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Ligand clusters for UniProt code Q6B856

Ligand clusters for Q6B856: Tubulin beta-2B chain from Bos taurus

Top 6 (of 9) ligand clusters


Cluster 1. 47 ligand types 150 ligands		Cluster 2. 28 ligand types 273 ligands		Cluster 3. 5 ligand types 25 ligands		Cluster 4. 3 ligand types 8 ligands		Cluster 5. 2 ligand types 72 ligands		Cluster 6. 3 ligand types 9 ligands

Representative protein: 5nqtB

Structures

PDB		Schematic diagram

5nqtB
4yj3B
4yj2B
5z4pB
5nm5B
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Cluster 1 contains 47 ligand types (of which only 20 are listed. Click for all)

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Ligand

Description

1. Ligand: LOC × 4

colchicine

N-[(7s)-1,2,3,10-Tetramethoxy-9-Oxo-6,7-Dihydro-5h- Benzo[d]heptalen-7-Yl]ethanamide

PDB codes: 3e22(B), 4o2b(B), 5itz(B), 5nm5(B).

2. Ligand: GOL × 2

glycerin

Glycerol

PDB codes: 4o2b(B), 5osk(B).

_Mg

3. Metal: _MG × 2

PDB codes: 5lov(B), 5o7a(B).

4. Ligand: POD × 1

podofilox

9-Hydroxy-5-(3,4,5-Trimethoxyphenyl)-5,8,8a,9- Tetrahydrofuro[3',4':6,7]naphtho[2,3-D][1,3]dioxol-
6(5ah)-One

PDB code: 1sa1(B).

5. Ligand: GTP × 96

Guanosine-5'-Triphosphate

PDB codes: 1jff(B), 1sa0(B), 1z2b(B), 2p4n(B), 2wbe(B), 2xrp(A), 3dco(B), 3e22(B), 3iz0(B), 4atu(A), 4atx(A), 4i4t(B), 4i50(B), 4i55(B), 4ihj(B), 4iij(B), 4o2a(B), 4o2b(B), 4o4h(B), 4o4i(B), 4o4j(B), 4o4l(B), 4tuy(B), 4tv8(B), 4tv9(B), 4wbn(B), 4yj2(B), 4yj3(B), 5eib(D), 5ezy(B), 5h74(B), 5h7o(B), 5hnw(B), 5hnx(B), 5hny(B), 5hnz(B), 5itz(B), 5iyz(B), 5j2t(D), 5j2u(B), 5jh7(B), 5la6(B), 5lov(B), 5lp6(B), 5lxs(B), 5lxt(B), 5lyj(B), 5m50(E), 5m54(E), 5m5c(E), 5m7e(B), 5m7g(B), 5m8d(B), 5m8g(B), 5mf4(B), 5nd2(B), 5nd3(B), 5nd4(B), 5nd7(B), 5nfz(B), 5ng1(B), 5njh(B), 5nm5(B), 5nqt(B), 5nqu(B), 5o7a(B), 5xlt(B), 5xlz(B), 5yz3(B), 5z4p(B), 5z4u(B), 5zxh(B), 6agk(B), 6eg5(B), 6fii(B), 6fjf(B), 6fjm(B), 6fkj(B), 6fkl(B), 6gze(B), 6i5c(B), 6knz(B), 6n47(B), 6ojq(B), 6qqn(B), 6qtn(B), 6s8k(B), 6s9e(B), 6ses(B), 6wvl(B), 6wvm(D), 6wvr(B), 6y6d(B), 6zwb(B), 6zwc(B), 7jfr(B).

6. Ligand: CN2 × 3

2-Mercapto-N-[1,2,3,10-Tetramethoxy-9-Oxo-5,6,7,9- Tetrahydro-Benzo[a]heptalen-7-Yl]acetamide

PDB codes: 1sa0(B), 1z2b(B), 3du7(B).

7. Ligand: 8WB × 2

2-Methoxy-5-(2,3,4-Trimethoxyphenyl)cyclohepta-2,4,6- Trien-1-One

PDB codes: 5nfz(B), 5ng1(B).

8. Ligand: 2GE × 1

N~4~-Cyclopropyl-6-(2,3-Dichlorophenyl)pyrimidine-2,4- Diamine

PDB code: 6qqn(B).

