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EBI Databases Structure Databases PDBsum

Ligand clusters for UniProt code P00800

Ligand clusters for P00800: Thermolysin from Bacillus thermoproteolyticus

Top 6 (of 38) ligand clusters
Cluster 1.
128 ligand types
590 ligands
 Cluster 2.
4 ligand types
4 ligands
 Cluster 3.
11 ligand types
14 ligands
 Cluster 4.
10 ligand types
63 ligands
 Cluster 5.
9 ligand types
56 ligands
 Cluster 6.
6 ligand types
88 ligands
Representative protein: 1fj3A  
JSmol
 

Structures

PDB   Schematic diagram
1fj3A    
6ig7A    
3do1A    
5lifE    
1gxwA    
 more ...

 

 Cluster 1 contains 128 ligand types (of which only 20 are listed. Click for all)

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Ligand Description

_Zn
 
1. Metal: _ZN × 226
PDB codes: 1fj3(A), 1fjo(A), 1fjq(A), 1fjt(A), 1fju(A), 1fjv(A), 1fjw(A), 1gxw(A), 1hyt(A), 1kei(A), 1kjo(A), 1kjp(A), 1kkk(A), 1kl6(A), 1kr6(A), 1kro(A), 1ks7(A), 1kto(A), 1l3f(E), 1lnd(E), 1lnf(E), 1os0(A), 1pe5(A), 1pe7(A), 1pe8(A), 1qf0(A), 1qf1(A), 1qf2(A), 1thl(A), 1tli(A), 1tlp(E), 1tlx(A), 1tmn(E), 1y3g(E), 1z9g(E), 1zdp(E), 2a7g(E), 2g4z(A), 2tli(A), 2tlx(A), 2tmn(E), 2whz(A), 2wi0(A), 3dnz(A), 3do0(A), 3do1(A), 3do2(A), 3f28(A), 3f2p(A), 3fcq(A), 3fgd(A), 3flf(A), 3for(A), 3fv4(A), 3fvp(A), 3fxp(A), 3ls7(A), 3ms3(A), 3msa(A), 3msf(A), 3msn(A), 3n21(A), 3nn7(A), 3p7p(E), 3p7q(E), 3p7r(E), 3p7s(E), 3p7t(E), 3p7u(E), 3p7v(E), 3p7w(E), 3qgo(A), 3qh1(A), 3qh5(A), 3ssb(A), 3t2h(E), 3t2i(E), 3t2j(E), 3t73(A), 3t74(A), 3t87(A), 3t8c(A), 3t8d(A), 3t8f(A), 3t8g(A), 3t8h(A), 3tli(A), 3tmn(E), 3zi6(A), 4d91(A), 4d9w(A), 4h57(A), 4mtw(E), 4mwp(E), 4mxj(E), 4mzn(E), 4n4e(E), 4n5p(E), 4n66(E), 4oi5(E), 4ow3(A), 4tli(A), 4tln(A), 4tmn(E), 4tnl(A), 5a3y(A), 5dpe(E), 5dpf(E), 5fsj(A), 5fsp(A), 5fss(A), 5fxn(A), 5js3(E), 5jss(E), 5jt9(E), 5jvi(E), 5jxn(E), 5k7t(A), 5l3u(E), 5l41(E), 5l8p(E), 5lif(E), 5lvd(E), 5lwd(E), 5m5f(E), 5m69(E), 5m9w(A), 5ma7(E), 5mnr(E), 5n2t(E), 5n2x(E), 5n2z(E), 5n31(E), 5n34(E), 5n3v(E), 5n3y(E), 5o8n(A), 5onr(A), 5t9i(A), 5t9k(A), 5t9q(A), 5tac(A), 5tad(A), 5tae(A), 5tai(A), 5taj(A), 5tak(A), 5tli(A), 5tln(A), 5tmn(E), 5un3(A), 5uu7(A), 5uu8(A), 5uu9(A), 5uua(A), 5uub(A), 5uuc(A), 5uud(A), 5uue(A), 6d5n(A), 6d5o(A), 6d5p(A), 6d5q(A), 6d5r(A), 6d5s(A), 6d5t(A), 6d5u(A), 6fj2(A), 6ig7(A), 6lzn(A), 6n4w(A), 6n4z(A), 6qar(A), 6qf2(A), 6qf3(A), 6sb9(E), 6sbk(E), 6sc0(E), 6sc1(E), 6sc3(E), 6sck(E), 6scu(E), 6sel(A), 6tli(A), 6tmn(E), 6zhj(A), 7akn(A), 7tli(A), 7tln(A), 8tli(A), 8tln(E).


 
2. Ligand: GOL × 81
glycerin
Glycerol
PDB codes: 3flf(A), 3fv4(A), 3fvp(A), 3ls7(A), 3ms3(A), 3msa(A), 3msf(A), 3ssb(A), 3t73(A), 3t74(A), 3t87(A), 3t8c(A), 3t8d(A), 3t8f(A), 3t8g(A), 3t8h(A), 4d9w(A), 4h57(A), 4mtw(E), 4mwp(E), 4mxj(E), 4mzn(E), 4n4e(E), 4n5p(E), 4n66(E), 5dpe(E), 5dpf(E), 5js3(E), 5jss(E), 5jt9(E), 5jvi(E), 5jxn(E), 5lif(E), 5lvd(E), 5lwd(E), 5m5f(E), 5m69(E), 5m9w(A), 5ma7(E), 6qar(A), 6sc1(E),


 
3. Ligand: DMS × 46
dimethyl sulfoxide
Dimethyl sulfoxide
PDB codes: 1qf0(A), 1qf1(A), 1qf2(A), 1y3g(E), 3fgd(A), 3fv4(A), 3fvp(A), 3t73(A), 3t74(A), 3t87(A), 3t8c(A), 3t8d(A), 3t8f(A), 3t8g(A), 3t8h(A), 4d91(A), 4d9w(A), 4h57(A), 4mtw(E), 4mwp(E), 4mxj(E), 4mzn(E), 4n4e(E), 4n5p(E), 4n66(E), 5dpe(E), 5dpf(E), 5js3(E), 5jss(E), 5jt9(E), 5jvi(E), 5jxn(E), 5l3u(E), 5l41(E), 5lif(E), 5lvd(E), 5lwd(E), 5m5f(E), 5m69(E), 5m9w(A), 5n2t(E), 5n2z(E), 6sb9(E), 6sbk(E), 6sc3(E), 6sck(E).


 
4. Ligand: IPA × 18
isopropyl alcohol
Isopropyl alcohol
PDB codes: 2tli(A), 3msa(A), 3tli(A), 4tli(A), 5k7t(A), 5tli(A), 6tli(A), 7tli(A), 8tli(A),


 
5. Ligand: TRS × 3
tromethamine
2-Amino-2-Hydroxymethyl-Propane-1,3-Diol
PDB codes: 6sbk(E), 6sc0(E), 6sck(E).


 
6. Ligand: ASP × 2
aspartic acid
PDB codes: 6qf3(A),


 
7. Ligand: ACY × 1
acetic acid
Acetic acid
PDB code: 2a7g(E).


 
8. Ligand: IPH × 1
phenol
Phenol
PDB code: 1fjw(A).


 
9. Ligand: LYS × 1
l-lysine
PDB code: 5fss(A).


 
10. Ligand: URE × 1
urea
Urea
PDB code: 3msf(A).


 
11. Ligand: VAL × 1
valine
PDB code: 5fss(A).

_Fe
 
12. Metal: _FE × 1
PDB code: 1lnb(E).

_Mn
 
13. Metal: _MN × 1
PDB code: 1lnc(E).


 
14. Ligand: VAL-LYS × 42
PDB codes: 1fjt(A), 1gxw(A), 1kei(A), 1lna(E), 1lnb(E), 1lnc(E), 1lnd(E), 1lne(E), 1lnf(E), 1tlx(A), 2tlx(A), 3dnz(A), 3do0(A), 3do1(A), 3do2(A), 3ls7(A), 3zi6(A), 5a3y(A), 5fsj(A), 5fsp(A), 5fxn(A), 5t9i(A), 5t9k(A), 5t9q(A), 5tac(A), 5tad(A), 5tae(A), 5tai(A), 5taj(A), 5tak(A), 6d5n(A), 6d5o(A), 6d5p(A), 6d5q(A), 6d5r(A), 6d5s(A), 6d5t(A), 6d5u(A), 6fj2(A), 6qar(A), 7akn(A), 8tln(E).


 
15. Ligand: MPD × 8
(4s)-2-Methyl-2,4-Pentanediol
PDB codes: 5mnr(E), 5n2x(E), 5n31(E), 5n34(E), 5n3v(E), 5n3y(E), 5uu7(A), 5uub(A).


 
16. Ligand: XYP × 7
Beta-D-Xylopyranose
PDB codes: 5un3(A), 5uu8(A), 5uu9(A), 5uua(A), 6d5p(A), 6d5r(A), 6n4z(A).

_Na
 
17. Metal: _NA × 6
PDB codes: 3t2h(E), 3t2i(E), 3t2j(E), 6qf3(A),


 
18. Ligand: 0A9 × 5
Methyl l-Phenylalaninate
PDB codes: 3qgo(A), 3qh5(A),


 
19. Ligand: ACN × 4
Acetone
PDB codes: 1fj3(A), 1fjo(A), 1fjq(A),


 
20. Ligand: DMF × 4
Dimethylformamide
PDB codes: 5uud(A),

 + more. Press for full list
 

 

 Cluster 2 contains 4 ligand types

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Ligand Description


 
1. Ligand: P33 × 1
3,6,9,12,15,18-Hexaoxaicosane-1,20-Diol
PDB code: 6qf3(A).


 
2. Ligand: P6G × 1
Hexaethylene glycol
PDB code: 3qgo(A).


 
3. Ligand: PE5 × 1
3,6,9,12,15,18,21,24-Octaoxahexacosan-1-Ol
PDB code: 6qf2(A).


 
4. Ligand: XYP × 1
Beta-D-Xylopyranose
PDB code: 6n4w(A).

 

 Cluster 3 contains 11 ligand types

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Ligand Description


 
1. Ligand: IPA × 1
isopropyl alcohol
Isopropyl alcohol
PDB code: 7tli(A).


 
2. Ligand: ACN × 2
Acetone
PDB codes: 1fjo(A), 1fjq(A).


 
3. Ligand: EDO × 2
1,2-Ethanediol
PDB codes: 6qf3(A),


 
4. Ligand: XYP × 2
Beta-D-Xylopyranose
PDB codes: 6n4w(A), 6n4z(A).


 
5. Ligand: 0A9 × 1
Methyl l-Phenylalaninate
PDB code: 6sc3(E).


 
6. Ligand: BET × 1
Trimethyl glycine
PDB code: 3t2j(E).


 
7. Ligand: DMF × 1
Dimethylformamide
PDB code: 6d5o(A).


 
8. Ligand: MPD × 1
(4s)-2-Methyl-2,4-Pentanediol
PDB code: 5uuc(A).


 
9. Ligand: TMO × 1
Trimethylamine oxide
PDB code: 3t2h(E).


 
10. Ligand: XYS × 1
Alpha-D-Xylopyranose
PDB code: 6n4w(A).

_Cl
 
11. Metal: _CL × 1
PDB code: 3t2h(E).

 

 Cluster 4 contains 10 ligand types

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Ligand Description


 
1. Ligand: DMS × 48
dimethyl sulfoxide
Dimethyl sulfoxide
PDB codes: 3qgo(A), 3t73(A), 3t74(A), 3t87(A), 3t8c(A), 3t8d(A), 3t8f(A), 3t8g(A), 3t8h(A), 4d91(A), 4d9w(A), 4h57(A), 4mtw(E), 4mwp(E), 4mxj(E), 4mzn(E), 4n4e(E), 4n5p(E), 4n66(E), 4oi5(E), 5dpe(E), 5dpf(E), 5js3(E), 5jss(E), 5jt9(E), 5jvi(E), 5jxn(E), 5l3u(E), 5l41(E), 5l8p(E), 5lif(E), 5lwd(E), 5m5f(E), 5m69(E), 5m9w(A), 5ma7(E), 5mnr(E), 5n2t(E), 5n2x(E), 5n2z(E), 5n31(E), 5n34(E), 5n3v(E), 5n3y(E), 6sc1(E), 6sck(E).


 
2. Ligand: IPA × 3
isopropyl alcohol
Isopropyl alcohol
PDB codes: 3ms3(A), 7tli(A), 8tli(A).


 
3. Ligand: GOL × 1
glycerin
Glycerol
PDB code: 3msf(A).


 
4. Ligand: POL × 1
propyl alcohol
N-Propanol
PDB code: 6lzn(A).


 
5. Ligand: XYP × 4
Beta-D-Xylopyranose
PDB codes: 5uu9(A), 5uua(A), 6n4w(A), 6n4z(A).


 
6. Ligand: EDO × 2
1,2-Ethanediol
PDB codes: 6qf2(A), 6qf3(A).


 
7. Ligand: MPD × 1
(4s)-2-Methyl-2,4-Pentanediol
PDB code: 5uuc(A).


 
8. Ligand: PEG × 1
Di(hydroxyethyl)ether
PDB code: 3qh5(A).


 
9. Ligand: PHN × 1
1,10-Phenanthroline
PDB code: 6lzo(A).


 
10. Ligand: SO4 × 1
Sulfate ion
PDB code: 2g4z(A).

 

