Ligand clusters for UniProt code Q9L5C8

Ligand clusters for Q9L5C8: Beta-lactamase from Escherichia coli

		Top 6 (of 18) ligand clusters Cluster 1. 28 ligand types 41 ligands Cluster 2. 9 ligand types 12 ligands Cluster 3. 5 ligand types 7 ligands Cluster 4. 3 ligand types 3 ligands Cluster 5. 2 ligand types 2 ligands Cluster 6. 3 ligand types 6 ligands
Representative protein: 1yljA

Structures

PDB		Schematic diagram
1yljA
3g30A
5ujoA
3hlwA
1ymsA
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Cluster 1 contains 28 ligand types (of which only 20 are listed. Click for all)

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Ligand		Description
		1. Ligand: CE3 × 2 cefotaxime (6r,7r)-3-(Acetyloxymethyl)-7-[[(2z)-2-(2-Amino-1,3- Thiazol-4-Yl)-2-Methoxyimino-Ethanoyl]amino]- 8-Oxo-5- Thia-1-Azabicyclo[4.2.0]oct-2-Ene-2-Carboxylic acid PDB codes: 3hlw(A),
		2. Ligand: DMS × 2 dimethyl sulfoxide Dimethyl sulfoxide PDB codes: 3g2z(A), 3g32(A).
__K		3. Metal: __K × 2 PDB codes: 2p74(A), 5kmt(A).
		4. Ligand: 1QL × 1 cefoxitin (2r)-5-[(Carbamoyloxy)methyl]-2-{(1s)-1-Methoxy-2-Oxo- 1-[(Thiophen-2-Ylacetyl)amino]ethyl}-3,6- Dihydro-2h-1, 3-Thiazine-4-Carboxylic acid PDB code: 1ymx(A).
		5. Ligand: PNN × 1 benzylpenicillin Penicillin g PDB code: 3huo(A).
		6. Ligand: WPP × 1 piperacillin Piperacillin PDB code: 3q07(A).
		7. Ligand: PO4 × 5 Phosphate ion PDB codes: 1ym1(A), 2p74(A), 3hre(A), 5kmt(A), 5kmu(A).
		8. Ligand: DN8 × 3 3-Bromo-N-[3-(1h-Tetrazol-5-Yl)phenyl]benzamide PDB codes: 4de3(A),
		9. Ligand: 0J7 × 2 3-(Pyrimidin-2-Yl)-N-[3-(1h-Tetrazol-5-Yl) phenyl]benzamide PDB codes: 4dds(A),
		10. Ligand: CE4 × 2 (2r)-2-[(R)-{[(2z)-2-(2-Amino-1,3-Thiazol-4-Yl)-2- (Methoxyimino)acetyl]amino}(carboxy)methyl]-5- Methylidene-5,6-Dihydro-2h-1,3-Thiazine-4-Carboxylic acid PDB codes: 6cyq(A), 6cyu(A).
		11. Ligand: DN6 × 2 N-[3-(1h-Tetrazol-5-Yl)phenyl]-3-(Trifluoromethyl) benzamide PDB codes: 4ddy(A),
		12. Ligand: YPP × 2 Hydrolyzed piperacillin PDB codes: 3q07(A), 3q1f(A).
		13. Ligand: 0J6 × 1 N-[3-(1h-Tetrazol-5-Yl)phenyl]-2h-Indazole-5- Carboxamide PDB code: 4de1(A).
		14. Ligand: 0JB × 1 N-[3-(1h-Tetrazol-5-Yl)phenyl]-1h-Benzimidazole-7- Carboxamide PDB code: 4de0(A).
		15. Ligand: 1CE-PO4 × 1 1CE=3-(1h-Tetrazol-5-Ylmethyl)-5,6,7,8- Tetrahydro[1]benzothieno[2,3-D]pyrimidin-4(3h)-One, PO4=Phosphate ion. PDB code: 3g34(A).
		16. Ligand: 2GK × 1 (2e)-3-[2-(Dihydroxyboranyl)-1-Benzothiophen-3-Yl]prop- 2-Enoic acid PDB code: 4len(A).
		17. Ligand: 3G3 × 1 2-[2-(1h-Tetrazol-5-Yl)ethyl]-1h-Isoindole-1,3(2h)- Dione PDB code: 3g32(A).
		18. Ligand: 8CY × 1 Ruthenocenyl-7-Aminodesacetoxycephalosporanic acid, Bound form PDB code: 5ujo(A).
		19. Ligand: DN3 × 1 3-[(Dimethylamino)methyl]-N-[3-(1h-Tetrazol-5-Yl) phenyl]benzamide PDB code: 4de2(A).
		20. Ligand: F13 × 1 3-Fluoro-N-[3-(1h-Tetrazol-5-Yl)phenyl]benzamide PDB code: 3g35(A).
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Cluster 2 contains 9 ligand types