9. Ligand: 2RR × 1

3-[(4-{1-[2-(4-Aminophenyl)-2-Oxoethyl]-1h- Benzimidazol-2-Yl}-1,2,5-Oxadiazol-3-
Yl) amino]propanenitrile

PDB code: 4o2a(B).

10. Ligand: 4ED × 1

5,6-Dimethyl-2-[(E)-2-(Pyridin-3-Yl)ethenyl]-1,3- Benzothiazole

PDB code: 4yj2(B).

11. Ligand: 4EE × 1

6-(4-Ethoxyphenyl)-3-(2-Methoxyphenyl)-7h-[1,2, 4]triazolo[3,4-B][1,3,4]thiadiazine

PDB code: 4yj3(B).

12. Ligand: 6FS × 1

N-[2-Methoxy-5-({[(E)-2-(2,4,6-Trimethoxyphenyl) ethenyl]sulfonyl}methyl)phenyl]glycine

PDB code: 5ov7(B).

13. Ligand: 6NL × 1

(2e)-3-(3-Hydroxy-4-Methoxyphenyl)-1-(7-Methoxy-2h-1,3- Benzodioxol-5-Yl)-2-Methylprop-2-En-1-One

PDB code: 5jvd(B).

14. Ligand: 6ZR × 1

(3r,4r)-4-(4-Methoxy-3-Oxidanyl-Phenyl)-3-Methyl-1-(3, 4,5-Trimethoxyphenyl)azetidin-2-One

PDB code: 5gon(B).

15. Ligand: 71P × 1

~{N}-[(7~{r})-1,2,3-Trimethoxy-10-Methylsulfanyl-9- Oxidanylidene-6,7-Dihydro-5~{h}-
Benzo[a]heptalen-7- Yl]ethanamide

PDB code: 5lp6(B).

16. Ligand: 7BA × 1

Combretastatin a4

PDB code: 5lyj(B).

17. Ligand: 7Q7 × 1

2-(1h-Indol-4-Yl)-4-(3,4,5-Trimethoxyphenyl)-1h- Imidazo[4,5-C]pyridine

PDB code: 5h7o(B).

18. Ligand: 84F × 1

(3s,4r)-4-(3-Hydroxy-4-Methoxyphenyl)-3-Methyl-1-(3,4, 5-Trimethoxyphenyl)azetidin-2-One

PDB code: 5xaf(B).

19. Ligand: 89O × 1

(5s,5ar,8ar,9r)-9-(3,5-Dimethoxy-4-Oxidanyl-Phenyl)-5- Oxidanyl-5a,6,8a,9-Tetrahydro-5h-
[2]benzofuro[6,5- F][1,3]benzodioxol-8-One

PDB code: 5xlt(B).

20. Ligand: 89U × 1

10-[(4-Methoxy-3-Oxidanyl-Phenyl)methylidene]anthracen- 9-One

PDB code: 5xlz(B).

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Cluster 2 contains 28 ligand types (of which only 20 are listed. Click for all)

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Ligand

Description

_Mg

1. Metal: _MG × 61

PDB codes: 1sa0(B), 4i4t(B), 4i50(B), 4i55(B), 4ihj(B), 4iij(B), 4o2a(B), 4o2b(B), 4o4h(B), 4o4i(B), 4o4j(B), 4o4l(B), 4tuy(B), 4tv8(B), 4tv9(B), 4yj2(B), 4yj3(B), 5ezy(B), 5gon(B), 5h74(B), 5h7o(B), 5iyz(B), 5jvd(B), 5la6(B), 5lov(B), 5lp6(B), 5lxs(B), 5lxt(B), 5lyj(B), 5m7e(B), 5m7g(B), 5m8d(B), 5m8g(B), 5mf4(B), 5nfz(B), 5ng1(B), 5o7a(B), 5osk(B), 5ov7(B), 5xaf(B), 5xag(B), 5xlt(B), 5xlz(B), 5yz3(B), 5z4p(B), 5z4u(B), 5zxh(B), 6eg5(B), 6f7c(B), 6fii(B), 6fjf(B), 6fjm(B), 6fkj(B), 6fkl(B), 6gf3(B), 6gj4(B), 6hx8(B), 6jcj(B), 6knz(B), 6qqn(B), 6qtn(B).

