Receptor
PDB id Resolution Class Description Source Keywords
1YV5 2 Å EC: 2.5.1.10 HUMAN FARNESYL DIPHOSPHATE SYNTHASE COMPLEXED WITH MG AND RI HOMO SAPIENS ISOPRENOID PATHWAY CHOLESTEROL SYNTHESIS BISPHOSPHONATE SGENOMICS STRUCTURAL GENOMICS CONSORTIUM SGC TRANSFERASE
Ref.: THE MOLECULAR MECHANISM OF NITROGEN-CONTAINING BISPHOSPHONATES AS ANTIOSTEOPOROSIS DRUGS. PROC.NATL.ACAD.SCI.USA V. 103 7829 2006
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MG A:907;
A:908;
A:909;
 Part of Protein;
Part of Protein;
Part of Protein;
 none;
none;
none;
 submit data
24.305 Mg [Mg+2...
PO4 A:1001;
A:1002;
 Invalid;
Invalid;
 none;
none;
 submit data
94.971 O4 P [O-]P...
RIS A:901;
 Valid;
 none;
 submit data
283.112 C7 H11 N O7 P2 c1cc(...
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 (65)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 1ZW5 - ZOL C5 H10 N2 O7 P2 c1cn(cn1)C....
2 1YV5 - RIS C7 H11 N O7 P2 c1cc(cnc1)....
3 4RXA ic50 = 1.8 uM 3F2 C32 H28 N6 O2 c1cc(cc(c1....
4 3N49 ic50 = 7 uM 3N4 C14 H10 O2 S c1ccc2c(c1....
5 5JV2 ic50 ~ 100 uM 6O3 C14 H13 N2 O3 P S Cc1ccc(cc1....
6 3N5J ic50 = 6 uM GO1 C11 H7 Cl2 N O4 c1c(cc(c2c....
7 2F9K - ZOL C5 H10 N2 O7 P2 c1cn(cn1)C....
8 3N45 - PO4 O4 P [O-]P(=O)(....
9 4LPH Kd = 9.2 uM YL3 C14 H14 N3 O3 P S Cc1ccc(cc1....
10 5JV1 ic50 = 0.86 uM YL6 C21 H18 Cl F N3 O3 P S Cc1ccc(cc1....
11 4LFV - YS4 C15 H20 N2 O7 P2 CC(C)Oc1cc....
12 4LPG Kd = 55.6 uM 1MV C14 H15 N3 O6 P2 S Cc1ccc(cc1....
13 2F94 - BFQ C9 H23 N O7 P2 CCCCC[N@](....
14 3N6K Kd = 180 nM BFH C15 H11 N O4 c1ccc2c(c1....
15 6OAH ic50 = 1.5 uM M2V C21 H19 Cl N3 O3 P S Cc1ccc(cc1....
16 5JV0 ic50 = 1.1 uM YL5 C21 H19 F N3 O3 P S Cc1ccc(cc1....
17 4H5E Kd = 0.86 uM YS4 C15 H20 N2 O7 P2 CC(C)Oc1cc....
18 3N5H ic50 = 2 uM GO0 C11 H7 Cl2 N O4 c1cc(c2c(c....
19 6OAG ic50 = 3.7 uM M2Y C21 H19 Cl N3 O3 P S Cc1ccc(cc1....
20 4H5D Kd = 0.58 uM YS4 C15 H20 N2 O7 P2 CC(C)Oc1cc....
21 2F8C - ZOL C5 H10 N2 O7 P2 c1cn(cn1)C....
22 4P0W - ZOL C5 H10 N2 O7 P2 c1cn(cn1)C....
23 3N46 - PO4 O4 P [O-]P(=O)(....
24 4P0X - 1WO C20 H26 O3 CC(C)C1=CC....
25 6N83 ic50 = 0.54 uM YL6 C21 H18 Cl F N3 O3 P S Cc1ccc(cc1....
26 4H5C - PO4 O4 P [O-]P(=O)(....
27 5DGN ic50 = 1.2 uM 59Y C20 H13 N O2 c1ccc2c(c1....
28 4DEM ic50 = 28 nM YS4 C15 H20 N2 O7 P2 CC(C)Oc1cc....
29 6N82 ic50 = 1.1 uM YF7 C21 H18 Cl F N3 O3 P S Cc1ccc(cc1....
30 3N1V ic50 > 500 uM 3N1 C11 H9 Cl O2 S Cc1c2cc(cc....
31 2OPM - NI9 C7 H11 F N O7 P2 c1cc(c[n+]....
32 5JA0 Kd = 5.3 uM FPP C15 H28 O7 P2 CC(=CCC/C(....
33 1YQ7 - RIS C7 H11 N O7 P2 c1cc(cnc1)....
34 6B07 - C6M C10 H18 N O6 P2 CCC[N]1=C(....
