Ligand clusters for UniProt code Q9NPB1

Ligand clusters for Q9NPB1: 5'(3')-deoxyribonucleotidase, mitochondrial from Homo sapiens

		Top 6 (of 16) ligand clusters Cluster 1. 22 ligand types 64 ligands Cluster 2. 5 ligand types 10 ligands Cluster 3. 3 ligand types 8 ligands Cluster 4. 3 ligand types 4 ligands Cluster 5. 4 ligand types 15 ligands Cluster 6. 2 ligand types 5 ligands
Representative protein: 4l6aA

Structures

PDB		Schematic diagram
4l6aA
1mh9A
2jauA
1z4pX
1z4kA
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Cluster 1 contains 22 ligand types (of which only 20 are listed. Click for all)

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Ligand		Description
_Mg		1. Metal: _MG × 20 PDB codes: 1mh9(A), 1q91(A), 1q92(A), 1z4i(A), 1z4j(A), 1z4k(A), 1z4l(A), 1z4m(A), 1z4p(X), 1z4q(A), 2jau(A), 2jaw(A), 4l6a(A), 4l6c(A), 4mum(A), 4nfl(A), 4yik(A), 6g22(A), 6g2l(A), 6g2m(A).
		2. Ligand: GOL × 16 glycerin Glycerol PDB codes: 1z4i(A), 1z4j(A), 1z4m(A), 4l6a(A), 4mum(A), 4mwo(A), 4nfl(A),
		3. Ligand: TRS × 2 tromethamine 2-Amino-2-Hydroxymethyl-Propane-1,3-Diol PDB codes: 4mum(A), 4yik(A).
__K		4. Metal: __K × 1 PDB code: 4mwo(A).
		5. Ligand: PO4 × 7 Phosphate ion PDB codes: 1mh9(A), 1q91(A), 4l6a(A), 4l6c(A), 4mum(A), 4mwo(A), 4nfl(A).
		6. Ligand: 2O2 × 2 1-{2-Deoxy-3,5-O-[Phenyl(phosphono)methylidene]-Beta-D- Threo-Pentofuranosyl}-5-[(E)-2- Phosphonoethenyl]pyrimidine-2,4(1h,3h)-Dione PDB codes: 4yik(A), 6g22(A).
		7. Ligand: 0BT × 1 1-{2-Deoxy-3,5-O-[(4-Iodophenyl)(phosphono) methylidene]-Beta-D-Threo-Pentofuranosyl}-5- Methylpyrimidine-2,4(1h,3h)-Dione PDB code: 4l6c(A).
		8. Ligand: 2E2 × 1 1-{3,5-O-[(4-Carboxyphenyl)(phosphono)methylidene]-2- Deoxy-Beta-D-Threo-Pentofuranosyl}-5- Methylpyrimidine- 2,4(1h,3h)-Dione PDB code: 4mwo(A).
		9. Ligand: 2JW × 1 1-{2-Deoxy-3,5-O-[(4-Nitrophenyl)(phosphono) methylidene]-Beta-D-Threo-Pentofuranosyl}-5- Methylpyrimidine-2,4(1h,3h)-Dione PDB code: 4nfl(A).
		10. Ligand: BVP × 1 (E)-5-(2-Bromovinyl)-2'-Deoxyuridine-5'-Monophosphate PDB code: 2jaw(A).
		11. Ligand: D4M × 1 [(5r)-5-(5-Methyl-2,4-Dioxo-3,4-Dihydropyrimidin- 1(2h)-Yl)-2,5-Dihydrofuran-2- Yl]methyl dihydrogen phosphate PDB code: 1z4q(A).
		12. Ligand: DGP × 1 2'-Deoxyguanosine-5'-Monophosphate PDB code: 1z4p(X).
		13. Ligand: DPB × 1 (S)-1-[2'-Deoxy-3',5'-O-(1-Phosphono)benzylidene-B-D- Threo-Pentofuranosyl]thymine PDB code: 1q91(A).
		14. Ligand: DRM × 1 {[(1r,2s)-2-(2,4-Dioxo-3,4-Dihydropyrimidin-1(2h)-Yl) cyclopentyl]oxy}methylphosphonic acid PDB code: 1q92(A).
		15. Ligand: EJ8 × 1 [(2~{r},4~{a}~{r},6~{r},7~{a}~{r})-6-[2,4- Bis(oxidanylidene)-5- (Phosphonomethylsulfanylmethyl) pyrimidin-1-Yl]-2-Phenyl-4~{a},6,7,7~{a}-Tetrahydro- 4~{h}- Furo[3,2-D][1,3]dioxin-2-Yl]phosphonic acid PDB code: 6g2l(A).
		16. Ligand: O84 × 1 [(2~{r},4~{a}~{r},6~{r},7~{a}~{r})-6-[2,4- Bis(oxidanylidene)-5-[(~{E})-3-Phosphonoprop-1- Enyl]pyrimidin-1-Yl]-2-Phenyl-4~{a},6,7,7~{a}- Tetrahydro-4~{h}-Furo[3,2-D][1,3]dioxin-2- Yl]phosphonic acid PDB code: 6g2m(A).
		17. Ligand: PO4-ATM × 1 PO4=Phosphate ion, ATM=3'-Azido-3'-Deoxythymidine-5'-Monophosphate. PDB code: 2jau(A).
		18. Ligand: T3P × 1 Thymidine-3'-Phosphate PDB code: 1z4k(A).
		19. Ligand: TMP × 1 Thymidine-5'-Phosphate PDB code: 1z4l(A).
		20. Ligand: U2P × 1 Phosphoric acid mono-[2-(2,4-Dioxo-3,4-Dihydro-2h- Pyrimidin-1-Yl)-4-Hydroxy-5-Hydroxymethyl- Tetrahydro- Furan-3-Yl] ester PDB code: 1z4j(A).
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Cluster 2 contains 5 ligand types

