Receptor
PDB id Resolution Class Description Source Keywords
3ICM 2.2 Å EC: 2.5.1.10 TRYPANOSOMA CRUZI FARNESYL DIPHOSPHATE SYNTHASE HOMODIMER IN WITH ISOPENTENYL PYROPHOSPHATE, MG2+ AND 1-(2-HYDROXY-2,2-BP HOSPHONO-ETHYL)-3-PHENYL-PYRIDINIUM TRYPANOSOMA CRUZI FARNESYL DIPHOSPHATE SYNTHASE FPPS BISPHOSPHONATE ZOLEDRORISEDRONATE MINODRONATE CHAGAS DISEASE ISOPRENE BIOSYNTHTRANSFERASE
Ref.: BINDING OF NITROGEN-CONTAINING BISPHOSPHONATES (N-B THE TRYPANOSOMA CRUZI FARNESYL DIPHOSPHATE SYNTHASE HOMODIMER. PROTEINS V. 78 888 2010
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
IPR A:900;
Valid;
none;
submit data
248.108 C5 H14 O7 P2 CC(C)...
MG A:401;
A:402;
A:403;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
submit data
24.305 Mg [Mg+2...
P2H A:363;
Valid;
none;
submit data
360.216 C13 H16 N O7 P2 c1ccc...
SO4 A:371;
Valid;
none;
submit data
96.063 O4 S [O-]S...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4DXJ 2.35 Å EC: 2.5.1.10 CRYSTAL STRUCTURE OF TRYPANOSOME CRUZI FARNESYL DIPHOSPHATE IN COMPLEX WITH [2-(N-PROPYLAMINO)ETHANE-1,1-DIYL]BISPHOSPHA ND MG2+ TRYPANOSOMA CRUZI GERANYL TRANSFERASE TRANSFERASE-TRANSFERASE INHIBITOR COMPL
Ref.: DESIGN, SYNTHESIS, CALORIMETRY, AND CRYSTALLOGRAPHI ANALYSIS OF 2-ALKYLAMINOETHYL-1,1-BISPHOSPHONATES A INHIBITORS OF TRYPANOSOMA CRUZI FARNESYL DIPHOSPHAT SYNTHASE. J.MED.CHEM. V. 55 6445 2012
Members (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 4DXJ ic50 = 38 nM 0M9 C5 H15 N O6 P2 CCCNCC(P(=....
2 3ICN - NI9 C7 H11 F N O7 P2 c1cc(c[n+]....
3 3ICK - IPR C5 H14 O7 P2 CC(C)CCO[P....
4 4DWB ic50 = 1.84 uM 0M7 C7 H19 N O6 P2 CCCCCNCC(P....
5 4DWG ic50 = 58 nM 0M8 C9 H23 N O6 P2 CCCCCCCNCC....
6 3ICM - P2H C13 H16 N O7 P2 c1ccc(cc1)....
7 3ICZ - PB6 C11 H18 N O6 P2 CC/C=C/c1c....
8 1YHL - RIS C7 H11 N O7 P2 c1cc(cnc1)....
9 3IBA - SO4 O4 S [O-]S(=O)(....
70% Homology Family (21)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 7 families.
1 4K10 Kd = 119.5 nM NI9 C7 H11 F N O7 P2 c1cc(c[n+]....
2 4RXE ic50 = 230 nM 3YQ C7 H12 N2 O6 P2 Cc1cccnc1N....
3 2EWG - M0N C9 H12 N2 O7 P2 c1ccn2c(c1....
4 5AFX ic50 = 1.2 uM PVZ C14 H29 N2 O7 P2 CCCCCCCCCn....
5 3DYH - 721 C11 H20 N O7 P2 CCCCOc1ccc....
6 2I19 - 1BY C7 H12 N2 O6 P2 c1ccnc(c1)....
7 3EGT Ki = 32 nM 722 C14 H26 N O7 P2 CCCCCCCOc1....
8 3EFQ - 714 C15 H28 N O7 P2 CCCCCCCCOc....
9 4RXD ic50 = 300 nM RIS C7 H11 N O7 P2 c1cc(cnc1)....
