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Receptor
PDB id Resolution Class Description Source Keywords
4M8E 2.4 Å NON-ENZYME: TRANSCRIPT_TRANSLATE CRYSTAL STRUCTURE OF HUMAN RETINOID X RECEPTOR ALPHA-LIGAND DOMAIN COMPLEX WITH (S) 4-METHYL 9CUAB30 COACTIVATOR PEPTID HOMO SAPIENS ANTIPARALLEL SANDWICH LIGAND BINDING COACTIVATOR BINDING DIMERIZATION ACTIVATION FUNCTION TRANSCRIPTION NUCLEAR RLIGAND BINDING DOMIAN LIGAND BINDING POCKET COACTIVATOR BSITE CANCER 4-METHYL 9CUAB30 ((2E4E6Z8E)-8-[(4-prime S)METHYDIHYDRO-1-prime (2-prime H)-NAPHTHALEN-1-prime -YLIDENE]-37-DIMETHYL-246- OCTATRIENOIC ACID)
Ref.: METHYL-SUBSTITUTED CONFORMATIONALLY CONSTRAINED REX AGONISTS FOR THE RETINOID X RECEPTORS DEMONSTRATE I EFFICACY FOR CANCER THERAPY AND PREVENTION. BIOORG.MED.CHEM. V. 22 178 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
29V A:500;
Valid;
none;
Kd = 13 nM
310.43 C21 H26 O2 C[C@H...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4M8E 2.4 Å NON-ENZYME: TRANSCRIPT_TRANSLATE CRYSTAL STRUCTURE OF HUMAN RETINOID X RECEPTOR ALPHA-LIGAND DOMAIN COMPLEX WITH (S) 4-METHYL 9CUAB30 COACTIVATOR PEPTID HOMO SAPIENS ANTIPARALLEL SANDWICH LIGAND BINDING COACTIVATOR BINDING DIMERIZATION ACTIVATION FUNCTION TRANSCRIPTION NUCLEAR RLIGAND BINDING DOMIAN LIGAND BINDING POCKET COACTIVATOR BSITE CANCER 4-METHYL 9CUAB30 ((2E4E6Z8E)-8-[(4-prime S)METHYDIHYDRO-1-prime (2-prime H)-NAPHTHALEN-1-prime -YLIDENE]-37-DIMETHYL-246- OCTATRIENOIC ACID)
Ref.: METHYL-SUBSTITUTED CONFORMATIONALLY CONSTRAINED REX AGONISTS FOR THE RETINOID X RECEPTORS DEMONSTRATE I EFFICACY FOR CANCER THERAPY AND PREVENTION. BIOORG.MED.CHEM. V. 22 178 2014
Members (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 291 families.
1 4M8E Kd = 13 nM 29V C21 H26 O2 C[C@H]1CC/....
2 3OZJ - BGV C17 H20 O5 C[C@@H]1C[....
3 5MK4 - I5W C22 H18 O3 Cc1ccc(cc1....
4 5EC9 - 5LO C26 H30 O3 CC1(CCC(c2....
5 3OAP Kd = 14 nM REA C20 H28 O2 CC1=C(C(CC....
6 4M8H Kd = 25 nM R4M C21 H26 O2 C[C@@H]1CC....
7 5MKU - J57 C18 H18 O3 CC(C)c1ccc....
70% Homology Family (30)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 247 families.
1 2P1T - 3TN C24 H28 O4 CC1(CCC(c2....
2 4OC7 - 2QO C18 H16 O3 C=CCc1cccc....
3 5MJ5 - 7O0 C22 H18 O3 c1ccc(cc1)....
4 4RMD Kd = 35 nM 3SW C24 H34 O2 CC(C)CCC1=....
5 4K4J - 1O8 C20 H22 O2 C/C(=CC(=O....
6 4PP5 Kd = 18 nM 2W0 C21 H24 O2 Cc1cccc2c1....
7 4PP3 Kd = 15 nM 2VZ C21 H24 O2 Cc1ccc2c(c....
8 4POH Kd = 10 nM 2VR C21 H24 O2 Cc1cccc2c1....
9 2P1U - 4TN C25 H30 O4 CCOc1cc2c(....
10 1MV9 - HXA C22 H32 O2 CCC=C/CC=C....
11 4RFW Kd = 9 nM 3RB C21 H24 O2 C/C(=CC(=O....
