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Ligand clusters for UniProt code Q9Y3Z3

Ligand clusters for Q9Y3Z3: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 from Homo sapiens

Top 6 (of 23) ligand clusters


Cluster 1. 27 ligand types 79 ligands		Cluster 2. 17 ligand types 107 ligands		Cluster 3. 16 ligand types 106 ligands		Cluster 4. 18 ligand types 78 ligands		Cluster 5. 2 ligand types 3 ligands		Cluster 6. 1 ligand type 1 ligand

Representative protein: 4bzbA

Structures

PDB		Schematic diagram

4bzbA
4to5A
6tx0A
4to1A
6dwjD
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Cluster 1 contains 27 ligand types (of which only 20 are listed. Click for all)

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Ligand

Description

_Zn

1. Metal: _ZN × 12

PDB codes: 3u1n(A), 4mz7(A), 4q7h(A), 4qg4(A), 4rxo(A), 6u6x(A), 6u6y(A), 6u6z(A),

_Fe

2. Metal: _FE × 7

PDB codes: 5ao0(A), 5ao1(A), 5ao2(A), 5ao3(A), 5ao4(A),

_Mg

3. Metal: _MG × 5

PDB codes: 6dw5(A), 6dwd(D), 6dwj(D), 6dwk(A).

_Mn

4. Metal: _MN × 3

PDB codes: 4bzc(A), 6txf(A), 6yom(A).

5. Ligand: GLY × 2

glycine

PDB codes: 6dw7(A), 6dwk(A).

6. Ligand: DCP × 8

2'-Deoxycytidine-5'-Triphosphate

PDB codes: 4qfy(A), 4rxr(A), 4tnp(A), 4to0(A), 4to1(A), 4to3(A), 4to4(A), 4to5(A).

7. Ligand: DGT × 6

2'-Deoxyguanosine-5'-Triphosphate

PDB codes: 4bzb(A), 4mz7(A), 4qfx(A), 4tny(A), 4to2(A), 4zwe(A).

8. Ligand: DTP × 5

2'-Deoxyadenosine 5'-Triphosphate

PDB codes: 4qg1(A), 4rxp(A), 4tnr(D), 4zwg(A), 6u6y(A).

9. Ligand: TTP × 5

Thymidine-5'-Triphosphate

PDB codes: 4qfz(A), 4rxs(A), 4tnq(A), 4tnz(C), 4to6(A).

10. Ligand: DZ4 × 3

2'-Deoxy-5'-O-[(R)-Hydroxy{[(r)-Hydroxy(phosphonooxy) phosphoryl]amino}phosphoryl]adenosine

PDB codes: 6tx0(A), 6txf(A), 6xu1(A).

11. Ligand: PO4 × 3

Phosphate ion

PDB codes: 3u1n(A), 4rxo(A),

12. Ligand: 0KX × 2

2'-Deoxy-5'-O-[(R)-Hydroxy{[(r)-Hydroxy(phosphonooxy) phosphoryl]amino}phosphoryl]cytidine

PDB codes: 6txc(A), 6yom(A).

13. Ligand: DG3 × 2

2'-3'-Dideoxyguanosine-5'-Triphosphate

PDB codes: 5ao0(A), 5ao1(A).

14. Ligand: DUT × 2

Deoxyuridine-5'-Triphosphate

PDB codes: 4qg0(A), 4rxq(A).

15. Ligand: T8T × 2

2'-Deoxyguanosine-5'-O-(1-Thiotriphosphate)

PDB codes: 4bzc(A), 7a5y(A).

16. Ligand: 1FZ × 1

5'-O-[(R)-Hydroxy{[(r)-Hydroxy(phosphonooxy) phosphoryl]amino}phosphoryl]thymidine

PDB code: 6txe(A).

17. Ligand: 3PO × 1

Triphosphate

PDB code: 4tnx(A).

18. Ligand: F6G × 1

6-Amino-3-{2-Deoxy-5-O-[(R)-Hydroxy{[(s)- Hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-Beta- D-
Erythro-Pentofuranosyl}-3,4-Dihydro-1,3,5-Triazin- 2(1h)-One

PDB code: 6cm2(D).

19. Ligand: GTF × 1

2'-Deoxy-2',2'-Difluorocytidine 5'-(Tetrahydrogen triphosphate)

PDB code: 6dw5(A).

20. Ligand: HDV × 1

9-{2-Deoxy-2-Fluoro-5-O-[(R)-Hydroxy{[(s)- Hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-Beta-
D-Arabinofuranosyl}-2-Methyl-9h-Purin-6-Amine

PDB code: 6dwd(D).

