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Receptor
PDB id Resolution Class Description Source Keywords
4x1f 2 Å EC: 2.3.1.48 CRYSTAL STRUCTURE OF THE HPXR-LBD IN COMPLEX WITH THE SYNTHE ESTROGEN 17ALPHA-ETHINYLESTRADIOL HOMO SAPIENS NUCLEAR RECEPTOR HORMONE RECEPTOR PREGNANE X RECEPTOR ESTGENE REGULATION
Ref.: SYNERGISTIC ACTIVATION OF HUMAN PREGNANE X RECEPTOR BINARY COCKTAILS OF PHARMACEUTICAL AND ENVIRONMENTA COMPOUNDS. NAT COMMUN V. 6 8089 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
3WF A:501;
 Valid;
 none;
 Ki = 11.5 uM
296.403 C20 H24 O2 C[C@]...
MPD A:503;
A:502;
 Invalid;
Invalid;
 none;
none;
 submit data
118.174 C6 H14 O2 C[C@@...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1M13 2.15 Å EC: 2.3.1.48 CRYSTAL STRUCTURE OF THE HUMAN PREGANE X RECEPTOR LIGAND BINDING DOMAIN IN COMPLEX WITH HYPERFORIN, A CONSTITUENT O F ST. JOHN'S WORT HOMO SAPIENS NUCLEAR RECEPTOR LIGAND BINDING DOMAIN PROTEIN-LIGAND COMPLEX TRANSCRIPTION
Ref.: 2.1 A CRYSTAL STRUCTURE OF HUMAN PXR IN COMPLEX WITH THE ST. JOHN'S WORT COMPOUND HYPERFORIN BIOCHEMISTRY V. 42 1430 2003
Members (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 46 families.
1 6DUP - HCJ C20 H15 F3 N2 O3 c1cc(cc(c1....
2 4XHD - 40U C23 H33 Cl N2 O3 CC(C)[C@H]....
3 3HVL - SRL C24 H42 O7 P2 CCOP(=O)(C....
4 1M13 Kd = 27 nM HYF C35 H52 O4 CC(C)C(=O)....
5 4X1G Kd = 11.5 uM 3WF C20 H24 O2 C[C@]12CC[....
6 4X1F Ki = 11.5 uM 3WF C20 H24 O2 C[C@]12CC[....
70% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 29 families.
1 6DUP - HCJ C20 H15 F3 N2 O3 c1cc(cc(c1....
2 4XHD - 40U C23 H33 Cl N2 O3 CC(C)[C@H]....
3 3HVL - SRL C24 H42 O7 P2 CCOP(=O)(C....
4 1M13 Kd = 27 nM HYF C35 H52 O4 CC(C)C(=O)....
5 4X1G Kd = 11.5 uM 3WF C20 H24 O2 C[C@]12CC[....
6 4X1F Ki = 11.5 uM 3WF C20 H24 O2 C[C@]12CC[....
50% Homology Family (42)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 209 families.
1 4Q0A Kd = 0.33 uM 4OA C24 H40 O3 C[C@H](CCC....
2 4X1F Ki = 11.5 uM 3WF C20 H24 O2 C[C@]12CC[....
3 5M24 - 9CR C20 H28 O2 CC1=C(C(CC....
4 1FCY Kd = 3 nM 564 C26 H26 O3 CC1(CCC(c2....
5 3A3Z - 2MV C29 H46 O4 C[C@H]1[C@....
6 1IE8 - KH1 C29 H48 O4 CCC(CC)(CC....
7 2HAS - C3O C30 H50 O4 CCCO[C@H]1....
8 1S0Z - EB1 C30 H46 O3 CCC(CC)(C=....
9 3AZ1 - DS2 C27 H38 O5 CCC(CC)(c1....
10 1IE9 - VDX C27 H44 O3 C[C@H](CCC....
11 2HAM - C33 C30 H50 O3 CCC[C@H]1[....
12 2HB8 - MVD C28 H46 O3 C[C@H]1[C@....
13 3CS4 - COV C28 H44 O4 C[C@]12CCC....
14 1S19 - MC9 C27 H40 O3 C[C@H](C=C....
15 3M7R - VDX C27 H44 O3 C[C@H](CCC....
16 3A40 - 23R C29 H46 O4 C[C@H]1[C@....