12 3FUG - 2E3 C24 H28 O3 Cc1cc2c(cc....
13 3E94 - TBY C12 H27 Sn CCCC[Sn](C....
14 4POJ Kd = 8 nM 2VP C21 H24 O2 Cc1ccc2c(c....
15 4K6I - 9RA C24 H28 O2 Cc1cc2c(cc....
16 2P1V - 5TN C26 H32 O4 CCCOc1cc2c....
17 4ZSH Kd = 90 nM 4XW C20 H36 O2 C[C@H]1CC=....
18 3KWY - T9T C18 H15 Sn c1ccc(cc1)....
19 4RME Kd = 9 nM 3T2 C24 H36 O2 CC(C)CCC1=....
20 1MZN - BM6 C24 H27 O4 CC1(CCC(c2....
21 1MVC - BM6 C24 H27 O4 CC1(CCC(c2....
22 5LYQ - 7BE C26 H30 O4 CC1(CCC(c2....
23 1XIU - REA C20 H28 O2 CC1=C(C(CC....
24 4M8E Kd = 13 nM 29V C21 H26 O2 C[C@H]1CC/....
25 3OZJ - BGV C17 H20 O5 C[C@@H]1C[....
26 5MK4 - I5W C22 H18 O3 Cc1ccc(cc1....
27 5EC9 - 5LO C26 H30 O3 CC1(CCC(c2....
28 3OAP Kd = 14 nM REA C20 H28 O2 CC1=C(C(CC....
29 4M8H Kd = 25 nM R4M C21 H26 O2 C[C@@H]1CC....
30 5MKU - J57 C18 H18 O3 CC(C)c1ccc....
50% Homology Family (30)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 209 families.
1 2P1T - 3TN C24 H28 O4 CC1(CCC(c2....
2 4OC7 - 2QO C18 H16 O3 C=CCc1cccc....
3 5MJ5 - 7O0 C22 H18 O3 c1ccc(cc1)....
4 4RMD Kd = 35 nM 3SW C24 H34 O2 CC(C)CCC1=....
5 4K4J - 1O8 C20 H22 O2 C/C(=CC(=O....
6 4PP5 Kd = 18 nM 2W0 C21 H24 O2 Cc1cccc2c1....
7 4PP3 Kd = 15 nM 2VZ C21 H24 O2 Cc1ccc2c(c....
8 4POH Kd = 10 nM 2VR C21 H24 O2 Cc1cccc2c1....
9 2P1U - 4TN C25 H30 O4 CCOc1cc2c(....
10 1MV9 - HXA C22 H32 O2 CCC=C/CC=C....
11 4RFW Kd = 9 nM 3RB C21 H24 O2 C/C(=CC(=O....
12 3FUG - 2E3 C24 H28 O3 Cc1cc2c(cc....
13 3E94 - TBY C12 H27 Sn CCCC[Sn](C....
14 4POJ Kd = 8 nM 2VP C21 H24 O2 Cc1ccc2c(c....
15 4K6I - 9RA C24 H28 O2 Cc1cc2c(cc....
16 2P1V - 5TN C26 H32 O4 CCCOc1cc2c....
17 4ZSH Kd = 90 nM 4XW C20 H36 O2 C[C@H]1CC=....
18 3KWY - T9T C18 H15 Sn c1ccc(cc1)....
19 4RME Kd = 9 nM 3T2 C24 H36 O2 CC(C)CCC1=....
20 1MZN - BM6 C24 H27 O4 CC1(CCC(c2....
21 1MVC - BM6 C24 H27 O4 CC1(CCC(c2....
22 5LYQ - 7BE C26 H30 O4 CC1(CCC(c2....
23 1XIU - REA C20 H28 O2 CC1=C(C(CC....
24 4M8E Kd = 13 nM 29V C21 H26 O2 C[C@H]1CC/....
25 3OZJ - BGV C17 H20 O5 C[C@@H]1C[....
26 5MK4 - I5W C22 H18 O3 Cc1ccc(cc1....
27 5EC9 - 5LO C26 H30 O3 CC1(CCC(c2....
28 3OAP Kd = 14 nM REA C20 H28 O2 CC1=C(C(CC....
29 4M8H Kd = 25 nM R4M C21 H26 O2 C[C@@H]1CC....