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Cluster 2 contains 17 ligand types

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Ligand

Description

1. Ligand: GLY × 1

glycine

PDB code: 6dwd(D).

2. Ligand: GTP × 35

Guanosine-5'-Triphosphate

PDB codes: 4q7h(A), 4qg1(A), 4qg2(A), 4qg4(A), 4rxo(A), 4rxp(A), 4rxq(A), 4rxr(A), 4rxs(A), 4tnp(A), 4tnq(A), 4tnr(D), 4tnx(A), 4tnz(C), 4to0(A), 4to1(A), 4to4(A), 4to5(A), 4zwg(A), 5ao3(A), 5ao4(A), 6cm2(D), 6dw3(D), 6dw4(D), 6dw5(A), 6dw7(A), 6dwd(D), 6dwj(D), 6dwk(A), 6txc(A), 6txe(A), 6xu1(A).

3. Ligand: DGT × 20

2'-Deoxyguanosine-5'-Triphosphate

PDB codes: 4bzb(A), 4mz7(A), 4qfx(A), 4qfy(A), 4qfz(A), 4qg0(A), 4tnx(A), 4tny(A), 4to2(A), 4to3(A), 4to4(A), 4to6(A), 4zwe(A), 5ao2(A).

4. Ligand: DTP × 19

2'-Deoxyadenosine 5'-Triphosphate

PDB codes: 4qfx(A), 4qg1(A), 4qg2(A), 4qg4(A), 4rxp(A), 4tnr(D), 4tny(A), 4tnz(C), 4to0(A), 4to6(A), 4zwg(A), 6dw3(D), 6dw5(A), 6dw7(A), 6dwj(D), 6dwk(A), 6txc(A), 6txe(A), 6yom(A).

5. Ligand: CZF × 4

[[(2~{r},3~{s},4~{r},5~{r})-5-[2,6-Bis(oxidanylidene)- 3~{h}-Purin-9-Yl]-3,4-Bis(oxidanyl)oxolan-2-
Yl]methoxy-Oxidanyl-Phosphoryl] phosphono hydrogen phosphate

PDB codes: 6tx0(A), 6txa(A), 6txf(A), 6yom(A).

6. Ligand: T8T × 4

2'-Deoxyguanosine-5'-O-(1-Thiotriphosphate)

PDB codes: 4bzc(A), 7a5y(A),

7. Ligand: TTP × 4

Thymidine-5'-Triphosphate

PDB codes: 4qfz(A), 4rxs(A), 4tnq(A), 4to5(A).

8. Ligand: DCP × 3

2'-Deoxycytidine-5'-Triphosphate

PDB codes: 4rxr(A), 4tnp(A), 4to1(A).

9. Ligand: DZ4 × 3

2'-Deoxy-5'-O-[(R)-Hydroxy{[(r)-Hydroxy(phosphonooxy) phosphoryl]amino}phosphoryl]adenosine

PDB codes: 6tx0(A), 6txf(A), 6xu1(A).

10. Ligand: SO4 × 3

Sulfate ion

PDB codes: 5ao1(A), 5ao3(A),

11. Ligand: _SC-_GS-_SC-_SC × 3

SC=2-Deoxy-Cytidine-5'-Thiophosphorate, GS=Guanosine-5'-Thio-Monophosphate.

PDB codes: 6u6x(A),

12. Ligand: DG3 × 2

2'-3'-Dideoxyguanosine-5'-Triphosphate

PDB codes: 5ao0(A), 5ao1(A).

13. Ligand: DUT × 2

Deoxyuridine-5'-Triphosphate

PDB codes: 4qg0(A), 4rxq(A).

14. Ligand: F6G × 1

6-Amino-3-{2-Deoxy-5-O-[(R)-Hydroxy{[(s)- Hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-Beta- D-
Erythro-Pentofuranosyl}-3,4-Dihydro-1,3,5-Triazin- 2(1h)-One

PDB code: 6cm2(D).

15. Ligand: HDV × 1

9-{2-Deoxy-2-Fluoro-5-O-[(R)-Hydroxy{[(s)- Hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-Beta-
D-Arabinofuranosyl}-2-Methyl-9h-Purin-6-Amine

PDB code: 6dwd(D).

16. Ligand: HF7 × 1

2'-Deoxy-2-Methyladenosine 5'-(Tetrahydrogen triphosphate)

PDB code: 6dw4(D).

