Ligand clusters for UniProt code P14350

Ligand clusters for P14350: Pro-Pol polyprotein from Human spumaretrovirus

		Top 6 (of 27) ligand clusters Cluster 1. 34 ligand types 173 ligands Cluster 2. 3 ligand types 42 ligands Cluster 3. 2 ligand types 9 ligands Cluster 4. 2 ligand types 9 ligands Cluster 5. 2 ligand types 2 ligands Cluster 6. 2 ligand types 3 ligands
Representative protein: 3oy9A

Structures

PDB		Schematic diagram
3oy9A
4e7kA
3s3oA
3oyeA
5uopA
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Cluster 1 contains 34 ligand types (of which only 20 are listed. Click for all)

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Ligand		Description
_Mg		1. Metal: _MG × 86 PDB codes: 2x6s(A), 3dlr(A), 3l2r(A), 3l2u(A), 3os0(A), 3os1(B), 3oya(A), 3oyb(A), 3oyc(A), 3oyd(A), 3oye(A), 3oyf(A), 3oyg(A), 3oyh(A), 3oyj(A), 3oyl(A), 3oyn(A), 3s3m(A), 3s3n(A), 3s3o(A), 4bac(A), 4bdy(A), 4bdz(A), 4be0(A), 4be1(A), 4be2(A), 4ikf(A), 4ztf(A), 4ztj(A), 5frm(A), 5fro(A), 5no1(A), 5uop(A), 5uoq(A), 6rny(K).
_Mn		2. Metal: _MN × 27 PDB codes: 2x6n(A), 3l2v(A), 3l2w(A), 3oy9(A), 3oyi(B), 3oyk(B), 3oym(A), 4e7i(A), 4e7k(A), 4e7l(A),
		3. Ligand: GOL × 5 glycerin Glycerol PDB codes: 3oym(B), 4e7h(B), 5mma(A), 5uop(A), 5uoq(A).
		4. Ligand: DLU × 3 dolutegravir (4r,12as)-N-(2,4-Difluorobenzyl)-7-Hydroxy-4-Methyl-6, 8-Dioxo-3,4,6,8,12,12a-Hexahydro-2h- Pyrido[1',2':4, 5]pyrazino[2,1-B][1,3]oxazine-9-Carboxamide PDB codes: 3s3m(A), 3s3n(A), 3s3o(A).
		5. Ligand: ELV × 2 elvitegravir 6-(3-Chloro-2-Fluorobenzyl)-1-[(1s)-1-(Hydroxymethyl)- 2-Methylpropyl]-7-Methoxy-4-Oxo-1,4- Dihydroquinoline- 3-Carboxylic acid PDB codes: 3l2u(A), 3l2w(A).
		6. Ligand: RLT × 2 raltegravir N-(4-Fluorobenzyl)-5-Hydroxy-1-Methyl-2-(1-Methyl-1- {[(5-Methyl-1,3,4-Oxadiazol-2- Yl) carbonyl]amino}ethyl)-6-Oxo-1,6-Dihydropyrimidine-4- Carboxamide PDB codes: 3l2v(A), 3oya(A).
		7. Ligand: SO4 × 14 Sulfate ion PDB codes: 4bdy(A), 4bdz(A), 4be0(A), 4be1(A), 4be2(A), 5frm(A), 5frn(A), 5fro(A), 5mma(A), 5mmb(A), 5no1(A), 7adu(A), 7adv(A),
		8. Ligand: MES × 5 2-(N-Morpholino)-Ethanesulfonic acid PDB codes: 4e7i(A), 5frm(A), 5mma(A), 5no1(A), 7adu(A).
		9. Ligand: ZZX × 4 (6s)-2-(3-Chloro-4-Fluorobenzyl)-8-Ethyl-10-Hydroxy-N, 6-Dimethyl-1,9-Dioxo-1,2,6,7,8,9- Hexahydropyrazino[1', 2':1,5]pyrrolo[2,3-D]pyridazine-4-Carboxamide PDB codes: 3oyb(A), 3oyj(A), 3oyl(A), 3oyn(A).
		10. Ligand: 19C × 1 2-[(3-Chloranyl-4-Fluoranyl-Phenyl)methyl]-6, 7-Bis(oxidanyl)isoindol-1-One PDB code: 4bdz(A).
		11. Ligand: 4RT × 1 (1r,2s,5r)-8'-(3-Chloro-4-Fluorobenzyl)-6'-Hydroxy-1- (Hydroxymethyl)-2'-Methyl-9',10'-Dihydro-2'H- Spiro[bicyclo[3.1.0]hexane-2,3'-Imidazo[5,1-A][2, 6]naphthyridine]-1',5',7'(8'H)-Trione PDB code: 4ztj(A).
		12. Ligand: 8G1 × 1 (3r)-8-[(3-Chloro-4-Fluorophenyl)methyl]-6-Hydroxy-1,5, 7-Trioxo-1,2',3',5,7,8,9,10-Octahydro-2h- Spiro[imidazo[5,1-A][2,6]naphthyridine-3,1'-Indene]- 7'-Carbonitrile PDB code: 5uoq(A).
		13. Ligand: 8G4 × 1 (1s,2s,5r)-8'-[(3-Chloro-4-Fluorophenyl)methyl]-2'-[2- (2,5-Dioxo-2,5-Dihydro-1h-Pyrrol-1- Yl)ethyl]-6'- Hydroxy-9',10'-Dihydro-2'H-Spiro[bicyclo[3.1.0]hexane- 2,3'-Imidazo[5,1- A][2,6]naphthyridine]-1',5',7'(8'H)- Trione PDB code: 5uop(A).
		14. Ligand: BF3 × 1 2-(3-Chloro-2-Fluorobenzyl)-4,5-Dihydroxy-1h-Isoindole- 1,3(2h)-Dione PDB code: 4be0(A).
		15. Ligand: CI4 × 1 2-(3-Chloro-2-Fluorobenzyl)-6,7-Dihydroxy-2,3-Dihydro- 1h-Isoindol-1-One PDB code: 4be1(A).
		16. Ligand: CIJ × 1 2-(3-Chloro-4-Fluorobenzyl)-4,5-Dihydroxy-1h-Isoindole- 1,3(2h)-Dione PDB code: 4bdy(A).
		17. Ligand: HEZ × 1 Hexane-1,6-Diol PDB code: 5no1(A).
		18. Ligand: M76 × 1 N-(4-Fluorobenzyl)-2,3-Dihydroxy-1-Oxo-1,2- Dihydroisoquinoline-4-Carboxamide PDB code: 4ikf(A).
		19. Ligand: OUY × 1 Methyl 3-[5-Azanyl-6-[[2,4-Bis(fluoranyl) phenyl]methylcarbamoyl]-8-Oxidanyl-7-Oxidanylidene-1, 8- Naphthyridin-3-Yl]propanoate PDB code: 5mmb(A).
		20. Ligand: QUW × 1 4-Azanyl-N-[[2,4-Bis(fluoranyl)phenyl]methyl]-1- Oxidanyl-2-Oxidanylidene-6-(5-Oxidanylpentyl)-1,8- Naphthyridine-3-Carboxamide PDB code: 5frn(A).
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Cluster 2 contains 3 ligand types

