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Receptor
PDB id Resolution Class Description Source Keywords
3dsu 1.9 Å EC: 2.5.1.60 CRYSTAL STRUCTURE OF RABGGTASE(DELTA LRR; DELTA IG)IN COMPLE FARNESYL 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...
FPP B:334;
Valid;
none;
Kd = 0.94 nM
382.326 C15 H28 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: FPP; Similar ligands found: 35
No: Ligand ECFP6 Tc MDL keys Tc
1 OTP 1 0.975
2 GRG 1 1
3 ZTP 1 0.975
4 FPP 1 1
5 VTP 1 0.975
6 GPP 0.911111 0.974359
7 DSL 0.744681 0.9
8 FJP 0.744681 0.923077
9 0K3 0.744681 0.9
10 FDF 0.727273 0.904762
11 FFF 0.714286 0.928571
12 FGG 0.590164 0.928571
13 2CF 0.57377 0.928571
14 FPF 0.57377 0.928571
15 10D 0.568627 0.785714
16 10E 0.568627 0.702128
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
35 9GB 0.415094 0.825
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: 94
This union binding pocket(no: 1) in the query (biounit: 3dst.bio1) has 71 residues
No: Leader PDB Ligand Sequence Similarity
1 2VWA PTY None
2 2BIF SIN 2.41692
3 4RW3 SHV 2.64901
4 4RW3 TDA 2.64901
5 4P8O 883 2.6738
6 3PMA SCR 2.7027
7 3R9V DXC 2.7972
8 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 3.40136
9 5IUY BOG 3.62538
10 4NTO 1PW 3.62538
11 4MRP GSH 3.92749
12 3MBC NAP 3.92749
13 4URN NOV 4
14 5EOO CIT 4.15094
15 5DXE EST 4.21456
16 1ZED PNP 4.22961
17 5B5S BOG 4.34783
18 4TV1 36M 4.38247
19 5W6Y TRP 4.43038
20 4FHT DHB 4.4586
21 5OPJ AHR 4.53172
22 5LX9 OLB 4.57746
23 6CB2 OLC 4.77816
24 5X3R 7Y3 4.87805
25 4G86 BNT 4.92958
26 5NE5 KIF 5.13595
27 3ET1 ET1 5.15464
28 2Y91 98J 5.28302
29 2HHP FLC 5.43807
30 4QGE 35O 5.43807
31 4OKD GLC GLC GLC 5.74018
32 1NF8 BOG 5.7971
33 2OKL BB2 5.94595
34 3I7V ATP 5.97015
35 1XVB 3BR 6.47059
36 4OKS 2T9 6.64653
37 3OKI OKI 6.86695
38 1NRL SRL 6.96203
39 4AZI OAN 7.25076
40 1YYE 196 7.46269
41 2YVE MBT 7.56757
42 2BHW NEX 7.75862
43 2BHW XAT 7.75862
44 2BHW LUX 7.75862
45 5VZ0 2BA 7.85498
46 1NVM OXL 7.85498
47 1OCU PIB 8.02469
48 4IHL 1F5 8.08511
49 1T0S BML 8.13953
50 1M2Z BOG 8.17121
51 1NU4 MLA 8.24742
52 1U3R 338 8.29876
53 3OLL EST 8.33333
54 5LWY OLB 8.41121
55 3X01 AMP 8.45921
56 2GJ5 VD3 8.64198
57 1DTL BEP 8.69565
58 3KO0 TFP 8.91089
59 4V3I ASP LEU THR ARG PRO 9.06344
60 4EKQ NPO 9.09091
61 5WGQ EST 9.1954
62 5WGD EST 9.1954
63 2BCG GER 9.2233
64 5HYR EST 9.30233
65 4MGA 27L 9.41177
66 5OCQ CIT 9.47368
67 3UUD EST 9.56175
68 3E3U NVC 10.6599
69 5V4R MGT 11.1111
70 5TDC NMM ILE PHE SER 11.8421
71 1KJ1 MAN 11.9266
72 1TV5 N8E 12.0846
73 2WDQ CBE 12.4031
74 4V1F BQ1 12.7907
75 4LWU 20U 12.9412
76 3GWN FAD 16.6667
77 6BVM EBV 18.5629
78 6BVK EAV 18.5629
79 4OGQ 7PH 20.5882
80 5OCA 9QZ 21.4286
81 6BOC EU7 29.6296
82 6BOC RIM 29.6296
83 4L9P FII 38.0665
84 3DRA GRG 38.8889
85 3Q78 FPS 43.2024
86 3SFX JAN 43.2024
87 3SFX FII 43.2024
88 1N4Q MGM 46.5257
89 1TN6 FII 49.5468
90 2R2L PB9 49.5468
91 2R2L FPP 49.5468
92 1MZC FPP 49.5468
93 1MZC BNE 49.5468
94 1KZO FPP 49.8489
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