Receptor
PDB id Resolution Class Description Source Keywords
1rdt 2.4 Å NON-ENZYME: SIGNAL_HORMONE CRYSTAL STRUCTURE OF A NEW REXINOID BOUND TO THE RXRALPHA LIGAND BINDING DOAMIN IN THE RXRALPHA/PPARGAMMA HETERODIMER HOMO SAPIENS HORMONE RECEPTOR POLYMORPHISM HORMONE/GROWTH FACTOR COMPLEX
Ref.: STRUCTURE-BASED DESIGN OF POTENT RETINOID X RECEPTOR ALPHA AGONISTS. J.MED.CHEM. V. 47 2010 2004
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
570 D:478;
Valid;
none;
submit data
546.612 C34 H30 N2 O5 Cc1c(...
L79 A:463;
Valid;
none;
Ki = 6 nM
378.504 C25 H30 O3 CC1(C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1RDT 2.4 Å NON-ENZYME: SIGNAL_HORMONE CRYSTAL STRUCTURE OF A NEW REXINOID BOUND TO THE RXRALPHA LIGAND BINDING DOAMIN IN THE RXRALPHA/PPARGAMMA HETERODIMER HOMO SAPIENS HORMONE RECEPTOR POLYMORPHISM HORMONE/GROWTH FACTOR COMPLEX
Ref.: STRUCTURE-BASED DESIGN OF POTENT RETINOID X RECEPTOR ALPHA AGONISTS. J.MED.CHEM. V. 47 2010 2004
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 224 families.
1 1RDT Ki = 6 nM L79 C25 H30 O3 CC1(CCC(c2....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 172 families.
1 1RDT Ki = 6 nM L79 C25 H30 O3 CC1(CCC(c2....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 145 families.
1 1RDT Ki = 6 nM L79 C25 H30 O3 CC1(CCC(c2....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 570; Similar ligands found: 4
No: Ligand ECFP6 Tc MDL keys Tc
1 570 1 1
2 GW4 0.733333 0.883333
3 544 0.657143 0.898305
4 MMB 0.40678 0.701493
Ligand no: 2; Ligand: L79; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 L79 1 1
Similar Binding Sites
Pocket no: 1; Query (leader) PDB : 1RDT; Ligand: 570; Similar sites found: 187
This union binding pocket (no: 1) in the query (biounit: 1rdt.bio1) has 20 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc)
1 1RDT 570 1.305e-16 1
2 1FM9 570 6.661e-16 0.99073
3 2P4Y C03 8.024e-12 0.86141
4 3G9E RO7 3.554e-12 0.84468
5 3LMP CEK 1.167e-11 0.82683
6 3KDU NKS 1.115e-10 0.7938
7 3B1M KRC 3.831e-10 0.76854
8 3GZ9 D32 1.53e-09 0.74826
9 2HFP NSI 1.372e-09 0.73806
10 3FEI CTM 4.126e-10 0.72074
11 2PRG BRL 1.404e-10 0.6736
12 1K7L 544 6.292e-09 0.66884
13 2NPA MMB 1.773e-09 0.66255
14 3SP6 IL2 1.831e-09 0.61547
15 2P54 735 2.784e-07 0.59347
16 3ET1 ET1 1.632e-08 0.58831
17 2B1Z 17M 3.252e-05 0.51742
18 3H0A D30 1.639e-05 0.51634
19 1SR7 MOF 0.0001211 0.49716
20 3KFC 61X 0.0001596 0.49656
21 3OKI OKI 0.0002225 0.49424
22 2QE4 JJ3 0.0004393 0.48174
