Ligand clusters for UniProt code P03369

Ligand clusters for P03369: Gag-Pol polyprotein OS=Human immunodeficiency virus type 1 group M subtype B (isolate ARV2/SF2) GN=gag-pol PE=1 SV=3

		Top 6 (of 21) ligand clusters Cluster 1. 108 ligand types 265 ligands Cluster 2. 1 ligand type 1 ligand Cluster 3. 6 ligand types 53 ligands Cluster 4. 4 ligand types 27 ligands Cluster 5. 4 ligand types 4 ligands Cluster 6. 5 ligand types 13 ligands
Representative protein: 3fsmA

Structures

PDB		Schematic diagram
3fsmA
3gi0A
3hloA
3nxnA
3iawA
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Cluster 1 contains 108 ligand types (of which only 20 are listed. Click for all)

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Ligand		Description
		1. Ligand: ACT × 42 acetic acid Acetate ion PDB codes: 1f7a(A), 1kj4(A), 1kj7(A), 1kjf(A), 1kjh(A), 1mt7(A), 1tsq(A), 2fns(A), 2fnt(A), 2j9k(A), 2je4(A), 2q3k(A), 2qhy(A), 2qi7(A), 3ekp(A), 3ekt(A), 3ekv(A), 3ekx(A), 3el0(A), 3el1(A), 3el5(A), 3em3(A), 3lzv(A), 3mxd(A), 3o9f(A), 3o9h(A), 3oxw(A), 3oy4(A), 4epj(A), 4f75(A).
		2. Ligand: 017 × 6 darunavir (3r,3as,6ar)-Hexahydrofuro[2,3-B]furan-3-Yl(1s,2r)-3- [[(4-Aminophenyl)sulfonyl](isobutyl)amino]-1- Benzyl-2- Hydroxypropylcarbamate PDB codes: 1t3r(A), 3ekt(A), 3em6(A), 3lzv(A), 3oxw(A), 3oy4(A).
		3. Ligand: DR7 × 6 atazanavir (3s,8s,9s,12s)-3,12-Bis(1,1-Dimethylethyl)-8-Hydroxy-4, 11-Dioxo-9-(Phenylmethyl)-6-[[4-(2- Pyridinyl) phenyl]methyl]-2,5,6,10,13-Pentaazatetradecanedioic acid dimethyl ester PDB codes: 3ekw(A), 3eky(A), 3el1(A), 3el9(A), 3em4(A), 3oxx(A).
		4. Ligand: 478 × 4 amprenavir {3-[(4-Amino-Benzenesulfonyl)-Isobutyl-Amino]-1-Benzyl- 2-Hydroxy-Propyl}-Carbamic acid tetrahydro- Furan-3-Yl ester PDB codes: 3ekp(A), 3ekv(A), 3em3(A), 3oxv(B).
		5. Ligand: 1UN × 3 nelfinavir 2-[2-Hydroxy-3-(3-Hydroxy-2-Methyl-Benzoylamino)-4- Phenyl sulfanyl-Butyl]-Decahydro-Isoquinoline- 3- Carboxylic acid tert-Butylamide PDB codes: 3ekx(A), 3el0(A), 3el5(A).
		6. Ligand: ROC × 2 saquinavir (2s)-N-[(2s,3r)-4-[(2s,3s,4as,8as)-3-(Tert- Butylcarbamoyl)-3,4,4a,5,6,7,8,8a-Octahydro-1h- Isoquinolin-2-Yl]-3-Hydroxy-1-Phenyl-Butan-2-Yl]-2- (Quinolin-2-Ylcarbonylamino)butanediamide PDB codes: 3ekq(A), 3el4(A).
		7. Ligand: DMS × 1 dimethyl sulfoxide Dimethyl sulfoxide PDB code: 4epj(A).
		8. Ligand: GLY × 1 glycine PDB code: 2fnt(A).
		9. Ligand: RIT × 1 ritonavir Ritonavir PDB code: 1n49(A).
		10. Ligand: PO4 × 4 Phosphate ion PDB codes: 1mt9(A), 1t3r(A),
		11. Ligand: EDO × 1 1,2-Ethanediol PDB code: 1kzk(A).
		12. Ligand: THK × 3 4-(4-Chloro-Phenyl)-1-{3-[2-(4-Fluoro-Phenyl)-[1, 3]dithiolan-2-Yl]-Propyl}-Piperidin-4-Ol PDB codes: 1aid(A), 2aid(A),
		13. Ligand: ARQ × 1 Benzoylamino-Benzyl-Methyl-[2-Hydroxy-3-[1-Methyl- Ethyl-Oxy-N-Formamidyl]-4-Phenyl-Butyl]-Ammonium PDB code: 3aid(A).
		14. Ligand: PI4 × 1 1-[2-(8-Carbamoylmethyl-6,9-Dioxo-2-Oxa-7,10-Diaza- Bicyclo[11.2.2]heptadeca- 1(16),13(17),14- Trien-11- Yl)-2-Hydroxy-Ethyl]-Piperidine-2-Carboxylic acid tert-Butylamide PDB code: 1b6l(A).
		15. Ligand: JE2 × 1 (4r)-3-{(2s,3s)-2-Hydroxy-3-[(3-Hydroxy-2- Methylbenzoyl)amino]-4-Phenylbutanoyl}-5,5-Dimethyl-N- (2-Methylbenzyl)-1,3-Thiazolidine-4-Carboxamide PDB code: 1kzk(A).
		16. Ligand: PI8 × 1 N-13-[(10s,13s)-9,12-Dioxo-10-(2-Butyl)-2-Oxa-8,11- Diazabicyclo [13.2.2] nonadeca-15,17,18- Triene] (2r)- Benzyl-(4s)-Hydroxy-5-Aminopentanoic (1r)-Hydroxy- (2s)-Indaneamide PDB code: 1d4k(A).
		17. Ligand: PI6 × 1 [1-Benzyl-3-(8-Sec-Butyl-7,10-Dioxo-2-Oxa-6,9-Diaza- Bicyclo[11.2.2] heptadeca-1(16),13(17),14- Trien-11- Ylamino)-2-Hydroxy-Propyl]-Carbamic acid tert-Butyl ester PDB code: 1b6m(A).
		18. Ligand: HBB × 1 N-{(2r)-2-Hydroxy-2-[(8s,11s)-8-Isopropyl-6,9-Dioxo-2- Oxa-7,10-Diazabicyclo[11.2.2]heptadeca- 1(15),13,16- Trien-11-Yl]ethyl}-N-Isopentylbenzenesulfonamide PDB code: 1z1h(A).
		19. Ligand: HBH × 1 2-[(8s,11s)-11-{(1r)-1-Hydroxy-2- [Isopentyl(phenylsulfonyl)amino]ethyl}-6,9-Dioxo-2- Oxa-7,10- Diazabicyclo[11.2.2]heptadeca-1(15),13,16- Trien-8-Yl]acetamide PDB code: 1z1r(A).
		20. Ligand: PI9 × 1 (10s,13s,1'R)-13-[1'-Hydroxy-2'-(N-P- Aminobenzenesulfonyl-1''-Amino-3''-Methylbutyl)ethyl]- 8,11- Dioxo-10-Isopropyl-2-Oxa-9,12-Diazabicyclo [13.2.2]nonadeca-15,17,18-Triene PDB code: 1d4l(A).
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Cluster 2 contains 1 ligand type