10 4RXC ic50 ~ 33 uM HRX C8 H13 N O7 P2 c1cc(cnc1)....
11 3DYG - NI9 C7 H11 F N O7 P2 c1cc(c[n+]....
12 2P1C Ki = 21 nM GG3 C14 H25 N O7 P2 C[N@](CCCC....
13 4DXJ ic50 = 38 nM 0M9 C5 H15 N O6 P2 CCCNCC(P(=....
14 3ICN - NI9 C7 H11 F N O7 P2 c1cc(c[n+]....
15 3ICK - IPR C5 H14 O7 P2 CC(C)CCO[P....
16 4DWB ic50 = 1.84 uM 0M7 C7 H19 N O6 P2 CCCCCNCC(P....
17 4DWG ic50 = 58 nM 0M8 C9 H23 N O6 P2 CCCCCCCNCC....
18 3ICM - P2H C13 H16 N O7 P2 c1ccc(cc1)....
19 3ICZ - PB6 C11 H18 N O6 P2 CC/C=C/c1c....
20 1YHL - RIS C7 H11 N O7 P2 c1cc(cnc1)....
21 3IBA - SO4 O4 S [O-]S(=O)(....
50% Homology Family (60)
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 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 = 8 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 ic50 = 4.5 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 ic50 = 0.022 uM 1MV C14 H15 N3 O6 P2 S Cc1ccc(cc1....
13 2F94 - BFQ C9 H23 N O7 P2 CCCCC[N@](....
14 3N6K ic50 = 0.2 uM BFH C15 H11 N O4 c1ccc2c(c1....
15 5JV0 ic50 = 1.1 uM YL5 C21 H19 F N3 O3 P S Cc1ccc(cc1....
16 4H5E Kd = 0.86 uM YS4 C15 H20 N2 O7 P2 CC(C)Oc1cc....
17 3N5H ic50 = 2 uM GO0 C11 H7 Cl2 N O4 c1cc(c2c(c....
18 4H5D Kd = 0.58 uM YS4 C15 H20 N2 O7 P2 CC(C)Oc1cc....
19 2F8C - ZOL C5 H10 N2 O7 P2 c1cn(cn1)C....
20 4P0W - ZOL C5 H10 N2 O7 P2 c1cn(cn1)C....
21 3N46 - PO4 O4 P [O-]P(=O)(....
22 4P0X - 1WO C20 H26 O3 CC(C)C1=CC....
23 4H5C - PO4 O4 P [O-]P(=O)(....
24 5DGN ic50 = 1.2 uM 59Y C20 H13 N O2 c1ccc2c(c1....
25 4DEM ic50 = 28 nM YS4 C15 H20 N2 O7 P2 CC(C)Oc1cc....
26 3N1V ic50 > 500 uM 3N1 C11 H9 Cl O2 S Cc1c2cc(cc....
27 2OPM - NI9 C7 H11 F N O7 P2 c1cc(c[n+]....
28 5JA0 Kd = 5.3 uM FPP C15 H28 O7 P2 CC(=CCC/C(....
29 1YQ7 - RIS C7 H11 N O7 P2 c1cc(cnc1)....
30 6B07 - C6M C10 H18 N O6 P2 CCC[N]1=C(....
31 6B04 - C6J C8 H14 N O6 P2 C[N]1=C(C=....
32 2Q58 - ZOL C5 H10 N2 O7 P2 c1cn(cn1)C....
33 3LDW Ki = 10.7 nM ZOL C5 H10 N2 O7 P2 c1cn(cn1)C....
34 3PH7 - GRG C20 H36 O7 P2 CC(=CCC/C(....
35 5HN7 ic50 = 120 uM 04M C26 H35 N O7 S CCCCCCCCOc....
36 5HN9 ic50 = 50 uM 04W C24 H31 N O6 CCCCCCCCCC....
37 1UBY - DMA C5 H12 O7 P2 CC(=CCO[P@....
38 1UBX - FPP C15 H28 O7 P2 CC(=CCC/C(....
39 1UBW - GPP C10 H20 O7 P2 CC(=CCC/C(....
40 4K10 Kd = 119.5 nM NI9 C7 H11 F N O7 P2 c1cc(c[n+]....
