Receptor
PDB id Resolution Class Description Source Keywords
2E8V 1.8 Å EC: 2.5.1.30 S. CEREVISIAE GERANYLGERANYL PYROPHOSPHATE SYNTHASE IN COMPLEX WITH PRODUCT GGPP (P21) SACCHAROMYCES CEREVISIAE PRENYLTRANSFERASE FARNESYL PYROPHOSPHATE BISPHOSPHONATE
Ref.: BISPHOSPHONATES TARGET MULTIPLE SITES IN BOTH CIS-AND TRANS-PRENYLTRANSFERASES PROC.NATL.ACAD.SCI.USA V. 104 10022 2007
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GRG A:1501;
B:1502;
Valid;
Valid;
none;
none;
submit data
450.443 C20 H36 O7 P2 CC(=C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2Z7I 2.1 Å EC: 2.5.1.30 S. CEREVISIAE GERANYLGERANYL PYROPHOSPHATE SYNTHASE IN COMPL INHIBITOR BPH-742 SACCHAROMYCES CEREVISIAE PRENYLTRANSFERASE GERANYLGERANYL PYROPHOSPHATE BISPHOSPHONCAROTENOID BIOSYNTHESIS ISOPRENE BIOSYNTHESIS MULTIFUNCTIENZYME PROTEIN TRANSPORT TRANSPORT TRANSFERASE TRANSFERTRANSFERASE INHIBITOR COMPLEX
Ref.: INHIBITION OF GERANYLGERANYL DIPHOSPHATE SYNTHASE B BISPHOSPHONATES: A CRYSTALLOGRAPHIC AND COMPUTATION INVESTIGATION J.MED.CHEM. V. 51 5594 2008
Members (21)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2E8X - GPP C10 H20 O7 P2 CC(=CCC/C(....
2 2ZEV - IPE C5 H12 O7 P2 CC(=C)CCO[....
3 2Z4V - GRG C20 H36 O7 P2 CC(=CCC/C(....
4 2E8W - IPE C5 H12 O7 P2 CC(=C)CCO[....
5 2Z7H Ki = 115 nM GG3 C14 H25 N O7 P2 C[N@](CCCC....
6 2Z4Y ic50 = 0.71 uM 252 C9 H22 O7 P2 CCCCCCCCC(....
7 2Z4W ic50 = 0.98 uM 749 C21 H38 O6 P2 CC(=CCC/C(....
8 2E93 - B29 C20 H18 O8 P2 c1ccc2c(c1....
9 2E8U - IPE C5 H12 O7 P2 CC(=C)CCO[....
10 2Z4X ic50 = 0.71 uM 252 C9 H22 O7 P2 CCCCCCCCC(....
11 2Z50 ic50 = 11.22 uM 028 C7 H18 O7 P2 CCCCCCC(O)....
12 2Z7I ic50 = 0.1 uM 742 C16 H38 O6 P3 CCCCCCCCCC....
13 2E94 - 364 C19 H20 N O7 P2 c1ccc(cc1)....
14 2E91 - ZOL C5 H10 N2 O7 P2 c1cn(cn1)C....
15 2ZEU - B71 C17 H32 N O7 P2 CCCCCCCCCC....
16 2Z4Z ic50 = 1.86 uM SC0 C17 H34 O6 P2 CCCCCC=CCC....
17 2E92 - M0N C9 H12 N2 O7 P2 c1ccn2c(c1....
18 2E8V - GRG C20 H36 O7 P2 CC(=CCC/C(....
19 2Z52 ic50 = 2.69 uM H23 C12 H28 O7 P2 CCCCCCCCCC....
20 2E8T - IPE C5 H12 O7 P2 CC(=C)CCO[....
21 2Z78 - H86 C23 H34 F2 N O7 P2 CCCCCCCCCC....
70% Homology Family (21)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2E8X - GPP C10 H20 O7 P2 CC(=CCC/C(....
2 2ZEV - IPE C5 H12 O7 P2 CC(=C)CCO[....
3 2Z4V - GRG C20 H36 O7 P2 CC(=CCC/C(....
4 2E8W - IPE C5 H12 O7 P2 CC(=C)CCO[....
5 2Z7H Ki = 115 nM GG3 C14 H25 N O7 P2 C[N@](CCCC....
6 2Z4Y ic50 = 0.71 uM 252 C9 H22 O7 P2 CCCCCCCCC(....
