Receptor
PDB id Resolution Class Description Source Keywords
4P0V 2.4 Å EC: 2.5.1.10 CRYSTAL STRUCTURE OF HUMAN FARNESYL DIPHOSPHOATE SYNTHASE IN WITH ZOLEDRONATE AND TAXODIONE HOMO SAPIENS HUMAN FPPS INHIBITOR COMPLEX SYNTHASE TRANSFERASE-TRANSINHIBITOR COMPLEX
Ref.: TAXODIONE AND ARENARONE INHIBIT FARNESYL DIPHOSPHAT SYNTHASE BY BINDING TO THE ISOPENTENYL DIPHOSPHATE PROC.NATL.ACAD.SCI.USA V. 111 E2530 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MG A:404;
A:405;
A:403;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
submit data
24.305 Mg [Mg+2...
ZOL A:401;
Valid;
none;
submit data
272.09 C5 H10 N2 O7 P2 c1cn(...
1WO A:402;
Valid;
none;
submit data
314.419 C20 H26 O3 CC(C)...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4LPG 2.35 Å EC: 2.5.1.10 CRYSTAL STRUCTURE OF HUMAN FPPS IN COMPLEX WITH CL01131 HOMO SAPIENS TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX
Ref.: MULTISTAGE SCREENING REVEALS CHAMELEON LIGANDS OF T FARNESYL PYROPHOSPHATE SYNTHASE: IMPLICATIONS TO DR DISCOVERY FOR NEURODEGENERATIVE DISEASES. J.MED.CHEM. V. 57 5764 2014
Members (38)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 1ZW5 - ZOL C5 H10 N2 O7 P2 c1cn(cn1)C....
2 1YV5 - RIS C7 H11 N O7 P2 c1cc(cnc1)....
3 6N7Y ic50 = 7.7 uM KFA C21 H20 N3 O3 P S Cc1ccc(cc1....
4 4QXS ic50 = 1.1 uM WC1 C21 H27 N O6 P2 C[C@H](c1c....
5 4P0V - ZOL C5 H10 N2 O7 P2 c1cn(cn1)C....
6 2F92 - AHD C4 H9 N O7 P2 C(CC(O)(P(....
7 5JUZ ic50 = 3 uM YL4 C22 H20 N3 O4 P S Cc1ccc(cc1....
8 4RXA ic50 = 1.8 uM 3F2 C32 H28 N6 O2 c1cc(cc(c1....
9 3N49 ic50 = 7 uM 3N4 C14 H10 O2 S c1ccc2c(c1....
10 5JV2 ic50 ~ 100 uM 6O3 C14 H13 N2 O3 P S Cc1ccc(cc1....
11 3N5J ic50 = 6 uM GO1 C11 H7 Cl2 N O4 c1c(cc(c2c....
12 2F9K - ZOL C5 H10 N2 O7 P2 c1cn(cn1)C....
13 3N45 - PO4 O4 P [O-]P(=O)(....
14 4LPH Kd = 9.2 uM YL3 C14 H14 N3 O3 P S Cc1ccc(cc1....
15 5JV1 ic50 = 0.86 uM YL6 C21 H18 Cl F N3 O3 P S Cc1ccc(cc1....
16 4LFV - YS4 C15 H20 N2 O7 P2 CC(C)Oc1cc....
17 4LPG Kd = 55.6 uM 1MV C14 H15 N3 O6 P2 S Cc1ccc(cc1....
18 2F94 - BFQ C9 H23 N O7 P2 CCCCC[N@](....
19 3N6K Kd = 180 nM BFH C15 H11 N O4 c1ccc2c(c1....
20 6OAH ic50 = 1.5 uM M2V C21 H19 Cl N3 O3 P S Cc1ccc(cc1....
21 5JV0 ic50 = 1.1 uM YL5 C21 H19 F N3 O3 P S Cc1ccc(cc1....
22 4H5E Kd = 0.86 uM YS4 C15 H20 N2 O7 P2 CC(C)Oc1cc....
23 3N5H ic50 = 2 uM GO0 C11 H7 Cl2 N O4 c1cc(c2c(c....
24 6OAG ic50 = 3.7 uM M2Y C21 H19 Cl N3 O3 P S Cc1ccc(cc1....
25 4H5D Kd = 0.58 uM YS4 C15 H20 N2 O7 P2 CC(C)Oc1cc....
26 2F8C - ZOL C5 H10 N2 O7 P2 c1cn(cn1)C....
27 4P0W - ZOL C5 H10 N2 O7 P2 c1cn(cn1)C....
28 3N46 - PO4 O4 P [O-]P(=O)(....
29 4P0X - 1WO C20 H26 O3 CC(C)C1=CC....
