Ligand clusters for UniProt code P53634

Ligand clusters for P53634: Dipeptidyl peptidase 1 from Homo sapiens

		Top 6 (of 14) ligand clusters Cluster 1. 20 ligand types 93 ligands Cluster 2. 4 ligand types 14 ligands Cluster 3. 2 ligand types 18 ligands Cluster 4. 3 ligand types 10 ligands Cluster 5. 1 ligand type 1 ligand Cluster 6. 1 ligand type 1 ligand
Representative protein: 3pdfA

Structures

PDB		Schematic diagram
3pdfA
4oemA
4oelA
4cdfB
6rniB
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Cluster 1 contains 20 ligand types

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Ligand		Description
		1. Ligand: NAG × 33 n-acetylglucosamine 2-Acetamido-2-Deoxy-Beta-D-Glucopyranose PDB codes: 1k3b(A), 2djf(A), 2djg(A), 3pdf(A), 4cdc(A), 4cdd(A), 4cde(A), 4oel(A), 4oem(A), 6ic5(A), 6ic6(A), 6ic7(A), 6rn6(A), 6rn7(A), 6rn9(A), 6rne(A), 6rni(A),
		2. Ligand: DMS × 14 dimethyl sulfoxide Dimethyl sulfoxide PDB codes: 6rn7(A), 6rn9(A), 6rne(A), 6rni(A),
		3. Ligand: 1ZB × 3 N-[(1s)-1-Benzyl-3-Diazen-1-Iumylidene-2- Oxopropyl]glycinamide PDB codes: 2djf(A),
		4. Ligand: 6AO × 3 (2s)-2-Azanyl-N-[(2s)-1-Azanylidene-3-(4-Phenylphenyl) propan-2-Yl]butanamide PDB codes: 4cdc(A),
		5. Ligand: GDI × 3 (2s)-N-[(2s)-1-Azanylidene-3-[4-(4-Cyanophenyl) phenyl]propan-2-Yl]piperidine-2-Carboxamide PDB codes: 4cdd(A),
		6. Ligand: H9B × 3 (2~{s})-~{N}-[(1~{r},2~{r})-1-(Aminomethyl)-2-[4-[4- (Trifluoromethyl)phenyl]phenyl]cyclopropyl]-2- Azanyl- Butanamide PDB codes: 6ic6(A),
		7. Ligand: H9H × 3 1-Azanyl-~{N}-[(1~{r},2~{r})-1-Cyano-2-[4-[4-(4- Methylpiperazin-1- Yl) sulfonylphenyl]phenyl]cyclopropyl]cyclohexane-1- Carboxamide PDB codes: 6ic7(A),
		8. Ligand: HB5 × 3 (2~{s})-2-Azanyl-~{N}-[(1~{r},2~{r})-1-(Iminomethyl)-2- [4-[4-(4-Methylpiperazin-1- Yl) sulfonylphenyl]phenyl]cyclopropyl]-3-Thiophen-2-Yl- Propanamide PDB codes: 6ic5(A),
		9. Ligand: K9W × 3 (2~{s})-~{N}-[(2~{s})-1-Azanyl-3-[4-(4-Cyanophenyl) phenyl]propan-2-Yl]pyrrolidine-2-Carboxamide PDB codes: 6rn7(A),
		10. Ligand: K9Z × 3 (2~{s},4~{s})-~{N}-[(2~{s})-1-Azanyl-3-[4-(4- Cyanophenyl)phenyl]propan-2-Yl]-4-Oxidanyl- Pyrrolidine-2-Carboxamide PDB codes: 6rn9(A),
		11. Ligand: KA8 × 3 (2~{s},4~{s})-~{N}-[(2~{s})-1-Azanyl-3-[4-(4- Cyanophenyl)phenyl]propan-2-Yl]-4-Fluoranyl- Pyrrolidine-2-Carboxamide PDB codes: 6rne(A),
		12. Ligand: KAQ × 3 (2~{s},4~{s})-~{N}-[(2~{s})-1-Azanyl-3-[4-(4- Cyanophenyl)phenyl]propan-2-Yl]-4-Methylsulfanyl- Pyrrolidine-2-Carboxamide PDB codes: 6rni(A),
		13. Ligand: U6B × 3 4-Azanyl-N-[(2s)-1-Azanylidene-3-[4-(4-Cyanophenyl) phenyl]propan-2-Yl]oxane-4-Carboxamide PDB codes: 4cde(A),
		14. Ligand: W2C × 3 (2s,4s)-N-[(2s)-1-Azanylidene-3-[4-(4-Cyanophenyl) phenyl]propan-2-Yl]-4-Oxidanyl-Piperidine-2- Carboxamide PDB codes: 4cdf(A),
		15. Ligand: ACT × 2 Acetate ion PDB codes: 6rne(B),
		16. Ligand: EDO × 2 1,2-Ethanediol PDB codes: 4oem(A),
		17. Ligand: GLY-LYS × 2 PDB codes: 4oem(A),
		18. Ligand: SER-TYR × 2 PDB codes: 4oel(A),
		19. Ligand: K9Q × 1 (2~{s},4~{r})-~{N}-[(2~{s})-1-Azanyl-3-(4- Phenylphenyl)propan-2-Yl]-4-Oxidanyl-Pyrrolidine-2- Carboxamide PDB code: 6rn6(F).
		20. Ligand: LXV × 1 2,5-Dibromo-N-{(3r,5s)-1-[(Z)-Iminomethyl]-5- Methylpyrrolidin-3-Yl}benzenesulfonamide PDB code: 3pdf(A).
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Cluster 2 contains 4 ligand types

