Receptor
PDB id Resolution Class Description Source Keywords
2P1T 1.8 Å NON-ENZYME: TRANSCRIPT_TRANSLATE CRYSTAL STRUCTURE OF THE LIGAND BINDING DOMAIN OF THE RETINOID X RECEPTOR ALPHA IN COMPLEX WITH 3-(2'-METHOXY)- T ETRAHYDRONAPHTYL CINNAMIC ACID AND A FRAGMENT OF THE CO ACTIVATOR TIF-2 HOMO SAPIENS PROTEIN-LIGAND COMPLEX HORMONE RECEPTOR
Ref.: MODULATORS OF THE STRUCTURAL DYNAMICS OF THE RETINOID X RECEPTOR TO REVEAL RECEPTOR FUNCTION. PROC.NATL.ACAD.SCI.USA V. 104 17323 2007
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
3TN A:201;
Valid;
none;
submit data
380.477 C24 H28 O4 CC1(C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4POJ 2 Å NON-ENZYME: TRANSCRIPT_TRANSLATE CRYSTAL STRUCTURE OF HUMAN RETINOID X RECEPTOR ALPHA-LIGAND DOMAIN COMPLEX WITH 7-METHYL UAB30 AND THE COACTIVATOR PEPT HOMO SAPIENS LIGAND BINDING DOMAIN NUCLEAR RECEPTOR CANCER LIPID TOXICREXINOID 7-METHYL UAB30 TRANSCRIPTION
Ref.: METHYL SUBSTITUTION OF A REXINOID AGONIST IMPROVES AND REVEALS SITE OF LIPID TOXICITY. J.MED.CHEM. V. 57 5370 2014
Members (21)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 257 families.
1 2P1T - 3TN C24 H28 O4 CC1(CCC(c2....
2 4OC7 - 2QO C18 H16 O3 C=CCc1cccc....
3 4RMD Kd = 35 nM 3SW C24 H34 O2 CC(C)CCC1=....
4 4K4J - 1O8 C20 H22 O2 C/C(=CC(=O....
5 4PP5 Kd = 18 nM 2W0 C21 H24 O2 Cc1cccc2c1....
6 4PP3 Kd = 15 nM 2VZ C21 H24 O2 Cc1ccc2c(c....
7 4POH Kd = 10 nM 2VR C21 H24 O2 Cc1cccc2c1....
8 2P1U - 4TN C25 H30 O4 CCOc1cc2c(....
9 1MV9 - HXA C22 H32 O2 CCC=C/CC=C....
10 4RFW Kd = 9 nM 3RB C21 H24 O2 C/C(=CC(=O....
11 3FUG - 2E3 C24 H28 O3 Cc1cc2c(cc....
12 3E94 - TBY C12 H27 Sn CCCC[Sn](C....
13 4POJ Kd = 8 nM 2VP C21 H24 O2 Cc1ccc2c(c....
14 4K6I - 9RA C24 H28 O2 Cc1cc2c(cc....
15 2P1V - 5TN C26 H32 O4 CCCOc1cc2c....
16 4ZSH Kd = 90 nM 4XW C20 H36 O2 C[C@H]1CC=....
17 3KWY - T9T C18 H15 Sn c1ccc(cc1)....
18 4RME Kd = 9 nM 3T2 C24 H36 O2 CC(C)CCC1=....
19 1MZN - BM6 C24 H27 O4 CC1(CCC(c2....
20 1MVC - BM6 C24 H27 O4 CC1(CCC(c2....
21 5LYQ - 7BE C26 H30 O4 CC1(CCC(c2....
70% Homology Family (27)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 222 families.
1 2P1T - 3TN C24 H28 O4 CC1(CCC(c2....
2 4OC7 - 2QO C18 H16 O3 C=CCc1cccc....
3 4RMD Kd = 35 nM 3SW C24 H34 O2 CC(C)CCC1=....
