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;
Atoms found LESS than expected: % Diff = 0;
Kd = 3.4 uM
638.722 n/a O=C(N...
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 (51)
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 1QCJ - APT C14 H13 N6 O3 c1cc(ccc1C....
45 1QCI - ADE C5 H5 N5 c1[nH]c2c(....
46 3LE7 - ADE C5 H5 N5 c1[nH]c2c(....
47 5Z3J - NCA C6 H6 N2 O c1cc(cnc1)....
48 5Z3I - ADE C5 H5 N5 c1[nH]c2c(....
49 3HIW Ki = 3.9 nM C2X C51 H72 N21 O29 P5 CO[C@@H]1[....
50 3HIV Ki = 7.5 nM TXN C37 H52 N15 O20 P3 CO[C@@H]1[....
51 3HIT Ki = 6.4 nM DYN C30 H47 N10 O17 P3 CO[C@@H]1[....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: ASP ASP MET GLY PHE GLY LEU PHE ASP; Similar ligands found: 53
No: Ligand ECFP6 Tc MDL keys Tc
1 ASP ASP ASP MET GLY PHE GLY LEU PHE ASP 1 1
2 ASP ASP MET GLY PHE GLY LEU PHE ASP 1 1
3 THR LEU MET THR GLY GLN LEU GLY LEU PHE 0.57732 0.911111
4 GLY ILE LEU GLY PHE VAL PHE THR LEU 0.530973 0.877551
5 GLY ILE LEU GLY LEU VAL PHE THR LEU 0.517857 0.857143
6 ASP SER GLY PHE SER PHE GLY SER LYS 0.505618 0.791667
7 LEU LEU TYR GLY PHE VAL ASN TYR VAL 0.495726 0.862745
8 ARG PRO GLY ASN PHE LEU GLN ASN ARG PRO 0.495726 0.740741
9 ARG GLN ALA ASN PHE LEU GLY LYS 0.495327 0.893617
10 LEU LEU TYR GLY PHE VAL ASN TYR ILE 0.479339 0.846154
11 LEU SER PRO ASP SER PHE LEU ASN ASP 0.472527 0.770833
12 ALA LEU ASP LEU PHE 0.461538 0.840909
13 LYS LEU LEU PHE 0.458333 0.787234
14 GLY ASN TYR SER PHE TYR ALA LEU 0.455357 0.796296
15 SER GLU ASP GLU PHE TYR ASP ALA LEU SER 0.455285 0.777778
16 LEU GLY TYR GLY PHE VAL ASN TYR ILE 0.454545 0.846154
17 ACE GLU ASN LEU TYR PHE GLN SER GLY THR 0.452991 0.740741
18 GLN VAL ASN PHE LEU GLY LYS 0.45 0.84
19 LYS VAL LEU PHE LEU ASP GLY 0.442478 0.893617
20 TYR GLY GLY PHE LEU 0.439252 0.86
21 GLY ASN PHE LEU GLN SER ARG 0.438017 0.724138
22 LEU ASP GLU GLU THR GLY GLU PHE LEU 0.436975 0.823529
23 GLY ASP GLU VAL LYS VAL PHE ARG 0.436508 0.759259
24 LYS PHE LYS 0.43617 0.666667
25 ARG GLN ALA ASN PHE LEU GLY LYS ILE ASN 0.429907 0.869565
26 GLU ASN LEU TYR PHE GLN 0.429825 0.754717
27 ASP PHE M3L THR ASP 0.428571 0.645161
28 ASP ASP LEU TYR GLY 0.427184 0.84
29 ASN ALA LEU LEU ARG TYR LEU LEU ASP 0.425 0.683333
30 PHE ARG TYR LEU GLY 0.422414 0.754386
31 LEU LEU PHE GLY TYR PRO VAL TYR VAL 0.422222 0.693548
32 LEU LEU PHE GLY PHE PRO VAL TYR VAL 0.422222 0.693548
33 ARG PRO GLY ASN PHE PHE GLN ASN ARG PRO 0.422018 0.8
34 CYS GLY ASP LEU LEU ASN LEU ASP LEU GLY 0.421053 0.791667
35 LEU LEU PHE GLY LYS PRO VAL TYR VAL 0.42029 0.671875
36 THR GLU ASN LEU TYR PHE GLN SER GLY THR 0.419847 0.785714
37 GLY PHE 0.419753 0.75
38 ILE ARG LYS ILE LEU PHE LEU ASP GLY ILE 0.419118 0.75
39 PHE LEU ARG GLY ARG ALA TYR GLY LEU 0.417323 0.741379
40 ARG PRO GLY ASN PHE LEU GLN SER SER PRO 0.415385 0.719298
41 TYR GLN GLU SER THR ASP PHE THR PHE LEU 0.415094 0.795918
42 GLY ILE LEU GLU PHE VAL PHE THR LEU 0.413223 0.86
43 PHE GLU ALA ASN GLY ASN LEU ILE 0.41129 0.84
44 GLY ILE TRP GLY PHE VAL PHE THR LEU 0.410448 0.785714
45 GLY GLY LYS LYS LYS TYR LYS LEU 0.409091 0.773585
46 LEU GLU PHE GLN GLY 0.407407 0.891304
47 GLU ASP GLU ASP PHE GLU ILE LEU SER LEU 0.40625 0.754717
48 ARG GLN VAL ASN PHE LEU GLY LYS ILE ASN 0.403509 0.869565
49 ILE GLY LEU LEU GLY GLY 0.402174 0.826087
50 THR PRO ASP TYR PHE LEU 0.401786 0.785714
51 ASP LEU TYR CYS TYR GLU GLN LEU ASN 0.401639 0.763636
52 SER LEU ARG PHE LEU TYR GLU GLY 0.401575 0.733333
53 PHE LEU SER TYR LYS 0.4 0.763636
Similar Binding Sites (Proteins are less than 50% similar to leader) APoc FAQ
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