Ligand clusters for UniProt code P9WKD3

Ligand clusters for P9WKD3: Beta-lactamase from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

		Top 6 (of 15) ligand clusters Cluster 1. 27 ligand types 67 ligands Cluster 2. 7 ligand types 24 ligands Cluster 3. 2 ligand types 2 ligands Cluster 4. 1 ligand type 1 ligand Cluster 5. 3 ligand types 3 ligands Cluster 6. 3 ligand types 7 ligands
Representative protein: 5nj2A

Structures

PDB		Schematic diagram
5nj2A
3iqaA
6b6fA
5oyoA
3ny4A
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Cluster 1 contains 27 ligand types (of which only 20 are listed. Click for all)

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Ligand		Description
		1. Ligand: 9F2 × 4 ceftriaxone Ceftriaxone PDB codes: 6b6c(A), 6b6d(A), 6b6e(A), 6b6f(A).
		2. Ligand: 1RG × 2 ertapenem (4r,5s)-3-({(3s,5s)-5-[(3-Carboxyphenyl) carbamoyl]pyrrolidin-3-Yl}sulfanyl)-5-[(1s,2r)-1- Formyl- 2-Hydroxypropyl]-4-Methyl-4,5-Dihydro-1h- Pyrrole-2-Carboxylic acid PDB codes: 3m6b(A),
		3. Ligand: SMX × 2 cefamandole (6r,7r)-7-{[(2r)-2-Hydroxy-2-Phenylacetyl]amino}-3- {[(1-Methyl-1h-Tetrazol-5-Yl)sulfanyl]methyl}- 8-Oxo-5- Thia-1-Azabicyclo[4.2.0]oct-2-Ene-2-Carboxylic acid PDB codes: 3ny4(A),
		4. Ligand: 9EP × 1 cefalotin (2r)-5-[(Acetyloxy)methyl]-2-{(1r)-2-Oxo-1-[(Thiophen- 2-Ylacetyl)amino]ethyl}-3,6-Dihydro-2h-1,3- Thiazine-4- Carboxylic acid PDB code: 3nde(A).
		5. Ligand: DXF × 1 cefuroxime (2r)-5-[(Carbamoyloxy)methyl]-2-[(1r)-1-{[(2z)-2- (Furan-2-Yl)-2-(Methoxyimino)acetyl]amino}-2- Oxoethyl]-3,6-Dihydro-2h-1,3-Thiazine-4-Carboxylic acid PDB code: 3nbl(A).
		6. Ligand: NFF × 1 nafcillin (2r,4s)-2-[(1r)-1-{[(2-Ethoxynaphthalen-1-Yl) carbonyl]amino}-2-Oxoethyl]-5,5-Dimethyl-1,3- Thiazolidine-4-Carboxylic acid PDB code: 3nck(A).
		7. Ligand: PO4 × 33 Phosphate ion PDB codes: 3cg5(A), 3iqa(A), 3m6b(A), 3m6h(A), 3n6i(A), 3n7w(A), 3n8l(A), 3n8r(A), 3nc8(A), 3nde(A), 3ny4(A), 3vfh(A), 4df6(A), 4ebl(A), 4ebn(A), 4ebp(A), 4jlf(A), 4qb8(A), 4qhc(A), 4x6t(A), 5nj2(A), 6b5x(A), 6b5y(A), 6b68(A), 6b69(A), 6b6a(A), 6n14(A),
		8. Ligand: ACT × 2 Acetate ion PDB codes: 5nj2(A), 5oyo(A).
		9. Ligand: FZS × 2 (2r)-2-[(1s)-1-{[(2z)-2-(2-Amino-1,3-Thiazol-4-Yl)-2- (Methoxyimino)acetyl]amino}-2-Hydroxyethyl]- 5- Methylidene-5,6-Dihydro-2h-1,3-Thiazine-4-Carboxylic acid PDB codes: 6b6d(A), 6b6e(A).
		10. Ligand: SO4 × 2 Sulfate ion PDB codes: 3zhh(A),
		11. Ligand: 1TE × 1 Tebipenem PDB code: 4qb8(A).
		12. Ligand: 2RG × 1 (2s,3r,4s)-4-({(3s,5s)-5-[(3-Carboxyphenyl) carbamoyl]pyrrolidin-3-Yl}sulfanyl)-2-[(1s,2r)-1- Formyl-2-Hydroxypropyl]-3-Methyl-3,4-Dihydro-2h- Pyrrole-5-Carboxylic acid PDB code: 3m6h(A).
		13. Ligand: 33V × 1 (3r,6r,7s)-7-[(2r,3ar)-Hexahydropyrazolo[1,5-C][1, 3]thiazin-2-Yl]-6-(Hydroxymethyl)-1,4- Thiazepane-3- Carboxylic acid PDB code: 4qhc(A).
		14. Ligand: 3Y6 × 1 3-[(2r)-2-(Dihydroxyboranyl)-2-{[(2r)-2-{[(4-Ethyl-2,3- Dioxo-3,4-Dihydropyrazin-1(2h)- Yl)carbonyl]amino}-2- (4-Hydroxyphenyl)acetyl]amino}ethyl]benzoic acid PDB code: 4x6t(A).
		15. Ligand: 7EP × 1 (2r,4s)-2-[(1r)-1-{[(2,6-Dimethoxyphenyl) carbonyl]amino}-2-Oxoethyl]-5,5-Dimethyl-1,3- Thiazolidine-4-Carboxylic acid PDB code: 3ndg(A).
		16. Ligand: AIX × 1 (2r,4s)-2-[(1r)-1-{[(2r)-2-Amino-2-Phenylacetyl]amino}- 2-Oxoethyl]-5,5-Dimethyl-1,3-Thiazolidine- 4-Carboxylic acid PDB code: 3n8l(A).
		17. Ligand: AXL × 1 2-{1-[2-Amino-2-(4-Hydroxy-Phenyl)-Acetylamino]-2-Oxo- Ethyl}-5,5-Dimethyl-Thiazolidine-4- Carboxylic acid PDB code: 3n7w(A).
		18. Ligand: CB9 × 1 (2r,4s)-2-[(1r)-1-{[(2s)-2-Carboxy-2- Phenylacetyl]amino}-2-Oxoethyl]-5,5-Dimethyl-1,3- Thiazolidine-4-Carboxylic acid PDB code: 3n8r(A).
		19. Ligand: CD8 × 1 (2r)-2-[(1s)-1-(Benzoylamino)-1-Methoxy-2-Oxoethyl]-5- Methylidene-5,6-Dihydro-2h-1,3-Thiazine-4- Carboxylic acid PDB code: 3vff(A).
		20. Ligand: DH4 × 1 2-[(1r)-1-{[(E)-Azepan-1-Ylmethylidene]amino}-2- Oxoethyl]-5,5-Dimethyl-1,3-Thiazolidine-4- Carboxylic acid PDB code: 3nc8(A).
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Cluster 2 contains 7 ligand types