4 4K4J - 1O8 C20 H22 O2 C/C(=CC(=O....
5 4PP5 Kd = 18 nM 2W0 C21 H24 O2 Cc1cccc2c1....
6 4PP3 Kd = 15 nM 2VZ C21 H24 O2 Cc1ccc2c(c....
7 4POH Kd = 10 nM 2VR C21 H24 O2 Cc1cccc2c1....
8 2P1U - 4TN C25 H30 O4 CCOc1cc2c(....
9 1MV9 - HXA C22 H32 O2 CCC=C/CC=C....
10 4RFW Kd = 9 nM 3RB C21 H24 O2 C/C(=CC(=O....
11 3FUG - 2E3 C24 H28 O3 Cc1cc2c(cc....
12 3E94 - TBY C12 H27 Sn CCCC[Sn](C....
13 4POJ Kd = 8 nM 2VP C21 H24 O2 Cc1ccc2c(c....
14 4K6I - 9RA C24 H28 O2 Cc1cc2c(cc....
15 2P1V - 5TN C26 H32 O4 CCCOc1cc2c....
16 4ZSH Kd = 90 nM 4XW C20 H36 O2 C[C@H]1CC=....
17 3KWY - T9T C18 H15 Sn c1ccc(cc1)....
18 4RME Kd = 9 nM 3T2 C24 H36 O2 CC(C)CCC1=....
19 1MZN - BM6 C24 H27 O4 CC1(CCC(c2....
20 1MVC - BM6 C24 H27 O4 CC1(CCC(c2....
21 5LYQ - 7BE C26 H30 O4 CC1(CCC(c2....
22 1XIU - REA C20 H28 O2 CC1=C(C(CC....
23 4M8E Kd = 13 nM 29V C21 H26 O2 C[C@H]1CC/....
24 3OZJ - BGV C17 H20 O5 C[C@@H]1C[....
25 5EC9 - 5LO C26 H30 O3 CC1(CCC(c2....
26 3OAP Kd = 14 nM REA C20 H28 O2 CC1=C(C(CC....
27 4M8H Kd = 25 nM R4M C21 H26 O2 C[C@@H]1CC....
50% Homology Family (27)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 185 families.
1 2P1T - 3TN C24 H28 O4 CC1(CCC(c2....
2 4OC7 - 2QO C18 H16 O3 C=CCc1cccc....
3 4RMD Kd = 35 nM 3SW C24 H34 O2 CC(C)CCC1=....
4 4K4J - 1O8 C20 H22 O2 C/C(=CC(=O....
5 4PP5 Kd = 18 nM 2W0 C21 H24 O2 Cc1cccc2c1....
6 4PP3 Kd = 15 nM 2VZ C21 H24 O2 Cc1ccc2c(c....
7 4POH Kd = 10 nM 2VR C21 H24 O2 Cc1cccc2c1....
8 2P1U - 4TN C25 H30 O4 CCOc1cc2c(....
9 1MV9 - HXA C22 H32 O2 CCC=C/CC=C....
10 4RFW Kd = 9 nM 3RB C21 H24 O2 C/C(=CC(=O....
11 3FUG - 2E3 C24 H28 O3 Cc1cc2c(cc....
12 3E94 - TBY C12 H27 Sn CCCC[Sn](C....
13 4POJ Kd = 8 nM 2VP C21 H24 O2 Cc1ccc2c(c....
14 4K6I - 9RA C24 H28 O2 Cc1cc2c(cc....
15 2P1V - 5TN C26 H32 O4 CCCOc1cc2c....
16 4ZSH Kd = 90 nM 4XW C20 H36 O2 C[C@H]1CC=....
17 3KWY - T9T C18 H15 Sn c1ccc(cc1)....
18 4RME Kd = 9 nM 3T2 C24 H36 O2 CC(C)CCC1=....
19 1MZN - BM6 C24 H27 O4 CC1(CCC(c2....
