Ligand clusters for UniProt code P00489

Ligand clusters for P00489: Glycogen phosphorylase, muscle form from Oryctolagus cuniculus

		Top 6 (of 27) ligand clusters Cluster 1. 176 ligand types 348 ligands Cluster 2. 31 ligand types 37 ligands Cluster 3. 26 ligand types 92 ligands Cluster 4. 5 ligand types 10 ligands Cluster 5. 4 ligand types 5 ligands Cluster 6. 2 ligand types 2 ligands
Representative protein: 3gpbA

Structures

PDB		Schematic diagram
3gpbA
3g2jA
3g2hA
3g2iA
3l7bA
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Cluster 1 contains 176 ligand types (of which only 20 are listed. Click for all)

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Ligand		Description
		1. Ligand: PO4 × 7 Phosphate ion PDB codes: 1axr(A), 1noj(A), 2g9q(A), 2g9u(A), 2g9v(A), 2skd(A).
		2. Ligand: G1P × 1 1-O-Phosphono-Alpha-D-Glucopyranose PDB code: 3gpb(A).
		3. Ligand: PLP × 128 pyridoxal phosphate Pyridoxal-5'-Phosphate PDB codes: 1axr(A), 1b4d(A), 1bx3(A), 1c50(A), 1c8k(A), 1c8l(A), 1e1y(A), 1fs4(A), 1ftq(A), 1ftw(A), 1fty(A), 1fu4(A), 1fu7(A), 1fu8(A), 1gfz(A), 1gg8(A), 1ggn(A), 1gpa(A), 1gpb(A), 1gpy(A), 1h5u(A), 1hlf(A), 1k06(A), 1k08(A), 1kti(A), 1lwn(A), 1lwo(A), 1noi(A), 1noj(A), 1nok(A), 1p29(A), 1p2b(A), 1p2d(A), 1p2g(A), 1p4g(A), 1p4h(A), 1p4j(A), 1uzu(A), 1wut(A), 1wuy(A), 1wv0(A), 1wv1(A), 1ww2(A), 1ww3(A), 1xc7(A), 1xkx(A), 1xl0(A), 1xl1(A), 1z62(A), 2amv(A), 2f3p(A), 2f3q(A), 2f3s(A), 2f3u(A), 2fet(A), 2ff5(A), 2ffr(A), 2gpa(A), 2gpb(A), 2pri(A), 2prj(A), 2qn7(A), 2qn8(A), 2qn9(A), 2skc(A), 2skd(A), 2ske(A), 3amv(A), 3bd7(A), 3bd8(A), 3bda(A), 3gpb(A), 3zcp(A), 3zcq(A), 3zcr(A), 3zcs(A), 3zct(A), 3zcu(A), 3zcv(A), 4ctm(A), 4ctn(A), 4cto(A), 4gpb(A), 4yi3(A), 4yi5(A), 4yua(A), 4z5x(A), 5gpb(A), 5jtt(A), 5jtu(A), 5lrc(A), 5lrd(A), 5lre(A), 5lrf(A), 5mcb(A), 5mem(A), 5o50(A), 5o52(A), 5o54(A), 5o56(A), 5owy(A), 5owz(A), 5ox0(A), 5ox1(A), 5ox3(A), 5ox4(A), 6f3j(A), 6f3l(A), 6f3r(A), 6f3s(A), 6f3u(A), 6gpb(A), 6qa6(A), 6qa7(A), 6qa8(A), 6r0h(A), 6r0i(A), 6s4h(A), 6s4k(A), 6s4o(A), 6s4p(A), 6s4r(A), 6s51(A), 6s52(A), 7gpb(A), 7o8e(A), 8gpb(A), 9gpb(A).
		4. Ligand: GLC × 11 d-glucose Alpha-D-Glucopyranose PDB codes: 1e1y(A), 1h5u(A), 1lwn(A), 1lwo(A), 2gpa(A), 2gpb(A), 2pyd(A), 2skc(A), 2skd(A), 2ske(A), 3amv(A).
		5. Ligand: DMS × 3 dimethyl sulfoxide Dimethyl sulfoxide PDB codes: 3g2h(A), 4ctn(A), 4yi3(A).
		6. Ligand: CFF × 2 caffeine Caffeine PDB codes: 1c8l(A), 1gfz(A).
		7. Ligand: GOL × 2 glycerin Glycerol PDB codes: 1c8l(A), 2amv(A).
		8. Ligand: AZZ × 1 zidovudine 3'-Azido-3'-Deoxythymidine PDB code: 3bcr(A).
		9. Ligand: H2P × 1 1-Deoxy-2-O-Phosphono-Alpha-D-Gluco-Hept-2-Ulopyranose PDB code: 6gpb(A).
		10. Ligand: GFP × 1 2-Deoxy-2-Fluoro-1-O-Phosphono-Alpha-D-Glucopyranose PDB code: 4gpb(A).
		11. Ligand: PO3 × 1 Phosphite ion PDB code: 2ske(A).
		12. Ligand: FPO × 1 Fluoro-Phosphite ion PDB code: 2skc(A).
		13. Ligand: CBF × 1 (2r,3r,4s,5s,6r)-2,3,4,5-Tetrahydroxy-6- (Hydroxymethyl)oxane-2-Carboxamide PDB code: 1p4j(A).
		14. Ligand: GLG × 1 Alpha-D-Glucopyranosyl-2-Carboxylic acid amide PDB code: 1gg8(A).
		15. Ligand: 1AB × 1 1,4-Dideoxy-1,4-Imino-D-Arabinitol PDB code: 2g9q(A).
		16. Ligand: NBG × 2 N-Acetyl-Beta-D-Glucopyranosylamine PDB codes: 1ww2(A), 2prj(A).
		17. Ligand: CR1 × 1 N-(Methoxycarbonyl)-Beta-D-Glucopyranosylamine PDB code: 1fu7(A).
		18. Ligand: GPM × 1 (1s)-1,5-Anhydro-1-(Phosphonomethyl)-D-Glucitol PDB code: 5gpb(A).
		19. Ligand: IFM × 1 5-Hydroxymethyl-3,4-Dihydroxypiperidine PDB code: 2g9v(A).
		20. Ligand: NTZ × 2 Nojirimycine tetrazole PDB codes: 1noj(A), 1nok(A).
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Cluster 2 contains 31 ligand types (of which only 20 are listed. Click for all)