17. Ligand: XG4 × 1

2'-Deoxy-5'-O-[(R)-Hydroxy{[(r)-Hydroxy(phosphonooxy) phosphoryl]amino}phosphoryl]guanosine

PDB code: 6txa(A).

Cluster 3 contains 16 ligand types

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Ligand

Description

_Mg

1. Metal: _MG × 3

PDB codes: 4bzc(A), 4tnr(D), 4zwe(A).

2. Ligand: GTP × 35

Guanosine-5'-Triphosphate

3. Ligand: DTP × 21

2'-Deoxyadenosine 5'-Triphosphate

PDB codes: 4mz7(A), 4qfx(A), 4qg1(A), 4qg2(A), 4qg4(A), 4rxp(A), 4tnr(D), 4tny(A), 4tnz(C), 4to0(A), 4to1(A), 4to6(A), 4zwg(A), 6dw3(D), 6dw5(A), 6dw7(A), 6dwj(D), 6dwk(A), 6txc(A), 6txe(A), 6yom(A).

4. Ligand: DGT × 19

2'-Deoxyguanosine-5'-Triphosphate

PDB codes: 4bzb(A), 4mz7(A), 4qfx(A), 4qfy(A), 4qfz(A), 4qg0(A), 4tnx(A), 4tny(A), 4to2(A), 4to3(A), 4to4(A), 4to6(A), 4zwe(A), 5ao2(A).

5. Ligand: CZF × 4

[[(2~{r},3~{s},4~{r},5~{r})-5-[2,6-Bis(oxidanylidene)- 3~{h}-Purin-9-Yl]-3,4-Bis(oxidanyl)oxolan-2-
Yl]methoxy-Oxidanyl-Phosphoryl] phosphono hydrogen phosphate

PDB codes: 6tx0(A), 6txa(A), 6txf(A), 6yom(A).

6. Ligand: T8T × 4

2'-Deoxyguanosine-5'-O-(1-Thiotriphosphate)

PDB codes: 4bzc(A), 7a5y(A),

7. Ligand: TTP × 4

Thymidine-5'-Triphosphate

PDB codes: 4qfz(A), 4rxs(A), 4tnq(A), 4to5(A).

8. Ligand: DZ4 × 3

2'-Deoxy-5'-O-[(R)-Hydroxy{[(r)-Hydroxy(phosphonooxy) phosphoryl]amino}phosphoryl]adenosine

PDB codes: 6tx0(A), 6txf(A), 6xu1(A).

9. Ligand: _SC-_GS-_SC-_SC × 3

SC=2-Deoxy-Cytidine-5'-Thiophosphorate, GS=Guanosine-5'-Thio-Monophosphate.

PDB codes: 6u6x(A),

10. Ligand: DCP × 2

2'-Deoxycytidine-5'-Triphosphate

PDB codes: 4rxr(A), 4tnp(A).

11. Ligand: DG3 × 2

2'-3'-Dideoxyguanosine-5'-Triphosphate

PDB codes: 5ao0(A), 5ao1(A).

12. Ligand: DUT × 2

Deoxyuridine-5'-Triphosphate

PDB codes: 4qg0(A), 4rxq(A).

13. Ligand: F6G × 1

6-Amino-3-{2-Deoxy-5-O-[(R)-Hydroxy{[(s)- Hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-Beta- D-
Erythro-Pentofuranosyl}-3,4-Dihydro-1,3,5-Triazin- 2(1h)-One

PDB code: 6cm2(D).

14. Ligand: HDV × 1

9-{2-Deoxy-2-Fluoro-5-O-[(R)-Hydroxy{[(s)- Hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-Beta-
D-Arabinofuranosyl}-2-Methyl-9h-Purin-6-Amine

PDB code: 6dwd(D).

15. Ligand: HF7 × 1

2'-Deoxy-2-Methyladenosine 5'-(Tetrahydrogen triphosphate)

PDB code: 6dw4(D).

16. Ligand: XG4 × 1

2'-Deoxy-5'-O-[(R)-Hydroxy{[(r)-Hydroxy(phosphonooxy) phosphoryl]amino}phosphoryl]guanosine

PDB code: 6txa(A).

Cluster 4 contains 18 ligand types

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Ligand

Description

1. Ligand: GLY × 1

glycine

PDB code: 6dwj(D).

_Mg

2. Metal: _MG × 1

PDB code: 4bzc(A).