30 5MKU - J57 C18 H18 O3 CC(C)c1ccc....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 29V; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 29V 1 1
2 R4M 0.621622 0.833333
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4M8E; Ligand: 29V; Similar sites found with APoc: 332
This union binding pocket(no: 1) in the query (biounit: 4m8e.bio1) has 25 residues
No: Leader PDB Ligand Sequence Similarity
1 2WOR 2AN None
2 4RJD TFP None
3 4V2O CLQ None
4 5BV6 35G None
5 6D28 NEC None
6 4WGF HX2 None
7 4IBF 1D5 None
8 1MFI FHC None
9 1JX6 AI2 None
10 5ET3 60C None
11 6BKL EU7 None
12 3L1N PLM None
13 5N8V KZZ None
14 6BKL RIM None
15 2PFC PLM None
16 5TVI O8N None
17 4IN9 SER TRP PHE PRO 1.20482
18 1RL4 BRR 1.59574
19 4P86 5GP 1.63934
20 5YW5 ADE 1.67598
21 2BHW NEX 1.7316
22 5V13 JH3 1.7316
23 4OR7 25U 1.81818
24 3PMD 11A 1.96078
25 3R9C ECL 2.1645
26 6C1R EFD 2.1645
27 4WX0 HXD 2.1645
28 3ZQE DXC 2.1645
29 5B0I BOG 2.1645
30 3LE7 ADE 2.1645
31 3CEV ARG 2.1645
32 6EWZ GTP 2.1645
33 5M37 9SZ 2.17391
34 5M36 9SZ 2.18341
35 2HJ9 AI2 2.26244
36 3R77 QLI 2.39234
37 4DOO DAO 2.43902
38 3AQT RCO 2.5974
39 1YC4 43P 2.5974
40 5DEY 59T 2.5974
41 4F06 PHB 2.5974
42 2CDC XYS 2.5974
43 4MC3 28U 2.5974
44 4G2R H1L 2.5974
45 4QEK GLC 2.5974
46 2BP1 FLC 2.5974
47 3GUZ PAF 2.84091
48 1A05 IPM 3.0303
49 5J32 IPM 3.0303
50 2CIX CEJ 3.0303
51 5LNW HG3 3.0303
52 6A0S NDP 3.0303
53 5LNW RP5 3.0303
54 3RWP ABQ 3.0303
55 6FK6 DOK 3.0303
56 3LXI CAM 3.0303
57 5C9P FUC 3.0303
58 1XMY ROL 3.0303
59 3THR C2F 3.0303
60 1ZPD CIT 3.0303
61 4QGE 35O 3.0303
62 1DE6 RNS 3.0303
63 5WS9 ATP 3.0303
64 5C1M OLC 3.2
65 5C1M CLR 3.2
66 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 3.4632
67 4V3I ASP LEU THR ARG PRO 3.4632
68 3HYW DCQ 3.4632
69 4NKW PLO 3.4632
70 4N6H EJ4 3.4632
71 1VRP IOM 3.4632
72 1U6R IOM 3.4632
73 1CZA ADP 3.4632
74 3COW 52H 3.4632
75 2EA1 GPG 3.4632
76 5B4B LP5 3.4632
77 2RH1 CLR 3.4632
78 1Q9I FAD 3.4632
79 1Q9I TEO 3.4632
80 1SBR VIB 3.5
81 5IUY BOG 3.53201
82 4RYV ZEA 3.87097
83 5C9J DAO 3.8961
84 5VRH OLB 3.8961
85 5AZC PGT 3.8961
86 1HFU NAG NDG 3.8961
87 5V3Y 5V8 3.8961
88 2QCX PF1 3.8961
89 3WQM B29 3.8961
90 5VRH OLC 3.8961
91 1D4D SIN 3.8961
92 3W5N RAM 3.8961
93 1TO9 HMH 3.8961
94 1ZDQ MSM 3.8961
95 2XEM SSV 4
96 4R29 SAM 4.01786
97 6MVU K4V 4.04172
98 5W7B MYR 4.25532
99 3FXU TSU 4.2623
100 4EKQ NPO 4.27807
101 3X01 AMP 4.3257
102 1IQ7 NAG 4.329
103 6F5W KG1 4.329
