Receptor
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
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CA B:333;
Part of Protein;
none;
submit data
40.078 Ca [Ca+2...
GRG B:334;
Valid;
none;
Kd = 0.83 nM
450.443 C20 H36 O7 P2 CC(=C...
ZN B:332;
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 = 0.94 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 = 123 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 = 0.94 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 = 123 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 = 0.94 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 = 123 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
Ligand no: 1; Ligand: GRG; Similar ligands found: 34
No: Ligand ECFP6 Tc MDL keys Tc
1 OTP 1 0.975
2 ZTP 1 0.975
3 GRG 1 1
4 FPP 1 1
5 VTP 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 FGG 0.590164 0.928571
13 FPF 0.57377 0.928571
14 2CF 0.57377 0.928571
15 10E 0.568627 0.702128
16 10D 0.568627 0.785714
17 MGM 0.5625 0.764706
18 DMA 0.5625 0.846154
19 A4S 0.558824 0.698113
20 3E9 0.555556 0.951219
21 FPS 0.551724 0.880952
22 GGS 0.551724 0.880952
23 H6P 0.54902 0.785714
24 FPQ 0.539683 0.826087
25 10G 0.538462 0.767442
26 FII 0.507937 0.666667
27 GST 0.482759 0.857143
28 PS7 0.48 0.906977
29 FHP 0.473684 0.761905
30 1NH 0.457831 0.770833
31 0FV 0.442623 0.904762
32 LA6 0.442623 0.904762
33 749 0.428571 0.897436
34 SZH 0.428571 0.655172
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3DST; Ligand: GRG; Similar sites found: 31
This union binding pocket(no: 1) in the query (biounit: 3dst.bio1) has 71 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2VWA PTY 0.01142 0.4711 None
2 4RW3 SHV 0.01876 0.46042 2.64901
3 4RW3 PLM 0.01886 0.4281 2.64901
4 4RW3 TDA 0.01299 0.42308 2.64901
5 3PMA SCR 0.03064 0.4381 2.7027
6 3TL1 JRO 0.01985 0.4508 3.77358
7 4URN NOV 0.01545 0.45713 4
8 3B6C SDN 0.01092 0.46588 4.70085
9 1M2Z BOG 0.04639 0.44063 8.17121
10 5UWA 8ND 0.01692 0.4046 8.37438
11 3E3U NVC 0.01506 0.44164 10.6599
12 5V4R MGT 0.004764 0.49161 11.1111
13 1TV5 N8E 0.01271 0.46206 12.0846
14 1RL4 BL5 0.03555 0.40309 12.234
15 4LWU 20U 0.0144 0.44269 12.9412
16 1LQY BB2 0.02064 0.42787 13.0435
17 4EI7 GDP 0.009471 0.42998 13.5952
18 4Q86 AMP 0.0278 0.42744 14.1994
19 4I67 G G G RPC 0.03144 0.43139 18.3908
20 4OAS 2SW 0.02152 0.43338 18.75
21 1G27 BB1 0.04613 0.40984 20.2381
22 4L9P FII 0.000000001157 0.41731 38.0665
23 3DRA GRG 0.00000003598 0.72945 38.8889
24 3Q78 FPS 0.00000009178 0.68418 43.2024
25 3SFX JAN 0.000000009717 0.43293 43.2024
26 3SFX FII 0.000000009717 0.43293 43.2024
27 1MZC BNE 0.0000000007455 0.50696 49.5468
28 1MZC FPP 0.0000000007455 0.50696 49.5468
29 2R2L FPP 0.0000000004697 0.46267 49.5468
30 2R2L PB9 0.0000000003106 0.46267 49.5468
31 1KZO FPP 0.00000001218 0.74446 49.8489
Feedback