20 1MVC - BM6 C24 H27 O4 CC1(CCC(c2....
21 5LYQ - 7BE C26 H30 O4 CC1(CCC(c2....
22 1XIU - REA C20 H28 O2 CC1=C(C(CC....
23 4M8E Kd = 13 nM 29V C21 H26 O2 C[C@H]1CC/....
24 3OZJ - BGV C17 H20 O5 C[C@@H]1C[....
25 5EC9 - 5LO C26 H30 O3 CC1(CCC(c2....
26 3OAP Kd = 14 nM REA C20 H28 O2 CC1=C(C(CC....
27 4M8H Kd = 25 nM R4M C21 H26 O2 C[C@@H]1CC....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 3TN; Similar ligands found: 6
No: Ligand ECFP6 Tc MDL keys Tc
1 3TN 1 1
2 4TN 0.73913 0.868421
3 5TN 0.708333 0.825
4 2E3 0.652174 0.941176
5 FER 0.476923 0.657143
6 4FE 0.432836 0.657143
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4POJ; Ligand: 2VP; Similar sites found: 161
This union binding pocket(no: 1) in the query (biounit: 4poj.bio1) has 25 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4WGF HX2 0.01558 0.42369 None
2 4IBF 1D5 0.007413 0.41686 None
3 3L1N PLM 0.01823 0.41415 None
4 5BVT PAM 0.005396 0.40873 None
5 2PFC PLM 0.01637 0.40426 None
6 5CSD ACD 0.01139 0.40145 None
7 1RL4 BRR 0.01556 0.41773 1.59574
8 1TZD ADP 0.02229 0.41104 1.7316
9 2Q8H TF4 0.003048 0.44768 2.1645
10 4WX0 HXD 0.005484 0.41909 2.1645
11 3LE7 ADE 0.02602 0.40769 2.1645
12 4DOO DAO 0.01035 0.40294 2.43902
13 3AQT RCO 0.001063 0.48099 2.5974
14 5DEY 59T 0.004184 0.4326 2.5974
15 2BP1 FLC 0.02128 0.42106 2.5974
16 1O6U PLM 0.01438 0.4033 2.5974
17 3GUZ PAF 0.0164 0.42039 2.84091
18 1A05 IPM 0.004355 0.44832 3.0303
19 5J32 IPM 0.007108 0.43754 3.0303
20 1J78 OLA 0.0343 0.40855 3.0303
21 3QCQ 3Q0 0.03581 0.40629 3.0303
22 1XMY ROL 0.02147 0.40621 3.0303
23 3LXI CAM 0.03269 0.40238 3.0303
24 5LIA 6XN 0.03393 0.40017 3.0303
25 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 0.01175 0.44178 3.4632
26 4V3I ASP LEU THR ARG PRO 0.01031 0.43423 3.4632
27 3HYW DCQ 0.01034 0.42956 3.4632
28 1U6R IOM 0.019 0.40813 3.4632
29 1I0B PEL 0.02944 0.40565 3.4632
30 3G58 988 0.02065 0.4031 3.4632
31 4N6H EJ4 0.03227 0.40115 3.4632
32 5B4B LP5 0.008265 0.40042 3.4632
33 1SBR VIB 0.005351 0.44185 3.5
34 3KYQ DPV 0.0163 0.41669 3.51759
35 3IX9 MTX 0.01975 0.40032 3.68421
36 1HFU NAG NDG 0.01909 0.41468 3.8961
37 4UCC ZKW 0.007978 0.41028 3.8961
38 2QCX PF1 0.0278 0.40571 3.8961
39 2XEM SSV 0.006346 0.42846 4
40 2F2G HMH 0.04028 0.40033 4.0724
41 2ALG DAO 0.02733 0.40485 4.34783