23 3BEJ MUF 5.444e-05 0.47807
24 3VHU SNL 0.0004709 0.46133
25 2AX9 BHM 0.002938 0.4601
26 2I0G I0G 0.001319 0.45931
27 3FAL LO2 0.000907 0.45871
28 4CSJ NN7 0.0004402 0.45406
29 3MNP DEX 0.001068 0.45393
30 4OHA HFT 0.0005476 0.45219
31 3V49 PK0 0.0008404 0.45195
32 2YJD YJD 0.0003003 0.44818
33 3RUU 37G 0.001043 0.44774
34 1U3R 338 0.0006159 0.4477
35 4OKX 198 0.0009978 0.44677
36 3VRV YSD 0.003101 0.44301
37 1OSH FEX 0.002036 0.44111
38 1M13 HYF 0.00115 0.44014
39 1DB1 VDX 0.003323 0.43679
40 3BQD DAY 0.001128 0.43625
41 3UUA 0CZ 1.803e-05 0.43519
42 4QJR PIZ 0.002431 0.43292
43 2Q7J TES 0.0005486 0.43143
44 2HC4 VDX 0.003321 0.43138
45 4POJ 2VP 0.002539 0.42865
46 2Q1H AS4 0.006955 0.42855
47 4DK7 0KS 0.001373 0.42791
48 3KMZ EQO 0.001979 0.42771
49 4FHH 0U3 0.00484 0.42663
50 1FCY 564 0.003144 0.4245
51 2C78 PUL 0.01314 0.42338
52 1NHZ 486 0.001294 0.42271
53 1YYE 196 0.0008064 0.42196
54 4MGB XDH 0.0004859 0.41952
55 1FCZ 156 0.00347 0.41894
56 3L0E G58 0.004062 0.41776
57 4WLB 3QQ 0.007773 0.41711
58 1DKF BMS 0.004127 0.41562
59 3L3X DHT 0.001285 0.41128
60 2ZCQ B65 0.01439 0.41044
61 3OLL EST 0.001294 0.41019
62 3WHB DCC 0.01445 0.40928
63 3QCP FAD 0.00634 0.40916
64 3DCT 064 0.005534 0.40809
65 4OKW 198 0.005578 0.40794
66 4MG8 27J 0.001295 0.40791
67 4QRS GLU 0.0164 0.40775
68 2EVL GAL 0.02744 0.40449
69 3KMR EQN 0.003524 0.4041
70 1M2Z DEX 0.006242 0.40382
71 3T58 FAD 0.01132 0.40118
72 4HBM 0Y7 0.0142 0.40108
73 1N8V BDD 0.01428 0.40098
74 4I4B 1CV 0.04908 0.40059
75 1G2N EPH 0.005734 0.40042
76 4BNU 9KQ 0.008362 0.4002
77 1T79 DHT 0.00131 0.399
78 2WTV ZZL 0.04811 0.39842
79 3FAL REA 0.002986 0.39794
80 1T27 PCW 0.02303 0.39753
81 2GIU FBR 0.0443 0.39588
82 1T74 DHT 0.001526 0.39587
83 4DM8 REA 0.01182 0.39538
84 4OAS 2SW 0.02029 0.39528
85 1T5Z DHT 0.002452 0.39395
86 2QZO KN1 0.003462 0.39381
87 2E3N 6CM 0.02782 0.39367
88 2R40 EPH 0.0119 0.39345
89 3VVY ET 0.01969 0.39179
90 3PLZ 470 0.02153 0.39002
91 3UUD EST 0.0004114 0.38992
92 2UXI G50 0.007754 0.38933
93 2ALG DAO 0.02227 0.3879
94 4P6W MOF 0.01603 0.38774
95 1FBY REA 0.02837 0.38593
96 3R1V AZB 0.0211 0.38584
97 4J24 EST 0.003895 0.38566
98 4P6X HCY 0.006688 0.38524
99 4OAR 2S0 0.01344 0.38459
100 2AO6 R18 0.003573 0.38398
101 4QRT GLU 0.04725 0.38383
102 4E2J MOF 0.01549 0.38313
103 2X5W K2B 0.02902 0.38266
104 1ATL 0QI 0.01933 0.3823
105 1T73 DHT 0.004781 0.37991
106 4MGD 27N 0.000699 0.3798
107 4O1Z MXM 0.02204 0.37979
