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Receptor
PDB id Resolution Class Description Source Keywords
3WYJ 2.1 Å EC: 2.5.1.31 STRUCTURE OF E. COLI UNDECAPRENYL DIPHOSPHATE SYNTHASE IN CO BPH-789 ESCHERICHIA COLI K-12 TRANSFERASE
Ref.: ANTIBACTERIAL DRUG LEADS: DNA AND ENZYME MULTITARGE J.MED.CHEM. 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
H78 A:900;
 Valid;
 none;
 ic50 = 1.9 uM
948.677 C34 H36 N2 O18 P4 S2 c1cc(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3WYJ 2.1 Å EC: 2.5.1.31 STRUCTURE OF E. COLI UNDECAPRENYL DIPHOSPHATE SYNTHASE IN CO BPH-789 ESCHERICHIA COLI K-12 TRANSFERASE
Ref.: ANTIBACTERIAL DRUG LEADS: DNA AND ENZYME MULTITARGE J.MED.CHEM. 2015
Members (13)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 2E9D - B76 C20 H20 O8 P2 c1ccc(cc1)....
2 1X09 Kd = 520 uM IPE C5 H12 O7 P2 CC(=C)CCO[....
3 3TH8 - TH9 C19 H27 N O5 CCCCCCOc1c....
4 5CQJ ic50 = 7.5 uM 53Q C21 H17 Cl O COc1ccc(cc....
5 1V7U - FPP C15 H28 O7 P2 CC(=CCC/C(....
6 2E9C - B75 C24 H23 N O9 P2 S c1ccc2cc(c....
7 2E9A - B28 C20 H20 O7 P2 c1ccc(cc1)....
8 1X06 - FPS C15 H28 O6 P2 S CC(=CCC/C(....
9 1X07 Kd = 520 uM IPE C5 H12 O7 P2 CC(=C)CCO[....
10 2E98 - B29 C20 H18 O8 P2 c1ccc2c(c1....
11 3WYJ ic50 = 1.9 uM H78 C34 H36 N2 O18 P4 S2 c1cc(cc(c1....
12 1X08 Kd = 520 uM IPE C5 H12 O7 P2 CC(=C)CCO[....
13 2E99 - B08 C20 H20 O7 P2 c1ccc(cc1)....
70% Homology Family (13)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 2E9D - B76 C20 H20 O8 P2 c1ccc(cc1)....
2 1X09 Kd = 520 uM IPE C5 H12 O7 P2 CC(=C)CCO[....
3 3TH8 - TH9 C19 H27 N O5 CCCCCCOc1c....
4 5CQJ ic50 = 7.5 uM 53Q C21 H17 Cl O COc1ccc(cc....
5 1V7U - FPP C15 H28 O7 P2 CC(=CCC/C(....
6 2E9C - B75 C24 H23 N O9 P2 S c1ccc2cc(c....
7 2E9A - B28 C20 H20 O7 P2 c1ccc(cc1)....
8 1X06 - FPS C15 H28 O6 P2 S CC(=CCC/C(....
9 1X07 Kd = 520 uM IPE C5 H12 O7 P2 CC(=C)CCO[....
10 2E98 - B29 C20 H18 O8 P2 c1ccc2c(c1....
11 3WYJ ic50 = 1.9 uM H78 C34 H36 N2 O18 P4 S2 c1cc(cc(c1....
12 1X08 Kd = 520 uM IPE C5 H12 O7 P2 CC(=C)CCO[....
13 2E99 - B08 C20 H20 O7 P2 c1ccc(cc1)....
50% Homology Family (24)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2E9D - B76 C20 H20 O8 P2 c1ccc(cc1)....
2 1X09 Kd = 520 uM IPE C5 H12 O7 P2 CC(=C)CCO[....
3 3TH8 - TH9 C19 H27 N O5 CCCCCCOc1c....
4 5CQJ ic50 = 7.5 uM 53Q C21 H17 Cl O COc1ccc(cc....
5 1V7U - FPP C15 H28 O7 P2 CC(=CCC/C(....
6 2E9C - B75 C24 H23 N O9 P2 S c1ccc2cc(c....
7 2E9A - B28 C20 H20 O7 P2 c1ccc(cc1)....
8 1X06 - FPS C15 H28 O6 P2 S CC(=CCC/C(....
