Receptor
PDB id Resolution Class Description Source Keywords
5HN7 2.15 Å EC: 7.-.-.- CRYSTAL STRUCTURE OF PLASMODIUM VIVAX GERANYLGERANYLPYROPHOS SYNTHASE COMPLEXED WITH BPH-1158 PLASMODIUM VIVAX TRANSFERASE TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX
Ref.: DYNAMIC STRUCTURE AND INHIBITION OF A MALARIA DRUG GERANYLGERANYL DIPHOSPHATE SYNTHASE. BIOCHEMISTRY V. 55 5180 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
04M B:401;
A:401;
F:401;
D:401;
E:401;
H:401;
G:401;
C:401;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
none;
none;
none;
none;
ic50 = 120 uM
505.624 C26 H35 N O7 S CCCCC...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3LDW 2.47 Å EC: 7.-.-.- CRYSTAL STRUCTURE OF PLASMODIUM VIVAX GERANYLGERANYLPYROPHOS SYNTHASE PVX_092040 WITH ZOLEDRONATE AND IPP BOUND PLASMODIUM VIVAX MALARIA FARNESYL PYROPHOSPHATE SYNTHASE DIPHOSPHATE LYASESTRUCTURAL GENOMICS ISOPRENE BIOSYNTHESIS TRANSFERASE STGENOMICS CONSORTIUM SGC
Ref.: MOLECULAR CHARACTERIZATION OF A NOVEL GERANYLGERANY PYROPHOSPHATE SYNTHASE FROM PLASMODIUM PARASITES. J.BIOL.CHEM. V. 286 3315 2011
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 293 families.
1 3LDW Ki = 10.7 nM ZOL C5 H10 N2 O7 P2 c1cn(cn1)C....
2 3PH7 - GRG C20 H36 O7 P2 CC(=CCC/C(....
3 5HN7 ic50 = 120 uM 04M C26 H35 N O7 S CCCCCCCCOc....
4 5HN9 ic50 = 50 uM 04W C24 H31 N O6 CCCCCCCCCC....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 250 families.
1 3LDW Ki = 10.7 nM ZOL C5 H10 N2 O7 P2 c1cn(cn1)C....
2 3PH7 - GRG C20 H36 O7 P2 CC(=CCC/C(....
3 5HN7 ic50 = 120 uM 04M C26 H35 N O7 S CCCCCCCCOc....
4 5HN9 ic50 = 50 uM 04W C24 H31 N O6 CCCCCCCCCC....
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: 04M; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 04M 1 1
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3LDW; 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: 3ldw.bio1) has 15 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 3LDW; Ligand: ZOL; Similar sites found with APoc: 2
This union binding pocket(no: 2) in the query (biounit: 3ldw.bio1) has 13 residues
No: Leader PDB Ligand Sequence Similarity
1 1RQJ RIS 8.3612
2 1YHM AHD 46.4088
Pocket No.: 3; Query (leader) PDB : 3LDW; 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: 3) in the query (biounit: 3ldw.bio1) has 31 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 3LDW; Ligand: ZOL; 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: 3ldw.bio1) has 35 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 3LDW; Ligand: ZOL; 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: 3ldw.bio2) has 28 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 3LDW; 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: 3ldw.bio2) has 28 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 7; Query (leader) PDB : 3LDW; 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: 7) in the query (biounit: 3ldw.bio2) has 25 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 8; Query (leader) PDB : 3LDW; Ligand: ZOL; 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: 3ldw.bio2) has 29 residues
No: Leader PDB Ligand Sequence Similarity
APoc FAQ
Feedback