42 1TV5 N8E 0.006394 0.43783 4.7619
43 4E28 9MZ 0.0296 0.40748 4.7619
44 4ORM 2V6 0.0257 0.4046 4.7619
45 4ORM FMN 0.0257 0.4046 4.7619
46 4ORM ORO 0.0257 0.4046 4.7619
47 1SQL GUN 0.01526 0.41893 4.79452
48 5UC9 MYR 0.01133 0.42032 4.86726
49 2BYC FMN 0.01656 0.4004 5.10949
50 3B9Z CO2 0.006303 0.45124 5.19481
51 3B99 U51 0.004531 0.43116 5.19481
52 1T0S BML 0.04561 0.40153 5.19481
53 3G4Q MCH 0.0162 0.40448 5.47945
54 3R1V AZB 0.00519 0.40171 5.51181
55 3R9V DXC 0.01983 0.41601 5.62771
56 4O4Z N2O 0.02672 0.40428 5.84416
57 2VWA PTY 0.02344 0.41347 5.94059
58 2ZE3 AKG 0.006841 0.43981 6.06061
59 5LX9 OLB 0.004158 0.42867 6.06061
60 4XCP PLM 0.02229 0.40692 6.06061
61 2WDQ CBE 0.02866 0.40578 6.08696
62 3RLB VIB 0.01737 0.40302 6.25
63 4RW3 TDA 0.01391 0.44274 6.49351
64 4MRP GSH 0.01206 0.42365 6.49351
65 4BTB PRO PRO PRO PRO PRO PRO PRO PRO PRO 0.01628 0.42305 6.49351
66 2JAP J01 0.01692 0.41148 6.49351
67 1XX4 BAM 0.01706 0.41145 6.49351
68 4QCK ASD 0.01456 0.40304 6.49351
69 4P3H 25G 0.001117 0.44221 6.73575
70 5V4R MGT 0.01465 0.43001 6.79012
71 2CB8 MYA 0.01374 0.42449 6.89655
72 3HP9 CF1 0.008425 0.43973 6.92641
73 2VPY PCI 0.03323 0.40048 6.92641
74 3TDC 0EU 0.01405 0.46364 7.35931
75 2VL8 UDP 0.00614 0.41315 7.35931
76 3EYK EYK 0.03069 0.42158 7.55814
77 3RET SAL 0.01109 0.40862 7.92079
78 3RET PYR 0.01109 0.40862 7.92079
79 3E3U NVC 0.01677 0.40014 8.12183
80 4URN NOV 0.03218 0.40121 8.44444
81 3W54 RNB 0.009967 0.40368 8.65801
82 5OCA 9QZ 0.008124 0.44155 8.73016
83 3TL1 JRO 0.01306 0.42169 8.80503
84 3RV5 DXC 0.00001241 0.49074 8.98876
85 1BRW URA 0.03221 0.40171 9.52381
86 2XCM ADP 0.01561 0.40161 9.78261
87 1DLL LAT 0.02384 0.40951 9.95671
88 2ZJ5 ADP 0.03322 0.40329 9.95671
89 1Y75 NAG 0.01461 0.41471 10.1695
90 2HHP FLC 0.00006656 0.61449 10.3896
91 1NF8 BOG 0.003031 0.4645 10.628
92 1NF8 ISC 0.01618 0.40451 10.628
93 3PMA SCR 0.02032 0.40401 10.8225
94 5HZ5 65X 0.003926 0.40503 11.194
95 2JHP GUN 0.02248 0.40853 12.1212
96 1DTL BEP 0.001772 0.45076 13.0435
97 2QJY UQ2 0.01459 0.4192 13.4199
98 3N7S 3N7 0.007027 0.4421 14.5833
99 1XVB 3BR 0.005179 0.43281 14.7059
100 2VDY HCY 0.02153 0.41201 15.1515
101 2YLD CMO 0.01377 0.42171 15.748
102 3B6R CRN 0.008497 0.40837 16.0173
103 3KO0 TFP 0.01 0.412 16.8317
104 3WBG 2AN 0.003779 0.42652 16.9935