7 2Z4W ic50 = 0.98 uM 749 C21 H38 O6 P2 CC(=CCC/C(....
8 2E93 - B29 C20 H18 O8 P2 c1ccc2c(c1....
9 2E8U - IPE C5 H12 O7 P2 CC(=C)CCO[....
10 2Z4X ic50 = 0.71 uM 252 C9 H22 O7 P2 CCCCCCCCC(....
11 2Z50 ic50 = 11.22 uM 028 C7 H18 O7 P2 CCCCCCC(O)....
12 2Z7I ic50 = 0.1 uM 742 C16 H38 O6 P3 CCCCCCCCCC....
13 2E94 - 364 C19 H20 N O7 P2 c1ccc(cc1)....
14 2E91 - ZOL C5 H10 N2 O7 P2 c1cn(cn1)C....
15 2ZEU - B71 C17 H32 N O7 P2 CCCCCCCCCC....
16 2Z4Z ic50 = 1.86 uM SC0 C17 H34 O6 P2 CCCCCC=CCC....
17 2E92 - M0N C9 H12 N2 O7 P2 c1ccn2c(c1....
18 2E8V - GRG C20 H36 O7 P2 CC(=CCC/C(....
19 2Z52 ic50 = 2.69 uM H23 C12 H28 O7 P2 CCCCCCCCCC....
20 2E8T - IPE C5 H12 O7 P2 CC(=C)CCO[....
21 2Z78 - H86 C23 H34 F2 N O7 P2 CCCCCCCCCC....
50% Homology Family (22)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2E8X - GPP C10 H20 O7 P2 CC(=CCC/C(....
2 2ZEV - IPE C5 H12 O7 P2 CC(=C)CCO[....
3 2Z4V - GRG C20 H36 O7 P2 CC(=CCC/C(....
4 2E8W - IPE C5 H12 O7 P2 CC(=C)CCO[....
5 2Z7H Ki = 115 nM GG3 C14 H25 N O7 P2 C[N@](CCCC....
6 2Z4Y ic50 = 0.71 uM 252 C9 H22 O7 P2 CCCCCCCCC(....
7 2Z4W ic50 = 0.98 uM 749 C21 H38 O6 P2 CC(=CCC/C(....
8 2E93 - B29 C20 H18 O8 P2 c1ccc2c(c1....
9 2E8U - IPE C5 H12 O7 P2 CC(=C)CCO[....
10 2Z4X ic50 = 0.71 uM 252 C9 H22 O7 P2 CCCCCCCCC(....
11 2Z50 ic50 = 11.22 uM 028 C7 H18 O7 P2 CCCCCCC(O)....
12 2Z7I ic50 = 0.1 uM 742 C16 H38 O6 P3 CCCCCCCCCC....
13 2E94 - 364 C19 H20 N O7 P2 c1ccc(cc1)....
14 2E91 - ZOL C5 H10 N2 O7 P2 c1cn(cn1)C....
15 2ZEU - B71 C17 H32 N O7 P2 CCCCCCCCCC....
16 2Z4Z ic50 = 1.86 uM SC0 C17 H34 O6 P2 CCCCCC=CCC....
17 2E92 - M0N C9 H12 N2 O7 P2 c1ccn2c(c1....
18 2E8V - GRG C20 H36 O7 P2 CC(=CCC/C(....
19 2Z52 ic50 = 2.69 uM H23 C12 H28 O7 P2 CCCCCCCCCC....
20 2E8T - IPE C5 H12 O7 P2 CC(=C)CCO[....
21 2Z78 - H86 C23 H34 F2 N O7 P2 CCCCCCCCCC....
22 6R4V Kd = 1.74 uM BFQ C9 H23 N O7 P2 CCCCC[N@](....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; 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: 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 : 2Z7I; Ligand: 742; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 2z7i.bio1) has 23 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 2Z7I; Ligand: 742; Similar sites found with APoc: 9
This union binding pocket(no: 2) in the query (biounit: 2z7i.bio1) has 65 residues
No: Leader PDB Ligand Sequence Similarity
1 4DXJ 0M9 10.5882
2 1YHM AHD 21.4706
3 1YHM AHD 21.4706
4 1YHM AHD 21.4706
5 3LDW ZOL 31.7647
6 4UMJ BFQ 38.5135
7 4UMJ BFQ 38.5135
8 2O1O RIS 39.1176
9 2O1O RIS 39.1176
APoc FAQ
Feedback