Ligand clusters for UniProt code I6Y9J2

Ligand clusters for I6Y9J2: L,D-transpeptidase 2 from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

		Top 6 (of 29) ligand clusters Cluster 1. 23 ligand types 26 ligands Cluster 2. 1 ligand type 3 ligands Cluster 3. 3 ligand types 11 ligands Cluster 4. 3 ligand types 8 ligands Cluster 5. 4 ligand types 6 ligands Cluster 6. 2 ligand types 5 ligands
Representative protein: 5dc2A

Structures

PDB		Schematic diagram
5dc2A
5dujA
5dzpA
5e1gA
5dzjA
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Cluster 1 contains 23 ligand types (of which only 20 are listed. Click for all)

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Ligand		Description
		1. Ligand: GOL × 1 glycerin Glycerol PDB code: 5d7h(A).
		2. Ligand: 2RG × 2 (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 codes: 6iyv(B), 6lqb(A).
		3. Ligand: 58U × 2 (4s)-4-Methyl-2,5,7-Trioxoheptanoic acid PDB codes: 5dc2(A), 5dcc(A).
		4. Ligand: 6B7 × 2 (2~{r},3~{r},4~{r})-4-Methyl-3-(2-Oxidanylidene-2- Propoxy-Ethyl)sulfanyl-5-[(2~{s},3~{r})-3- Oxidanyl-1- Oxidanylidene-Butan-2-Yl]-3,4-Dihydro-2~{h}-Pyrrole-2- Carboxylic acid PDB codes: 5dzj(A), 5dzp(A).
		5. Ligand: 3V5 × 1 (3s,5s)-3-({[(Aminomethyl)amino]methyl}sulfanyl)-5- [(2s)-1,3-Dioxobutan-2-Yl]-L-Proline PDB code: 4qtf(A).
		6. Ligand: 6B8 × 1 (2s,3r,4r)-2-[(2s,3r)-3-Hydroxy-1-Oxobutan-2-Yl]-3- Methyl-4-(Methylsulfanyl)-3,4-Dihydro-2h- Pyrrole-5- Carboxylic acid PDB code: 5e1i(A).
		7. Ligand: 6CL × 1 6-Carboxylysine PDB code: 7kem(A).
		8. Ligand: 6QR × 1 (2~{s},3~{r},4~{r})-4-(1~{h}-Indol-3-Ylsulfanyl)-3- Methyl-2-[(2~{s},3~{s})-3-Oxidanyl-1- Oxidanylidene- Butan-2-Yl]-3,4-Dihydro-2~{h}-Pyrrole-5-Carboxylic acid PDB code: 5k69(A).
		9. Ligand: BME × 1 Beta-Mercaptoethanol PDB code: 5duj(A).
		10. Ligand: BT6 × 1 Benzenethiol PDB code: 7a0z(A).
		11. Ligand: DGF × 1 (2r,5r)-2-[(2s,3r)-3-Hydroxy-1-Oxobutan-2-Yl]-5-[(2r)- Tetrahydrofuran-2-Yl]-2,5-Dihydro-1,3- Thiazole-4- Carboxylic acid PDB code: 5duj(A).
		12. Ligand: DGL × 1 D-Glutamic acid PDB code: 7kem(A).
		13. Ligand: DRW × 1 (2s,3r,4s)-2-[(2s,3r)-3-Hydroxy-1-Oxobutan-2-Yl]-3- Methyl-4-({(3s,5s)-5- [(Sulfamoylamino) methyl]pyrrolidin-3-Yl}sulfanyl)-3,4-Dihydro-2h- Pyrrole-5-Carboxylic acid PDB code: 5dvp(A).
		14. Ligand: DWZ × 1 (2s,3r,4s)-4-{[(3s,5s)-5-(Dimethylcarbamoyl)pyrrolidin- 3-Yl]sulfanyl}-2-[(1s,2r)-1-Formyl-2- Hydroxypropyl]-3- Methyl-3,4-Dihydro-2h-Pyrrole-5-Carboxylic acid PDB code: 4qr7(A).
		15. Ligand: IM2 × 1 (5r)-5-[(1s,2r)-1-Formyl-2-Hydroxypropyl]-3-[(2-{[(E)- Iminomethyl]amino}ethyl)sulfanyl]-4,5- Dihydro-1h- Pyrrole-2-Carboxylic acid PDB code: 6iyw(A).
		16. Ligand: MNB × 1 5-Mercapto-2-Nitro-Benzoic acid PDB code: 5lb1(A).
		17. Ligand: MXR × 1 (2s,3r,4s)-4-{[(3s,5r)-5-(Dimethylcarbamoyl)pyrrolidin- 3-Yl]sulfanyl}-2-[(2s,3r)-3-Hydroxy-1- Oxobutan-2-Yl]- 3-Methyl-3,4-Dihydro-2h-Pyrrole-5-Carboxylic acid PDB code: 3vyp(A).
		18. Ligand: QU5 × 1 4-Methoxycyclohexa-2,5-Diene-1-Thione PDB code: 7a10(A).
		19. Ligand: SDQ × 1 Phenylmethanethiol PDB code: 7a1e(A).
		20. Ligand: SO4 × 1 Sulfate ion PDB code: 6iyv(B).
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Cluster 2 contains 1 ligand type

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Ligand		Description
		1. Ligand: MLD × 3 Glcnac(beta1-4)-Murnac(1,6-Anhydro)-L-Ala-Gamma-D-Glu- Meso-A2pm-D-Ala PDB codes: 4qr7(A), 4qrb(A), 4qtf(A).

Cluster 3 contains 3 ligand types

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Ligand		Description
		1. Ligand: GOL × 4 glycerin Glycerol PDB codes: 5e1i(A), 5k69(A), 6iyw(A), 6lqb(A).
		2. Ligand: PEG × 5 Di(hydroxyethyl)ether PDB codes: 5dc2(A), 5dcc(A), 6iyv(B).
		3. Ligand: PGE × 2 Triethylene glycol PDB codes: 5dc2(A), 5dcc(A).

Cluster 4 contains 3 ligand types

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Ligand		Description
		1. Ligand: GOL × 5 glycerin Glycerol PDB codes: 3vyp(A), 5k69(A), 6iyv(B), 6iyw(A), 6lqb(A).
		2. Ligand: PGE × 2 Triethylene glycol PDB codes: 5dc2(A), 5dcc(A).
		3. Ligand: 0JC × 1 Di-Mu-Iodobis(ethylenediamine)diplatinum(ii) PDB code: 7kem(A).

Cluster 5 contains 4 ligand types

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Ligand		Description
		1. Ligand: DMS × 1 dimethyl sulfoxide Dimethyl sulfoxide PDB code: 7a1c(A).
		2. Ligand: ACT × 2 Acetate ion PDB codes: 7a11(A), 7a1e(A).
		3. Ligand: SO4 × 2 Sulfate ion PDB codes: 5dc2(A), 5dcc(A).
		4. Ligand: 0JC × 1 Di-Mu-Iodobis(ethylenediamine)diplatinum(ii) PDB code: 7kem(A).

Cluster 6 contains 2 ligand types

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Ligand		Description
		1. Ligand: GOL × 3 glycerin Glycerol PDB codes: 5d7h(A), 5dc2(A), 5dcc(A).
		2. Ligand: PEG × 2 Di(hydroxyethyl)ether PDB codes: 5dc2(A), 5dcc(A).