Ligand clusters for UniProt code Q9BY41

Ligand clusters for Q9BY41: Histone deacetylase 8 from Homo sapiens

		Top 6 (of 30) ligand clusters Cluster 1. 32 ligand types 186 ligands Cluster 2. 1 ligand type 1 ligand Cluster 3. 1 ligand type 1 ligand Cluster 4. 3 ligand types 5 ligands Cluster 5. 3 ligand types 4 ligands Cluster 6. 2 ligand types 4 ligands
Representative protein: 4qa0A

Structures

PDB		Schematic diagram
4qa0A
1t67A
5dc5A
3rqdA
6odbA
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Cluster 1 contains 32 ligand types (of which only 20 are listed. Click for all)

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Ligand		Description
		1. Ligand: GOL × 13 glycerin Glycerol PDB codes: 3ew8(A), 3mz4(A), 3mz7(A), 4qa0(A), 4qa1(A), 4qa3(A), 4qa7(A), 5dc6(A), 5dc7(A), 5dc8(A).
		2. Ligand: SHH × 7 vorinostat Octanedioic acid hydroxyamide phenylamide PDB codes: 1t69(A), 4qa0(A), 4qa2(A), 7jvu(A),
_Zn		3. Metal: _ZN × 49 PDB codes: 1t64(A), 1t67(A), 1t69(A), 1vkg(A), 1w22(A), 2v5w(A), 2v5x(A), 3ew8(A), 3ewf(A), 3ezp(A), 3ezt(A), 3f06(A), 3f07(A), 3f0r(A), 3rqd(A), 3sff(A), 3sfh(A), 4qa0(A), 4qa1(A), 4qa2(A), 4qa3(A), 4qa4(A), 4qa5(A), 4qa6(A), 4qa7(A), 4rn0(A), 4rn1(A), 4rn2(A), 5bwz(A), 5d1b(A), 5d1c(A), 5d1d(A), 5dc5(A), 5dc6(A), 5dc7(A), 5dc8(A), 5fcw(A), 5ths(A), 5tht(A), 5thu(A), 5thv(A), 5vi6(A), 6hsk(A), 6odb(A), 6odc(A), 7jvu(A), 7jvv(A), 7jvw(A).
		4. Ligand: B3N × 28 4-(Dimethylamino)-N-[7-(Hydroxyamino)-7- Oxoheptyl]benzamide PDB codes: 1t67(A), 3ew8(A), 3ezp(A), 3ezt(A), 3f06(A), 3mz3(A), 3mz4(A), 3mz6(A), 3mz7(A), 4qa1(A), 4qa4(A), 5dc5(A), 5ths(A), 5tht(A), 5thu(A), 5thv(A), 7jvw(A),
		5. Ligand: EDO × 16 1,2-Ethanediol PDB codes: 5ths(A), 5tht(A), 5thv(A), 5vi6(A), 7jvu(A), 7jvv(A).
		6. Ligand: ACE-ARG-HIS-ALY-ALY-MCM × 13 ACE=Acetyl group, ALY=N(6)-Acetyllysine, MCM=7-Amino-4-Methyl-Chromen-2-One. PDB codes: 2v5w(A), 5d1c(A), 5d1d(A), 5dc6(A), 5dc7(A), 5dc8(A), 7jvv(A),
		7. Ligand: TSN × 8 Trichostatin a PDB codes: 1t64(A), 3f0r(A), 4qa3(A), 5d1b(A),
		8. Ligand: ACE-ARG-HIS-ALY-ALY × 7 ACE=Acetyl group, ALY=N(6)-Acetyllysine. PDB codes: 3ewf(A), 4qa5(A), 4qa6(A), 4qa7(A).
		9. Ligand: MCM × 7 7-Amino-4-Methyl-Chromen-2-One PDB codes: 3ewf(A), 4qa5(A), 4qa6(A), 4qa7(A).
		10. Ligand: 5YA × 4 4-Naphthalen-1-Yl-~{N}-Oxidanyl-Benzamide PDB codes: 5fcw(A),
		11. Ligand: BME × 3 Beta-Mercaptoethanol PDB codes: 3ezp(A), 3ezt(A), 3f06(A).
		12. Ligand: 02G-GLY-BB9-03Y-VAL × 2 02G=(3s,4e)-3-Hydroxy-7-Sulfanylhept-4-Enoic acid, BB9=(2z)-2-Amino-3-Sulfanylprop-2-Enoic acid, 03Y=2-Methyl-L-Cysteine. PDB codes: 3rqd(A),
		13. Ligand: CRI × 2 5-(4-Methyl-Benzoylamino)-Biphenyl-3,4'-Dicarboxylic acid 3-Dimethylamide-4'-Hydroxyamide PDB codes: 1vkg(A),
		14. Ligand: IMD × 2 Imidazole PDB codes: 4rn0(A), 4rn1(A).
		15. Ligand: L6G × 2 (5r,8s,11s)-5-Methyl-8-(Propan-2-Yl)-11-[(1e)-4- Sulfanylbut-1-En-1-Yl]-3,17-Dithia-7,10,14,19,20- Pentaazatricyclo[14.2.1.1~2,5~]icosa-1(18),2(20), 16(19)-Triene-6,9,13-Trione PDB codes: 4rn0(A),
		16. Ligand: L7G × 2 (5r,8s,11s)-5-Methyl-8-(Propan-2-Yl)-11-[(1e)-4- Sulfanylbut-1-En-1-Yl]-3-Thia-7,10,14,17,21- Pentaazatricyclo[14.3.1.1~2,5~]henicosa-1(20),2(21), 16,18-Tetraene-6,9,13-Trione PDB codes: 4rn2(A),
		17. Ligand: L8G × 2 (5r,8s,11s)-5-Methyl-8-(Propan-2-Yl)-11-[(1e)-4- Sulfanylbut-1-En-1-Yl]-3-Thia-7,10,14,20,21- Pentaazatricyclo[14.3.1.1~2,5~]henicosa-1(20),2(21), 16,18-Tetraene-6,9,13-Trione PDB codes: 4rn1(A),
		18. Ligand: NHB × 2 N-Hydroxy-4-(Methyl{[5-(2-Pyridinyl)-2- Thienyl]sulfonyl}amino)benzamide PDB codes: 1w22(A),
		19. Ligand: V5X × 2 (2r)-N~8~-Hydroxy-2-{[(5-Methoxy-2-Methyl-1h-Indol-3- Yl)acetyl]amino}-N~1~-[2-(2-Phenyl-1h-Indol- 3-Yl) ethyl]octanediamide PDB codes: 2v5x(A),
		20. Ligand: XCH × 2 Droxinostat PDB codes: 5bwz(A),
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Cluster 2 contains 1 ligand type