17 3AUR - CA9 C27 H42 O3 C[C@H]1[C@....
18 3KPZ - ZNE C28 H41 N O3 S C[C@H](CCC....
19 1TXI - TX5 C27 H40 O3 C[C@H](CC#....
20 1DB1 Kd = 0.55 nM VDX C27 H44 O3 C[C@H](CCC....
21 4G2I - 0VQ C25 H26 F6 O3 CC/C(=CC=C....
22 3CS6 - 0CO C28 H44 O4 C[C@]12CCC....
23 3AZ2 - DS3 C30 H44 O5 CCC(CC)(c1....
24 3AZ3 - DS6 C31 H46 O5 CCC(CC)(c1....
25 5YT2 - 90O C29 H48 O4 C[C@H](CCC....
26 5GIE Kd = 769.2 nM VDP C37 H53 N O4 C[C@H](C[C....
27 2HB7 - O1C C30 H50 O4 C[C@H](CCC....
28 3VHW - VHW C34 H50 O7 CCC1(CC/C(....
29 2HAR - OCC C30 H50 O5 C[C@H](CCC....
30 5GID Kd = 769.2 nM VDP C37 H53 N O4 C[C@H](C[C....
31 3TKC - FMV C28 H40 O4 C[C@H](c1c....
32 4ITE - TEY C30 H48 N4 O3 C[C@H](CCC....
33 5GIC Kd = 330.9 nM DLC C35 H51 N O4 C[C@H]1/C(....
34 3P8X - ZYD C27 H44 O3 CC(C)(CCCC....
35 5YSY - 90L C29 H48 O4 C[C@H](CCC....
36 1PQ9 - BNS C6 H6 O3 S c1ccc(cc1)....
37 4RAK Ki = 14 nM 652 C28 H29 Cl N2 O3 S CC(C)(c1cc....
38 1UPV - 444 C17 H12 F9 N O3 S c1ccc(cc1)....
39 1PQ6 - 965 C33 H31 Cl F3 N O3 c1ccc(cc1)....
40 1UPW - 444 C17 H12 F9 N O3 S c1ccc(cc1)....
41 5JY3 Ki = 12 nM 6OX C29 H28 Cl2 F2 N2 O4 S CC(C)(c1cn....
42 3KFC ic50 = 2.8 nM 61X C23 H16 F3 N O3 S CS(=O)(=O)....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 3WF; Similar ligands found: 12
No: Ligand ECFP6 Tc MDL keys Tc
1 3WF 1 1
2 7EE 0.646341 0.795455
3 EST 0.546667 0.942857
4 J3Z 0.519481 0.833333
5 ESL 0.506329 0.868421
6 EZT 0.505263 0.829268
7 ESZ 0.493827 0.794872
8 6WV 0.455556 0.704545
9 6WM 0.434783 0.837838
10 HE7 0.431579 0.804878
11 6WN 0.430108 0.769231
12 7FQ 0.425532 0.756098
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1M13; Ligand: HYF; Similar sites found with APoc: 367
This union binding pocket(no: 1) in the query (biounit: 1m13.bio1) has 32 residues
No: Leader PDB Ligand Sequence Similarity
1 2YLD CMO None
2 5NNT DPV None
3 4F4S EFO None
4 1UO4 PIH None
5 1UO5 PIH None
6 6CS9 PIO None
7 1N8V BDD None
8 2VWA PTY None
9 4WG0 CHD None
10 1TUK PGM None
11 1FK5 OLA None
12 3L1N PLM 1.03093
13 3AQT RCO 1.22449
14 6B21 C9V 1.26582
15 4OKD GLC GLC GLC 1.26582
16 5U83 ZN8 1.41509
17 5NM7 GLY 1.50376
18 4YMX ARG 1.53846
19 3X01 AMP 1.58228
20 3B99 U51 1.58228
21 4JZX 476 1.58228
22 3CL5 SIO 1.58228
23 6H8S FSZ 1.66113
24 1M1B SPV 1.69492
25 4MNS 2AX 1.88679
26 1R6N 434 1.89573
27 3E70 GDP 1.89873
28 4YUS FMN 1.89873
29 2XN3 ID8 1.89873
30 3HYW DCQ 1.89873
