Receptor
PDB id Resolution Class Description Source Keywords
2I19 2.28 Å EC: 2.5.1.10 T. BRUCEI FARNESYL DIPHOSPHATE SYNTHASE COMPLEXED WITH BISPHOSPHONATE TRYPANOSOMA BRUCEI PROTEIN-BISPHOSPHONATE COMPLEX TRANSFERASE
Ref.: SOLID-STATE NMR, CRYSTALLOGRAPHIC, AND COMPUTATIONAL INVESTIGATION OF BISPHOSPHONATES AND FARNESYL DIPHOSPHATE SYNTHASE-BISPHOSPHONATE COMPLEXES. J.AM.CHEM.SOC. V. 128 14485 2006
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
1BY A:3001;
B:4001;
Valid;
Valid;
none;
none;
submit data
282.128 C7 H12 N2 O6 P2 c1ccn...
MG A:3002;
A:3003;
A:3004;
B:4002;
B:4003;
B:4004;
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...
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: 1BY; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 1BY 1 1
Similar Ligands (3D)
Ligand no: 1; Ligand: 1BY; Similar ligands found: 54
No: Ligand Similarity coefficient
1 HRX 0.9361
2 C6J 0.9293
3 M0N 0.9192
4 RIS 0.9172
5 CBQ 0.9150
6 NI9 0.9121
7 BZS 0.9048
8 CXA 0.9032
9 ING 0.8961
10 3NF 0.8913
11 HHV 0.8889
12 TH4 0.8878
13 3D8 0.8878
14 1KM 0.8871
15 HO6 0.8839
16 U19 0.8822
17 12R 0.8808
18 0M7 0.8803
19 NRD 0.8790
20 ZOL 0.8790
21 3B4 0.8779
22 FUZ 0.8771
23 WL3 0.8746
24 RBE 0.8739
25 531 0.8729
26 23N 0.8719
27 A4V 0.8716
28 SLY 0.8712
29 AUY 0.8710
30 JGM 0.8699
31 AOY 0.8696
32 0M9 0.8691
33 ACE PHE 0.8690
34 KWB 0.8680
35 7UZ 0.8670
36 5E4 0.8657
37 PRO LEU 0.8641
38 2B4 0.8639
39 3YQ 0.8639
40 028 0.8638
41 FC3 0.8635
42 4GU 0.8618
43 3IP 0.8612
44 F40 0.8610
45 6J3 0.8604
46 2D2 0.8585
47 H35 0.8582
48 ID8 0.8579
49 AYS 0.8571
50 ALA PHE 0.8565
51 NIY 0.8551
52 CMG 0.8532
53 CJZ 0.8526
54 VJJ 0.8521
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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