2. Ligand: TA1 × 36

paclitaxel

Taxol

PDB codes: 1jff(B), 2p4n(B), 2wbe(B), 3dco(B), 3iz0(B), 4aqv(B), 4aqw(B), 4ck5(B), 4ck6(B), 4ck7(B), 4uxo(B), 4uxp(B), 4uxr(B), 4uxs(B), 4uxt(B), 4uxy(B), 4uy0(B), 5hnw(B), 5hnx(B), 5hny(B), 5hnz(B), 5m50(E), 5m54(E), 5m5c(E), 5m5i(B), 5m5l(B), 5m5m(B), 5m5n(B), 5m5o(B), 5nd2(B), 5nd3(B), 5nd4(B), 5nd7(B), 6wvl(B), 6wvm(D), 6wvr(B).

3. Ligand: GOL × 21

glycerin

Glycerol

PDB codes: 4o2b(B), 4o4h(B), 4yj2(B), 5gon(B), 5ng1(B), 5osk(B), 5ov7(B), 5xaf(B), 5xag(B), 5z4p(B), 6fii(B), 6fkj(B), 6fkl(B), 6qtn(B), 6s9e(B), 6y6d(B).

4. Ligand: 6K9 × 1

eribulin

(1s,3s,6s,9s,12s,14r,16r,18s,20r,21r,22s,26r,29s,31r, 32s,33r,35r,36s)-20-[(2s)-3-Amino-2-
Hydroxypropyl]-21- Methoxy-14-Methyl-8,15-Dimethylidene-2,19,30,34,37,39, 40,41-
Octaoxanonacyclo[24.9.2.1~3,32~.1~3,33~.1~6, 9~.1~12,16~.0~18,22~.0~29,36~.0~31,35~]hentetracontan-
24-One (non-Preferred name)

PDB code: 5jh7(B).

5. Ligand: VLB × 1

vinblastine

(2alpha,2'Beta,3beta,4alpha,5beta)-Vincaleukoblastine

PDB code: 1z2b(B).

6. Ligand: GDP × 130

Guanosine-5'-Diphosphate

PDB codes: 1jff(B), 1sa0(B), 1sa1(B), 1z2b(B), 2p4n(B), 2wbe(B), 2xrp(A), 3dco(B), 3du7(B), 3e22(B), 3iz0(B), 4aqv(B), 4aqw(B), 4atu(A), 4atx(A), 4ck5(B), 4ck6(B), 4ck7(B), 4i4t(B), 4i50(B), 4i55(B), 4ihj(B), 4iij(B), 4o2a(B), 4o2b(B), 4o4h(B), 4o4i(B), 4o4j(B), 4o4l(B), 4tuy(B), 4tv8(B), 4tv9(B), 4uxo(B), 4uxp(B), 4uxr(B), 4uxs(B), 4uxt(B), 4uxy(B), 4uy0(B), 4wbn(B), 4yj2(B), 4yj3(B), 5ezy(B), 5gon(B), 5h74(B), 5h7o(B), 5hnw(B), 5hnx(B), 5hny(B), 5hnz(B), 5itz(B), 5iyz(B), 5j2t(D), 5j2u(B), 5jh7(B), 5jvd(B), 5la6(B), 5lov(B), 5lp6(B), 5lxs(B), 5lxt(B), 5lyj(B), 5m50(E), 5m54(E), 5m5c(E), 5m5i(B), 5m5l(B), 5m5m(B), 5m5n(B), 5m5o(B), 5m7e(B), 5m7g(B), 5m8d(B), 5m8g(B), 5mf4(B), 5nd2(B), 5nd3(B), 5nd4(B), 5nd7(B), 5nfz(B), 5ng1(B), 5njh(B), 5nm5(B), 5nqt(B), 5nqu(B), 5o7a(B), 5osk(B), 5ov7(B), 5xaf(B), 5xag(B), 5xlt(B), 5xlz(B), 5yz3(B), 5z4p(B), 5z4u(B), 5zxh(B), 6agk(B), 6bbn(B), 6eg5(B), 6f7c(B), 6fii(B), 6fjf(B), 6fjm(B), 6fkj(B), 6fkl(B), 6gf3(B), 6gj4(B), 6gze(B), 6hx8(B), 6i5c(B), 6jcj(B), 6k9v(B), 6knz(B), 6n47(B), 6qqn(B), 6qtn(B), 6rev(b), 6rf2(B), 6rf8(b), 6rfd(B), 6s8k(B), 6s9e(B), 6ses(B), 6wvl(B), 6wvm(D), 6wvr(B), 6y6d(B), 6zwb(B), 6zwc(B), 7jfr(B).

