Receptor
PDB id Resolution Class Description Source Keywords
4H5E 2.04 Å EC: 2.5.1.10 CRYSTAL STRUCTURE OF HUMAN FPPS IN TERNARY COMPLEX WITH YS04 ISOPENTENYL PYROPHOSPHATE HOMO SAPIENS TRANSFERASE TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX
Ref.: TERNARY COMPLEX STRUCTURES OF HUMAN FARNESYL PYROPH SYNTHASE BOUND WITH A NOVEL INHIBITOR AND SECONDARY PROVIDE INSIGHTS INTO THE MOLECULAR DETAILS OF THE ACTIVE SITE CLOSURE. BMC STRUCT.BIOL. V. 12 32 2012
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
IPR F:402;
 Valid;
 none;
 submit data
248.108 C5 H14 O7 P2 CC(C)...
MG F:403;
F:404;
F:405;
 Part of Protein;
Part of Protein;
Part of Protein;
 none;
none;
none;
 submit data
24.305 Mg [Mg+2...
YS4 F:401;
 Valid;
 none;
 Kd = 0.86 uM
402.276 C15 H20 N2 O7 P2 CC(C)...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4LPG 2.35 Å EC: 2.5.1.10 CRYSTAL STRUCTURE OF HUMAN FPPS IN COMPLEX WITH CL01131 HOMO SAPIENS TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX
Ref.: MULTISTAGE SCREENING REVEALS CHAMELEON LIGANDS OF T FARNESYL PYROPHOSPHATE SYNTHASE: IMPLICATIONS TO DR DISCOVERY FOR NEURODEGENERATIVE DISEASES. J.MED.CHEM. V. 57 5764 2014
Members (38)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 1ZW5 - ZOL C5 H10 N2 O7 P2 c1cn(cn1)C....
2 1YV5 - RIS C7 H11 N O7 P2 c1cc(cnc1)....
3 6N7Y ic50 = 7.7 uM KFA C21 H20 N3 O3 P S Cc1ccc(cc1....
4 4QXS ic50 = 1.1 uM WC1 C21 H27 N O6 P2 C[C@H](c1c....
5 4P0V - ZOL C5 H10 N2 O7 P2 c1cn(cn1)C....
6 2F92 - AHD C4 H9 N O7 P2 C(CC(O)(P(....
7 5JUZ ic50 = 3 uM YL4 C22 H20 N3 O4 P S Cc1ccc(cc1....
8 4RXA ic50 = 1.8 uM 3F2 C32 H28 N6 O2 c1cc(cc(c1....
9 3N49 ic50 = 7 uM 3N4 C14 H10 O2 S c1ccc2c(c1....
10 5JV2 ic50 ~ 100 uM 6O3 C14 H13 N2 O3 P S Cc1ccc(cc1....
11 3N5J ic50 = 6 uM GO1 C11 H7 Cl2 N O4 c1c(cc(c2c....
12 2F9K - ZOL C5 H10 N2 O7 P2 c1cn(cn1)C....
13 3N45 - PO4 O4 P [O-]P(=O)(....
14 4LPH Kd = 9.2 uM YL3 C14 H14 N3 O3 P S Cc1ccc(cc1....
15 5JV1 ic50 = 0.86 uM YL6 C21 H18 Cl F N3 O3 P S Cc1ccc(cc1....
16 4LFV - YS4 C15 H20 N2 O7 P2 CC(C)Oc1cc....
17 4LPG Kd = 55.6 uM 1MV C14 H15 N3 O6 P2 S Cc1ccc(cc1....
18 2F94 - BFQ C9 H23 N O7 P2 CCCCC[N@](....
19 3N6K Kd = 180 nM BFH C15 H11 N O4 c1ccc2c(c1....
20 6OAH ic50 = 1.5 uM M2V C21 H19 Cl N3 O3 P S Cc1ccc(cc1....
21 5JV0 ic50 = 1.1 uM YL5 C21 H19 F N3 O3 P S Cc1ccc(cc1....
22 4H5E Kd = 0.86 uM YS4 C15 H20 N2 O7 P2 CC(C)Oc1cc....
23 3N5H ic50 = 2 uM GO0 C11 H7 Cl2 N O4 c1cc(c2c(c....
24 6OAG ic50 = 3.7 uM M2Y C21 H19 Cl N3 O3 P S Cc1ccc(cc1....
25 4H5D Kd = 0.58 uM YS4 C15 H20 N2 O7 P2 CC(C)Oc1cc....
26 2F8C - ZOL C5 H10 N2 O7 P2 c1cn(cn1)C....