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Ligand		Description
		1. Ligand: GOL × 39 glycerin Glycerol PDB codes: 3l2r(B), 3oy9(B), 3oya(B), 3oyb(B), 3oyc(B), 3oyd(B), 3oye(B), 3oyf(B), 3oyg(B), 3oyh(B), 3oyi(B), 3oyj(B), 3oyk(B), 3oyl(B), 3oym(B), 3oyn(B), 3s3m(B), 3s3n(B), 3s3o(B), 4bdy(B), 4bdz(B), 4be0(B), 4be1(B), 4be2(B), 4e7h(B), 4e7i(B), 4ikf(B), 4ztf(B), 4ztj(B), 5frm(B), 5frn(B), 5fro(B), 5mma(B), 5mmb(B), 5no1(B), 5uop(B), 5uoq(B), 7adu(B), 7adv(B).
		2. Ligand: HEZ × 2 Hexane-1,6-Diol PDB codes: 5mma(A), 5mmb(A).
		3. Ligand: SO4 × 1 Sulfate ion PDB code: 7adv(A).

Cluster 3 contains 2 ligand types

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Ligand		Description
		1. Ligand: GOL × 3 glycerin Glycerol PDB codes: 5frm(A), 5frn(A), 5fro(A).
		2. Ligand: HEZ × 6 Hexane-1,6-Diol PDB codes: 3s3m(A), 3s3o(A), 4e7i(A), 4ikf(A), 5mma(A), 5mmb(A).

Cluster 4 contains 2 ligand types

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Ligand		Description
		1. Ligand: GOL × 3 glycerin Glycerol PDB codes: 5frm(B), 5frn(B), 5fro(B).
		2. Ligand: HEZ × 6 Hexane-1,6-Diol PDB codes: 3s3m(B), 3s3o(B), 4e7i(B), 4ikf(B), 5mma(B), 5mmb(B).

Cluster 5 contains 2 ligand types

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Ligand		Description
		1. Ligand: HEZ × 1 Hexane-1,6-Diol PDB code: 3oym(B).
		2. Ligand: SO4 × 1 Sulfate ion PDB code: 5no1(A).

Cluster 6 contains 2 ligand types

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Ligand		Description
		1. Ligand: SO4 × 2 Sulfate ion PDB codes: 7adu(A), 7adv(A).
		2. Ligand: HEZ × 1 Hexane-1,6-Diol PDB code: 4e7h(A).