108 1ZDU P3A 0.02651 0.37976
109 2BJ4 OHT 0.01083 0.37922
110 1YMT DR9 0.0251 0.3791
111 1BH2 GSP 0.03762 0.37893
112 4DOL PLM 0.004407 0.37683
113 1VGV UD1 0.03123 0.37657
114 4M8E 29V 0.02613 0.37653
115 3GN8 DEX 0.01508 0.37624
116 4JA8 1K9 0.03518 0.37585
117 1DKF OLA 0.00839 0.37584
118 1OQC FAD 0.03997 0.37486
119 3L3Z DHT 0.006936 0.37485
120 4J26 EST 0.003844 0.3748
121 1T65 DHT 0.007109 0.37393
122 4KWD JF2 0.04296 0.37343
123 1T7F DHT 0.007322 0.37314
124 1YP0 PEF 0.02149 0.37264
125 4HW3 19G 0.03237 0.37242
126 1T7M DHT 0.007925 0.37126
127 1LRI CLR 0.02819 0.37103
128 1ZDT PEF 0.03157 0.36999
129 1YUC EPH 0.03189 0.36998
130 3S0E EOL 0.01879 0.36947
131 1JR8 FAD 0.04882 0.3694
132 3AHQ FAD 0.04538 0.36927
133 3KZE ARG 0.008993 0.36868
134 1NRL SRL 0.01877 0.36782
135 1EYQ NAR 0.0205 0.36767
136 2BCG GER 0.009816 0.36693
137 1T7R DHT 0.006959 0.36606
138 4RC8 STE 0.04931 0.366
139 3KZE SER 0.04577 0.36573
140 4MGA 27L 0.0002601 0.36288
141 4LRL DGT 0.02258 0.36141
142 1Q1Y BB2 0.02402 0.36123
143 2QA8 GEN 0.007258 0.35927
144 4MG7 27H 0.01646 0.35726
145 3SE5 ANP 0.03354 0.35682
146 4U0S ADP 0.02903 0.35428
147 2RH1 CLR 0.04784 0.35307
148 1NQ7 ARL 0.02466 0.35285
149 4KG1 PCG 0.03837 0.35251
150 3V78 ET 0.04062 0.35244
151 3KTI OTT 0.04873 0.35234
152 4FH7 TBP 0.03955 0.34966
153 3W68 VIV 0.03399 0.34956
154 1LOX RS7 0.04828 0.34891
155 3LA3 2FT 0.01623 0.34861
156 3UU7 2OH 0.009666 0.3461
157 3UYT 0CK 0.04417 0.34573
158 2UW1 GVM 0.006874 0.34543
159 2XHK AKG 0.02007 0.34457
160 1XN0 ROL 0.03699 0.34415
161 1RPJ ALL 0.03447 0.34335
162 2XKO AKG 0.02753 0.34135
163 4D1J DGJ 0.0158 0.34092
164 2QEH SRO 0.04056 0.33996
165 1T76 DHT 0.01591 0.33889
166 3RLF MAL 0.01285 0.33795
167 1ALW ISA 0.02473 0.33666
168 3ETG GWD 0.001386 0.33642
169 3TL1 JRO 0.0364 0.33603
170 3HP9 CF1 0.007691 0.33495
171 4MA7 P2Z 0.02442 0.33493
172 2IOY RIP 0.03893 0.33189
173 4MG9 27K 0.005563 0.33043
174 1KSK URA 0.0374 0.32638
175 3KV4 OGA 0.03644 0.32325
176 3CV2 COA 0.0218 0.32282
177 2WDA L42 0.01744 0.32267
178 3SXU ASP 0.0008506 0.32082
179 3TDC 0EU 0.0006951 0.32048
180 1VPD TLA 0.01763 0.32005
181 4QXB OGA 0.04608 0.31587
182 4NY3 PRO 0.03262 0.3157
183 1HBK COA 0.04182 0.3098
184 3F33 PFL 0.01058 0.3087
185 2CIX CEJ 0.007633 0.30691
186 4QEK GLC 0.01889 0.30664
187 4G9Z C 0.04967 0.29666
Pocket no: 2; Query (leader) PDB : 1RDT; Ligand: L79; Similar sites found: 164
