Receptor
PDB id Resolution Class Description Source Keywords
4rxe 2.5 Å EC: 2.5.1.10 T. BRUCEI FARNESYL DIPHOSPHATE SYNTHASE COMPLEXED WITH BISPH BPH-14 TRYPANOSOMA BRUCEI TRANSFERASE TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX
Ref.: FARNESYL DIPHOSPHATE SYNTHASE INHIBITORS WITH UNIQU LIGAND-BINDING GEOMETRIES. ACS MED CHEM LETT V. 6 349 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MG B:4003;
A:3004;
A:3003;
B:4002;
B:4004;
A:3002;
 Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
 none;
none;
none;
none;
none;
none;
 submit data
24.305 Mg [Mg+2...
3YQ B:4001;
A:3001;
 Valid;
Valid;
 none;
none;
 ic50 = 230 nM
282.128 C7 H12 N2 O6 P2 Cc1cc...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2P1C 2.45 Å EC: 2.5.1.10 T. BRUCEI FARNESYL DIPHOSPHATE SYNTHASE COMPLEXED WITH BISPH BPH-210 TRYPANOSOMA BRUCEI PROTEIN-BISPHOSPHONATE COMPLEX TRANSFERASE
Ref.: STRUCTURES OF A POTENT PHENYLALKYL BISPHOSPHONATE I BOUND TO FARNESYL AND GERANYLGERANYL DIPHOSPHATE SY PROTEINS V. 73 431 2008
Members (11)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 4RXE ic50 = 230 nM 3YQ C7 H12 N2 O6 P2 Cc1cccnc1N....
2 2EWG - M0N C9 H12 N2 O7 P2 c1ccn2c(c1....
3 5AFX ic50 = 1.2 uM PVZ C14 H29 N2 O7 P2 CCCCCCCCCn....
4 3DYH - 721 C11 H20 N O7 P2 CCCCOc1ccc....
5 2I19 - 1BY C7 H12 N2 O6 P2 c1ccnc(c1)....
6 3EGT Ki = 1.26 nM 722 C14 H26 N O7 P2 CCCCCCCOc1....
7 3EFQ - 714 C15 H28 N O7 P2 CCCCCCCCOc....
8 4RXD ic50 = 300 nM RIS C7 H11 N O7 P2 c1cc(cnc1)....
9 4RXC ic50 ~ 33 uM HRX C8 H13 N O7 P2 c1cc(cnc1)....
10 3DYG - NI9 C7 H11 F N O7 P2 c1cc(c[n+]....
11 2P1C Ki = 21 nM GG3 C14 H25 N O7 P2 C[N@](CCCC....
70% Homology Family (22)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 6WW1 - 476 C11 H20 N O6 P2 CCCCc1ccc[....
2 4K10 Kd = 119.5 nM NI9 C7 H11 F N O7 P2 c1cc(c[n+]....
3 4RXE ic50 = 230 nM 3YQ C7 H12 N2 O6 P2 Cc1cccnc1N....
4 2EWG - M0N C9 H12 N2 O7 P2 c1ccn2c(c1....
5 5AFX ic50 = 1.2 uM PVZ C14 H29 N2 O7 P2 CCCCCCCCCn....
6 3DYH - 721 C11 H20 N O7 P2 CCCCOc1ccc....
7 2I19 - 1BY C7 H12 N2 O6 P2 c1ccnc(c1)....
8 3EGT Ki = 1.26 nM 722 C14 H26 N O7 P2 CCCCCCCOc1....
9 3EFQ - 714 C15 H28 N O7 P2 CCCCCCCCOc....
10 4RXD ic50 = 300 nM RIS C7 H11 N O7 P2 c1cc(cnc1)....
11 4RXC ic50 ~ 33 uM HRX C8 H13 N O7 P2 c1cc(cnc1)....
12 3DYG - NI9 C7 H11 F N O7 P2 c1cc(c[n+]....
13 2P1C Ki = 21 nM GG3 C14 H25 N O7 P2 C[N@](CCCC....
14 4DXJ ic50 = 38 nM 0M9 C5 H15 N O6 P2 CCCNCC(P(=....
15 3ICN - NI9 C7 H11 F N O7 P2 c1cc(c[n+]....
16 3ICK - M0N C9 H12 N2 O7 P2 c1ccn2c(c1....
17 4DWB ic50 = 1840 nM 0M7 C7 H19 N O6 P2 CCCCCNCC(P....
18 4DWG ic50 = 58 nM 0M8 C9 H23 N O6 P2 CCCCCCCNCC....
19 3ICM - P2H C13 H16 N O7 P2 c1ccc(cc1)....
20 3ICZ - PB6 C11 H18 N O6 P2 CC/C=C/c1c....
21 1YHL - RIS C7 H11 N O7 P2 c1cc(cnc1)....
22 3IBA - SO4 O4 S [O-]S(=O)(....
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: 3YQ; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 3YQ 1 1
Similar Ligands (3D)
Ligand no: 1; Ligand: 3YQ; Similar ligands found: 50
No: Ligand Similarity coefficient
1 RIS 0.9376
2 C6J 0.9269
3 CBQ 0.9248
4 ZOL 0.9118
5 NI9 0.9070
6 787 0.9046
7 7UZ 0.8911
8 L69 0.8848
9 1Z8 0.8839
10 NZ2 0.8798
11 BZS 0.8773
12 OBP 0.8772
13 NZ3 0.8751
14 2B4 0.8745
15 ID8 0.8742
16 256 0.8741
17 SQP 0.8730
18 WUB 0.8717
19 6J9 0.8715
20 WS6 0.8711
21 X6P 0.8706
22 WOE 0.8687
23 ACE PHE 0.8685
24 KW8 0.8675
25 CH9 0.8674
26 F16 0.8661
27 MOK 0.8639
28 AVI 0.8639
29 1BY 0.8639
30 BPY 0.8627
31 X11 0.8624
32 QZ8 0.8617
33 TLF 0.8615
34 9X5 0.8613
35 61O 0.8611
36 CK2 0.8609
37 5VL 0.8608
38 AHR FUB 0.8606
39 2J2 0.8605
40 1KM 0.8597
41 SQ4 0.8585
42 TVP 0.8583
43 DNB 0.8573
44 K3Y 0.8568
45 SLY 0.8567
46 791 0.8567
47 1XA 0.8548
48 XZ8 0.8547
49 SQ7 0.8543
50 CK1 0.8510
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2P1C; Ligand: GG3; Similar sites found with APoc: 2
This union binding pocket(no: 1) in the query (biounit: 2p1c.bio1) has 30 residues
No: Leader PDB Ligand Sequence Similarity
1 2O1O RIS 42.3913
2 2O1O RIS 42.3913
Pocket No.: 2; Query (leader) PDB : 2P1C; Ligand: GG3; Similar sites found with APoc: 2
This union binding pocket(no: 2) in the query (biounit: 2p1c.bio1) has 29 residues
No: Leader PDB Ligand Sequence Similarity
1 2O1O RIS 42.3913
2 2O1O RIS 42.3913
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