104 1E4I NFG 4.329
105 4KIB 56D 4.329
106 3TKY N7I 4.329
107 2OCI TYC 4.329
108 1MRH FMC 4.329
109 5DRB 5FJ 4.329
110 5OLK DTP 4.329
111 5CX8 TG6 4.329
112 2ALG DAO 4.34783
113 6BSX E7S 4.49438
114 1UGX GAL MGC 4.51128
115 3ZJQ NCA 4.61538
116 6BR8 6OU 4.7619
117 1TV5 N8E 4.7619
118 4UMJ BFQ 4.7619
119 2D09 FLV 4.7619
120 6D5H FV7 4.7619
121 6D5L FW7 4.7619
122 6D5M FW4 4.7619
123 6D5J FV4 4.7619
124 6D5E FVG 4.7619
125 6D56 FVM 4.7619
126 6BR8 PGV 4.7619
127 6D59 FVJ 4.7619
128 1SQL GUN 4.79452
129 5UC9 MYR 4.86726
130 3D78 NBB 5.04202
131 2BYC FMN 5.10949
132 2GBB CIT 5.12821
133 1T0S BML 5.19481
134 6DIO CIT 5.19481
135 3B9Z CO2 5.19481
136 3B99 U51 5.19481
137 2JAJ D20 5.19481
138 3DZT EAH 5.19481
139 4XU6 TDA 5.2381
140 5C79 PBU 5.33333
141 3G4Q MCH 5.47945
142 4G9N NGA 5.59441
143 6BJO DUY 5.6
144 1HBK MYR 5.61798
145 2HZL PYR 5.62771
146 5OKL PAM 5.62771
147 3R9V DXC 5.62771
148 5OSW DIU 5.62771
149 2B7N NTM 5.62771
150 5YAS FAC 5.62771
151 3N75 G4P 5.62771
152 4LHD GLY 5.62771
153 4IA6 EIC 5.62771
154 5WL1 CUY 5.62771
155 4OUJ LBT 5.62771
156 4O4Z N2O 5.84416
157 2VWA PTY 5.94059
158 5CX6 CDP 6.06061
159 2Z49 AMG 6.06061
160 5Z3I ADE 6.06061
161 2Z48 NGA 6.06061
162 2ZE3 AKG 6.06061
163 5LX9 OLB 6.06061
164 3O01 DXC 6.06061
165 4XCP PLM 6.06061
166 3D9F N6C 6.06061
167 4RGA 3PV 6.06061
168 2WDQ CBE 6.08696
169 6GMN F4E 6.18557
170 3RLB VIB 6.25
171 4DE3 DN8 6.49351
172 4MRP GSH 6.49351
173 4RW3 TDA 6.49351
174 1EWF PC1 6.49351
175 4BTB PRO PRO PRO PRO PRO PRO PRO PRO PRO 6.49351
176 2JAP J01 6.49351
177 1XX4 BAM 6.49351
178 5CQG 55C 6.49351
179 3NJQ NJQ 6.73575
180 5V4R MGT 6.79012
181 2CB8 MYA 6.89655
182 1XZ3 ICF 6.89655
183 3HP9 CF1 6.92641
184 3A51 VDY 6.92641
185 6AP8 BNY 6.92641
186 3KU0 ADE 6.92641
187 2VPY PCI 6.92641
188 3TFC PEP 6.92641
189 5I8F ML1 7.27273
190 4G86 BNT 7.35931
191 3G3N TC8 7.35931
192 2VL8 UDP 7.35931
193 1M2W MTL 7.35931
194 3EYK EYK 7.55814
195 4YSX E23 7.69231
196 2BCG GER 7.76699
197 3GL0 HXX 7.79221
198 2PZI AXX 7.79221
199 3RET SAL 7.92079
200 3RET PYR 7.92079
201 3E3U NVC 8.12183
202 1HGX 5GP 8.19672
203 5FPN KYD 8.22511
204 1ZED PNP 8.22511
205 3GFZ FMN 8.22511
206 3ZOK GLY 8.22511
207 4URN NOV 8.44444
208 4MUV PCG 8.4507
209 3W54 RNB 8.65801
210 3NB0 G6P 8.65801
211 3CHT 4NB 8.65801
212 5W6Y TRP 8.65801
213 4BHL ARG 8.65801
214 5OCA 9QZ 8.73016
215 3TL1 JRO 8.80503
216 1BWO LPC 8.88889
217 2VQ5 HBA 8.95522
218 3RV5 DXC 8.98876
219 2UW1 GVM 9.09091