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Ligand		Description
		1. Ligand: DMS × 1 dimethyl sulfoxide Dimethyl sulfoxide PDB code: 4de1(A).
		2. Ligand: PO4 × 3 Phosphate ion PDB codes: 1ym1(A), 2p74(A), 3hre(A).
		3. Ligand: SO4 × 2 Sulfate ion PDB codes: 1ylj(A),
		4. Ligand: 0J7 × 1 3-(Pyrimidin-2-Yl)-N-[3-(1h-Tetrazol-5-Yl) phenyl]benzamide PDB code: 4dds(A).
		5. Ligand: DN3 × 1 3-[(Dimethylamino)methyl]-N-[3-(1h-Tetrazol-5-Yl) phenyl]benzamide PDB code: 4de2(A).
		6. Ligand: DN8 × 1 3-Bromo-N-[3-(1h-Tetrazol-5-Yl)phenyl]benzamide PDB code: 4de3(A).
		7. Ligand: F13 × 1 3-Fluoro-N-[3-(1h-Tetrazol-5-Yl)phenyl]benzamide PDB code: 3g35(A).
		8. Ligand: G30 × 1 (1s,2r)-2-[(2,5-Difluorophenyl) carbamoyl]cyclopropanecarboxylic acid PDB code: 3g30(A).
		9. Ligand: YPP × 1 Hydrolyzed piperacillin PDB code: 3q1f(A).

Cluster 3 contains 5 ligand types

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Ligand		Description
		1. Ligand: PNN × 2 benzylpenicillin Penicillin g PDB codes: 3huo(A),
		2. Ligand: DMS × 1 dimethyl sulfoxide Dimethyl sulfoxide PDB code: 4ddy(A).
		3. Ligand: DN6 × 2 N-[3-(1h-Tetrazol-5-Yl)phenyl]-3-(Trifluoromethyl) benzamide PDB codes: 4ddy(A),
		4. Ligand: DN8 × 1 3-Bromo-N-[3-(1h-Tetrazol-5-Yl)phenyl]benzamide PDB code: 4de3(A).
		5. Ligand: SO4 × 1 Sulfate ion PDB code: 1ylj(A).

Cluster 4 contains 3 ligand types

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Ligand		Description
		1. Ligand: GF1 × 1 (2s)-2-[(3ar,4r,7s,7as)-1,3-Dioxooctahydro-2h-4,7- Methanoisoindol-2-Yl]propanoic acid PDB code: 3g31(A).
		2. Ligand: LSI × 1 Ruthenocenyl-7-Aminodesacetoxycephalosporanic acid PDB code: 5ujo(A).
		3. Ligand: SO4 × 1 Sulfate ion PDB code: 1ylj(A).

Cluster 5 contains 2 ligand types

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Ligand		Description
		1. Ligand: GLC-FRU × 1 GLC=Alpha-D-Glucopyranose, FRU=Beta-D-Fructofuranose. PDB code: 1ylj(A).
		2. Ligand: PEG × 1 Di(hydroxyethyl)ether PDB code: 5kmu(A).

Cluster 6 contains 3 ligand types

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Ligand		Description
		1. Ligand: DMS × 4 dimethyl sulfoxide Dimethyl sulfoxide PDB codes: 3g2z(A), 3g31(A), 4ddy(A), 4de3(A).
		2. Ligand: GF1 × 1 (2s)-2-[(3ar,4r,7s,7as)-1,3-Dioxooctahydro-2h-4,7- Methanoisoindol-2-Yl]propanoic acid PDB code: 3g31(A).
		3. Ligand: PO4 × 1 Phosphate ion PDB code: 5kmt(A).