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Receptor
PDB id Resolution Class Description Source Keywords
4DEM 1.85 Å EC: 2.5.1.10 CRYSTAL STRUCTURE OF HUMAN FPPS IN COMPLEX WITH YS_04_70 HOMO SAPIENS MEVALONATE PATHWAY ISOPRENE BIOSYNTHESIS CHOLESTEROL BIOSYBISPHOSPHONATE TRANSFERASE TRANSFERASE-TRANSFERASE INHIBICOMPLEX
Ref.: DESIGN AND SYNTHESIS OF ACTIVE SITE INHIBITORS OF T FARNESYL PYROPHOSPHATE SYNTHASE: APOPTOSIS AND INHI ERK PHOSPHORYLATION IN MULTIPLE MYELOMA CELLS. J.MED.CHEM. V. 55 3201 2012
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MG F:402;
F:403;
F:404;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
submit data
24.305 Mg [Mg+2...
YS4 F:401;
Valid;
none;
ic50 = 28 nM
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 (33)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 1ZW5 - ZOL C5 H10 N2 O7 P2 c1cn(cn1)C....
2 1YV5 - RIS C7 H11 N O7 P2 c1cc(cnc1)....
3 4QXS ic50 = 1.1 uM WC1 C21 H27 N O6 P2 C[C@H](c1c....
4 4P0V - ZOL C5 H10 N2 O7 P2 c1cn(cn1)C....
5 2F92 - AHD C4 H9 N O7 P2 C(CC(O)(P(....
6 5JUZ ic50 = 3 uM YL4 C22 H20 N3 O4 P S Cc1ccc(cc1....
7 4RXA ic50 = 1.8 uM 3F2 C32 H28 N6 O2 c1cc(cc(c1....
8 3N49 ic50 = 7 uM 3N4 C14 H10 O2 S c1ccc2c(c1....
9 5JV2 ic50 = 100 uM 6O3 C14 H13 N2 O3 P S Cc1ccc(cc1....
10 3N5J ic50 = 8 uM GO1 C11 H7 Cl2 N O4 c1c(cc(c2c....
11 2F9K - ZOL C5 H10 N2 O7 P2 c1cn(cn1)C....
12 3N45 - PO4 O4 P [O-]P(=O)(....
13 4LPH ic50 = 4.5 uM YL3 C14 H14 N3 O3 P S Cc1ccc(cc1....
14 5JV1 ic50 = 0.86 uM YL6 C21 H18 Cl F N3 O3 P S Cc1ccc(cc1....
15 4LFV - YS4 C15 H20 N2 O7 P2 CC(C)Oc1cc....
16 4LPG ic50 = 0.022 uM 1MV C14 H15 N3 O6 P2 S Cc1ccc(cc1....
17 2F94 - BFQ C9 H23 N O7 P2 CCCCC[N@](....
18 3N6K ic50 = 0.2 uM BFH C15 H11 N O4 c1ccc2c(c1....
19 5JV0 ic50 = 1.1 uM YL5 C21 H19 F N3 O3 P S Cc1ccc(cc1....
20 4H5E Kd = 0.86 uM YS4 C15 H20 N2 O7 P2 CC(C)Oc1cc....
21 3N5H ic50 = 2 uM GO0 C11 H7 Cl2 N O4 c1cc(c2c(c....
22 4H5D Kd = 0.58 uM YS4 C15 H20 N2 O7 P2 CC(C)Oc1cc....
23 2F8C - ZOL C5 H10 N2 O7 P2 c1cn(cn1)C....
24 4P0W - ZOL C5 H10 N2 O7 P2 c1cn(cn1)C....
25 3N46 - PO4 O4 P [O-]P(=O)(....
26 4P0X - 1WO C20 H26 O3 CC(C)C1=CC....
27 4H5C - PO4 O4 P [O-]P(=O)(....
28 5DGN ic50 = 1.2 uM 59Y C20 H13 N O2 c1ccc2c(c1....
29 4DEM ic50 = 28 nM YS4 C15 H20 N2 O7 P2 CC(C)Oc1cc....
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)....
70% Homology Family (36)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 7 families.
1 1ZW5 - ZOL C5 H10 N2 O7 P2 c1cn(cn1)C....