105 5HZ9 5M8 0.004131 0.42474 19.2593
106 2XN5 FUN 0.0148 0.41029 20
107 5APK 76E 0.00002622 0.50129 23.3766
108 5NTW 98N 0.00008933 0.48266 23.3766
109 5IXK 6EW 0.0004381 0.45569 23.6842
110 4ZOM 4Q3 0.0001982 0.42822 24
111 5G5W R8C 0.0000005287 0.53553 24.2424
112 1NHZ 486 0.00001278 0.51097 24.2424
113 1M2Z DEX 0.0000003936 0.58675 27.2727
114 4P6W MOF 0.0000005675 0.56688 27.2727
115 4LSJ LSJ 0.000000218 0.56529 27.2727
116 3BQD DAY 0.0000003952 0.55311 27.2727
117 1M2Z BOG 0.004235 0.47206 27.2727
118 4P6X HCY 0.0000003241 0.55013 28.1385
119 3RY9 1CA 0.00000009007 0.63005 29.4372
120 3GN8 DEX 0.0000002492 0.59529 29.4372
121 4E2J MOF 0.0000001343 0.59275 29.4372
122 5UFS 1TA 0.0000009045 0.55851 29.4372
123 1SR7 MOF 0.0000001695 0.5985 29.8701
124 4OAR 2S0 0.000002273 0.55399 29.8701
125 2Q1H AS4 0.00000004262 0.57693 32.9004
126 3DCT 064 0.00007327 0.46781 32.9004
127 5ICK FEZ 0.0002579 0.47017 33.1878
128 3RUU 37G 0.00007923 0.44783 33.1878
129 4S15 4D8 0.000458 0.4507 33.7662
130 1N46 PFA 0.001122 0.43055 33.7662
131 3VRV YSD 0.0002653 0.48299 34.1991
132 2O4J VD4 0.0006567 0.4223 34.1991
133 4Q0A 4OA 0.001292 0.43942 34.632
134 4DK7 0KS 0.001314 0.4391 34.632
135 3JZB 4HY 0.001056 0.40879 35.0649
136 3L0E G58 0.0004069 0.42916 35.9307
137 5HCV 60R 0.00000008236 0.61597 36.3636
138 2A3I C0R 0.0000001919 0.5931 36.3636
139 3KFC 61X 0.000134 0.42574 36.3636
140 5L7G 6QE 0.000000003409 0.64363 36.7965
141 4UDB CV7 0.00000001466 0.61441 36.7965
142 1M13 HYF 0.00217 0.42611 37.2294
143 4B6C B5U 0.008816 0.4096 38.4615
144 3FUR Z12 0.00006763 0.50697 38.5281
145 3G9E RO7 0.000032 0.50623 38.5281
146 3V49 PK0 0.0000151 0.49607 38.5281
147 2AX9 BHM 0.000001697 0.44552 38.5281
148 5K13 6Q7 0.0001177 0.45719 42.4242
149 3KMZ EQO 0.0002509 0.43588 42.4242
150 4J26 EST 0.00000001883 0.68955 42.8571
151 4J24 EST 0.00000003542 0.67637 42.8571
152 1YYE 196 0.00000002253 0.67569 42.8571
153 2I0G I0G 0.00000004423 0.65283 42.8571
154 1U3R 338 0.000000001179 0.62231 42.8571
155 3KDU NKS 0.0001914 0.48926 46.1538
156 3SP6 IL2 0.0004812 0.45827 46.1538
157 3FEI CTM 0.001302 0.42449 46.1538
158 2W3L DRO 0.02123 0.41226 46.1538
159 5B25 4QJ 0.01481 0.40268 46.1538
160 5TWO 7MV 0.0002325 0.44025 46.6667
161 2PJL 047 0.004203 0.41008 48.583
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