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Ligand		Description
		1. Ligand: DMS × 1 dimethyl sulfoxide Dimethyl sulfoxide PDB code: 2pyd(A).
		2. Ligand: IMK × 1 2-(Beta-D-Glucopyranosyl)-5-Methyl-1-Benzimidazole PDB code: 1xkx(A).
		3. Ligand: BZD × 2 N-[(Phenylcarbonyl)carbamoyl]-Beta-D- Glucopyranosylamine PDB codes: 1k06(A), 1k08(A).
		4. Ligand: 2TH × 1 2-Chloro-N-[(1r,2r)-1-Hydroxy-2,3-Dihydro-1h-Inden-2- Yl]-6h-Thieno[2,3-B]pyrrole-5-Carboxamide PDB code: 2gj4(A).
		5. Ligand: CHI × 3 5-Chloro-1h-Indole-2-Carboxylic acid [1-(4- Fluorobenzyl)-2-(4-Hydroxypiperidin-1yl)-2- Oxoethyl]amide PDB codes: 1c50(A), 1h5u(A), 1lwo(A).
		6. Ligand: 3TH × 1 2-Chloro-N-[(3r)-2-Oxo-1,2,3,4-Tetrahydroquinolin-3- Yl]-6h-Thieno[2,3-B]pyrrole-5-Carboxamide PDB code: 2gm9(A).
		7. Ligand: FRY × 2 (2s)-N-[(3s)-1-(2-Amino-2-Oxoethyl)-2-Oxo-1,2,3,4- Tetrahydroquinolin-3-Yl]-2-Chloro-2h-Thieno[2,3- B]pyrrole-5-Carboxamide PDB codes: 2ieg(A),
		8. Ligand: FRX × 2 (S)-2-Chloro-N-(1-(2-(2-Hydroxyethylamino)-2- Oxoethyl)-2-Oxo-1,2,3,4-Tetrahydroquinolin-3-Yl)-6h- Thieno[2,3-B]pyrrole-5-Carboxamide PDB codes: 2iei(A),
		9. Ligand: BZD × 1 N-[(Phenylcarbonyl)carbamoyl]-Beta-D- Glucopyranosylamine PDB code: 2qnb(A).
		10. Ligand: KS3 × 2 (2~{r},3~{s},4~{r},5~{r},6~{s})-2-(Hydroxymethyl)-6-(3- Naphthalen-2-Yl-1~{h}-1,2,4-Triazol-5- Yl)oxane-3,4,5- Triol PDB codes: 5lre(A), 5lrf(A).
		11. Ligand: 12E × 1 N-{[(2e)-2-(Pyridin-4-Ylmethylidene) hydrazino]carbonothioyl}-Beta-D-Glucopyranosylamine PDB code: 3mrt(A).
		12. Ligand: 16F × 1 N-({(2z)-2-[(3-Hydroxyphenyl) methylidene]hydrazino}carbonothioyl)-Beta-D- Glucopyranosylamine PDB code: 3mrv(A).
		13. Ligand: 16O × 1 N-({(2e)-2-[(4-Bromophenyl) methylidene]hydrazino}carbonothioyl)-Beta-D- Glucopyranosylamine PDB code: 3mt7(A).
		14. Ligand: 17S × 1 N-({(2e)-2-[(4-Methoxyphenyl) methylidene]hydrazino}carbonothioyl)-Beta-D- Glucopyranosylamine PDB code: 3mrx(A).
		15. Ligand: 17T × 1 N-({(2e)-2-[(4-Chlorophenyl) methylidene]hydrazino}carbonothioyl)-Beta-D- Glucopyranosylamine PDB code: 3mt8(A).
		16. Ligand: 18O × 1 N-({(2e)-2-[(4-Nitrophenyl) methylidene]hydrazino}carbonothioyl)-Beta-D- Glucopyranosylamine PDB code: 3mt9(A).
		17. Ligand: 18S × 1 N-({(2e)-2-[(4-Methylphenyl) methylidene]hydrazino}carbonothioyl)-Beta-D- Glucopyranosylamine PDB code: 3ms2(A).
		18. Ligand: 20X × 1 N-({(2e)-2-[(4-Fluorophenyl) methylidene]hydrazino}carbonothioyl)-Beta-D- Glucopyranosylamine PDB code: 3mqf(A).
		19. Ligand: 21N × 1 N-{[(2e)-2-{[4-(Trifluoromethyl) phenyl]methylidene}hydrazino]carbonothioyl}-Beta-D- Glucopyranosylamine PDB code: 3ms4(A).
		20. Ligand: 22O × 1 N-({(2e)-2-[(3-Bromophenyl) methylidene]hydrazino}carbonothioyl)-Beta-D- Glucopyranosylamine PDB code: 3mta(A).
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Cluster 3 contains 26 ligand types (of which only 20 are listed. Click for all)