9 1X07 Kd = 520 uM IPE C5 H12 O7 P2 CC(=C)CCO[....
10 2E98 - B29 C20 H18 O8 P2 c1ccc2c(c1....
11 3WYJ ic50 = 1.9 uM H78 C34 H36 N2 O18 P4 S2 c1cc(cc(c1....
12 1X08 Kd = 520 uM IPE C5 H12 O7 P2 CC(=C)CCO[....
13 2E99 - B08 C20 H20 O7 P2 c1ccc(cc1)....
14 6ACS - CIT C6 H8 O7 C(C(=O)O)C....
15 2VG2 - IPE C5 H12 O7 P2 CC(=C)CCO[....
16 4ONC Kd = 410 nM 40B C19 H18 O7 P2 c1ccc(cc1)....
17 2VG3 - GPP C10 H20 O7 P2 CC(=CCC/C(....
18 5HC8 - PIS H3 O6 P2 S OP(=O)(O)O....
19 5HC7 - DST C5 H14 O6 P2 S CC(C)CCS[P....
20 4Q9O Kd = 1.7 uM 2ZW C20 H19 Cl N2 O2 Cc1c(c(no1....
21 4Q9M Kd = 66 nM 2ZW C20 H19 Cl N2 O2 Cc1c(c(no1....
22 4U82 ic50 = 0.39 uM FPS C15 H28 O6 P2 S CC(=CCC/C(....
23 2VG1 - FPP C15 H28 O7 P2 CC(=CCC/C(....
24 2VG0 - GPP C10 H20 O7 P2 CC(=CCC/C(....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: H78; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 H78 1 1
2 B75 0.722222 0.966102
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3WYJ; Ligand: H78; Similar sites found with APoc: 383
This union binding pocket(no: 1) in the query (biounit: 3wyj.bio1) has 64 residues
No: Leader PDB Ligand Sequence Similarity
1 4F4S EFO None
2 2WOR 2AN None
3 4V1F BQ1 None
4 1U9L ASN ARG PRO ILE LEU SER LEU None
5 6FA4 D1W None
6 5NNT DPV None
7 1XX4 BAM None
8 4WG0 CHD None
9 1N8V BDD None
10 4ELG 52J None
11 1UO5 PIH None
12 3RLB VIB None
13 5N17 8FK None
14 1MID LAP None
15 4ELG 52I None
16 1TUK PGM None
17 4HBM 0Y7 None
18 1TIQ COA 1.11111
19 5KJW 53C 1.18577
20 3W68 VIV 1.18577
21 3T03 3T0 1.18577
22 3W68 PBU 1.18577
23 2HFP NSI 1.18577
24 3ET3 ET1 1.18577
25 4BTB PRO PRO PRO PRO PRO PRO PRO PRO PRO 1.25523
26 6CB2 OLC 1.58103
27 3B9Z CO2 1.58103
28 4OAR 2S0 1.58103
29 4ZGM 32M 1.63934
30 5F5R ANP 1.68067
31 4COL DTP 1.97628
32 4V3I ASP LEU THR ARG PRO 1.97628
33 3B12 FAH 1.97628
34 3HYW DCQ 1.97628
35 3G58 988 1.97628
36 1R5L VIV 1.97628
37 4QWT ACD 1.97628
38 3UST FAD 1.97628
39 4JE7 BB2 2.03046
40 4WUJ FMN 2.04082
41 3UEC ALA ARG TPO LYS 2.05479
42 5URY PAM 2.05479
43 4UCC ZKW 2.14592
44 2OKL BB2 2.16216
45 1S17 GNR 2.22222
46 4HIA FMN 2.27273
47 3N8K D1X 2.32558
48 2G30 ALA ALA PHE 2.37154
49 4G86 BNT 2.37154
50 1TV5 N8E 2.37154
51 3QPB URA 2.37154
52 5K53 STE 2.37154
53 1YYE 196 2.37154
54 6D28 NEC 2.37154
55 2IO8 CYS 2.37154
56 5CX6 CDP 2.37154
57 3B99 U51 2.37154
58 3F70 MLZ 2.37154
59 1NHZ 486 2.37154
60 5G5W R8C 2.37154
61 1U3R 338 2.48963