This union binding pocket (no: 2) in the query (biounit: 1rdt.bio1) has 17 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc)
1 1RDT L79 7.772e-16 1
2 4POJ 2VP 1.679e-13 0.92783
3 4M8E 29V 9.115e-14 0.92175
4 1FM9 9CR 3.593e-12 0.80878
5 3H0A 9RA 1.82e-11 0.79974
6 1FBY REA 6.184e-10 0.76697
7 3FAL REA 4.377e-10 0.71865
8 2I0G I0G 2.956e-07 0.65594
9 2B1Z 17M 1.158e-07 0.65433
10 2QE4 JJ3 9.572e-07 0.63038
11 1U3R 338 1.933e-07 0.62618
12 1DKF OLA 2.584e-08 0.6257
13 3VHU SNL 7.002e-07 0.61158
14 1SR7 MOF 2.498e-06 0.59654
15 2Q1H AS4 9.872e-06 0.58412
16 4MG8 27J 7.411e-07 0.57805
17 2YJD YJD 2.083e-06 0.57158
18 3OLL EST 1.22e-06 0.56797
19 3MNP DEX 1.765e-05 0.55505
20 2AX9 BHM 0.0001018 0.54937
21 1YYE 196 5.636e-06 0.54834
22 4MG7 27H 1.46e-06 0.54476
23 4E2J MOF 1.026e-05 0.54271
24 4OAR 2S0 1.348e-05 0.5372
25 2Q7J TES 1.183e-05 0.5336
26 1XIU REA 5.633e-05 0.52859
27 3FS1 MYR 3.684e-07 0.52775
28 4J24 EST 7.018e-06 0.52543
29 4OKX 198 5.608e-05 0.52065
30 4J26 EST 5.099e-06 0.52027
31 2QZO KN1 1.745e-05 0.51828
32 4WLB 3QQ 0.0001198 0.51777
33 4P6W MOF 4.923e-05 0.51634
34 4MGB XDH 1.802e-05 0.50999
35 1PZL MYR 3.345e-06 0.50876
36 4OHA HFT 7.902e-05 0.50668
37 3UU7 2OH 8.306e-07 0.50071
38 2A3I C0R 9.028e-05 0.49886
39 3V49 PK0 0.0002053 0.49572
40 2HFP NSI 0.000457 0.49482
41 2BJ4 OHT 8.686e-05 0.49396
42 3GN8 DEX 0.000107 0.48981
43 1FCY 564 0.0002499 0.48965
44 3RY9 1CA 7.612e-05 0.48951
45 1FCZ 156 0.0002324 0.48692
46 3KFC 61X 0.0006 0.48477
47 1NHZ 486 0.000163 0.48427
48 3L3X DHT 0.0001102 0.48239
49 4OKW 198 0.000266 0.4819
50 3BQD DAY 0.0002447 0.48124
51 3KMR EQN 0.0001911 0.48109
52 1M2Z DEX 0.0002669 0.47948
53 3L3Z DHT 6.592e-05 0.47777
54 3FAL LO2 0.0008873 0.47345
55 2QA8 GEN 5.033e-05 0.47289
56 1T65 DHT 9.84e-05 0.47208
57 1XAP TTB 0.0001858 0.47175
58 1T7M DHT 9.011e-05 0.4702
59 1T74 DHT 0.0001031 0.46893
60 3UUD EST 2.252e-05 0.46811
61 1T7R DHT 5.742e-05 0.46669
62 1T7F DHT 0.0001122 0.46596
63 1T73 DHT 0.0001352 0.46362
64 3GZ9 D32 0.002846 0.46183
65 1T5Z DHT 0.0002166 0.46166
66 1T79 DHT 0.0001558 0.46155
67 2HC4 VDX 0.001501 0.46076
68 3KDU NKS 0.002553 0.45985
69 4CSJ NN7 0.0007024 0.45984
70 1DKF BMS 0.0008735 0.45973
71 1ZDU P3A 0.0009229 0.4586
72 4DM8 REA 0.0009995 0.45697
73 3KMZ EQO 0.001035 0.45415
74 4P6X HCY 0.0004845 0.45348
75 4FHH 0U3 0.002612 0.45183
76 3B1M KRC 0.00398 0.45015
77 2AO6 R18 0.0003039 0.44929
78 3G9E RO7 0.003135 0.44653
79 2P4Y C03 0.006708 0.44477
80 3RUU 37G 0.002537 0.44328
81 1YUC EPH 0.001456 0.44279