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Ligand		Description
		1. Ligand: PO4 × 6 Phosphate ion PDB codes: 1axr(A), 1noj(A), 1p4h(A), 2g9q(A), 2g9u(A), 2g9v(A).
		2. Ligand: G1P × 1 1-O-Phosphono-Alpha-D-Glucopyranose PDB code: 3gpb(A).
		3. Ligand: G6P × 1 6-O-Phosphono-Alpha-D-Glucopyranose PDB code: 1gpy(A).
		4. Ligand: DMS × 18 dimethyl sulfoxide Dimethyl sulfoxide PDB codes: 2pyd(A), 2pyi(A), 2qrp(A), 2qrq(A), 3cuv(A), 3mrv(A), 5jtt(A), 5jtu(A), 5lrd(A), 5lre(A), 5lrf(A), 6qa6(A), 6s4h(A), 7o8e(A).
		5. Ligand: D6G × 1 2-Deoxy-6-O-Phosphono-Alpha-D-Glucopyranose PDB code: 2pri(A).
		6. Ligand: GFP × 1 2-Deoxy-2-Fluoro-1-O-Phosphono-Alpha-D-Glucopyranose PDB code: 4gpb(A).
		7. Ligand: GPM × 1 (1s)-1,5-Anhydro-1-(Phosphonomethyl)-D-Glucitol PDB code: 5gpb(A).
		8. Ligand: IMP × 9 Inosinic acid PDB codes: 1abb(A), 1b4d(A), 1ftq(A), 1gfz(A), 1gg8(A), 2prj(A), 2skc(A), 2skd(A), 2ske(A).
		9. Ligand: AMP × 4 Adenosine monophosphate PDB codes: 1pyg(A), 6gpb(A), 7gpb(A), 8gpb(A).
		10. Ligand: BN3 × 1 4-[3-Chloro-4-({[(2,4-Dichlorobenzoyl) amino]carbonyl}amino)phenoxy]butanoic acid PDB code: 1wuy(A).
		11. Ligand: BN4 × 1 4-[4-({[(2,4-Dichlorobenzoyl)amino]carbonyl}amino)-2,3- Dimethylphenoxy]butanoic acid PDB code: 1wv0(A).
		12. Ligand: BN5 × 1 5-[3-({[(2,4-Dichlorobenzoyl)amino]carbonyl}amino)-2- Methylphenoxy]pentanoic acid PDB code: 1wv1(A).
		13. Ligand: IAA × 2 ({[(3e)-2'-Oxo-2',7'-Dihydro-2,3'-Biindol-3(7h)- Ylidene]amino}oxy)acetic acid PDB codes: 1z62(A),
		14. Ligand: BN2 × 1 7-[2,6-Dichloro-4-({[(2-Chlorobenzoyl) amino]carbonyl}amino)phenoxy]heptanoic acid PDB code: 1wut(A).
		15. Ligand: BIN × 3 2,3-Dicarboxy-4-(2-Chloro-Phenyl)-1-Ethyl-5- Isopropoxycarbonyl-6-Methyl-Pyridinium PDB codes: 1c8l(A), 2amv(A), 3amv(A).
		16. Ligand: 194 × 1 4-{2-[(3-Nitrobenzoyl)amino]phenoxy}phthalic acid PDB code: 1z6p(A).
		17. Ligand: 195 × 1 4-{2,4-Bis[(3-Nitrobenzoyl)amino]phenoxy}phthalic acid PDB code: 1z6q(A).
		18. Ligand: IMP × 19 Inosinic acid PDB codes: 2qn7(A), 2qn9(A), 3e3o(A), 3g2h(A), 3zcr(A), 3zcs(A), 3zct(A), 4yi3(A), 4yi5(A), 5o50(A), 5o54(A), 5owy(A), 5owz(A), 5ox0(A), 5ox3(A), 5ox4(A), 6f3j(A), 6f3u(A), 6s4o(A).
		19. Ligand: SO4 × 12 Sulfate ion PDB codes: 1abb(A), 1gpa(A), 1xc7(A), 2gj4(A), 2qn8(A), 3e3l(A), 3e3n(A), 3e3o(A), 7gpb(A), 9gpb(A),
		20. Ligand: PO4 × 2 Phosphate ion PDB codes: 3zcq(A), 4cto(A).
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Cluster 4 contains 5 ligand types