41 4RXE ic50 = 230 nM 3YQ C7 H12 N2 O6 P2 Cc1cccnc1N....
42 2EWG - M0N C9 H12 N2 O7 P2 c1ccn2c(c1....
43 5AFX ic50 = 1.2 uM PVZ C14 H29 N2 O7 P2 CCCCCCCCCn....
44 3DYH - 721 C11 H20 N O7 P2 CCCCOc1ccc....
45 2I19 - 1BY C7 H12 N2 O6 P2 c1ccnc(c1)....
46 3EGT Ki = 32 nM 722 C14 H26 N O7 P2 CCCCCCCOc1....
47 3EFQ - 714 C15 H28 N O7 P2 CCCCCCCCOc....
48 4RXD ic50 = 300 nM RIS C7 H11 N O7 P2 c1cc(cnc1)....
49 4RXC ic50 ~ 33 uM HRX C8 H13 N O7 P2 c1cc(cnc1)....
50 3DYG - NI9 C7 H11 F N O7 P2 c1cc(c[n+]....
51 2P1C Ki = 21 nM GG3 C14 H25 N O7 P2 C[N@](CCCC....
52 4DXJ ic50 = 38 nM 0M9 C5 H15 N O6 P2 CCCNCC(P(=....
53 3ICN - NI9 C7 H11 F N O7 P2 c1cc(c[n+]....
54 3ICK - IPR C5 H14 O7 P2 CC(C)CCO[P....
55 4DWB ic50 = 1.84 uM 0M7 C7 H19 N O6 P2 CCCCCNCC(P....
56 4DWG ic50 = 58 nM 0M8 C9 H23 N O6 P2 CCCCCCCNCC....
57 3ICM - P2H C13 H16 N O7 P2 c1ccc(cc1)....
58 3ICZ - PB6 C11 H18 N O6 P2 CC/C=C/c1c....
59 1YHL - RIS C7 H11 N O7 P2 c1cc(cnc1)....
60 3IBA - SO4 O4 S [O-]S(=O)(....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: IPR; Similar ligands found: 19
No: Ligand ECFP6 Tc MDL keys Tc
1 IPR 1 1
2 IS3 0.666667 0.918919
3 EIP 0.631579 0.864865
4 P23 0.542857 0.885714
5 DED 0.5 0.772727
6 P25 0.475 0.842105
7 IPE 0.475 0.820513
8 P22 0.457143 0.771429
9 BHI 0.454545 0.780488
10 43W 0.45 0.805556
11 0CH 0.45 0.74359
12 0CJ 0.44186 0.842105
13 0JX 0.439024 0.828571
14 0K2 0.428571 0.805556
15 DST 0.425 0.837838
16 0O3 0.418605 0.707317
17 DP6 0.416667 0.8
18 0CM 0.414634 0.777778
19 3E9 0.413793 0.829268
Ligand no: 2; Ligand: P2H; Similar ligands found: 3
No: Ligand ECFP6 Tc MDL keys Tc
1 P2H 1 1
2 364 0.763636 1
3 NI9 0.518519 0.867925
Ligand no: 3; Ligand: SO4; Similar ligands found: 3
No: Ligand ECFP6 Tc MDL keys Tc
1 SO4 1 1
2 THJ 0.555556 0.875
3 PSL 0.454545 0.88
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4DXJ; Ligand: IPE; 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: 4dxj.bio1) has 14 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 4DXJ; Ligand: IPE; 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: 4dxj.bio1) has 32 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 4DXJ; Ligand: 0M9; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 4dxj.bio1) has 13 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 4DXJ; Ligand: 0M9; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 4dxj.bio1) has 30 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 4DXJ; Ligand: IPE; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 4dxj.bio2) has 15 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 4DXJ; Ligand: IPE; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 4dxj.bio2) has 15 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 7; Query (leader) PDB : 4DXJ; Ligand: 0M9; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 7) in the query (biounit: 4dxj.bio2) has 16 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 8; Query (leader) PDB : 4DXJ; Ligand: 0M9; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 8) in the query (biounit: 4dxj.bio2) has 16 residues
No: Leader PDB Ligand Sequence Similarity
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