31 5AHS COA 1.89873
32 4V1T ADP 1.89873
33 1RVV INI 1.94805
34 4RW3 PLM 1.98676
35 4RW3 TDA 1.98676
36 3KU0 ADE 1.99203
37 2XIG CIT 2
38 4RHP PEF 2.12766
39 1RL4 BL5 2.12766
40 3EWK FAD 2.20264
41 1E4I NFG 2.21519
42 3EBL GA4 2.21519
43 4D1J DGJ 2.21519
44 5MBC FMN 2.21519
45 5B0I BOG 2.21519
46 4P42 PEE 2.21519
47 4BVM VCA 2.25564
48 3P9T TCL 2.28311
49 1XZ3 ICF 2.29885
50 3LE7 ADE 2.29885
51 3OQJ 3CX 2.33463
52 6BMM OLB 2.38908
53 5F5N 5VD 2.42215
54 5XJ7 87O 2.48756
55 2HHP FLC 2.53165
56 3BJC WAN 2.53165
57 1Q7E MET 2.53165
58 1ZPD CIT 2.53165
59 4XRZ SI6 2.53165
60 3JUQ AJD 2.7027
61 3JUQ AKD 2.7027
62 3GXO MQA 2.71003
63 1GEG GLC 2.73438
64 3W54 RNB 2.8481
65 3TDC 0EU 2.8481
66 4DS8 A8S 2.8481
67 2ZJF BSU 2.8481
68 4LIT AKG 2.8481
69 5N8V KZZ 2.89855
70 5FQK 6NT 2.97398
71 4UCC ZKW 3.00429
72 1AUA BOG 3.04054
73 3I7S PYR 3.08219
74 3IX9 MTX 3.15789
75 2RH1 CLR 3.16456
76 6BR9 6OU 3.16456
77 1J78 OLA 3.16456
78 2UW1 GVM 3.16456
79 5IM3 DTP 3.16456
80 2O1V ADP 3.16456
81 3D9F FAD 3.16456
82 6BR9 PGV 3.16456
83 3D9F N6C 3.16456
84 1UBY DMA 3.16456
85 2BP1 FLC 3.33333
86 4BTB PRO PRO PRO PRO PRO PRO PRO PRO PRO 3.34728
87 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 3.40136
88 4DE3 DN8 3.42205
89 2BHW NEX 3.44828
90 4QO5 NAG 3.48101
91 3HP9 CF1 3.48101
92 4AIG FLX 3.48259
93 6AYH C3G 3.48259
94 5V3Y 5V8 3.4965
95 4V3I ASP LEU THR ARG PRO 3.50195
96 2CIX CEJ 3.67893
97 4NYT PC 3.68664
98 5V4R MGT 3.7037
99 2QX0 PH2 3.77358
100 1EWF PC1 3.79747
101 5Z9S BGC 3.79747
102 2QES ADE 3.83142
103 3B6C SDN 3.84615
104 5C1M OLC 4
105 1ZGA HMK 4.11392
106 1VR0 3SL 4.11392
107 3TKY N7I 4.11392
108 4BH1 SIA GAL NAG 4.21687
109 1JGS SAL 4.34783
110 2ALG DAO 4.34783
111 5OLK DTP 4.4186
112 3B9Z CO2 4.43038
113 1YKD CMP 4.43038
114 1EYQ NAR 4.5045
115 5XXH E0D 4.51128
116 1T0S BML 4.65116
117 4G86 BNT 4.74684
118 2HZL PYR 4.74684
119 2Q8G AZX 4.74684
120 6DIO CIT 4.74684
121 3NB0 G6P 4.74684
122 4KCF AKM 4.74684
123 3B96 MYA 4.74684
124 1XIM XYL 4.74684
125 3JRS A8S 4.80769
126 5UC9 MYR 4.86726
127 4DOO DAO 4.87805
128 6FS8 E4Z 4.87805
129 3DFR MTX 4.93827
130 5W7B MYR 4.96454
131 1DTL BEP 4.96894
132 5AZC PGT 5
133 6AYI C3G 5.02513
134 1TV5 N8E 5.06329
135 4MRP GSH 5.06329
136 4URX FK1 5.06329
137 5KLP IHP 5.06329
138 1TMX HGX 5.11945
139 2QJY UQ2 5.20446
140 4URN NOV 5.33333
141 5OSW DIU 5.37975
142 6BVK EAV 5.38922
143 6BVM EBV 5.38922
144 6BVJ EAS 5.38922
