Receptor
PDB id Resolution Class Description Source Keywords
3PZ2 2.35 Å EC: 2.5.1.60 CRYSTAL STRUCTURE OF RABGGTASE(DELTA LRR; DELTA IG) IN COMPL BMS3 AND LIPID SUBSTRATE GGPP RATTUS NORVEGICUS PROTEIN PRENYLATION FUSION PROTEIN CHIMERA PROTEIN TRANSFTRANSFERASE INHIBITOR COMPLEX
Ref.: STRUCTURE-GUIDED DEVELOPMENT OF SELECTIVE RABGGTASE INHIBITORS. ANGEW.CHEM.INT.ED.ENGL. V. 50 4957 2011
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
3PZ B:333;
 Valid;
 none;
 ic50 = 724 nM
527.637 C29 H29 N5 O3 S Cn1cn...
CA B:332;
 Part of Protein;
 none;
 submit data
40.078 Ca [Ca+2...
GRG B:334;
 Valid;
 none;
 submit data
450.443 C20 H36 O7 P2 CC(=C...
ZN B:1;
 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: 3PZ; Similar ligands found: 7
No: Ligand ECFP6 Tc MDL keys Tc
1 3PZ 1 1
2 7TQ 0.776786 0.925
3 7TO 0.771429 0.925
4 7TR 0.743119 0.936709
5 7TM 0.675 0.840909
6 7TP 0.578512 0.911392
7 PZ3 0.571429 0.86747
Ligand no: 2; Ligand: GRG; Similar ligands found: 39
No: Ligand ECFP6 Tc MDL keys Tc
1 VTP 1 0.975
2 GRG 1 1
3 OTP 1 0.975
4 FPP 1 1
5 ZTP 1 0.975
6 GPP 0.911111 0.974359
7 DSL 0.744681 0.9
8 0K3 0.744681 0.9
9 FJP 0.744681 0.923077
10 FDF 0.727273 0.904762
11 FFF 0.714286 0.928571
12 HZZ 0.680851 0.897436
13 FGG 0.590164 0.928571
14 FPF 0.57377 0.928571
15 2CF 0.57377 0.928571
16 ELU 0.571429 0.951219
17 ELR 0.571429 0.951219
18 10E 0.568627 0.702128
19 10D 0.568627 0.785714
20 MGM 0.5625 0.764706
21 DMA 0.5625 0.846154
22 A4S 0.558824 0.698113
23 3E9 0.555556 0.951219
24 FPS 0.551724 0.880952
25 GGS 0.551724 0.880952
26 H6P 0.54902 0.785714
27 FPQ 0.539683 0.826087
28 10G 0.538462 0.767442
29 FII 0.507937 0.666667
30 GST 0.482759 0.857143
31 PS7 0.48 0.906977
32 C0X 0.477612 0.744681
33 FHP 0.473684 0.761905
34 1NH 0.457831 0.770833
35 0FV 0.442623 0.904762
36 LA6 0.442623 0.904762
37 SZH 0.428571 0.655172
38 749 0.428571 0.897436
39 9GB 0.415094 0.825
Similar Ligands (3D)
Ligand no: 1; Ligand: 3PZ; Similar ligands found: 0
No: Ligand Similarity coefficient
Ligand no: 2; Ligand: GRG; 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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