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Ligand		Description
		1. Ligand: ACE-ARG-HIS-ALY-ALY × 1 ACE=Acetyl group, ALY=N(6)-Acetyllysine. PDB code: 3ewf(A).

Cluster 3 contains 1 ligand type

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Ligand		Description
		1. Ligand: TSN × 1 Trichostatin a PDB code: 3f0r(A).

Cluster 4 contains 3 ligand types

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Ligand		Description
		1. Ligand: GOL × 2 glycerin Glycerol PDB codes: 6odb(A),
		2. Ligand: EDO × 2 1,2-Ethanediol PDB codes: 5thv(A),
		3. Ligand: DIO × 1 1,4-Diethylene dioxide PDB code: 5vi6(A).

Cluster 5 contains 3 ligand types

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Ligand		Description
		1. Ligand: GOL × 2 glycerin Glycerol PDB codes: 4qa4(A), 4qa5(A).
		2. Ligand: BME × 1 Beta-Mercaptoethanol PDB code: 3ew8(A).
		3. Ligand: EDO × 1 1,2-Ethanediol PDB code: 5ths(A).

Cluster 6 contains 2 ligand types

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Ligand		Description
		1. Ligand: GOL × 1 glycerin Glycerol PDB code: 4qa3(A).
		2. Ligand: EDO × 3 1,2-Ethanediol PDB codes: 5ths(A), 6odc(A), 7jvv(A).