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 (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1RDT; