Ligand clusters for UniProt code P12499

Ligand clusters for P12499: Gag-Pol polyprotein from Human immunodeficiency virus type 1 group M subtype D (isolate Z2/CDC-Z34)

		Top 6 (of 19) ligand clusters Cluster 1. 14 ligand types 33 ligands Cluster 2. 6 ligand types 10 ligands Cluster 3. 3 ligand types 6 ligands Cluster 4. 6 ligand types 12 ligands Cluster 5. 4 ligand types 5 ligands Cluster 6. 3 ligand types 5 ligands
Representative protein: 1hxwA

Structures

PDB		Schematic diagram
1hxwA
4e43A
4dqeA
4dqhA
2xyeA
		more ...

Cluster 1 contains 14 ligand types

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Ligand		Description
		1. 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: 4dqb(A), 4dqc(A), 4dqe(A), 4dqf(A), 4dqh(A).
		2. Ligand: GOL × 4 glycerin Glycerol PDB codes: 4dqg(A), 4ejl(A),
		3. Ligand: DMS × 2 dimethyl sulfoxide Dimethyl sulfoxide PDB codes: 3kfn(A), 4ej8(A).
		4. Ligand: RIT × 1 ritonavir Ritonavir PDB code: 1hxw(A).
		5. Ligand: A88 × 1 (5r,6r)-2,4-Bis-(4-Hydroxy-3-Methoxybenzyl)-1,5- Dibenzyl-3-Oxo-6-Hydroxy-1,2,4-Triazacycloheptane PDB code: 1pro(A).
		6. Ligand: BAY × 2 N-(1-Benzyl-2,3-Dihydroxy-4-{3-Methyl-2-[2-(2-Methyl- Propane-2-Sulfonylmethyl)-3-Naphthalen-1-Yl- Propionylamino]-Butyrylamino}-5-Phenyl-Pentyl)-3- Methyl-2-[2-(2-Methyl-Propane-2- Sulfonylmethyl)-3- Naphthalen-1-Yl-Propionylamino]-Butyramide PDB codes: 1vij(A), 1vik(A).
		7. Ligand: 3TL × 8 Benzyl [(1s,4s,7s,8r,9r,10s,13s,16s)-7,10-Dibenzyl-8,9- Dihydroxy-1,16-Dimethyl-4,13-Bis(1- Methylethyl)-2,5, 12,15,18-Pentaoxo-20-Phenyl-19-Oxa-3,6,11,14,17- Pentaazaicos-1-Yl]carbamate PDB codes: 3kf0(A), 3kfn(A), 3kfp(A), 3kfr(A), 3kfs(A), 4k4p(A), 4k4q(A), 4k4r(A).
		8. Ligand: 5AH × 2 Methyl [(1s)-1-({2-[(3s)-3-Benzyl-3-Hydroxy-4-{[(1s, 2r)-2-Hydroxy-2,3-Dihydro-1h-Inden-1- Yl]amino}-4- Oxobutyl]-2-(4-Pyridin-2-Ylbenzyl)hydrazino}carbonyl)- 2,2-Dimethylpropyl]carbamate PDB codes: 2wkz(A), 2wl0(A).
		9. Ligand: IVA-VAL-VAL-STA-ALA-STA × 2 IVA=Isovaleric acid, STA=Statine. PDB codes: 4ejd(A), 4ejk(A).
		10. Ligand: 06B-06B × 1 06B=3-Bromo-2,6-Dimethoxybenzoic acid. PDB code: 4k4q(A).
		11. Ligand: ASN-LEU-LEU-GLN-LYS-LYS × 1 PDB code: 4e43(A).
		12. Ligand: C7J × 1 (3r,3as,4r,6as)-4-Chlorohexahydrofuro[2,3-B]furan-3-Yl [(2s,3r)-4-{[(4-Aminophenyl)sulfonyl](2- Methylpropyl) amino}-3-Hydroxy-1-Phenylbutan-2-Yl]carbamate PDB code: 5ah7(A).
		13. Ligand: CXG × 1 Methyl n-[(2s)-1-[2-[(4r)-5-[[(2s)-3,3-Dimethyl-1- Methylamino-1-Oxo-Butan-2-Yl]amino]-4-Hydroxy-5- Oxo-4- (Phenylmethyl)pentyl]-2-[(4-Phenylphenyl) methyl]hydrazinyl]-3,3-Dimethyl-1-Oxo-Butan-2- Yl]carbamate PDB code: 2xye(A).
		14. Ligand: G40 × 1 Methyl n-[(2s)-1-[2-[(4r)-5-[[(2s)-3,3-Dimethyl-1- Methylamino-1-Oxo-Butan-2-Yl]amino]-4-Hydroxy-5- Oxo-4- (Phenylmethyl)pentyl]-2-[(4-Thiophen-3-Ylphenyl) methyl]hydrazinyl]-3,3-Dimethyl-1-Oxo- Butan-2- Yl]carbamate PDB code: 2xyf(A).

Cluster 2 contains 6 ligand types

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Ligand		Description
		1. Ligand: DMS × 3 dimethyl sulfoxide Dimethyl sulfoxide PDB codes: 3kfp(A), 3kfs(A).
		2. Ligand: GOL × 2 glycerin Glycerol PDB codes: 4e43(A), 4ejl(A).
		3. Ligand: 4DX × 2 (1s,2s)-2-Methylcyclohexanol PDB codes: 3kf0(A), 3kfn(A).
		4. Ligand: 27B × 1 1-Bromonaphthalene-2-Carboxylic acid PDB code: 4k4r(A).
		5. Ligand: ACT × 1 Acetate ion PDB code: 4e43(A).
		6. Ligand: HGU × 1 N-Hydroxyguanidine PDB code: 4dqg(A).

Cluster 3 contains 3 ligand types

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Ligand		Description
		1. Ligand: 1F1 × 2 1h-Indole-6-Carboxylic acid PDB codes: 4ej8(A), 4ejd(A).
		2. Ligand: IOP × 2 Indolylpropionic acid PDB codes: 4ejk(A), 4ejl(A).
		3. Ligand: NO3 × 2 Nitrate ion PDB codes: 4k4q(A), 4k4r(A).

Cluster 4 contains 6 ligand types

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Ligand		Description
		1. Ligand: DMS × 7 dimethyl sulfoxide Dimethyl sulfoxide PDB codes: 3kf0(A), 3kfn(A), 4e43(A), 4ej8(A).
		2. Ligand: GOL × 1 glycerin Glycerol PDB code: 4e43(A).
		3. Ligand: EDO × 1 1,2-Ethanediol PDB code: 4ej8(A).
		4. Ligand: NO3 × 1 Nitrate ion PDB code: 4k4q(A).
		5. Ligand: PEG × 1 Di(hydroxyethyl)ether PDB code: 4ejl(A).
_Cl		6. Metal: _CL × 1 PDB code: 5ah7(A).

Cluster 5 contains 4 ligand types

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Ligand		Description
__K		1. Metal: __K × 2 PDB codes: 3kf0(A), 3kfn(A).
		2. Ligand: DMS × 1 dimethyl sulfoxide Dimethyl sulfoxide PDB code: 4e43(A).
		3. Ligand: GOL × 1 glycerin Glycerol PDB code: 4e43(A).
		4. Ligand: EDO × 1 1,2-Ethanediol PDB code: 4dqf(B).

Cluster 6 contains 3 ligand types

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Ligand		Description
		1. Ligand: GOL × 2 glycerin Glycerol PDB codes: 4dqc(A), 4e43(A).
		2. Ligand: DMS × 1 dimethyl sulfoxide Dimethyl sulfoxide PDB code: 3kfs(A).
		3. Ligand: EDO × 2 1,2-Ethanediol PDB codes: 4dqb(A),