Receptor
PDB id Resolution Class Description Source Keywords
3HXB 2.25 Å EC: 2.5.1.60 ENGINEERED RABGGTASE IN COMPLEX WITH A PEPTIDOMIMETIC INHIBI (COMPOUND 6) RATTUS NORVEGICUS PROTEIN PRENYLATION INHIBITION METAL-BINDING PRENYLTRANSFETRANSFERASE ZINC
Ref.: DESIGN, SYNTHESIS, AND CHARACTERIZATION OF PEPTIDE-GERANYLGERANYL TRANSFERASE INHIBITORS J.MED.CHEM. V. 52 8025 2009
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
BD5 B:332;
 Valid;
 none;
 submit data
625.668 C35 H35 N3 O8 c1ccc...
ZN B:333;
 Part of Protein;
 none;
 submit data
65.409 Zn [Zn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3DST 1.9 Å EC: 2.5.1.60 CRYSTAL STRUCTURE OF RABGGTASE(DELTA LRR; DELTA IG)IN COMPLE GERANYLGERANYL PYROPHOSPHATE RATTUS NORVEGICUS PROTEIN PRENYLATION METAL-BINDING PRENYLTRANSFERASE TRANSZINC PHOSPHOPROTEIN
Ref.: STRUCTURES OF RABGGTASE-SUBSTRATE/PRODUCT COMPLEXES INSIGHTS INTO THE EVOLUTION OF PROTEIN PRENYLATION EMBO J. V. 27 2444 2008
Members (16)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 3PZ2 ic50 = 724 nM 3PZ C29 H29 N5 O3 S Cn1cncc1CN....
2 4GTS ic50 = 12.8 nM 7TP C33 H32 N4 O6 S Cn1cncc1CN....
3 3PZ3 ic50 = 141 nM PZ3 C41 H39 N5 O7 S Cn1cncc1CN....
4 4GTT ic50 = 6 nM 7TQ C37 H36 N6 O5 S Cn1cncc1CN....
5 3DST Kd = 0.83 nM GRG C20 H36 O7 P2 CC(=CCC/C(....
6 3DSU Kd = 94 nM FPP C15 H28 O7 P2 CC(=CCC/C(....
7 3HXC - BD6 C35 H37 N7 O6 CN([C@@H](....
8 3C72 ic50 = 22.7 uM CX1 C33 H35 N5 O7 CN([C@@H](....
9 3DSV - GER C20 H34 CC=C(/C)CC....
10 3HXE - BD8 C43 H57 N7 O5 CCCCCCCCCC....
11 3PZ1 ic50 = 724 nM 3PZ C29 H29 N5 O3 S Cn1cncc1CN....
12 3DSW - GER C20 H34 CC=C(/C)CC....
13 4GTV ic50 = 38 nM 7TR C34 H38 N6 O5 S CCN(CC)C(=....
14 3HXB - BD5 C35 H35 N3 O8 c1ccc(cc1)....
15 3DSX - GER C20 H34 CC=C(/C)CC....
16 3HXF - BD9 C40 H55 N9 O5 CCCCCCCCCC....
70% Homology Family (16)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 3PZ2 ic50 = 724 nM 3PZ C29 H29 N5 O3 S Cn1cncc1CN....
2 4GTS ic50 = 12.8 nM 7TP C33 H32 N4 O6 S Cn1cncc1CN....
3 3PZ3 ic50 = 141 nM PZ3 C41 H39 N5 O7 S Cn1cncc1CN....
4 4GTT ic50 = 6 nM 7TQ C37 H36 N6 O5 S Cn1cncc1CN....
5 3DST Kd = 0.83 nM GRG C20 H36 O7 P2 CC(=CCC/C(....
6 3DSU Kd = 94 nM FPP C15 H28 O7 P2 CC(=CCC/C(....
7 3HXC - BD6 C35 H37 N7 O6 CN([C@@H](....
8 3C72 ic50 = 22.7 uM CX1 C33 H35 N5 O7 CN([C@@H](....
9 3DSV - GER C20 H34 CC=C(/C)CC....
10 3HXE - BD8 C43 H57 N7 O5 CCCCCCCCCC....
