Receptor
PDB id Resolution Class Description Source Keywords
5GU4 1.55 Å EC: 3.2.2.22 RRNA N-GLYCOSYLASE RTA RICINUS COMMUNIS RICIN RIBOSOME-INACTIVATING PROTEIN RIBOSOMAL P STALK PROTRIBOSOME HYDROLASE
Ref.: CRYSTAL STRUCTURE OF RIBOSOME-INACTIVATING PROTEIN CHAIN IN COMPLEX WITH THE C-TERMINAL PEPTIDE OF THE RIBOSOMAL STALK PROTEIN P2 TOXINS V. 8 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ASP ASP MET GLY PHE GLY LEU PHE ASP C:2;
D:2;
Valid;
Valid;
Atoms found LESS than expected: % Diff = 0.352;
Atoms found LESS than expected: % Diff = 0.352;
Kd = 3.4 uM
638.722 n/a O=C([...
GOL B:301;
Invalid;
none;
submit data
92.094 C3 H8 O3 C(C(C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5GU4 1.55 Å EC: 3.2.2.22 RRNA N-GLYCOSYLASE RTA RICINUS COMMUNIS RICIN RIBOSOME-INACTIVATING PROTEIN RIBOSOMAL P STALK PROTRIBOSOME HYDROLASE
Ref.: CRYSTAL STRUCTURE OF RIBOSOME-INACTIVATING PROTEIN CHAIN IN COMPLEX WITH THE C-TERMINAL PEPTIDE OF THE RIBOSOMAL STALK PROTEIN P2 TOXINS V. 8 2016
Members (22)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 13 families.
1 5DDZ - ASP ASP ASP MET GLY PHE GLY LEU PHE ASP n/a n/a
2 4MX5 ic50 = 28 uM 5MX C17 H17 N7 O4 c1ccc(cc1)....
3 4HV7 ic50 = 300 uM 19J C11 H11 N7 O5 c1c(nc2c(n....
4 3PX8 ic50 = 230 uM JP2 C7 H5 N5 O3 c1c(nc2c(n....
5 5GU4 Kd = 3.4 uM ASP ASP MET GLY PHE GLY LEU PHE ASP n/a n/a
6 1BR6 Ki = 0.6 mM PT1 C14 H12 N6 O3 c1cc(ccc1C....
7 4ESI ic50 = 70 uM 0RB C10 H9 N9 O2 c1c([nH]nn....
8 4HV3 ic50 = 115 uM 19L C21 H20 N8 O6 c1ccc2c(c1....
9 1BR5 Ki = 2 mM NEO C9 H11 N5 O4 c1c(nc2c(n....
10 3EJ5 ic50 = 0.27 mM EJ5 C14 H15 N3 O4 c1cc(ccc1C....
11 4MX1 ic50 = 209 uM 1MX C16 H16 N8 O3 c1ccc(cc1)....
12 3PX9 ic50 = 380 uM JP3 C12 H10 N6 O3 c1cc(oc1)C....
13 4HUO ic50 = 20 uM RS8 C18 H17 N7 O5 c1ccc(cc1)....
14 2P8N Kd = 700 uM ADE C5 H5 N5 c1[nH]c2c(....
15 1J1M - TRE C12 H22 O11 C([C@@H]1[....
16 4Q2V - 0XE C21 H18 O11 c1ccc(cc1)....
17 4HUP ic50 = 15 uM 19M C27 H26 N8 O6 c1ccc(cc1)....
18 1IFS - ADE C5 H5 N5 c1[nH]c2c(....
19 1IFU - FMC C10 H13 N5 O4 c1nc2c(c(n....
20 3HIO - C2X C51 H72 N21 O29 P5 CO[C@@H]1[....
21 2PJO Kd = 900 mM NMU C2 H6 N2 O CNC(=O)N
22 2R3D Kd = 1.4 M ACM C2 H5 N O CC(=O)N
70% Homology Family (22)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 5DDZ - ASP ASP ASP MET GLY PHE GLY LEU PHE ASP n/a n/a
2 4MX5 ic50 = 28 uM 5MX C17 H17 N7 O4 c1ccc(cc1)....
3 4HV7 ic50 = 300 uM 19J C11 H11 N7 O5 c1c(nc2c(n....
4 3PX8 ic50 = 230 uM JP2 C7 H5 N5 O3 c1c(nc2c(n....
5 5GU4 Kd = 3.4 uM ASP ASP MET GLY PHE GLY LEU PHE ASP n/a n/a
6 1BR6 Ki = 0.6 mM PT1 C14 H12 N6 O3 c1cc(ccc1C....
7 4ESI ic50 = 70 uM 0RB C10 H9 N9 O2 c1c([nH]nn....
8 4HV3 ic50 = 115 uM 19L C21 H20 N8 O6 c1ccc2c(c1....
9 1BR5 Ki = 2 mM NEO C9 H11 N5 O4 c1c(nc2c(n....
10 3EJ5 ic50 = 0.27 mM EJ5 C14 H15 N3 O4 c1cc(ccc1C....
11 4MX1 ic50 = 209 uM 1MX C16 H16 N8 O3 c1ccc(cc1)....
12 3PX9 ic50 = 380 uM JP3 C12 H10 N6 O3 c1cc(oc1)C....
13 4HUO ic50 = 20 uM RS8 C18 H17 N7 O5 c1ccc(cc1)....
14 2P8N Kd = 700 uM ADE C5 H5 N5 c1[nH]c2c(....
15 1J1M - TRE C12 H22 O11 C([C@@H]1[....
16 4Q2V - 0XE C21 H18 O11 c1ccc(cc1)....
17 4HUP ic50 = 15 uM 19M C27 H26 N8 O6 c1ccc(cc1)....
18 1IFS - ADE C5 H5 N5 c1[nH]c2c(....
19 1IFU - FMC C10 H13 N5 O4 c1nc2c(c(n....
20 3HIO - C2X C51 H72 N21 O29 P5 CO[C@@H]1[....
21 2PJO Kd = 900 mM NMU C2 H6 N2 O CNC(=O)N
22 2R3D Kd = 1.4 M ACM C2 H5 N O CC(=O)N
50% Homology Family (47)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 5DDZ - ASP ASP ASP MET GLY PHE GLY LEU PHE ASP n/a n/a
2 4MX5 ic50 = 28 uM 5MX C17 H17 N7 O4 c1ccc(cc1)....
3 4HV7 ic50 = 300 uM 19J C11 H11 N7 O5 c1c(nc2c(n....
4 3PX8 ic50 = 230 uM JP2 C7 H5 N5 O3 c1c(nc2c(n....
5 5GU4 Kd = 3.4 uM ASP ASP MET GLY PHE GLY LEU PHE ASP n/a n/a
6 1BR6 Ki = 0.6 mM PT1 C14 H12 N6 O3 c1cc(ccc1C....
7 4ESI ic50 = 70 uM 0RB C10 H9 N9 O2 c1c([nH]nn....
8 4HV3 ic50 = 115 uM 19L C21 H20 N8 O6 c1ccc2c(c1....
9 1BR5 Ki = 2 mM NEO C9 H11 N5 O4 c1c(nc2c(n....
10 3EJ5 ic50 = 0.27 mM EJ5 C14 H15 N3 O4 c1cc(ccc1C....
11 4MX1 ic50 = 209 uM 1MX C16 H16 N8 O3 c1ccc(cc1)....
12 3PX9 ic50 = 380 uM JP3 C12 H10 N6 O3 c1cc(oc1)C....
13 4HUO ic50 = 20 uM RS8 C18 H17 N7 O5 c1ccc(cc1)....
14 2P8N Kd = 700 uM ADE C5 H5 N5 c1[nH]c2c(....
15 1J1M - TRE C12 H22 O11 C([C@@H]1[....
16 4Q2V - 0XE C21 H18 O11 c1ccc(cc1)....
17 4HUP ic50 = 15 uM 19M C27 H26 N8 O6 c1ccc(cc1)....
18 1IFS - ADE C5 H5 N5 c1[nH]c2c(....
19 1IFU - FMC C10 H13 N5 O4 c1nc2c(c(n....
20 3HIO - C2X C51 H72 N21 O29 P5 CO[C@@H]1[....
21 2PJO Kd = 900 mM NMU C2 H6 N2 O CNC(=O)N
22 2R3D Kd = 1.4 M ACM C2 H5 N O CC(=O)N
23 3KU0 - ADE C5 H5 N5 c1[nH]c2c(....
24 2QET - ADE C5 H5 N5 c1[nH]c2c(....
25 1LPC - CMP C10 H12 N5 O6 P c1nc(c2c(n....
26 1GIU - ADE C5 H5 N5 c1[nH]c2c(....
27 1MRK - FMC C10 H13 N5 O4 c1nc2c(c(n....
28 1QD2 - ADE C5 H5 N5 c1[nH]c2c(....
29 1TCS - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
30 1MRJ - ADN C10 H13 N5 O4 c1nc(c2c(n....
31 1NLI Kd = 260 uM ADE C5 H5 N5 c1[nH]c2c(....
32 1GIS - DA C10 H14 N5 O6 P c1nc(c2c(n....
33 1AHB - FMP C10 H14 N5 O7 P c1nc2c(c(n....
34 1AHA - ADE C5 H5 N5 c1[nH]c2c(....
35 3N1N - GUN C5 H5 N5 O c1[nH]c2c(....
36 3V2K - ADE C5 H5 N5 c1[nH]c2c(....
37 3RL9 - ADE C5 H5 N5 c1[nH]c2c(....
38 3SJ6 - RIP C5 H10 O5 C1[C@H]([C....
39 1MRH - FMC C10 H13 N5 O4 c1nc2c(c(n....
40 3U6Z - ADE C5 H5 N5 c1[nH]c2c(....
41 1MRG - ADN C10 H13 N5 O4 c1nc(c2c(n....
42 1J1S - FMP C10 H14 N5 O7 P c1nc2c(c(n....
43 1D6A - GUN C5 H5 N5 O c1[nH]c2c(....
44 1QCI - ADE C5 H5 N5 c1[nH]c2c(....
45 3LE7 - ADE C5 H5 N5 c1[nH]c2c(....
46 3HIW Ki = 3.9 nM C2X C51 H72 N21 O29 P5 CO[C@@H]1[....
47 3HIV Ki = 7.5 nM TXN C37 H52 N15 O20 P3 CO[C@@H]1[....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: ASP ASP MET GLY PHE GLY LEU PHE ASP; Similar ligands found: 58
No: Ligand ECFP6 Tc MDL keys Tc
1 ASP ASP MET GLY PHE GLY LEU PHE ASP 1 1
2 ASP ASP ASP MET GLY PHE GLY LEU PHE ASP 1 1
3 THR LEU MET THR GLY GLN LEU GLY LEU PHE 0.57732 0.888889
4 ARG PRO GLY ASN PHE LEU GLN ASN ARG PRO 0.513043 0.722222
5 ASP SER GLY PHE SER PHE GLY SER LYS 0.505618 0.787234
6 GLY ILE LEU GLY LEU VAL PHE THR LEU 0.504425 0.854167
7 ARG GLN ALA ASN PHE LEU GLY LYS 0.495327 0.87234
8 LEU LEU TYR GLY PHE VAL ASN TYR VAL 0.487395 0.843137
9 GLY ILE LEU GLY PHE VAL PHE THR LEU 0.482456 0.895833
10 LEU LEU TYR GLY PHE VAL ASN TYR ILE 0.479675 0.826923
11 LYS VAL LEU PHE LEU ASP GLY 0.477064 0.891304
12 LEU SER PRO ASP SER PHE LEU ASN ASP 0.472527 0.765957
13 GLN VAL ASN PHE LEU GLY LYS 0.470085 0.82
14 LEU GLY TYR GLY PHE VAL ASN TYR ILE 0.466667 0.826923
15 GLY ASN TYR SER PHE TYR ALA LEU 0.464286 0.777778
16 LYS LEU LEU PHE 0.463158 0.76087
17 GLY ASP GLU VAL LYS VAL PHE ARG 0.454545 0.740741
18 GLY ASN PHE LEU GLN SER ARG 0.453782 0.706897
19 ASP PHE GLU ASP TYR GLU PHE ASP 0.448598 0.686275
20 ALA LEU ASP LEU PHE 0.445652 0.837209
21 GLU THR LEU LEU ASP LEU ASP PHE LEU GLU 0.442308 0.782609
22 ACE GLU ASN LEU TYR PHE GLN SER GLY THR 0.441667 0.722222
23 ASP PHE M3L THR ASP 0.441441 0.639344
24 ILE ARG LYS ILE LEU PHE LEU ASP GLY ILE 0.439394 0.732143
25 TYR GLY GLY PHE LEU 0.439252 0.857143
26 LEU ASP GLU GLU THR GLY GLU PHE LEU 0.436975 0.82
27 SER GLU ASP GLU PHE TYR ASP ALA LEU SER 0.435484 0.773585
28 LYS PHE LYS 0.430108 0.638298
29 ARG GLN ALA ASN PHE LEU GLY LYS ILE ASN 0.429907 0.847826
30 ASP ASP LEU TYR GLY 0.427184 0.836735
31 ARG PRO GLY ASN PHE PHE GLN ASN ARG PRO 0.425926 0.78
32 ASN ALA LEU LEU ARG TYR LEU LEU ASP 0.425926 0.705882
33 TYR GLN GLU SER THR ASP PHE THR PHE LEU 0.424528 0.791667
34 PHE ARG TYR LEU GLY 0.422414 0.736842
35 ALA GLU THR PHE TYR VAL ASP GLY 0.422414 0.730769
36 GLY ALA GLU VAL PHE TYR VAL ASP GLY ALA 0.421488 0.84
37 PHE LEU ARG GLY ARG ALA TYR GLY LEU 0.420635 0.724138
38 PHE GLU ALA ASN GLY ASN LEU ILE 0.419355 0.82
39 GLY ARG PHE GLN VAL THR 0.418182 0.711538
40 CYS GLY ASP LEU LEU ASN LEU ASP LEU GLY 0.416667 0.75
41 THR GLU ASN LEU TYR PHE GLN SER GLY THR 0.416667 0.767857
42 GLY GLY LYS LYS LYS TYR LYS LEU 0.416667 0.769231
43 ARG GLN VAL ASN PHE LEU GLY LYS ILE ASN 0.415929 0.847826
44 GLU ASN LEU TYR PHE GLN 0.412281 0.735849
45 PHE LEU ARG GLY ARG ALA TYR VAL LEU 0.410448 0.724138
46 ALA PHE THR SER 0.408163 0.708333
47 LEU LEU PHE GLY PHE PRO VAL TYR VAL 0.405797 0.688525
48 LEU LEU PHE GLY TYR PRO VAL TYR VAL 0.405797 0.688525
49 GLY LEU TYR ALA SER LYS LEU ALA 0.403509 0.740741
50 CYS VAL ASN GLY SER CYS PHE THR VAL 0.403226 0.769231
51 GLY PHE 0.402439 0.674419
52 GLY ILE LEU GLU PHE VAL PHE THR LEU 0.401639 0.836735
53 PHE GLU ASP ASN PHE VAL PRO 0.401639 0.688525
54 GLY ALA GLU THR PHE TYR VAL ASP GLY ALA 0.401575 0.792453
55 LEU LEU PHE GLY LYS PRO VAL TYR VAL 0.401408 0.677419
56 GLY ILE TRP GLY PHE VAL PHE THR LEU 0.4 0.781818
57 ILE LEU GLY LYS PHE LEU HIS ARG LEU 0.4 0.66129
58 GLY GLY LYS LYS LYS TYR GLN LEU 0.4 0.754717
Similar Binding Sites (Proteins are less than 50% similar to leader)
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