Receptor
PDB id Resolution Class Description Source Keywords
1YHL 1.95 Å EC: 2.5.1.10 STRUCTURE OF THE COMPLEX OF TRYPANOSOMA CRUZI FARNESYL DIPHO SYNTHASE WITH RISEDRONATE, DMAPP AND MG+2 TRYPANOSOMA CRUZI FARNESYL DIPHOSPHATE SYNTHASE BISPHOSPHONATE DIMETHYL ALLYPYROPHOSPHATE SULFATE FPPS TRANSFERASE
Ref.: STRUCTURE AND MECHANISM OF THE FARNESYL DIPHOSPHATE FROM TRYPANOSOMA CRUZI: IMPLICATIONS FOR DRUG DESIG PROTEINS V. 62 80 2005
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
DMA A:1301;
 Valid;
 none;
 submit data
246.092 C5 H12 O7 P2 CC(=C...
MG A:1401;
A:1402;
A:1403;
 Part of Protein;
Part of Protein;
Part of Protein;
 none;
none;
none;
 submit data
24.305 Mg [Mg+2...
RIS A:1400;
 Valid;
 none;
 submit data
283.112 C7 H11 N O7 P2 c1cc(...
SO4 A:1405;
 Invalid;
 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 - M0N C9 H12 N2 O7 P2 c1ccn2c(c1....
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 - M0N C9 H12 N2 O7 P2 c1ccn2c(c1....
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 (64)
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 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 1UBY - DMA C5 H12 O7 P2 CC(=CCO[P@....
42 1UBX - FPP C15 H28 O7 P2 CC(=CCC/C(....
43 1UBW - GPP C10 H20 O7 P2 CC(=CCC/C(....
44 4K10 Kd = 119.5 nM NI9 C7 H11 F N O7 P2 c1cc(c[n+]....
45 4RXE ic50 = 230 nM 3YQ C7 H12 N2 O6 P2 Cc1cccnc1N....
46 2EWG - M0N C9 H12 N2 O7 P2 c1ccn2c(c1....
47 5AFX ic50 = 1.2 uM PVZ C14 H29 N2 O7 P2 CCCCCCCCCn....
48 3DYH - 721 C11 H20 N O7 P2 CCCCOc1ccc....
49 2I19 - 1BY C7 H12 N2 O6 P2 c1ccnc(c1)....
50 3EGT Ki = 32 nM 722 C14 H26 N O7 P2 CCCCCCCOc1....
51 3EFQ - 714 C15 H28 N O7 P2 CCCCCCCCOc....
52 4RXD ic50 = 300 nM RIS C7 H11 N O7 P2 c1cc(cnc1)....
53 4RXC ic50 ~ 33 uM HRX C8 H13 N O7 P2 c1cc(cnc1)....
54 3DYG - NI9 C7 H11 F N O7 P2 c1cc(c[n+]....
55 2P1C Ki = 21 nM GG3 C14 H25 N O7 P2 C[N@](CCCC....
56 4DXJ ic50 = 38 nM 0M9 C5 H15 N O6 P2 CCCNCC(P(=....
57 3ICN - NI9 C7 H11 F N O7 P2 c1cc(c[n+]....
58 3ICK - M0N C9 H12 N2 O7 P2 c1ccn2c(c1....
59 4DWB ic50 = 1.84 uM 0M7 C7 H19 N O6 P2 CCCCCNCC(P....
60 4DWG ic50 = 58 nM 0M8 C9 H23 N O6 P2 CCCCCCCNCC....
61 3ICM - P2H C13 H16 N O7 P2 c1ccc(cc1)....
62 3ICZ - PB6 C11 H18 N O6 P2 CC/C=C/c1c....
63 1YHL - RIS C7 H11 N O7 P2 c1cc(cnc1)....
64 3IBA - SO4 O4 S [O-]S(=O)(....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: DMA; Similar ligands found: 21
No: Ligand ECFP6 Tc MDL keys Tc
1 DMA 1 1
2 H6P 0.684211 0.815789
3 10E 0.666667 0.72093
4 10G 0.625 0.794872
5 10D 0.625 0.815789
6 GPP 0.613636 0.868421
7 4LR 0.588235 0.909091
8 ZTP 0.5625 0.825
9 OTP 0.5625 0.825
10 FPP 0.5625 0.846154
11 VTP 0.5625 0.825
12 GRG 0.5625 0.846154
13 FFF 0.5 0.785714
14 0CN 0.463415 0.771429
15 FDF 0.454545 0.761905
16 P23 0.447368 0.710526
17 P22 0.444444 0.794118
18 0CJ 0.431818 0.682927
19 LA6 0.431373 0.804878
20 0FV 0.431373 0.804878
21 IPE 0.428571 0.794872
Ligand no: 2; 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 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: 2
This union binding pocket(no: 2) in the query (biounit: 4dxj.bio1) has 32 residues
No: Leader PDB Ligand Sequence Similarity
1 3KRO IPE 31.8644
2 3KRO DST 31.8644
Pocket No.: 3; Query (leader) PDB : 4DXJ; Ligand: 0M9; Similar sites found with APoc: 5
This union binding pocket(no: 3) in the query (biounit: 4dxj.bio1) has 13 residues
No: Leader PDB Ligand Sequence Similarity
1 6R4V BFQ 10.4235
2 6R4V BFQ 10.4235
3 2Z7I 742 10.5882
4 3KRO IPE 31.8644
5 3KRO DST 31.8644
Pocket No.: 4; Query (leader) PDB : 4DXJ; Ligand: 0M9; Similar sites found with APoc: 2
This union binding pocket(no: 4) in the query (biounit: 4dxj.bio1) has 30 residues
No: Leader PDB Ligand Sequence Similarity
1 3KRO IPE 31.8644
2 3KRO DST 31.8644
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: 1
This union binding pocket(no: 7) in the query (biounit: 4dxj.bio2) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 2O1O RIS 41.1602
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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