Receptor
PDB id Resolution Class Description Source Keywords
2e8x 2.04 Å EC: 2.5.1.30 S. CEREVISIAE GERANYLGERANYL PYROPHOSPHATE SYNTHASE IN COMPLEX WITH MAGNESIUM AND GPP 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
GPP A:1001;
B:1002;
 Valid;
Valid;
 none;
none;
 submit data
314.209 C10 H20 O7 P2 CC(=C...
MG A:1301;
A:1302;
B:1303;
B:1304;
 Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
 none;
none;
none;
none;
 submit data
24.305 Mg [Mg+2...
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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: GPP; Similar ligands found: 40
No: Ligand ECFP6 Tc MDL keys Tc
1 GPP 1 1
2 ZTP 0.911111 0.95
3 GRG 0.911111 0.974359
4 VTP 0.911111 0.95
5 OTP 0.911111 0.95
6 FPP 0.911111 0.974359
7 HZZ 0.704545 0.921053
8 FFF 0.672727 0.904762
9 FJP 0.659574 0.897436
10 0K3 0.659574 0.875
11 DSL 0.659574 0.875
12 FDF 0.654545 0.880952
13 10E 0.617021 0.717391
14 10D 0.617021 0.804878
15 DMA 0.613636 0.868421
16 H6P 0.595745 0.804878
17 10G 0.583333 0.785714
18 A4S 0.545455 0.711538
19 FPF 0.533333 0.904762
20 2CF 0.533333 0.904762
21 FGG 0.52459 0.904762
22 GST 0.518519 0.878049
23 3E9 0.516129 0.926829
24 ELU 0.507937 0.926829
25 ELR 0.507937 0.926829
26 MGM 0.5 0.745098
27 FPS 0.482759 0.857143
28 GGS 0.482759 0.857143
29 FPQ 0.47619 0.804348
30 0FV 0.473684 0.926829
31 LA6 0.473684 0.926829
32 749 0.461538 0.871795
33 1NH 0.444444 0.787234
34 FII 0.444444 0.649123
35 SZH 0.432432 0.637931
36 PS7 0.426667 0.883721
37 9GB 0.42 0.846154
38 C0X 0.41791 0.723404
39 FHP 0.403509 0.738095
40 9AX 0.4 0.826087
Similar Ligands (3D)
Ligand no: 1; Ligand: GPP; Similar ligands found: 2
No: Ligand Similarity coefficient
1 RZ5 0.8765
2 86B 0.8716
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
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