35 6B04 - C6J C8 H14 N O6 P2 C[N]1=C(C=....
36 2Q58 - ZOL C5 H10 N2 O7 P2 c1cn(cn1)C....
37 3LDW Ki = 10.7 nM ZOL C5 H10 N2 O7 P2 c1cn(cn1)C....
38 3PH7 - GRG C20 H36 O7 P2 CC(=CCC/C(....
39 5HN7 ic50 = 120 uM 04M C26 H35 N O7 S CCCCCCCCOc....
40 5HN9 ic50 = 50 uM 04W C24 H31 N O6 CCCCCCCCCC....
41 6WW1 - 476 C11 H20 N O6 P2 CCCCc1ccc[....
42 4K10 Kd = 119.5 nM NI9 C7 H11 F N O7 P2 c1cc(c[n+]....
43 1UBY - DMA C5 H12 O7 P2 CC(=CCO[P@....
44 1UBX - FPP C15 H28 O7 P2 CC(=CCC/C(....
45 1UBW - GPP C10 H20 O7 P2 CC(=CCC/C(....
46 4RXE ic50 = 230 nM 3YQ C7 H12 N2 O6 P2 Cc1cccnc1N....
47 2EWG - M0N C9 H12 N2 O7 P2 c1ccn2c(c1....
48 5AFX ic50 = 1.2 uM PVZ C14 H29 N2 O7 P2 CCCCCCCCCn....
49 3DYH - 721 C11 H20 N O7 P2 CCCCOc1ccc....
50 2I19 - 1BY C7 H12 N2 O6 P2 c1ccnc(c1)....
51 3EGT Ki = 1.26 nM 722 C14 H26 N O7 P2 CCCCCCCOc1....
52 3EFQ - 714 C15 H28 N O7 P2 CCCCCCCCOc....
53 4RXD ic50 = 300 nM RIS C7 H11 N O7 P2 c1cc(cnc1)....
54 4RXC ic50 ~ 33 uM HRX C8 H13 N O7 P2 c1cc(cnc1)....
55 3DYG - NI9 C7 H11 F N O7 P2 c1cc(c[n+]....
56 2P1C Ki = 21 nM GG3 C14 H25 N O7 P2 C[N@](CCCC....
57 4DXJ ic50 = 38 nM 0M9 C5 H15 N O6 P2 CCCNCC(P(=....
58 3ICN - NI9 C7 H11 F N O7 P2 c1cc(c[n+]....
59 3ICK - M0N C9 H12 N2 O7 P2 c1ccn2c(c1....
60 4DWB ic50 = 1840 nM 0M7 C7 H19 N O6 P2 CCCCCNCC(P....
61 4DWG ic50 = 58 nM 0M8 C9 H23 N O6 P2 CCCCCCCNCC....
62 3ICM - P2H C13 H16 N O7 P2 c1ccc(cc1)....
63 3ICZ - PB6 C11 H18 N O6 P2 CC/C=C/c1c....
64 1YHL - RIS C7 H11 N O7 P2 c1cc(cnc1)....
65 3IBA - SO4 O4 S [O-]S(=O)(....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: RIS; Similar ligands found: 3
No: Ligand ECFP6 Tc MDL keys Tc
1 RIS 1 1
2 HRX 0.590909 0.947368
3 2E4 0.411765 0.8
Similar Ligands (3D)
Ligand no: 1; Ligand: RIS; Similar ligands found: 46
No: Ligand Similarity coefficient
1 ZOL 0.9829
2 NI9 0.9755
3 C6J 0.9569
4 L69 0.9395
5 3YQ 0.9376
6 CBQ 0.9302
7 BZS 0.9185
8 1BY 0.9172
9 M0N 0.9081
10 ING 0.9057
11 ACE PHE 0.9037
12 NZ3 0.9019
13 AHD 0.8988
14 2B4 0.8985
15 DNB 0.8966
16 AVJ 0.8931
17 NZ2 0.8905
18 7UZ 0.8896
19 PIR 0.8868
20 AVI 0.8848
21 49N 0.8838
22 AVO 0.8800
23 1Z8 0.8792
24 0M9 0.8790
25 GTC 0.8746
26 T2D 0.8745
27 7QD 0.8731
28 212 0.8724
29 MOK 0.8703
30 SQP 0.8692
31 61O 0.8678
32 C6M 0.8661
33 6J9 0.8658
34 NRD 0.8638
35 BPY 0.8638
36 B2Y 0.8632
37 HCA 0.8601
38 5UD 0.8601
39 DMA 0.8585
40 S2T 0.8577
41 3GV 0.8575
42 THM 0.8568
43 9PL 0.8567
44 42R 0.8564
45 BTM 0.8538
46 1KM 0.8525
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
APoc FAQ
Feedback