30 6N83 ic50 = 0.54 uM YL6 C21 H18 Cl F N3 O3 P S Cc1ccc(cc1....
31 4H5C - PO4 O4 P [O-]P(=O)(....
32 5DGN ic50 = 1.2 uM 59Y C20 H13 N O2 c1ccc2c(c1....
33 4DEM ic50 = 28 nM YS4 C15 H20 N2 O7 P2 CC(C)Oc1cc....
34 6N82 ic50 = 1.1 uM YF7 C21 H18 Cl F N3 O3 P S Cc1ccc(cc1....
35 3N1V ic50 > 500 uM 3N1 C11 H9 Cl O2 S Cc1c2cc(cc....
36 2OPM - NI9 C7 H11 F N O7 P2 c1cc(c[n+]....
37 5JA0 Kd = 5.3 uM FPP C15 H28 O7 P2 CC(=CCC/C(....
38 1YQ7 - RIS C7 H11 N O7 P2 c1cc(cnc1)....
70% Homology Family (41)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 1ZW5 - ZOL C5 H10 N2 O7 P2 c1cn(cn1)C....
2 1YV5 - RIS C7 H11 N O7 P2 c1cc(cnc1)....
3 6N7Y ic50 = 7.7 uM KFA C21 H20 N3 O3 P S Cc1ccc(cc1....
4 4QXS ic50 = 1.1 uM WC1 C21 H27 N O6 P2 C[C@H](c1c....
5 4P0V - ZOL C5 H10 N2 O7 P2 c1cn(cn1)C....
6 2F92 - AHD C4 H9 N O7 P2 C(CC(O)(P(....
7 5JUZ ic50 = 3 uM YL4 C22 H20 N3 O4 P S Cc1ccc(cc1....
8 4RXA ic50 = 1.8 uM 3F2 C32 H28 N6 O2 c1cc(cc(c1....
9 3N49 ic50 = 7 uM 3N4 C14 H10 O2 S c1ccc2c(c1....
10 5JV2 ic50 ~ 100 uM 6O3 C14 H13 N2 O3 P S Cc1ccc(cc1....
11 3N5J ic50 = 6 uM GO1 C11 H7 Cl2 N O4 c1c(cc(c2c....
12 2F9K - ZOL C5 H10 N2 O7 P2 c1cn(cn1)C....
13 3N45 - PO4 O4 P [O-]P(=O)(....
14 4LPH Kd = 9.2 uM YL3 C14 H14 N3 O3 P S Cc1ccc(cc1....
15 5JV1 ic50 = 0.86 uM YL6 C21 H18 Cl F N3 O3 P S Cc1ccc(cc1....
16 4LFV - YS4 C15 H20 N2 O7 P2 CC(C)Oc1cc....
17 4LPG Kd = 55.6 uM 1MV C14 H15 N3 O6 P2 S Cc1ccc(cc1....
18 2F94 - BFQ C9 H23 N O7 P2 CCCCC[N@](....
19 3N6K Kd = 180 nM BFH C15 H11 N O4 c1ccc2c(c1....
20 6OAH ic50 = 1.5 uM M2V C21 H19 Cl N3 O3 P S Cc1ccc(cc1....
21 5JV0 ic50 = 1.1 uM YL5 C21 H19 F N3 O3 P S Cc1ccc(cc1....
22 4H5E Kd = 0.86 uM YS4 C15 H20 N2 O7 P2 CC(C)Oc1cc....
23 3N5H ic50 = 2 uM GO0 C11 H7 Cl2 N O4 c1cc(c2c(c....
24 6OAG ic50 = 3.7 uM M2Y C21 H19 Cl N3 O3 P S Cc1ccc(cc1....
25 4H5D Kd = 0.58 uM YS4 C15 H20 N2 O7 P2 CC(C)Oc1cc....
26 2F8C - ZOL C5 H10 N2 O7 P2 c1cn(cn1)C....
27 4P0W - ZOL C5 H10 N2 O7 P2 c1cn(cn1)C....
28 3N46 - PO4 O4 P [O-]P(=O)(....
29 4P0X - 1WO C20 H26 O3 CC(C)C1=CC....
30 6N83 ic50 = 0.54 uM YL6 C21 H18 Cl F N3 O3 P S Cc1ccc(cc1....
31 4H5C - PO4 O4 P [O-]P(=O)(....
32 5DGN ic50 = 1.2 uM 59Y C20 H13 N O2 c1ccc2c(c1....
33 4DEM ic50 = 28 nM YS4 C15 H20 N2 O7 P2 CC(C)Oc1cc....
34 6N82 ic50 = 1.1 uM YF7 C21 H18 Cl F N3 O3 P S Cc1ccc(cc1....
35 3N1V ic50 > 500 uM 3N1 C11 H9 Cl O2 S Cc1c2cc(cc....
