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Receptor
PDB id Resolution Class Description Source Keywords
4RXD 2 Å EC: 2.5.1.10 T. BRUCEI FARNESYL DIPHOSPHATE SYNTHASE COMPLEXED WITH RISED TRYPANOSOMA BRUCEI TRANSFERASE
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 A:1403;
C:1601;
B:1503;
C:1603;
B:1502;
B:1501;
C:1602;
A:1402;
A:1401;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
24.305 Mg [Mg+2...
RIS B:1504;
C:1600;
A:1404;
Valid;
Valid;
Valid;
none;
none;
none;
ic50 = 300 nM
283.112 C7 H11 N O7 P2 c1cc(...
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 9 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 = 32 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 (21)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 7 families.
1 4K10 Kd = 119.5 nM NI9 C7 H11 F N O7 P2 c1cc(c[n+]....
2 4RXE ic50 = 230 nM 3YQ C7 H12 N2 O6 P2 Cc1cccnc1N....
3 2EWG - M0N C9 H12 N2 O7 P2 c1ccn2c(c1....
4 5AFX ic50 = 1.2 uM PVZ C14 H29 N2 O7 P2 CCCCCCCCCn....
5 3DYH - 721 C11 H20 N O7 P2 CCCCOc1ccc....
6 2I19 - 1BY C7 H12 N2 O6 P2 c1ccnc(c1)....
7 3EGT Ki = 32 nM 722 C14 H26 N O7 P2 CCCCCCCOc1....
8 3EFQ - 714 C15 H28 N O7 P2 CCCCCCCCOc....
9 4RXD ic50 = 300 nM RIS C7 H11 N O7 P2 c1cc(cnc1)....
10 4RXC ic50 ~ 33 uM HRX C8 H13 N O7 P2 c1cc(cnc1)....
11 3DYG - NI9 C7 H11 F N O7 P2 c1cc(c[n+]....
12 2P1C Ki = 21 nM GG3 C14 H25 N O7 P2 C[N@](CCCC....
13 4DXJ ic50 = 38 nM 0M9 C5 H15 N O6 P2 CCCNCC(P(=....
14 3ICN - NI9 C7 H11 F N O7 P2 c1cc(c[n+]....
15 3ICK - IPR C5 H14 O7 P2 CC(C)CCO[P....
16 4DWB ic50 = 1.84 uM 0M7 C7 H19 N O6 P2 CCCCCNCC(P....
17 4DWG ic50 = 58 nM 0M8 C9 H23 N O6 P2 CCCCCCCNCC....
18 3ICM - P2H C13 H16 N O7 P2 c1ccc(cc1)....
19 3ICZ - PB6 C11 H18 N O6 P2 CC/C=C/c1c....
20 1YHL - RIS C7 H11 N O7 P2 c1cc(cnc1)....
21 3IBA - SO4 O4 S [O-]S(=O)(....
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: RIS; Similar ligands found: 3
No: Ligand ECFP6 Tc MDL keys Tc
1 RIS 1 1
2 HRX 0.590909 0.947368
3 2E4 0.411765 0.8
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: 233
This union binding pocket(no: 1) in the query (biounit: 2p1c.bio1) has 30 residues
No: Leader PDB Ligand Sequence Similarity
1 3KPE TM3 None
2 1HBK MYR None
3 5ET3 60C None
4 4WG0 CHD None
5 2ALG DAO None
6 5CX6 CDP 1.28205
7 2VK2 GZL 1.30719
8 3O0W MAN MAN MAN GLC 1.4652
9 1TMX HGX 1.70648
10 5V3Y 5V8 1.74825
11 4IA6 EIC 1.79487
12 3HYW DCQ 1.79487
13 3ZPG 5GP 1.83246
14 1ZED PNP 1.8595
15 1XX4 BAM 1.91571
16 3KU0 ADE 1.99203
17 6DAW ARG 2.04678
18 5OSW DIU 2.05128
19 3SDV 911 2.05128
20 3SP6 IL2 2.10526
21 6CIB ADP 2.12202
22 5ZQ4 AMP 2.12202
23 3KDU NKS 2.16606
24 2HZL PYR 2.19178
25 4YEF 4CQ 2.24719
26 5NM7 GLY 2.25564
27 6A0S NDP 2.40964
28 3W54 RNB 2.43161
29 4CT7 TRP 2.46914
30 4KWD JF2 2.54777
31 5FPN KYD 2.5641