3. Ligand: GTP × 23

Guanosine-5'-Triphosphate

PDB codes: 4qg1(A), 4qg2(A), 4qg4(A), 4tnp(A), 4tnq(A), 4tnr(D), 4tnx(A), 4tnz(C), 4to0(A), 4to1(A), 4to4(A), 4to5(A), 4zwg(A), 6cm2(D), 6dw3(D), 6dw4(D), 6dw5(A), 6dw7(A), 6dwd(D), 6dwj(D), 6dwk(A), 6txc(A), 6txe(A).

4. Ligand: DTP × 18

2'-Deoxyadenosine 5'-Triphosphate

PDB codes: 4qfx(A), 4qg1(A), 4qg2(A), 4qg4(A), 4tnr(D), 4tny(A), 4tnz(C), 4to0(A), 4to1(A), 4to6(A), 4zwg(A), 6dw3(D), 6dw5(A), 6dw7(A), 6dwj(D), 6dwk(A), 6txc(A), 6txe(A).

5. Ligand: DGT × 17

2'-Deoxyguanosine-5'-Triphosphate

PDB codes: 4bzb(A), 4qfx(A), 4qfy(A), 4qfz(A), 4qg0(A), 4tnx(A), 4tny(A), 4to2(A), 4to3(A), 4to4(A), 4to6(A), 4zwe(A),

6. Ligand: T8T × 3

2'-Deoxyguanosine-5'-O-(1-Thiotriphosphate)

PDB codes: 4bzc(A), 7a5y(A).

7. Ligand: TTP × 3

Thymidine-5'-Triphosphate

PDB codes: 4qfz(A), 4tnq(A), 4to5(A).

8. Ligand: _SC-_GS-_SC-_SC × 2

SC=2-Deoxy-Cytidine-5'-Thiophosphorate, GS=Guanosine-5'-Thio-Monophosphate.

PDB codes: 6u6x(A),

9. Ligand: CZF × 1

[[(2~{r},3~{s},4~{r},5~{r})-5-[2,6-Bis(oxidanylidene)- 3~{h}-Purin-9-Yl]-3,4-Bis(oxidanyl)oxolan-2-
Yl]methoxy-Oxidanyl-Phosphoryl] phosphono hydrogen phosphate

PDB code: 6txa(A).

10. Ligand: DCP × 1

2'-Deoxycytidine-5'-Triphosphate

PDB code: 4tnp(A).

11. Ligand: DUT × 1

Deoxyuridine-5'-Triphosphate

PDB code: 4qg0(A).

12. Ligand: DZ4 × 1

2'-Deoxy-5'-O-[(R)-Hydroxy{[(r)-Hydroxy(phosphonooxy) phosphoryl]amino}phosphoryl]adenosine

PDB code: 6xu1(A).

13. Ligand: F6G × 1

6-Amino-3-{2-Deoxy-5-O-[(R)-Hydroxy{[(s)- Hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-Beta- D-
Erythro-Pentofuranosyl}-3,4-Dihydro-1,3,5-Triazin- 2(1h)-One

PDB code: 6cm2(D).

14. Ligand: HDV × 1

9-{2-Deoxy-2-Fluoro-5-O-[(R)-Hydroxy{[(s)- Hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-Beta-
D-Arabinofuranosyl}-2-Methyl-9h-Purin-6-Amine

PDB code: 6dwd(D).

15. Ligand: HF7 × 1

2'-Deoxy-2-Methyladenosine 5'-(Tetrahydrogen triphosphate)

PDB code: 6dw4(D).

16. Ligand: SO4 × 1

Sulfate ion

PDB code: 5ao3(A).

17. Ligand: XG4 × 1

2'-Deoxy-5'-O-[(R)-Hydroxy{[(r)-Hydroxy(phosphonooxy) phosphoryl]amino}phosphoryl]guanosine

PDB code: 6txa(A).

_Na

18. Metal: _NA × 1

PDB code: 6dwd(D).

Cluster 5 contains 2 ligand types

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Ligand

Description

1. Ligand: GLY × 1

glycine

PDB code: 6dwd(D).

2. Ligand: SO4 × 2

Sulfate ion

PDB codes: 6txa(A), 6txc(A).

Ligand clusters for UniProt code Q9Y3Z3

Ligand clusters for Q9Y3Z3: Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 from Homo sapiens

Structures

Cluster 1 contains 27 ligand types (of which only 20 are listed. Click for all)

Cluster 2 contains 17 ligand types

Cluster 3 contains 16 ligand types

Cluster 4 contains 18 ligand types

Cluster 5 contains 2 ligand types

Cluster 6 contains 1 ligand type