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Ligand		Description
		1. Ligand: PHE-LEU-GLN-SER-ARG-PRO × 1 PDB code: 4qj2(A).

Cluster 3 contains 6 ligand types

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Ligand		Description
		1. Ligand: ACT × 8 acetic acid Acetate ion PDB codes: 1kjg(A), 1mt7(A), 1tsq(A), 2j9j(B), 3ekv(A), 3el0(A), 3em6(A), 4f73(A).
		2. Ligand: EDO × 1 1,2-Ethanediol PDB code: 1kzk(A).
		3. Ligand: PO4 × 20 Phosphate ion PDB codes: 2fgu(A), 2fgv(A), 2fnt(A), 2qi0(A), 2qi1(A), 2qi3(A), 2qi4(A), 2qi6(A), 2qi7(A), 3ekp(A), 3el9(A), 3gi4(A), 3lzv(A), 3mxd(A), 3o9g(A), 3o9h(A), 3o9i(A), 3r4b(A), 4ep2(A), 4eq0(A).
		4. Ligand: SO4 × 15 Sulfate ion PDB codes: 1b6j(A), 1b6k(A), 1b6l(A), 1b6m(A), 1b6p(A), 1cpi(A), 1d4l(A), 1mtr(A), 1z1h(A), 1z1r(A), 2j9j(A), 3bxr(A), 3bxs(A), 3hau(A), 3nxn(A).
		5. Ligand: GOL × 6 Glycerol PDB codes: 4f75(A), 4obh(A), 4obj(A), 4obk(A), 4qj9(A).
		6. Ligand: EDO × 3 1,2-Ethanediol PDB codes: 4eqj(A), 4obf(A), 4obg(A).

Cluster 4 contains 4 ligand types

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Ligand		Description
		1. Ligand: ACT × 3 acetic acid Acetate ion PDB codes: 1mt7(A), 3el5(A), 4obf(A).
		2. Ligand: SO4 × 17 Sulfate ion PDB codes: 1b6j(A), 1b6k(A), 1b6l(A), 1b6m(A), 1b6p(A), 1cpi(A), 1d4l(A), 1mtr(A), 1z1h(A), 1z1r(A), 2j9j(A), 2j9k(A), 2je4(A), 3bxr(A), 3bxs(A), 3nwx(A).
		3. Ligand: PO4 × 5 Phosphate ion PDB codes: 2fgu(A), 2fgv(A), 2q3k(A), 2qi5(A), 3oy4(A).
		4. Ligand: GOL × 2 Glycerol PDB codes: 2j9j(B), 4qj9(A).

Cluster 5 contains 4 ligand types

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Ligand		Description
		1. Ligand: ACT × 1 acetic acid Acetate ion PDB code: 2qhy(A).
		2. Ligand: EDO × 1 1,2-Ethanediol PDB code: 1kzk(A).
		3. Ligand: GOL × 1 Glycerol PDB code: 4qj8(A).
		4. Ligand: SO4 × 1 Sulfate ion PDB code: 1d4k(A).

Cluster 6 contains 5 ligand types

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Ligand		Description
		1. Ligand: ACT × 4 acetic acid Acetate ion PDB codes: 1tsq(A), 2q3k(A), 2qhy(A), 4eq0(A).
		2. Ligand: EDO × 1 1,2-Ethanediol PDB code: 1kzk(A).
		3. Ligand: GOL × 6 Glycerol PDB codes: 2j9j(A), 2j9k(A), 2je4(A), 3oxx(A), 4obj(A).
		4. Ligand: EDO × 1 1,2-Ethanediol PDB code: 4eqj(A).
		5. Ligand: PO4 × 1 Phosphate ion PDB code: 2fnt(A).