62 2YJD YJD 2.5
63 4J24 EST 2.5
64 3OLL EST 2.5
65 4J26 EST 2.5
66 5M6N 7H9 2.54237
67 4DR9 BB2 2.60417
68 4MTI 2DX 2.6087
69 1Q1Y BB2 2.6178
70 4JLS 3ZE 2.63158
71 5L83 ASP TRP GLU ILE VAL 2.67857
72 3HP9 CF1 2.6971
73 3G5K BB2 2.73224
74 2GWH PCI 2.7668
75 5V3Y 5V8 2.7668
76 5VRH OLB 2.7668
77 1LOX RS7 2.7668
78 2WH8 II2 2.7668
79 1SJD NPG 2.7668
80 6BR9 6OU 2.7668
81 4ZH7 FUC GAL NAG GAL FUC 2.7668
82 3T3Z 9PL 2.7668
83 8CAT NDP 2.7668
84 4RF7 ARG 2.7668
85 3PMA SCR 2.7668
86 2HHP FLC 2.7668
87 2WPX ACO 2.7668
88 5WIU AQD 2.7668
89 3ET1 ET1 2.7668
90 6BR8 PGV 2.77778
91 6BR8 6OU 2.77778
92 4E2J MOF 2.8
93 6GNO XDI 2.96296
94 5ICK FEZ 3.05677
95 4XPL ACO 3.06748
96 4F0B GDS 3.125
97 3D04 SAK 3.14465
98 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 3.16206
99 2J5V PCA 3.16206
100 4MGA 27L 3.16206
101 1GPM AMP 3.16206
102 1M2Z BOG 3.16206
103 4TUZ 36J 3.16206
104 4MG8 27J 3.16206
105 5DXE EST 3.16206
106 4U0S ADP 3.16206
107 5HYR EST 3.16206
108 5WGD EST 3.16206
109 5WGQ EST 3.16206
110 1N6B DMZ 3.16206
111 4MGB XDH 3.16206
112 4MGD 27N 3.16206
113 1KPG 16A 3.16206
114 5KD8 TNR 3.16206
115 1UWC FER 3.16206
116 4MG7 27H 3.16206
117 3BQD DAY 3.16206
118 5DXG EST 3.16206
119 5DX3 EST 3.16206
120 5AHS COA 3.16206
121 3A51 VDY 3.16302
122 2BJ4 OHT 3.1746
123 5AAV GW5 3.1746
124 4TV1 36M 3.18725
125 3UUD EST 3.18725
126 2HJ3 FAD 3.2
127 2O5L MNR 3.26797
128 6C1R EFD 3.31754
129 4RHP PEF 3.40426
130 5LX9 OLB 3.55731
131 3FXU TSU 3.55731
132 3OQJ 3CX 3.55731
133 6GNF GLC 3.55731
134 1BII ARG GLY PRO GLY ARG ALA PHE VAL THR ILE 3.55731
135 4MRP GSH 3.55731
136 5U97 PIT 3.55731
137 4GBD MCF 3.55731
138 1UBY DMA 3.55731
139 3H2K BOG 3.55731
140 1D1G MTX 3.57143
141 5UC1 486 3.6036
142 5DCH 1YO 3.64583
143 1DTL BEP 3.72671
144 4K30 NLG 3.75
145 3SQP 3J8 3.76569
146 6FS0 E4W 3.77358
147 2BHW NEX 3.87931
148 5YW5 ADE 3.91061
149 5M36 9SZ 3.93013
150 5YSI NCA 3.94737
151 3TDC 0EU 3.95257
152 5KAU RHQ 3.95257
153 1XQP 8HG 3.95257
154 5MUA GAL 3.95257
155 6BMS POV 3.95257
156 1HK8 DGT 3.95257
157 1RJW ETF 3.95257
158 5UC9 MYR 3.9823
159 2IYG FMN 4.03226
160 5HW4 SAM 4.03226
161 4WQ2 3SU 4.04624
162 4ZB8 GDS 4.05405
163 5DYO FLU 4.12844
164 1YRX FMN 4.13223
165 1G27 BB1 4.16667
166 1NBU PH2 4.20168
167 1JE1 GMP 4.23729
168 1RL4 BL5 4.25532
169 6B21 C9V 4.34783
170 4URX FK1 4.34783
171 6DIO CIT 4.34783
172 3UW4 MAA CHG PRO 0DQ 4.34783
173 6BVK EAV 4.34783