27 4P0W - ZOL C5 H10 N2 O7 P2 c1cn(cn1)C....
28 3N46 - PO4 O4 P [O-]P(=O)(....
29 4P0X - 1WO C20 H26 O3 CC(C)C1=CC....
30 6N83 ic50 = 0.54 uM YL6 C21 H18 Cl F N3 O3 P S Cc1ccc(cc1....
31 4H5C - PO4 O4 P [O-]P(=O)(....
32 5DGN ic50 = 1.2 uM 59Y C20 H13 N O2 c1ccc2c(c1....
33 4DEM ic50 = 28 nM YS4 C15 H20 N2 O7 P2 CC(C)Oc1cc....
34 6N82 ic50 = 1.1 uM YF7 C21 H18 Cl F N3 O3 P S Cc1ccc(cc1....
35 3N1V ic50 > 500 uM 3N1 C11 H9 Cl O2 S Cc1c2cc(cc....
36 2OPM - NI9 C7 H11 F N O7 P2 c1cc(c[n+]....
37 5JA0 Kd = 5.3 uM FPP C15 H28 O7 P2 CC(=CCC/C(....
38 1YQ7 - RIS C7 H11 N O7 P2 c1cc(cnc1)....
70% Homology Family (41)
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 6N7Y ic50 = 7.7 uM KFA C21 H20 N3 O3 P S Cc1ccc(cc1....
4 4QXS ic50 = 1.1 uM WC1 C21 H27 N O6 P2 C[C@H](c1c....
5 4P0V - ZOL C5 H10 N2 O7 P2 c1cn(cn1)C....
6 2F92 - AHD C4 H9 N O7 P2 C(CC(O)(P(....
7 5JUZ ic50 = 3 uM YL4 C22 H20 N3 O4 P S Cc1ccc(cc1....
8 4RXA ic50 = 1.8 uM 3F2 C32 H28 N6 O2 c1cc(cc(c1....
9 3N49 ic50 = 7 uM 3N4 C14 H10 O2 S c1ccc2c(c1....
10 5JV2 ic50 ~ 100 uM 6O3 C14 H13 N2 O3 P S Cc1ccc(cc1....
11 3N5J ic50 = 6 uM GO1 C11 H7 Cl2 N O4 c1c(cc(c2c....
12 2F9K - ZOL C5 H10 N2 O7 P2 c1cn(cn1)C....
13 3N45 - PO4 O4 P [O-]P(=O)(....
14 4LPH Kd = 9.2 uM YL3 C14 H14 N3 O3 P S Cc1ccc(cc1....
15 5JV1 ic50 = 0.86 uM YL6 C21 H18 Cl F N3 O3 P S Cc1ccc(cc1....
16 4LFV - YS4 C15 H20 N2 O7 P2 CC(C)Oc1cc....
17 4LPG Kd = 55.6 uM 1MV C14 H15 N3 O6 P2 S Cc1ccc(cc1....
18 2F94 - BFQ C9 H23 N O7 P2 CCCCC[N@](....
19 3N6K Kd = 180 nM BFH C15 H11 N O4 c1ccc2c(c1....
20 6OAH ic50 = 1.5 uM M2V C21 H19 Cl N3 O3 P S Cc1ccc(cc1....
21 5JV0 ic50 = 1.1 uM YL5 C21 H19 F N3 O3 P S Cc1ccc(cc1....
22 4H5E Kd = 0.86 uM YS4 C15 H20 N2 O7 P2 CC(C)Oc1cc....
23 3N5H ic50 = 2 uM GO0 C11 H7 Cl2 N O4 c1cc(c2c(c....
24 6OAG ic50 = 3.7 uM M2Y C21 H19 Cl N3 O3 P S Cc1ccc(cc1....
25 4H5D Kd = 0.58 uM YS4 C15 H20 N2 O7 P2 CC(C)Oc1cc....
26 2F8C - ZOL C5 H10 N2 O7 P2 c1cn(cn1)C....
27 4P0W - ZOL C5 H10 N2 O7 P2 c1cn(cn1)C....
28 3N46 - PO4 O4 P [O-]P(=O)(....
29 4P0X - 1WO C20 H26 O3 CC(C)C1=CC....
30 6N83 ic50 = 0.54 uM YL6 C21 H18 Cl F N3 O3 P S Cc1ccc(cc1....
31 4H5C - PO4 O4 P [O-]P(=O)(....
32 5DGN ic50 = 1.2 uM 59Y C20 H13 N O2 c1ccc2c(c1....
33 4DEM ic50 = 28 nM YS4 C15 H20 N2 O7 P2 CC(C)Oc1cc....