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Ligand		Description
		1. Ligand: NAG × 5 n-acetylglucosamine 2-Acetamido-2-Deoxy-Beta-D-Glucopyranose PDB codes: 2djf(A), 3pdf(A), 4cdf(A), 4oel(A), 6rn6(A).
		2. Ligand: NAG-NAG × 5 NAG=2-Acetamido-2-Deoxy-Beta-D-Glucopyranose. PDB codes: 4cdd(A), 6rn7(A), 6rn9(A), 6rne(A), 6rni(A).
		3. Ligand: NAG-NAG-BMA-MAN-MAN × 3 NAG=2-Acetamido-2-Deoxy-Beta-D-Glucopyranose, BMA=Beta-D-Mannopyranose, MAN=Alpha-D-Mannopyranose. PDB codes: 6ic5(A), 6ic6(A), 6ic7(A).
		4. Ligand: NAG-NAG-BMA-BMA-BMA × 1 NAG=2-Acetamido-2-Deoxy-Beta-D-Glucopyranose, BMA=Beta-D-Mannopyranose. PDB code: 2djg(A).

Cluster 3 contains 2 ligand types

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Ligand		Description
		1. Ligand: NAG × 17 n-acetylglucosamine 2-Acetamido-2-Deoxy-Beta-D-Glucopyranose PDB codes: 2djf(B), 2djg(B), 4cdc(B), 4cdd(B), 4cde(B), 4cdf(B), 4oel(A), 4oem(A), 6ic5(B), 6ic6(B), 6ic7(B), 6rn6(B), 6rn7(B), 6rn9(B), 6rne(B), 6rni(B).
		2. Ligand: NAG-NAG × 1 NAG=2-Acetamido-2-Deoxy-Beta-D-Glucopyranose. PDB code: 3pdf(A).

Cluster 4 contains 3 ligand types

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Ligand		Description
		1. Ligand: DMS × 8 dimethyl sulfoxide Dimethyl sulfoxide PDB codes: 6rn7(A), 6rn9(A), 6rne(A), 6rni(A),
		2. Ligand: EDO × 1 1,2-Ethanediol PDB code: 4oem(A).
		3. Ligand: PEG × 1 Di(hydroxyethyl)ether PDB code: 6rne(B).

Cluster 5 contains 1 ligand type

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Ligand		Description
		1. Ligand: NAG × 1 n-acetylglucosamine 2-Acetamido-2-Deoxy-Beta-D-Glucopyranose PDB code: 2djf(A).

Cluster 6 contains 1 ligand type

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Ligand		Description
		1. Ligand: NAG × 1 n-acetylglucosamine 2-Acetamido-2-Deoxy-Beta-D-Glucopyranose PDB code: 4cdc(B).