174 6BVM EBV 4.34783
175 3BJC WAN 4.34783
176 1H3F TYE 4.34783
177 2CIX CEJ 4.34783
178 3SHZ 5CO 4.34783
179 1S4P GDP 4.34783
180 3KN5 ANP 4.34783
181 4YJK URA 4.36508
182 4WGF HX2 4.39024
183 2O66 FLC 4.44444
184 2GBB CIT 4.48718
185 1HBK MYR 4.49438
186 1M48 FRG 4.51128
187 3P9T TCL 4.56621
188 1ELR ACE MET GLU GLU VAL ASP 4.58015
189 1XW6 GSH 4.58716
190 2C4J GSO 4.58716
191 4DOL PLM 4.60829
192 4Z7X 3CX 4.62185
193 1R6N 434 4.73934
194 1I0B PEL 4.74308
195 2NZ5 226 4.74308
196 5B25 4QJ 4.74308
197 5AWM ANP 4.74308
198 3AI3 SOE 4.74308
199 4KCF AKM 4.74308
200 1UUY PPI 4.79042
201 4EKQ NPO 4.81283
202 5B4B LP5 4.83871
203 5I8F ML1 4.84848
204 2W3L DRO 4.86111
205 5UNJ RJW 4.89796
206 4DS0 A2G GAL NAG FUC 4.90798
207 5MWE TCE 4.93827
208 3RET PYR 4.9505
209 3RET SAL 4.9505
210 3SAO DBH 5
211 5SVV FMN 5.10949
212 3O01 DXC 5.13834
213 3ZQE DXC 5.13834
214 4N6H EJ4 5.13834
215 2O1V ADP 5.13834
216 5HC0 NPO 5.13834
217 2YOO K2B 5.13834
218 1XMU ROF 5.13834
219 1NU4 MLA 5.15464
220 3KXC PLM 5.15464
221 5A4W QCT 5.18868
222 4XCP PLM 5.29412
223 2AK3 AMP 5.30973
224 3CYI ATP 5.45455
225 2D5X L35 5.47945
226 2YLD CMO 5.51181
227 5A8E XTK 5.5336
228 3F8C HT1 5.55556
229 1BWO LPC 5.55556
230 5K52 OCD 5.66038
231 4QBK 3NZ 5.6701
232 3FAL REA 5.78512
233 4NSQ COA 5.78947
234 5MTE BB2 5.83942
235 4DOO DAO 5.85366
236 5YBL AKG 5.92885
237 3HR1 PF9 5.92885
238 1J78 OLA 5.92885
239 3JRX S1A 5.92885
240 3KVY URA 5.92885
241 6FQZ 6PG 5.92885
242 1ODJ GMP 5.95745
243 2ZFU SAH 6.04651
244 4RJD TFP 6.06061
245 4CVZ TYR GLU LEU ASP GLU LYS PHE ASP ARG LEU 6.12245
246 3H0A D30 6.14035
247 3X01 AMP 6.32411
248 1IYK MYA 6.32411
249 4O4K 2PK 6.32411
250 1W96 S1A 6.32411
251 3R9V DXC 6.32411
252 4N14 WR7 6.32411
253 4GK9 MAN BMA MAN MAN MAN 6.32411
254 2C9E PID 6.32411
255 5W7B MYR 6.38298
256 5C1M OLC 6.4
257 5C1M CLR 6.4
258 2XG5 EC5 6.42202
259 2XG5 EC2 6.42202
260 1LQY BB2 6.52174
261 5CHR 4NC 6.56934
262 3E70 GDP 6.71937
263 2BCG GER 6.79612
264 4EJ1 FOL 6.91824
265 3CM2 X23 6.92308
266 3FS1 ALA ALA LEU ALA ALA LEU LEU ALA ALA 6.95652
267 1KJM ALA GLN PHE SER ALA SER ALA SER ARG 7
268 3W5N RAM 7.11462
269 1B4N GUA 7.11462
270 6CI7 ACP 7.11462
271 5N26 CPT 7.14286
272 4ZB6 GDS 7.17489
273 3QKD HI0 7.18232
274 6BJO DUY 7.2
275 1NF8 BOG 7.24638
276 5UWA 8ND 7.38916
277 3W54 RNB 7.50988
278 3UW5 MAA CHG PRO 0DQ 7.50988
279 5OLK DTP 7.50988
280 3I9U DTU 7.50988