145 6BVL EBY 5.38922
146 6BVI EC4 5.38922
147 6CB2 OLC 5.46075
148 2WTN FER 5.6962
149 3HR1 PF9 5.6962
150 5HC0 NPO 5.6962
151 1NF8 BOG 5.7971
152 4HBM 0Y7 5.83333
153 5O22 C3R 5.88235
154 4DO1 ANN 6.01266
155 5N26 CPT 6.04396
156 1UCD U5P 6.31579
157 6AP8 BNY 6.3197
158 1SO2 666 6.32911
159 3ROE THM 6.41509
160 2IYG FMN 6.45161
161 4XCP PLM 6.47059
162 3MBG FAD 6.47482
163 2BYC FMN 6.56934
164 1YRX FMN 6.61157
165 5K53 STE 6.64557
166 5LWY OLB 6.72269
167 2OZ5 7XY 6.75676
168 4WGF HX2 6.82927
169 2CB8 MYA 6.89655
170 3KO0 TFP 6.93069
171 6D28 NEC 6.95971
172 1A05 IPM 6.96203
173 3H55 GLA 6.96203
174 3BKR PLM 7.14286
175 4O4Z N2O 7.14286
176 1YC4 43P 7.19697
177 1OQC FAD 7.2
178 3O55 FAD 7.2
179 3V78 ET 7.21154
180 3CV2 COA 7.27848
181 6BR8 6OU 7.27848
182 4YSX E23 7.27848
183 6BR8 PGV 7.27848
184 2VPY PCI 7.27848
185 4OAS 2SW 7.29167
186 4R29 SAM 7.58929
187 1GVE CIT 7.59494
188 5TVI MYR 7.6087
189 2GWH PCI 7.71812
190 4P3H 25G 7.77202
191 5C9J DAO 8.08081
192 5C9J STE 8.08081
193 5LX9 OLB 8.09859
194 1B4N GUA 8.22785
195 1RV1 IMZ 8.23529
196 4LWU 20U 8.23529
197 4RYV ZEA 8.3871
198 2HFN FMN 8.49673
199 3ETG GTP 8.5443
200 4X6F 3XU 8.57143
201 5UC4 83S 8.63636
202 5CHR 4NC 8.75912
203 1MID LAP 8.79121
204 2O1O RIS 8.86076
205 3RMK BML 8.86076
206 1POC GEL 8.95522
207 2WOR 2AN 9
208 4RJD TFP 9.09091
209 5WL1 CUY 9.09091
210 3HUJ AGH 9.09091
211 1I0B PEL 9.17722
212 3KP6 SAL 9.27152
213 1NU4 MLA 9.27835
214 1X8D RNS 9.61539
215 2GBB CIT 9.61539
216 1X0P FAD 9.79021
217 4KU7 PCG 9.80392
218 1ZED PNP 9.81013
219 3RUG DB6 10.101
220 3SCM LGN 10.101
221 1XMU ROF 10.1266
222 3WBG 2AN 10.4575
223 6GMN F4E 10.5769
224 1MT1 AG2 10.6195
225 1N13 AG2 10.6195
226 2QQD AG2 10.7143
227 2QQC AG2 10.7143
228 5WGD EST 11.1111
229 5WGQ EST 11.1111
230 5JAX 6J7 11.1111
231 4PEG 5GP 11.3924
232 5DXE EST 11.4943
233 5DXG EST 11.4943
234 4V1F BQ1 11.6279
235 2QZO KN1 11.6279
236 2QA8 GEN 11.6279
237 2D5X L35 11.6438
238 5X3R 7Y3 11.7073
239 4MGD 27N 11.7647
240 4TUZ 36J 11.7647
241 4MG8 27J 11.7647
242 4MGB XDH 11.7647
243 4MG7 27H 11.7647
244 4MG9 27K 11.7647
245 4MGA 27L 11.7647
246 5HZ9 5M8 11.8519
247 5OCA 9QZ 11.9048
248 5AAV GW5 11.9048
249 4TV1 36M 11.9522
250 2QE4 JJ3 12.0968
251 1YRO UDP 12.1951
252 5MWE TCE 12.8571
253 3WYJ H78 13.0435
254 4V2O CLQ 13.4146
255 4RC8 STE 13.5135
256 2BCG GER 13.5922
257 3WFD AXO 13.6986
258 5U9J GER 14.2012