34 6N82 ic50 = 1.1 uM YF7 C21 H18 Cl F N3 O3 P S Cc1ccc(cc1....
35 3N1V ic50 > 500 uM 3N1 C11 H9 Cl O2 S Cc1c2cc(cc....
36 2OPM - NI9 C7 H11 F N O7 P2 c1cc(c[n+]....
37 5JA0 Kd = 5.3 uM FPP C15 H28 O7 P2 CC(=CCC/C(....
38 1YQ7 - RIS C7 H11 N O7 P2 c1cc(cnc1)....
39 1UBY - DMA C5 H12 O7 P2 CC(=CCO[P@....
40 1UBX - FPP C15 H28 O7 P2 CC(=CCC/C(....
41 1UBW - GPP C10 H20 O7 P2 CC(=CCC/C(....
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: IPR; Similar ligands found: 20
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 IPE 0.475 0.820513
7 P25 0.475 0.842105
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 0O3 0.418605 0.707317
16 DP6 0.416667 0.8
17 0CM 0.414634 0.777778
18 3E9 0.413793 0.829268
19 ELR 0.40678 0.829268
20 ELU 0.40678 0.829268
Ligand no: 2; Ligand: YS4; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 YS4 1 1
Similar Ligands (3D)
Ligand no: 1; Ligand: IPR; Similar ligands found: 81
No: Ligand Similarity coefficient
1 DMA 0.9903
2 H6P 0.9393
3 P3S 0.9335
4 2JA 0.9299
5 ISY 0.9280
6 DST 0.9256
7 PMV 0.9213
8 DG2 0.9116
9 58X 0.9112
10 DLT 0.9111
11 43Q 0.9098
12 AZM 0.9037
13 0CG 0.9003
14 6FR 0.8989
15 DX5 0.8986
16 HPO 0.8909
17 G01 0.8893
18 G6Q 0.8886
19 5SP 0.8875
20 ATX 0.8863
21 MGB 0.8859
22 STX 0.8852
23 2E5 0.8850
24 VFG 0.8846
25 AGP 0.8836
26 M3L 0.8819
27 NFZ 0.8815
28 G88 0.8811
29 DI9 0.8792
30 NBB 0.8786
31 ZZU 0.8783
32 A5P 0.8781
33 M3C 0.8765
34 GRQ 0.8762
35 PAU 0.8752
36 LXP 0.8742
37 5TO 0.8728
38 BGT 0.8710
39 2J3 0.8708
40 PML 0.8705
41 DXP 0.8696
42 AHL 0.8687
43 6C9 0.8684
44 ARG 0.8681
45 GVA 0.8679
46 ILO 0.8678
47 PA5 0.8672
48 DAR 0.8672
49 ALA GLU 0.8670
50 HSA 0.8667
51 PTB 0.8654
52 LGT 0.8650
53 GGB 0.8648
54 HAR 0.8647
55 R5P 0.8646
56 GGG 0.8645
57 EXY 0.8639
58 CXA 0.8638
59 VFM 0.8638
60 I58 0.8635
61 S6P 0.8633
62 3CX 0.8633
63 FM4 0.8630
64 MZM 0.8630
65 IOP 0.8629
66 F6R 0.8624
67 TX4 0.8617
68 PAN 0.8599
69 ING 0.8595
70 D1G 0.8592
71 WT2 0.8580
72 2OR 0.8578
73 HLP 0.8577
74 6C5 0.8568
75 CIR 0.8567
76 3PO 0.8565
77 XOG 0.8563
78 M6R 0.8545
79 5PV 0.8535
80 3W6 0.8515
81 FSA 0.8510
Ligand no: 2; Ligand: YS4; Similar ligands found: 5
No: Ligand Similarity coefficient
1 B28 0.9040
2 722 0.8946
3 714 0.8739
4 721 0.8717
5 PVZ 0.8552
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4LPG; Ligand: 1MV; Similar sites found with APoc: 10
This union binding pocket(no: 1) in the query (biounit: 4lpg.bio1) has 76 residues
No: Leader PDB Ligand Sequence Similarity
1 3KRO PPV 30.8475
2 3KRO PPV 30.8475
3 6W7I 476 49.5601
4 6VJC 476 49.5601
5 6W7I 476 49.5601
6 6VJC 476 49.5601
7 4JZB P2H 49.5601
8 4JZX 476 49.5601
9 4JZX 476 49.5601
10 4JZB P2H 49.5601
Pocket No.: 2; Query (leader) PDB : 4LPG; Ligand: 1MV; 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: 4lpg.bio1) has 76 residues
No: Leader PDB Ligand Sequence Similarity
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