281 5TVI O8N 7.6087
282 2ALG DAO 7.6087
283 2ALG HP6 7.6087
284 4RYV ZEA 7.74194
285 6FBA D48 7.90514
286 3WCA FPS 7.90514
287 5V4R MGT 8.02469
288 5OSW DIU 8.3004
289 2RH1 CAU 8.3004
290 5OSW AE4 8.3004
291 3T4L ZEA 8.3004
292 2RH1 CLR 8.3004
293 5LWY OLB 8.41121
294 5E5U MLI 8.54271
295 5UGW GSH 8.57143
296 3H0L ADP 8.69565
297 5CXI 5TW 8.86699
298 2V5E SCR 8.91089
299 2VWA PTY 8.91089
300 2QQC AG2 8.92857
301 4F06 PHB 9.09091
302 6C0B PAM 9.09091
303 6EOP F15 9.09091
304 5FUI APY 9.09091
305 4A7W GTP 9.16667
306 5F7Y GLC GAL NAG GAL FUC A2G 9.16667
307 5F7N NAG GAL FUC FUC A2G 9.16667
308 5H94 LYS MET ASN THR GLN PHE THR ALA VAL 9.18367
309 2CB8 MYA 9.1954
310 1T0S BML 9.30233
311 4IBF 1D5 9.30233
312 3MBG FAD 9.35252
313 5OFW 9TW 9.41704
314 5OQW A4E 9.48617
315 3ROE THM 9.48617
316 1N13 AG2 9.73451
317 5F7J ADE 9.88142
318 4YUS FMN 9.88142
319 4JGX PLM 10.0775
320 3BM1 FMN 10.3825
321 2B4D COA 10.5263
322 3GFZ FMN 10.6719
323 6BYM HC3 10.8374
324 2IOR ADP 11.0638
325 1SO2 666 11.0672
326 3ZF8 GDP 11.0672
327 6FS8 E4Z 11.2195
328 6CAY ERG 11.2426
329 5AZC PGT 11.4625
330 5IUY BOG 11.4625
331 4RC8 STE 11.7117
332 5DKK FMN 11.7241
333 5CYV WCA 12.3288
334 5OCA 9QZ 12.9032
335 1NRL SRL 13.0435
336 1M13 HYF 13.0435
337 3L1N PLM 13.4021
338 1FK5 OLA 13.9785
339 6GH1 ARG LEU PRO ALA LYS ALA PRO LEU LEU 14
340 3KYO LYS LEU PRO ALA GLN PHE TYR ILE LEU 14
341 5C9J DAO 14.1414
342 5C9J STE 14.1414
343 5U98 VAL THR THR ASP ILE GLN VAL LYS VAL 14.1414
344 1ZPD CIT 14.2292
345 5XS3 VAL ARG SER ARG ARG CYS LEU ARG LEU 14.2857
346 1J54 TMP 14.5161
347 1YC4 43P 14.6245
348 5Y02 HBX 15.8879
349 5N8V KZZ 15.942
350 2Z6C FMN 16.2791
351 5XJ7 87O 16.4179
352 3N7S 3N7 16.5217
353 4YSX E23 16.6667
354 5MB4 NAG 16.996
355 2YNC YNC 16.996
356 3KP6 SAL 17.8808
357 5DJT FMN 18.0328
358 5DJU FMN 18.0328
359 3VKX T3 18.5771
360 3KO0 TFP 18.8119
361 5UC4 83S 20.9091
362 1XVB 3BR 21.3439
363 5C83 4YN 21.8182
364 1TLG GAL 23.2
365 3WQM B29 23.7154
366 4OGQ 1O2 24.186
367 4OGQ SQD 24.186
368 4OGQ 7PH 24.186
369 4OGQ 2WD 24.186
370 2Y69 CHD 26.9841
371 5Z84 CHD 36.1702
372 5W97 CHD 36.1702
373 5ZCO CHD 36.1702
374 5ZCO PEK 36.1702
375 5Z84 PEK 36.1702
376 2DYS PGV 36.1702
377 5ZCO PGV 36.1702
378 5Z84 PGV 36.1702
379 2DYS TGL 36.1702
380 2DYR PGV 36.1702
381 2DYR TGL 36.1702
382 5XK9 GST 42.2414
383 5XK9 DMA 42.2414
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