259 3F8C HT1 14.2857
260 2ZSH GA3 14.5455
261 1PZ4 PLM 14.6552
262 4UYF 73B 14.9351
263 5L7G 6QE 15.4098
264 5MWY YNU 15.4098
265 5L7G LYS SER LEU LEU GLN GLN LEU LEU THR GLU 15.4098
266 1LNX URI 16.0494
267 4UDB CV7 17.2794
268 1XVB 3BR 17.6471
269 3ZKN WZV 17.6471
270 5ZQ4 AMP 17.9487
271 2Y69 CHD 18.3432
272 2V5E SCR 19.802
273 1HBK MYR 20.2247
274 2YJD YJD 20.4167
275 4J26 EST 20.4167
276 3OLL EST 20.4167
277 4J24 EST 20.4167
278 2BJ4 OHT 20.5696
279 5Z84 CHD 21.0884
280 5W97 CHD 21.0884
281 5ZCO CHD 21.0884
282 5ZCO PGV 21.0884
283 5G5W R8C 21.4286
284 1NHZ 486 21.4286
285 2HJ3 FAD 21.6
286 5Y02 HBX 22.4299
287 1SR7 MOF 23.166
288 4OAR 2S0 23.2558
289 4E2J MOF 23.6
290 4LSJ LSJ 23.6434
291 3GN8 DEX 23.6948
292 5UFS 1TA 23.7903
293 4P6X HCY 23.9216
294 5XJD 87L 24.0909
295 1M2Z DEX 24.1245
296 1M2Z BOG 24.1245
297 4P6W MOF 25
298 4OGQ 7PH 25.8065
299 4OGQ SQD 25.8065
300 4OGQ 1O2 25.8065
301 4OGQ UMQ 25.8065
302 3RY9 1CA 26
303 3V49 PK0 27.0677
304 2Q1H AS4 27.2
305 2AX9 BHM 28.125
306 5UC1 486 28.3784
307 3GYT DL4 28.6885
308 5HYR EST 29.7468
309 6FX0 E9T 29.7468
310 3SP6 IL2 29.8246
311 1HG4 LPP 30.1075
312 1G2N EPH 30.6818
313 2NPA MMB 31.1111
314 2E2R 2OH 31.1475
315 1N4H REA 32.0463
316 4QJR PIZ 33.8776
317 1YOK P6L 33.9844
318 3ET3 ET1 34.2466
319 1ZDT PEF 34.4398
320 1N83 CLR 34.8148
321 6AD9 KK4 34.8432
322 1YUC EPH 34.902
323 1YMT DR9 34.9594
324 1PZL MYR 35.0211
325 3JZB 4HY 35.206
326 3T03 3T0 35.2113
327 3B1M KRC 35.3357
328 4HEE 14R 35.461
329 1RDT 570 35.5372
330 1RDT L79 35.5372
331 2LBD REA 35.5805
332 1N46 PFA 35.6589
333 3KMZ EQO 35.7143
334 1YP0 PEF 35.9833
335 3FS1 ALA ALA LEU ALA ALA LEU LEU ALA ALA 36.087
336 3FS1 MYR 36.087
337 2P4Y C03 36.1011
338 5UNJ RJW 36.3265
339 1ZDU P3A 36.3265
340 5DX3 EST 36.3985
341 4S15 4D8 36.7188
342 5TWO 7MV 36.7647
343 1FM9 570 36.7647
344 1FM9 9CR 36.7647
345 3FUR Z12 36.7647
346 2R40 20E 36.8421
347 2R40 EPH 36.8421
348 4POJ 2VP 37.2294
349 3GZ9 D32 37.9182
350 5NI5 8YB 38.1944
351 1XAP TTB 38.2022
352 5K13 6Q7 38.6179
353 3L0E G58 38.7352
354 6ESN BWE 40.0749
355 1DKF BMS 40.4255
356 1FCZ 156 40.4255
357 1DKF OLA 40.4255
358 4WPF 3SN 40.5303
359 3FAL LO2 40.6015
360 3FAL REA 40.6015
361 3KFC 61X 41.1067
362 5NTW 98N 41.2451
363 5NTP 98E 42.0168
364 5IXK 6EW 42.5439
365 3OKI OKI 44.6352
366 6A5Y 9R0 46.4912
367 6A5Y 9CR 46.4912
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