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Ligand		Description
		1. Ligand: DMS × 3 dimethyl sulfoxide Dimethyl sulfoxide PDB codes: 2pyd(A), 2qrq(A), 3cuv(A).
		2. Ligand: GLC-GLC-GLC-GLC-GLC × 4 GLC=Alpha-D-Glucopyranose. PDB codes: 1p29(A), 1p2b(A), 5gpb(A), 6gpb(A).
		3. Ligand: GLC-GLC × 1 GLC=Alpha-D-Glucopyranose. PDB code: 1p2d(A).
		4. Ligand: GLC-GLC-GLC-GLC-GLC-GLC-GLC-GLC × 1 GLC=Alpha-D-Glucopyranose. PDB code: 1p2g(A).
		5. Ligand: SO4 × 1 Sulfate ion PDB code: 2gj4(A).

Cluster 5 contains 4 ligand types

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Ligand		Description
		1. Ligand: AMP × 2 Adenosine monophosphate PDB codes: 1pyg(A), 7gpb(A).
		2. Ligand: IMP × 1 Inosinic acid PDB code: 1abb(A).
		3. Ligand: AMP × 1 Adenosine monophosphate PDB code: 3e3n(A).
		4. Ligand: IMP × 1 Inosinic acid PDB code: 3e3o(A).

Cluster 6 contains 2 ligand types

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Ligand		Description
		1. Ligand: QUE × 1 3,5,7,3',4'-Pentahydroxyflavone PDB code: 4mra(A).
		2. Ligand: Z15 × 1 (1s)-1,5-Anhydro-1-(4-Chloro-2,5-Dihydroxyphenyl)-D- Glucitol PDB code: 3np7(A).