220 5LWY OLB 9.34579
221 1VC9 ATP 9.52381
222 1SO0 GAL 9.52381
223 1BRW URA 9.52381
224 4YFY 0FX 9.52381
225 2XCM ADP 9.78261
226 4ZGM 32M 9.83607
227 5N26 CPT 9.89011
228 2ZJ5 ADP 9.95671
229 1Y75 NAG 10.1695
230 5FLJ QUE 10.2151
231 2HHP FLC 10.3896
232 6CB2 OLC 10.3896
233 1NF8 BOG 10.628
234 2ATJ BHO 10.8225
235 3PMA SCR 10.8225
236 5KOD IAC 11.2554
237 4DXJ 0M9 11.2554
238 5IM3 DTP 11.2554
239 5N5U 7N8 11.6883
240 2QLX RM4 12.037
241 2JHP GUN 12.1212
242 1FX8 BOG 12.5541
243 4W9N TCL 12.5541
244 5OCM 9RH 12.5541
245 1DTL BEP 13.0435
246 5UGW GSH 13.1429
247 2QJY UQ2 13.4199
248 2YOO K2B 13.4199
249 3N7S 3N7 14.5833
250 1XVB 3BR 14.7059
251 2CHT TSA 14.9606
252 2VDY HCY 15.1515
253 4WT2 3UD 15.2381
254 1L0I PSR 15.3846
255 2YLD CMO 15.748
256 5UC4 83S 15.9091
257 3B6R CRN 16.0173
258 5MTE BB2 16.7883
259 3KO0 TFP 16.8317
260 1ZEI CRS 16.9811
261 3WBG 2AN 16.9935
262 4HDK 13X 17.316
263 2XN3 ID8 17.5
264 5CKS GAL 17.7489
265 5MWE TCE 18.5185
266 4V1F BQ1 18.6047
267 1MID LAP 18.6813
268 5Y02 HBX 18.6916
269 5Y02 MXN 18.6916
270 1RV1 IMZ 18.8235
271 2XN5 FUN 20
272 5Z84 CHD 20.1835
273 5ZCO CHD 20.1835
274 5W97 CHD 20.1835
275 2D5X L35 21.2329
276 2Y69 CHD 22.8571
277 5NTP 98E 23.3766
278 5APK 76E 23.3766
279 5NTW 98N 23.3766
280 5IXK 6EW 23.6842
281 4OGQ UMQ 24.1379
282 4OGQ 7PH 24.1379
283 5G5W R8C 24.2424
284 1NHZ 486 24.2424
285 3BQD DAY 27.2727
286 4LSJ LSJ 27.2727
287 1M2Z DEX 27.2727
288 4P6W MOF 27.2727
289 1M2Z BOG 27.2727
290 4P6X HCY 28.1385
291 3RY9 1CA 29.4372
292 4E2J MOF 29.4372
293 3GN8 DEX 29.4372
294 5UFS 1TA 29.4372
295 1SR7 MOF 29.8701
296 4OAR 2S0 29.8701
297 5UC1 486 30.1802
298 2Q1H AS4 32.9004
299 3OKI OKI 32.9004
300 3DCT 064 32.9004
301 3RUU 37G 33.1878
302 5ICK FEZ 33.1878
303 4S15 4D8 33.7662
304 1N46 PFA 33.7662
305 4OIV XX9 34.0708
306 3VRV YSD 34.1991
307 2O4J VD4 34.1991
308 5XPL 8C9 34.1991
309 4DK7 0KS 34.632
310 4Q0A 4OA 34.632
311 3JZB 4HY 35.0649
312 3L0E G58 35.9307
313 5MWY YNU 36.3636
314 5HCV 60R 36.3636
315 2A3I C0R 36.3636
316 3KFC 61X 36.3636
317 5L7G 6QE 36.7965
318 4UDB CV7 36.7965
319 3FUR Z12 38.5281
320 3V49 PK0 38.5281
321 2AX9 BHM 38.5281
322 3G9E RO7 38.5281
323 5K13 6Q7 42.4242
324 3KMZ EQO 42.4242
325 6FX0 E9T 42.4242
326 4J26 EST 42.8571
327 4J24 EST 42.8571
328 1YYE 196 42.8571
329 1U3R 338 42.8571
330 2I0G I0G 42.8571
331 1Q3A NGH 45.4545
332 5TWO 7MV 46.6667
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