82 4QJR PIZ 0.002981 0.44157
83 3VRV YSD 0.005997 0.44118
84 4MG9 27K 4.583e-06 0.43954
85 1T76 DHT 5.142e-05 0.43952
86 3L0L HC3 0.002122 0.43739
87 1DB1 VDX 0.006236 0.4357
88 3OKI OKI 0.006972 0.43565
89 3BEJ MUF 0.001846 0.43564
90 2JF9 OHT 0.0104 0.43407
91 3PLZ 470 0.00442 0.4333
92 2R40 20E 0.003318 0.43036
93 2O4J VD4 0.004373 0.43022
94 3L0E G58 0.004096 0.42982
95 3UUA 0CZ 0.0002348 0.42917
96 1OSH FEX 0.006872 0.42842
97 3LMP CEK 0.01063 0.42296
98 1YMT DR9 0.005332 0.42065
99 2E2R 2OH 0.04242 0.41405
100 1YP0 PEF 0.005972 0.41209
101 3DCT 064 0.00823 0.41176
102 4MGD 27N 0.000348 0.41003
103 1PME SB2 0.0389 0.40279
104 3JZB 4HY 0.03111 0.40081
105 3GWT 066 0.0341 0.39879
106 1DFO FFO 0.01223 0.39767
107 4EKQ NPO 0.024 0.3947
108 1MI5 PHE 0.04878 0.39398
109 3GFZ FMN 0.01325 0.39386
110 1OSV CHC 0.01033 0.3936
111 3KRO DST 0.02848 0.39259
112 2R40 EPH 0.02275 0.39086
113 3D78 NBB 0.0481 0.39015
114 3M00 2CF 0.03463 0.38986
115 1ZDT PEF 0.02015 0.38962
116 4MGA 27L 0.0002654 0.38925
117 4D09 788 0.03641 0.38879
118 1RQJ RIS 0.01958 0.38817
119 2FR3 REA 0.02705 0.38728
120 3MG1 ECH 0.04768 0.38563
121 4F3C BIG 0.04281 0.38394
122 1N46 PFA 0.03827 0.38334
123 2XCG XCG 0.04444 0.38314
124 1G2N EPH 0.02911 0.38211
125 3K3K A8S 0.0347 0.38211
126 4DOO DAO 0.03211 0.3801
127 1M13 HYF 0.04346 0.37908
128 3GYT DL4 0.0412 0.37854
129 4PXZ 6AD 0.04882 0.3782
130 3B2Q ATP 0.04129 0.37676
131 3SP6 IL2 0.02007 0.37546
132 4IX4 ADP 0.04802 0.37362
133 4IEU 2CO 0.01157 0.37315
134 2FP2 TSA 0.04675 0.37237
135 3AQT RCO 0.001154 0.36771
136 1YC4 43P 0.04284 0.36536
137 3DFR MTX 0.04795 0.36362
138 1QCI ADE 0.03828 0.36112
139 1MRH FMC 0.04662 0.35958
140 4IN9 SER 0.04456 0.359
141 3OGN 3OG 0.04181 0.35586
142 1IIU RTL 0.04949 0.35469
143 4APO ALA 0.04206 0.3511
144 2WMI A2G 0.04797 0.34767
145 3KU0 ADE 0.01927 0.34755
146 4MRP GSH 0.003728 0.34537
147 3PB9 1BN 0.03834 0.34468
148 2RBK VN4 0.0112 0.34192
149 3LE7 ADE 0.02325 0.33859
150 1L0I PSR 0.02213 0.33689
151 4IA6 EIC 0.01316 0.3343
152 3HP9 CF1 0.03692 0.33286
153 4QEK GLC 0.005276 0.33262
154 4UMX VVS 0.04738 0.32978
155 1LES GLC 0.04418 0.32793
156 3O01 DXC 0.003524 0.32695
157 1N13 AG2 0.04537 0.32654
158 2WDA L42 0.04643 0.32632
159 4G31 0WH 0.03427 0.32496
160 2XN3 ID8 0.03325 0.32472
161 3F33 PFL 0.01047 0.32452
162 2BHW NEX 0.005866 0.32278
163 1FEE SUC 0.001912 0.31539
164 2CIX CEJ 0.02381 0.31266
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