-Aminopurin-9- Yl)-3,4-Bis(oxidanyl)oxolan-2-Yl]methoxy- Oxidanyl- Phosphoryl]oxy-Oxidanyl-Phosphoryl]oxymethyl]-2,4- Bis(oxidanyl)oxolan-3- Yl] tetradecanoate PDB codes: 4y6q(A), 6l72(A).
		5. Ligand: 3LX × 3 Tridecanethial PDB codes: 4r8m(A), 4x3p(A), 6l66(A).
		6. Ligand: BME × 3 Beta-Mercaptoethanol PDB codes: 5yql(A), 5yqm(A),
		7. Ligand: EDO × 3 1,2-Ethanediol PDB codes: 3zgo(A), 4rmj(A), 5mar(A).
		8. Ligand: NAD × 3 Nicotinamide-Adenine-Dinucleotide PDB codes: 4rmg(A), 5dy4(A), 6l66(A).
		9. Ligand: PRO-LYS-LYS-THR-GLY × 3 PDB codes: 4r8m(A), 4x3o(A), 4x3p(A).
		10. Ligand: SO4 × 3 Sulfate ion PDB codes: 5fyq(A), 5mat(A).
		11. Ligand: 3TE × 2 2-[(4,6-Dimethylpyrimidin-2-Yl)sulfanyl]-N-[5- (Naphthalen-1-Ylmethyl)-1,3-Thiazol-2-Yl]acetamide PDB codes: 4rmg(A), 4rmh(A).
		12. Ligand: 4I5 × 2 (6s)-2-Chloro-5,6,7,8,9,10- Hexahydrocyclohepta[b]indole-6-Carboxamide PDB codes: 5d7q(A),
		13. Ligand: ACT × 2 Acetate ion PDB codes: 3zgv(A),
		14. Ligand: CNA × 2 Carba-Nicotinamide-Adenine-Dinucleotide PDB codes: 4x3p(A), 5g4c(A).
		15. Ligand: F4R × 2 N-Dodecylmethanethioamide PDB codes: 7bos(A), 7bot(A).
		16. Ligand: OCZ × 2 (1s)-6-Chloro-2,3,4,9-Tetrahydro-1h-Carbazole-1- Carboxamide PDB codes: 5d7p(A),
		17. Ligand: PRO-ARG-LYS-GLN-LEU-ALA × 2 PDB codes: 6l66(A), 6l71(A).
		18. Ligand: 3TK × 1 N-(5-Benzyl-1,3-Thiazol-2-Yl)-2-[(4,6- Dimethylpyrimidin-2-Yl)sulfanyl]acetamide PDB code: 4rmi(A).
		19. Ligand: 3Y0 × 1 [[(2r,3s,4r,5r)-5-(6-Aminopurin-9-Yl)-3,4- Bis(oxidanyl)oxolan-2-Yl]methoxy-Oxidanyl- Phosphoryl] [(2r,3r,4r,5r)-3-Oxidanyl-5-Sulfanyl-4-Tridecoxy- Oxolan-2- Yl]methyl hydrogen phosphate PDB code: 4x3o(A).
		20. Ligand: 5GN × 1 N-{5-[(7-Bromonaphthalen-1-Yl)methyl]-1,3-Thiazol-2- Yl}-2-[(4,6-Dimethylpyrimidin-2- Yl)sulfanyl]acetamide PDB code: 5dy4(A).
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Cluster 2 contains 1 ligand type

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Ligand		Description
		1. Ligand: 8K9 × 1 (1~{r},9~{s})-11-[(2~{r})-3-[2,4-Bis(2-Methylbutan-2- Yl)phenoxy]-2-Oxidanyl-Propyl]-7,11- Diazatricyclo[7.3.1.0^{2,7}]trideca-2,4-Dien-6-One PDB code: 5y0z(A).

Cluster 3 contains 2 ligand types

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Ligand		Description
		1. Ligand: GOL × 1 glycerin Glycerol PDB code: 5mar(A).
		2. Ligand: P6G × 1 Hexaethylene glycol PDB code: 3zgo(A).

Cluster 4 contains 5 ligand types

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Ligand		Description
		1. Ligand: DMS × 1 dimethyl sulfoxide Dimethyl sulfoxide PDB code: 5mar(A).
		2. Ligand: GOL × 1 glycerin Glycerol PDB code: 6nr0(A).
		3. Ligand: EDO × 3 1,2-Ethanediol PDB codes: 4x3o(A), 4x3p(A), 5dy5(A).
		4. Ligand: ACT × 1 Acetate ion PDB code: 3zgv(A).
		5. Ligand: BME × 1 Beta-Mercaptoethanol PDB code: 5yql(A).

Cluster 5 contains 4 ligand types

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Ligand		Description
		1. Ligand: BME × 1 Beta-Mercaptoethanol PDB code: 5yqm(A).
		2. Ligand: EDO × 1 1,2-Ethanediol PDB code: 4x3o(A).
		3. Ligand: PEG × 1 Di(hydroxyethyl)ether PDB code: 5yqn(A).
		4. Ligand: SO4 × 1 Sulfate ion PDB code: 5mat(A).

Cluster 6 contains 2 ligand types

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Ligand		Description
		1. Ligand: SO4 × 3 Sulfate ion PDB codes: 5mat(A), 6nr0(A).
		2. Ligand: MES × 1 2-(N-Morpholino)-Ethanesulfonic acid PDB code: 4l3o(A).