2 1YV5 - RIS C7 H11 N O7 P2 c1cc(cnc1)....
3 4QXS ic50 = 1.1 uM WC1 C21 H27 N O6 P2 C[C@H](c1c....
4 4P0V - ZOL C5 H10 N2 O7 P2 c1cn(cn1)C....
5 2F92 - AHD C4 H9 N O7 P2 C(CC(O)(P(....
6 5JUZ ic50 = 3 uM YL4 C22 H20 N3 O4 P S Cc1ccc(cc1....
7 4RXA ic50 = 1.8 uM 3F2 C32 H28 N6 O2 c1cc(cc(c1....
8 3N49 ic50 = 7 uM 3N4 C14 H10 O2 S c1ccc2c(c1....
9 5JV2 ic50 = 100 uM 6O3 C14 H13 N2 O3 P S Cc1ccc(cc1....
10 3N5J ic50 = 8 uM GO1 C11 H7 Cl2 N O4 c1c(cc(c2c....
11 2F9K - ZOL C5 H10 N2 O7 P2 c1cn(cn1)C....
12 3N45 - PO4 O4 P [O-]P(=O)(....
13 4LPH ic50 = 4.5 uM YL3 C14 H14 N3 O3 P S Cc1ccc(cc1....
14 5JV1 ic50 = 0.86 uM YL6 C21 H18 Cl F N3 O3 P S Cc1ccc(cc1....
15 4LFV - YS4 C15 H20 N2 O7 P2 CC(C)Oc1cc....
16 4LPG ic50 = 0.022 uM 1MV C14 H15 N3 O6 P2 S Cc1ccc(cc1....
17 2F94 - BFQ C9 H23 N O7 P2 CCCCC[N@](....
18 3N6K ic50 = 0.2 uM BFH C15 H11 N O4 c1ccc2c(c1....
19 5JV0 ic50 = 1.1 uM YL5 C21 H19 F N3 O3 P S Cc1ccc(cc1....
20 4H5E Kd = 0.86 uM YS4 C15 H20 N2 O7 P2 CC(C)Oc1cc....
21 3N5H ic50 = 2 uM GO0 C11 H7 Cl2 N O4 c1cc(c2c(c....
22 4H5D Kd = 0.58 uM YS4 C15 H20 N2 O7 P2 CC(C)Oc1cc....
23 2F8C - ZOL C5 H10 N2 O7 P2 c1cn(cn1)C....
24 4P0W - ZOL C5 H10 N2 O7 P2 c1cn(cn1)C....
25 3N46 - PO4 O4 P [O-]P(=O)(....
26 4P0X - 1WO C20 H26 O3 CC(C)C1=CC....
27 4H5C - PO4 O4 P [O-]P(=O)(....
28 5DGN ic50 = 1.2 uM 59Y C20 H13 N O2 c1ccc2c(c1....
29 4DEM ic50 = 28 nM YS4 C15 H20 N2 O7 P2 CC(C)Oc1cc....
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 1UBY - DMA C5 H12 O7 P2 CC(=CCO[P@....
35 1UBX - FPP C15 H28 O7 P2 CC(=CCC/C(....
36 1UBW - GPP C10 H20 O7 P2 CC(=CCC/C(....