 Cluster 5 contains 9 ligand types

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Ligand Description


 
1. Ligand: DMS × 17
dimethyl sulfoxide
Dimethyl sulfoxide
PDB codes: 3t73(A), 4h57(A), 5mnr(E), 5n2t(E), 5n2x(E), 5n2z(E), 5n31(E), 5n34(E), 5n3v(E), 5n3y(E), 5uu9(A), 6sb9(E), 6sbk(E), 6sc1(E), 6sck(E).

_Zn
 
2. Metal: _ZN × 17
PDB codes: 1l3f(E), 3t2h(E), 3t2i(E), 3t2j(E), 5un3(A), 5uu7(A), 5uua(A), 5uub(A), 5uuc(A), 5uud(A), 5uue(A), 6n4w(A), 6n4z(A).


 
3. Ligand: XYP × 10
Beta-D-Xylopyranose
PDB codes: 5un3(A), 5uu8(A), 5uu9(A), 5uua(A), 5uub(A), 6n4z(A).

_Cl
 
4. Metal: _CL × 4
PDB codes: 2g4z(A), 3t2h(E), 5uud(A), 5uue(A).


 
5. Ligand: EDO × 3
1,2-Ethanediol
PDB codes: 6qf2(A), 6qf3(A),


 
6. Ligand: TMO × 2
Trimethylamine oxide
PDB codes: 3t2h(E), 6fj2(A).


 
7. Ligand: BET × 1
Trimethyl glycine
PDB code: 3t2j(E).


 
8. Ligand: P6G × 1
Hexaethylene glycol
PDB code: 3qgo(A).


 
9. Ligand: PG4 × 1
Tetraethylene glycol
PDB code: 3qh5(A).

 

 Cluster 6 contains 6 ligand types

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Ligand Description


 
1. Ligand: DMS × 76
dimethyl sulfoxide
Dimethyl sulfoxide
PDB codes: 1fj3(A), 1fjo(A), 1fjq(A), 1fjt(A), 1fju(A), 1fjv(A), 1fjw(A), 1hyt(A), 1lna(E), 1lnb(E), 1lnc(E), 1lnd(E), 1lne(E), 1lnf(E), 1os0(A), 1pe7(A), 1pe8(A), 1qf0(A), 1qf1(A), 1qf2(A), 1tli(A), 1tlx(A), 1y3g(E), 2tli(A), 2tlx(A), 3f2p(A), 3for(A), 3fvp(A), 3ls7(A), 3ms3(A), 3t2j(E), 3t74(A), 3t8d(A), 3t8f(A), 3t8g(A), 3t8h(A), 3tli(A), 4mzn(E), 4n5p(E), 4n66(E), 4tli(A), 5a3y(A), 5dpe(E), 5dpf(E), 5js3(E), 5jss(E), 5jt9(E), 5jvi(E), 5jxn(E), 5k7t(A), 5l3u(E), 5l41(E), 5l8p(E), 5lif(E), 5lvd(E), 5lwd(E), 5m5f(E), 5m69(E), 5m9w(A), 5ma7(E), 5mnr(E), 5n2t(E), 5n2x(E), 5n2z(E), 5n31(E), 5n34(E), 5n3y(E), 5tli(A), 6fj2(A), 6qar(A), 6sb9(E), 6sck(E), 6tli(A), 7tli(A), 8tli(A), 8tln(E).


 
2. Ligand: IPA × 2
isopropyl alcohol
Isopropyl alcohol
PDB codes: 7tli(A), 8tli(A).


 
3. Ligand: XYP × 6
Beta-D-Xylopyranose
PDB codes: 5un3(A), 5uu8(A), 5uu9(A), 5uua(A), 5uub(A), 6n4w(A).


 
4. Ligand: MRD × 2
(4r)-2-Methylpentane-2,4-Diol
PDB codes: 6d5s(A), 6d5t(A).


 
5. Ligand: DMF × 1
Dimethylformamide
PDB code: 6d5o(A).


 
6. Ligand: PHN × 1
1,10-Phenanthroline
PDB code: 6lzo(A).

 

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