11 3PZ1 ic50 = 724 nM 3PZ C29 H29 N5 O3 S Cn1cncc1CN....
12 3DSW - GER C20 H34 CC=C(/C)CC....
13 4GTV ic50 = 38 nM 7TR C34 H38 N6 O5 S CCN(CC)C(=....
14 3HXB - BD5 C35 H35 N3 O8 c1ccc(cc1)....
15 3DSX - GER C20 H34 CC=C(/C)CC....
16 3HXF - BD9 C40 H55 N9 O5 CCCCCCCCCC....
50% Homology Family (16)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 3PZ2 ic50 = 724 nM 3PZ C29 H29 N5 O3 S Cn1cncc1CN....
2 4GTS ic50 = 12.8 nM 7TP C33 H32 N4 O6 S Cn1cncc1CN....
3 3PZ3 ic50 = 141 nM PZ3 C41 H39 N5 O7 S Cn1cncc1CN....
4 4GTT ic50 = 6 nM 7TQ C37 H36 N6 O5 S Cn1cncc1CN....
5 3DST Kd = 0.83 nM GRG C20 H36 O7 P2 CC(=CCC/C(....
6 3DSU Kd = 94 nM FPP C15 H28 O7 P2 CC(=CCC/C(....
7 3HXC - BD6 C35 H37 N7 O6 CN([C@@H](....
8 3C72 ic50 = 22.7 uM CX1 C33 H35 N5 O7 CN([C@@H](....
9 3DSV - GER C20 H34 CC=C(/C)CC....
10 3HXE - BD8 C43 H57 N7 O5 CCCCCCCCCC....
11 3PZ1 ic50 = 724 nM 3PZ C29 H29 N5 O3 S Cn1cncc1CN....
12 3DSW - GER C20 H34 CC=C(/C)CC....
13 4GTV ic50 = 38 nM 7TR C34 H38 N6 O5 S CCN(CC)C(=....
14 3HXB - BD5 C35 H35 N3 O8 c1ccc(cc1)....
15 3DSX - GER C20 H34 CC=C(/C)CC....
16 3HXF - BD9 C40 H55 N9 O5 CCCCCCCCCC....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: BD5; Similar ligands found: 27
No: Ligand ECFP6 Tc MDL keys Tc
1 BD5 1 1
2 TI2 0.635135 0.837209
3 CX1 0.556701 0.719298
4 FVF 0.534884 0.690909
5 186 0.53012 0.840909
6 NX6 0.507042 0.727273
7 343 0.485981 0.66129
8 AG6 0.484848 0.77551
9 3EF 0.46789 0.634921
10 3ES 0.46789 0.634921
11 MP2 0.455696 0.729167
12 PHQ DAS 0.445946 0.659091
13 BBL 0.444444 0.714286
14 KI2 PHE GLU GLU NH2 0.444444 0.745098
15 33Z 0.443396 0.612903
16 THR ASN GLU PHE TYR PHE 0.44086 0.734694
17 3NF 0.428571 0.72093
18 PHQ DGL 0.428571 0.659091
19 THR PRO ASP TYR PHE LEU 0.425743 0.616667
20 PHP 0.423529 0.660714
21 PHQ LEU VAL ARG TYR 0.423423 0.706897
22 ING 0.42029 0.608696
23 ASP PHE GLU ASP TYR GLU PHE ASP 0.42 0.692308
24 PHE TYR ARG TYR GLY PHE VAL ALA ASN PHE 0.405941 0.698113
25 BWX 0.402439 0.644444
26 ASP ASN ARG LEU GLY LEU VAL TYR GLN PHE 0.401961 0.72
27 SBA 0.4 0.705882
Similar Ligands (3D)
Ligand no: 1; Ligand: BD5; Similar ligands found: 0
No: Ligand Similarity coefficient
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3DST; Ligand: GRG; Similar sites found with APoc: 3
This union binding pocket(no: 1) in the query (biounit: 3dst.bio1) has 71 residues
No: Leader PDB Ligand Sequence Similarity
1 4L9P FII 38.0665
2 3DRA GRG 38.8889
3 1KZO FPP 49.8489
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