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: YS4; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 YS4 1 1
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: 131
This union binding pocket(no: 1) in the query (biounit: 4lpg.bio1) has 76 residues
No: Leader PDB Ligand Sequence Similarity
1 3KPE TM3 None
2 4F4S EFO None
3 5KZV HCD None
4 5NNT DPV None
5 6BMS POV 1.46628
6 4OAR 2S0 1.55039
7 6C28 WCA 1.6129
8 2GMH UQ5 1.86667
9 2OBM ADP 2.01729
10 5B0I BOG 2.04082
11 6CB2 OLC 2.04778
12 3W54 RNB 2.12766
13 2HHP FLC 2.13333
14 6C1R EFD 2.13333
15 1M7G AV2 2.36967
16 5IUY BOG 2.4
17 6CS8 F9Y 2.4
18 6B21 C9V 2.4
19 2C9E PID 2.44648
20 5V3Y 5V8 2.44755
21 5O9W AKG 2.45232
22 5EY0 GTP 2.55474
23 1XMY ROL 2.66667
24 1XM4 PIL 2.66667
25 5FPN KYD 2.66667
26 1XMU ROF 2.66667
27 4BNU 9KQ 2.66667
28 5XNA SHV 2.89855
29 2E9L PLM 2.93333
30 1E4I NFG 2.93333
31 3RLF MAL 3.04054
32 4O08 PO6 3.11526
33 4G86 BNT 3.16901
34 1Q19 SSC 3.2
35 5OSW DIU 3.2
36 4WGF HX2 3.41463
37 5WJ6 B4A 3.46667
38 4MRP GSH 3.46667
39 4V1F BQ1 3.48837
40 3EYK EYK 3.48837
41 1W55 GPP 3.50404
42 3SP6 IL2 3.50877
43 2WW4 ADP 3.53357
44 4OKZ 3E9 3.56164
45 6BR8 6OU 3.57143
46 6BR8 PGV 3.57143
47 2WPB ZZI 3.61842
48 3GF4 U5P 3.73333
49 4IBF 1D5 3.87597
50 2BCG GER 3.8835
51 1J78 OLA 4
52 3AQT RCO 4.08163
53 3G58 988 4.26667
54 1DTL BEP 4.34783
55 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 4.42177
56 5KD8 TNR 4.53333
57 1NHZ 486 4.64286
58 6FTB M0E 4.7619
59 1RL4 BL5 4.78723
60 1TV5 N8E 4.8
61 4EKQ NPO 4.81283
62 6A56 LAT 4.87805
63 3LKF PC 5.01672
64 4LSJ LSJ 5.03876
65 1M2Z BOG 5.05837
66 1R6N 434 5.21327
67 5UC1 486 5.40541
68 1MID LAP 5.49451
69 2YLD CMO 5.51181
70 5C1M OLC 5.6
71 2HJ3 FAD 5.6
72 4RYV ZEA 5.80645
73 3B6C SDN 5.98291
74 5M37 9SZ 6.08696
75 1H9G COA MYR 6.17284
76 3TL1 JRO 6.28931
77 5LX9 OLB 6.33803
78 5W7B MYR 6.38298
79 6BR9 6OU 6.40669
80 4JLS 3ZE 6.57895
81 1S8G DAO 6.61157
82 2BJ4 OHT 6.74603
83 5UGW GSH 6.85714
84 3O01 DXC 7.14286
85 3TDC 0EU 7.2
86 2GJ5 VD3 7.40741
87 2OFW ADX 7.69231
88 4O4Z N2O 7.79221
89 1RDT 570 7.85124
90 5M36 9SZ 7.89474
91 1XPJ TLA 7.93651
92 4I67 G G G RPC 8.04598
93 1DKF BMS 8.15451
94 1NU4 MLA 8.24742
95 5HV0 AKG 8.29493
96 4BTB PRO PRO PRO PRO PRO PRO PRO PRO PRO 8.3682
97 1L6O SER LEU LYS LEU MET THR THR VAL 8.42105
98 2PEZ DAT 8.93855
99 1ZPD CIT 9.33333
100 5EE7 5MV 9.51327
101 4WBD CIT 9.86667
102 5CHR 4NC 10.9489
103 1HBK MYR 11.236
104 4IA6 EIC 12
105 5U97 PIT 13.3333
106 2VWA PTY 13.8614
107 5YZC 95C 14.8936
108 2WOR 2AN 15
109 4LWU 20U 15.2941
110 2Y69 CHD 15.7088
111 5OCA 9QZ 15.873
112 5TCI 79V 16.5854
113 5LWY OLB 16.8224
114 3RMK BML 16.8675
115 4OGQ 7PH 19.3548
116 4OGQ 2WD 19.3548
117 4OGQ UMQ 19.3548
118 4OGQ SQD 19.3548
119 5ZCO CHD 19.5652
120 5W97 CHD 19.5652
121 5Z84 CHD 19.5652
122 3KO0 TFP 21.7822
123 4YSX E23 23.0769
124 5MWE TCE 25.7143
125 3WJO IPE 29.0801
126 4OAS 2SW 30.2083
127 2J1P GRG 30.3754
128 2Z7I 742 30.5882
129 3KRO PPV 30.8475
130 3KRO IPE 30.8475
131 3KRO DST 30.8475
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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