32 4OPC PGT 2.5641
33 4DDY DN6 2.5641
34 2XN5 FUN 2.57143
35 6BMS PLM 2.6393
36 6CS8 F9Y 2.64026
37 5GUE GGS 2.71903
38 3AJM 4IP 2.8169
39 4JLZ UTP 2.82051
40 5UNJ RJW 2.85714
41 2YJD YJD 2.91667
42 2WPX ACO 2.94985
43 4UCC ZKW 3.00429
44 2QCX PF1 3.04183
45 6BR9 6OU 3.06407
46 6BR9 PGV 3.06407
47 2WR1 NAG 3.07692
48 5YZC 95C 3.07692
49 1NRL SRL 3.16456
50 2GVV DI9 3.18471
51 2AEL SAZ 3.20856
52 2UW1 GVM 3.25444
53 5TCI 79V 3.26087
54 1S8G DAO 3.30579
55 2HFN FMN 3.33333
56 3QTP 2PG 3.33333
57 2BCG GER 3.39806
58 2X1L MET 3.43511
59 5A5D 5LC 3.46021
60 4V1F BQ1 3.48837
61 5B0I BOG 3.49854
62 6BR8 6OU 3.57143
63 1N8V BDD 3.57143
64 6BR8 PGV 3.57143
65 3VET TOY 3.58974
66 3VET CP 3.58974
67 3VET ADP 3.58974
68 1XQD DND 3.58974
69 1RTW MP5 3.63636
70 4QEK GLC 3.65448
71 4EKQ NPO 3.74332
72 1W55 GPP 3.77358
73 1DKF BMS 3.82979
74 3B6C SDN 3.84615
75 4EIL FOL 3.84615
76 5EE7 5MV 3.84615
77 4OAR 2S0 3.87597
78 5M36 9SZ 3.93013
79 5AZC PGT 4
80 5C9J DAO 4.0404
81 3OF1 CMP 4.06504
82 4ZES MMA 4.08163
83 3AQT RCO 4.08163
84 4OKZ 3E9 4.10256
85 2D5X L35 4.10959
86 5UV1 0FV 4.11862
87 3IX9 MTX 4.21053
88 3L9R L9R 4.24028
89 3MBG FAD 4.31655
90 5TVI O8N 4.34783
91 1Q19 SSC 4.35897
92 3GFZ FMN 4.35897
93 2BYC FMN 4.37956
94 5X3R 7Y3 4.39024
95 5N26 CPT 4.3956
96 1KI6 AHU 4.53172
97 3X01 AMP 4.61538
98 5NTP 98E 4.61538
99 1TV5 N8E 4.61538
100 5IM3 DTP 4.61538
101 3NJQ NJQ 4.66321
102 3TVQ DQH 4.73373
103 5EY0 GTP 4.74453
104 1J78 OLA 4.80349
105 5X20 AOT 4.80769
106 5FQK 6NT 4.83271
107 1K7L 544 4.86111
108 4D1J DGJ 4.87179
109 5WL1 CUY 5
110 5WL1 D3D 5
111 4HBM 0Y7 5
112 5MZI FYK 5.12821
113 6CGN DA 5.14286
114 5ERM 210 5.23416
115 3LLZ GAL NGA 5.26316
116 4NB5 2JT 5.26316
117 3FAL REA 5.26316
118 5K53 STE 5.34351
119 1NHZ 486 5.35714
120 3V1V GST 5.38462
121 5KAU RHQ 5.45455
122 2GJ5 VD3 5.55556
123 3OO6 GAL 5.64103
124 1Q7E MET 5.64103
125 3TDC 0EU 5.64103
126 3UG4 AHR 5.64103
127 2YIV YIV 5.64103
128 4YSX E23 5.67376
129 5KD8 TNR 5.89744
130 5MBC FMN 5.94901
131 3W5N RAM 6.15385
132 5V4R MGT 6.17284
133 2Z6C FMN 6.20155
134 4OAS 2SW 6.25
135 4BTB PRO PRO PRO PRO PRO PRO PRO PRO PRO 6.27615
136 1XZ3 ICF 6.32184
137 2RH1 CLR 6.41026
138 2BHW NEX 6.46552
139 2QES ADE 6.51341
140 3KP6 SAL 6.62252
141 2GJ3 FAD 6.66667
142 2PEH LYS ARG LYS SER ARG TRP ASP GLU THR PRO 6.66667
143 4RW3 TDA 6.95364
144 4Q0A 4OA 6.95364
145 4RW3 PLM 6.95364
146 1T0S BML 6.97674
147 1MT1 AG2 7.07965
148 1N13 AG2 7.07965
149 5W7B MYR 7.0922
150 5OCA 9QZ 7.14286
151 2NZU BG6 7.14286
152 3JZ0 APC 7.31707
153 2OZ5 7XY 7.43243
154 4O08 PO6 7.47664
155 5Y02 HBX 7.47664
156 5Y02 MXN 7.47664
157 3KMZ EQO 7.5188
158 1I0B PEL 7.53012
159 3ET1 ET1 7.56014
160 4RHP PEF 7.65957
161 4RYV ZEA 7.74194
162 2RKN LP3 7.79221
163 6CB2 OLC 7.84983
164 3KO0 TFP 7.92079