7. Ligand: _EP × 2

Epothilone a

PDB codes: 4o4i(B), 4o4l(B).

8. Ligand: 03S × 1

Methanesulfonic acid

PDB code: 5jh7(B).

9. Ligand: 4Q5 × 1

N-Methyl-L-Valyl-N-[(3r,4s,5s)-1-{(2s)-2-[(1r,2r)-3- {[(1s,2r)-1-Hydroxy-1-Phenylpropan-2-
Yl]amino}-1- Methoxy-2-Methyl-3-Oxopropyl]pyrrolidin-1-Yl}-3- Methoxy-5-Methyl-1-Oxoheptan-4-Yl]-
N-Methyl-L- Valinamide

PDB code: 5iyz(B).

10. Ligand: 6DO × 1

(2~{s})-2-[[(2~{r},3~{r})-3-Methoxy-3-[(2~{s})-1- [(3~{r},4~{s},5~{s})-3-Methoxy-5-Methyl-4-
[Methyl- [(2~{s})-3-Methyl-2-[[(2~{s})-3-Methyl-2-
(Methylamino) butanoyl]amino]butanoyl]amino]heptanoyl]pyrrolidin-2- Yl]-2-Methyl-
Propanoyl]amino]-3-Phenyl-Propanoic acid

PDB code: 5j2u(B).

11. Ligand: 71E × 1

Dz 2384

PDB code: 5lov(B).

12. Ligand: 7AK × 1

(+)-Discodermolide

PDB code: 5lxt(B).

13. Ligand: 7AO × 1

[(3~{z},5~{s},6~{s},7~{s},8~{r},9~{s},11~{z},13~{s}, 14~{s},15~{s},16~{z},18~{s})-19-
[(2~{s},3~{r},4~{s}, 5~{r})-3,5-Dimethyl-4-Oxidanyl-6-Oxidanylidene-Oxan-2- Yl]-5,7,9,11,13,15-
Hexamethyl-8,14,18-Tris(oxidanyl) nonadeca-1,3,11,16-Tetraen-6-Yl] ~{n}-[3-[(3-
Azidophenyl)carbonylamino]propyl]carbamate

PDB code: 5lxs(B).

14. Ligand: 7LG × 1

(2~{s},4~{r})-4-[[2-[(1~{r},3~{r})-1-Acetyloxy-3- [Hexyl-[(2~{s},3~{s})-3-Methyl-2-[[(2~{r})-1-
Methylpiperidin-2-Yl]carbonylamino]pentanoyl]amino]-4- Methyl-Pentyl]-1,3-Thiazol-4-
Yl]carbonylamino]-5-(4- Fluorophenyl)-2-Methyl-Pentanoic acid

PDB code: 5h74(B).

15. Ligand: 7LZ × 1

(3~{z},5~{e},7~{r},8~{s},10~{s},11~{z},13~{s},14~{r}, 15~{s},17~{s},20~{r},21~{s},22~{s})-22-
[(2~{s},3~{z})- Hexa-3,5-Dien-2-Yl]-7,13,15,17,21-Pentamethyl-8,10,14, 20-Tetrakis(oxidanyl)-1-
Oxacyclodocosa-3,5,11-Trien-2- One

PDB code: 5mf4(B).

16. Ligand: 8WE × 1

(2~{z},4~{e})-~{N}-[(~{S})-Oxidanyl-[(1~{s},2~{e}, 5~{s},11~{r},17~{s},19~{r})-3,11,19-Trimethyl-
7,13- Bis(oxidanylidene)-6,21-Dioxabicyclo[15.3.1]henicos-2- En-5-Yl]methyl]hexa-2,4-Dienamide

PDB code: 5ng1(B).