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Ligand		Description
		1. Ligand: GOL × 4 glycerin Glycerol PDB codes: 4l6c(A), 4mum(A), 4nfl(A).
		2. Ligand: BME × 3 Beta-Mercaptoethanol PDB codes: 6g22(A), 6g2l(A), 6g2m(A).
		3. Ligand: PEG × 1 Di(hydroxyethyl)ether PDB code: 4nfl(A).
		4. Ligand: PG4 × 1 Tetraethylene glycol PDB code: 4mum(A).
_Cl		5. Metal: _CL × 1 PDB code: 4mum(A).

Cluster 3 contains 3 ligand types

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Ligand		Description
		1. Ligand: GOL × 6 glycerin Glycerol PDB codes: 4l6a(A), 4l6c(A), 4mum(A), 4nfl(A), 4yik(A), 6g2m(A).
		2. Ligand: TRS × 1 tromethamine 2-Amino-2-Hydroxymethyl-Propane-1,3-Diol PDB code: 4nfl(A).
		3. Ligand: PEG × 1 Di(hydroxyethyl)ether PDB code: 4l6a(A).

Cluster 4 contains 3 ligand types

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Ligand		Description
__K		1. Metal: __K × 2 PDB codes: 4l6a(A), 6g2m(A).
		2. Ligand: PEG × 1 Di(hydroxyethyl)ether PDB code: 4nfl(A).
		3. Ligand: PO4 × 1 Phosphate ion PDB code: 4yik(A).

Cluster 5 contains 4 ligand types

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Ligand		Description
		1. Ligand: GOL × 8 glycerin Glycerol PDB codes: 4l6a(A), 4l6c(A), 4mum(A), 4nfl(A), 4yik(A), 6g22(A), 6g2l(A).
_Mg		2. Metal: _MG × 5 PDB codes: 1z4j(A), 1z4l(A), 1z4q(A), 2jau(A), 2jaw(A).
__K		3. Metal: __K × 1 PDB code: 4mwo(A).
		4. Ligand: EDO × 1 1,2-Ethanediol PDB code: 6g2m(A).

Cluster 6 contains 2 ligand types

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Ligand		Description
		1. Ligand: GOL × 2 glycerin Glycerol PDB codes: 1q92(A), 4l6c(A).
		2. Ligand: PEG × 3 Di(hydroxyethyl)ether PDB codes: 4l6a(A), 4nfl(A), 4yik(A).