36 2OPM - NI9 C7 H11 F N O7 P2 c1cc(c[n+]....
37 5JA0 Kd = 5.3 uM FPP C15 H28 O7 P2 CC(=CCC/C(....
38 1YQ7 - RIS C7 H11 N O7 P2 c1cc(cnc1)....
39 1UBY - DMA C5 H12 O7 P2 CC(=CCO[P@....
40 1UBX - FPP C15 H28 O7 P2 CC(=CCC/C(....
41 1UBW - GPP C10 H20 O7 P2 CC(=CCC/C(....
50% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 212 families.
1 6N7Y ic50 = 7.7 uM KFA C21 H20 N3 O3 P S Cc1ccc(cc1....
2 4QXS ic50 = 1.1 uM WC1 C21 H27 N O6 P2 C[C@H](c1c....
3 4P0V - ZOL C5 H10 N2 O7 P2 c1cn(cn1)C....
4 2F92 - AHD C4 H9 N O7 P2 C(CC(O)(P(....
5 5JUZ ic50 = 3 uM YL4 C22 H20 N3 O4 P S Cc1ccc(cc1....
6 2O1O Ki = 0.38 nM RIS C7 H11 N O7 P2 c1cc(cnc1)....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: ZOL; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 ZOL 1 1
Ligand no: 2; Ligand: 1WO; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 1WO 1 1
Similar Ligands (3D)
Ligand no: 1; Ligand: ZOL; Similar ligands found: 35
No: Ligand Similarity coefficient
1 RIS 0.9829
2 NI9 0.9420
3 C6J 0.9402
4 AHD 0.9365
5 AVJ 0.9212
6 3YQ 0.9118
7 AVI 0.9020
8 BZS 0.9014
9 212 0.8986
10 NZ3 0.8971
11 GTC 0.8898
12 ACE PHE 0.8871
13 NZ2 0.8865
14 AVO 0.8862
15 FLC 0.8809
16 49N 0.8803
17 DNB 0.8799
18 0M9 0.8797
19 1BY 0.8790
20 HCA 0.8775
21 2B4 0.8773
22 L69 0.8757
23 CIT 0.8739
24 7UZ 0.8733
25 PIR 0.8699
26 61O 0.8687
27 B2Y 0.8634
28 787 0.8620
29 5ZZ 0.8610
30 60Q 0.8604
31 DMA 0.8580
32 1KM 0.8567
33 210 0.8552
34 BPS 0.8532
35 256 0.8504
Ligand no: 2; Ligand: 1WO; Similar ligands found: 50
No: Ligand Similarity coefficient
1 M3F 0.9050
2 1YL 0.9038
3 XTS 0.9011
4 A9H 0.8956
5 AZN 0.8922
6 RHN 0.8919
7 EMO 0.8899
8 CZ0 0.8875
9 5XL 0.8868
10 DNQ 0.8847
11 GAL FUC 0.8835
12 JRO 0.8831
13 TXQ 0.8797
14 8SK 0.8793
15 NOM 0.8776
16 EST 0.8759
17 AOX 0.8749
18 JY4 0.8749
19 LFN 0.8748
20 EQU 0.8736
21 19E 0.8721
22 1EL 0.8718
23 17M 0.8710
24 9CE 0.8695
25 NRA 0.8683
26 ADL 0.8680
27 IXM 0.8674
28 5AD 0.8668
29 3UG 0.8656
30 HRM 0.8655
31 NQ8 0.8652
32 2J1 0.8647
33 R18 0.8643
34 DY9 0.8638
35 HC8 0.8637
36 J3Z 0.8635
37 5XK 0.8621
38 ASD 0.8598
39 ESR 0.8594
40 ESZ 0.8593
41 CX6 0.8592
42 DT9 0.8592
43 6VW 0.8589
44 3L1 0.8575
45 3WF 0.8573
46 AFT 0.8551
47 BGC BGC 0.8551
48 CNI 0.8541
49 AOI 0.8540
50 AD3 0.8534
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4LPG; Ligand: 1MV; Similar sites found with APoc: 10
This union binding pocket(no: 1) in the query (biounit: 4lpg.bio1) has 76 residues
No: Leader PDB Ligand Sequence Similarity
1 3KRO PPV 30.8475
2 3KRO PPV 30.8475
3 6W7I 476 49.5601
4 6VJC 476 49.5601
5 6W7I 476 49.5601
6 6VJC 476 49.5601
7 4JZB P2H 49.5601
8 4JZX 476 49.5601
9 4JZX 476 49.5601
10 4JZB P2H 49.5601
Pocket No.: 2; Query (leader) PDB : 4LPG; Ligand: 1MV; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 4lpg.bio1) has 76 residues
No: Leader PDB Ligand Sequence Similarity
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