17. Ligand: 8Z8 × 1

5-Chloranyl-7-[(1~{r},5~{s})-3-Methoxy-8- Azabicyclo[3.2.1]octan-8-Yl]-6-[2,4,6-
Tris(fluoranyl) phenyl]-[1,2,4]triazolo[1,5-A]pyrimidine

PDB code: 5njh(B).

18. Ligand: AF3 × 1

Aluminum fluoride

PDB code: 6s9e(B).

19. Ligand: G2P × 1

Phosphomethylphosphonic acid guanylate ester

PDB code: 6ojq(B).

20. Ligand: GTP × 1

Guanosine-5'-Triphosphate

PDB code: 5eib(D).

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Cluster 3 contains 5 ligand types

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Ligand

Description

1. Ligand: GOL × 3

glycerin

Glycerol

PDB codes: 4i4t(B), 5jvd(B).

2. Ligand: MES × 16

2-(N-Morpholino)-Ethanesulfonic acid

PDB codes: 4i55(B), 4ihj(B), 4wbn(B), 4yj2(B), 5ezy(B), 5h74(B), 5xlt(B), 5xlz(B), 5z4u(B), 5zxh(B), 6agk(B), 6eg5(B), 6i5c(B), 6knz(B), 6n47(B), 6s9e(B).

3. Ligand: IMD × 2

Imidazole

PDB codes: 5jh7(B),

4. Ligand: LLM × 2

Laulimalide

PDB codes: 4o4h(B), 4o4i(B).

5. Ligand: POU × 2

Peloruside a

PDB codes: 4o4j(B), 4o4l(B).

Cluster 4 contains 3 ligand types

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Ligand

Description

1. Ligand: GOL × 6

glycerin

Glycerol

PDB codes: 4o2b(B), 5gon(B), 5osk(B), 5xaf(B), 5xag(B), 5z4p(B).

2. Ligand: PG4 × 1

Tetraethylene glycol

PDB code: 6fkj(B).

3. Ligand: TYR × 1

PDB code: 4i4t(B).

Cluster 5 contains 2 ligand types

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Ligand

Description

1. Ligand: GOL × 7

glycerin

Glycerol

PDB codes: 4i4t(B), 4i50(B), 4o2a(B), 4tv9(B), 5jh7(B), 5jvd(B), 5mf4(B).

2. Ligand: MES × 65

2-(N-Morpholino)-Ethanesulfonic acid

PDB codes: 4i4t(B), 4i50(B), 4i55(B), 4ihj(B), 4iij(B), 4o2a(B), 4o2b(B), 4o4i(B), 4o4l(B), 4tuy(B), 4tv8(B), 4tv9(B), 4wbn(B), 4yj2(B), 4yj3(B), 5ezy(B), 5gon(B), 5h74(B), 5h7o(B), 5iyz(B), 5jh7(B), 5jvd(B), 5lov(B), 5lp6(B), 5lxs(B), 5lxt(B), 5lyj(B), 5m7e(B), 5m7g(B), 5m8d(B), 5m8g(B), 5mf4(B), 5nfz(B), 5ng1(B), 5osk(B), 5ov7(B), 5xaf(B), 5xag(B), 5xlt(B), 5xlz(B), 5yz3(B), 5z4p(B), 5z4u(B), 5zxh(B), 6agk(B), 6eg5(B), 6f7c(B), 6fii(B), 6fjf(B), 6fjm(B), 6fkj(B), 6fkl(B), 6gf3(B), 6gj4(B), 6gze(B), 6hx8(B), 6i5c(B), 6k9v(B), 6knz(B), 6n47(B), 6qqn(B), 6qtn(B), 6s9e(B), 6ses(B), 6y6d(B).

Cluster 6 contains 3 ligand types

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Ligand

Description

1. Ligand: GOL × 6

glycerin

Glycerol

PDB codes: 4o2b(B), 5gon(B), 5ov7(B), 5xaf(B), 5xag(B), 5z4p(B).

2. Ligand: PEG × 2

Di(hydroxyethyl)ether

PDB codes: 4o2b(B), 6fjf(B).

3. Ligand: EDO × 1

1,2-Ethanediol

PDB code: 6gf3(B).