165 2WOR 2AN 8
166 4WUJ FMN 8.16327
167 4LWU 20U 8.23529
168 4WGF HX2 8.29268
169 2BJ4 OHT 8.33333
170 2WUL GSH 8.47458
171 4MGA 27L 8.62745
172 4MG9 27K 8.62745
173 4TUZ 36J 8.62745
174 6GMN F4E 8.65385
175 5AAV GW5 8.73016
176 4TV1 36M 8.76494
177 2QE4 JJ3 8.87097
178 3ANY 2A3 9.12547
179 4I67 G G G RPC 9.1954
180 4F4S EFO 9.21053
181 5X13 HC4 9.57447
182 4IBF 1D5 10.0775
183 1EX7 5GP 10.2151
184 2HJ3 FAD 10.4
185 1YRX FMN 10.7438
186 2Z7I 742 10.8824
187 5IVX ARG GLY PRO GLY ARG ALA PHE VAL THR ILE 11
188 1NF8 BOG 11.1111
189 3QUZ QUV 11.1111
190 2F2G HMH 11.3122
191 2Q4X HMH 11.3122
192 2O1V ADP 11.7949
193 2P4Y C03 11.9134
194 5TWO 7MV 12.1324
195 3FUR Z12 12.1324
196 2PRG BRL 12.1771
197 1DTL BEP 12.4224
198 3JUQ AJD 12.4324
199 5Z3I ADE 12.4528
200 5LX9 OLB 12.7036
201 2ZSC BTN 12.766
202 5C1M OLC 12.8
203 3WUR O4B 12.8655
204 5LWY OLB 13.3562
205 5Z84 CHD 13.5593
206 5W97 CHD 13.5593
207 5ZCO CHD 13.5593
208 5ZCO PGV 13.5593
209 5MWE TCE 13.5802
210 4WH9 3M8 13.6612
211 1ID0 ANP 13.8158
212 1J1R ADE 14.1762
213 3RMK BML 14.4578
214 2CB8 MYA 14.9425
215 2XN3 ID8 15
216 1LNX URI 16.0494
217 6H8S FSZ 16.2791
218 2YLD CMO 17.3228
219 2Y69 CHD 18.5714
220 4OGQ 7PH 18.9189
221 4OGQ SQD 18.9189
222 4OGQ UMQ 18.9189
223 4OGQ 1O2 18.9189
224 3EYK EYK 19.186
225 1XVB 3BR 19.4118
226 1X0P FAD 19.5804
227 4LBP 1WG 23
228 2J1P GRG 23.8908
229 3WJO IPE 24.0356
230 3KRO IPE 28.4746
231 3KRO DST 28.4746
232 3KRO PPV 28.4746
233 2O1O RIS 42.3913
Pocket No.: 2; Query (leader) PDB : 2P1C; Ligand: GG3; Similar sites found with APoc: 49
This union binding pocket(no: 2) in the query (biounit: 2p1c.bio1) has 29 residues
No: Leader PDB Ligand Sequence Similarity
1 1UO4 PIH None
2 4LY9 1YY 1.28205
3 1GNI OLA 1.53846
4 5IUY BOG 1.53846
5 4G86 BNT 1.76056
6 2IOY RIP 2.4735
7 1YYE 196 2.61194
8 5HYR EST 2.71318
9 1M2Z BOG 2.72374
10 3P9T TCL 2.73973
11 3RY9 1CA 2.8
12 1U3R 338 2.90456
13 1N20 3AG 3.33333
14 3R9V DXC 3.4965
15 4MYD 164 3.57143
16 5E70 RCD 3.84615
17 4DOL PLM 4.14747
18 5TZ6 7OD 4.22078
19 1R6N 434 4.2654
20 1DRJ RIP 4.42804
21 5HCN DAO 4.5977
22 3G58 988 4.72441
23 3UPY FOM 4.87179
24 3B99 U51 4.87179
25 1M3U KPL 4.92424
26 1NQ7 HIS LYS ILE LEU HIS ARG LEU LEU GLN GLU 5.12821
27 3ETG GWD 5.12821
28 1XMY ROL 5.64103
29 1XMU ROF 5.64103
30 5B4B LP5 5.64516
31 5OES 3GC 5.89744
32 4V1T ADP 5.89744
33 5XJD 87L 7.27273
34 2C3Q GTX 7.28745
35 3FS1 ALA ALA LEU ALA ALA LEU LEU ALA ALA 7.3913
36 1MID LAP 7.69231
37 6AYI C3G 8.0402
38 3UUA 0CZ 8.76494
39 3W5J GDP 8.82353
40 5U9J GER 10.0592
41 2IYG FMN 10.4839
42 3KJQ B94 12.6316
43 3OCP CMP 12.9496
44 5Z84 PGV 13.5593
45 4V2O CLQ 14.6341
46 6CS9 PIO 14.6341
47 2E2R 2OH 15.5738
48 4RLT FSE 19.6203
49 5VOM 9GY 21.4765
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