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Ligand		Description
		1. Ligand: 9F2 × 8 ceftriaxone Ceftriaxone PDB codes: 6b5y(A), 6b68(A), 6b69(A), 6b6a(A),
		2. Ligand: PO4 × 10 Phosphate ion PDB codes: 3vfh(A), 4ebl(A), 4ebn(A), 4ebp(A), 4jlf(A), 4q8i(A), 4qb8(A), 4x6t(A),
		3. Ligand: FZS × 2 (2r)-2-[(1s)-1-{[(2z)-2-(2-Amino-1,3-Thiazol-4-Yl)-2- (Methoxyimino)acetyl]amino}-2-Hydroxyethyl]- 5- Methylidene-5,6-Dihydro-2h-1,3-Thiazine-4-Carboxylic acid PDB codes: 6b68(A), 6b6a(A).
		4. Ligand: ACT × 1 Acetate ion PDB code: 5nj2(A).
		5. Ligand: CD6 × 1 (2r)-5-Methylidene-2-{(1r)-2-Oxo-1-[(Phenylacetyl) amino]ethyl}-5,6-Dihydro-2h-1,3-Thiazine-4- Carboxylic acid PDB code: 3vfh(A).
		6. Ligand: CUG × 1 (2r)-2-[(S)-{[(2e)-2-(2-Amino-1,3-Thiazol-4-Yl)-2- (Methoxyimino)acetyl]amino}(carboxy)methyl]-5- (Hydroxymethyl)-3,6-Dihydro-2h-1,3-Thiazine-4- Carboxylic acid PDB code: 6b69(A).
		7. Ligand: SO4 × 1 Sulfate ion PDB code: 3zhh(A).

Cluster 3 contains 2 ligand types

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Ligand		Description
		1. Ligand: SMX × 1 cefamandole (6r,7r)-7-{[(2r)-2-Hydroxy-2-Phenylacetyl]amino}-3- {[(1-Methyl-1h-Tetrazol-5-Yl)sulfanyl]methyl}- 8-Oxo-5- Thia-1-Azabicyclo[4.2.0]oct-2-Ene-2-Carboxylic acid PDB code: 3ny4(A).
		2. Ligand: ACT × 1 Acetate ion PDB code: 5oyo(A).

Cluster 4 contains 1 ligand type

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Ligand		Description
		1. Ligand: SMX × 1 cefamandole (6r,7r)-7-{[(2r)-2-Hydroxy-2-Phenylacetyl]amino}-3- {[(1-Methyl-1h-Tetrazol-5-Yl)sulfanyl]methyl}- 8-Oxo-5- Thia-1-Azabicyclo[4.2.0]oct-2-Ene-2-Carboxylic acid PDB code: 3ny4(A).

Cluster 5 contains 3 ligand types

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Ligand		Description
		1. Ligand: ACT × 1 Acetate ion PDB code: 5oyo(A).
		2. Ligand: PGE × 1 Triethylene glycol PDB code: 5oyo(A).
		3. Ligand: PO4 × 1 Phosphate ion PDB code: 4x6t(A).

Cluster 6 contains 3 ligand types

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Ligand		Description
		1. Ligand: PO4 × 5 Phosphate ion PDB codes: 3cg5(A), 4ebn(A), 4jlf(A), 4q8i(A), 4qhc(A).
		2. Ligand: ACT × 1 Acetate ion PDB code: 5nj2(A).
		3. Ligand: SO4 × 1 Sulfate ion PDB code: 3zhh(A).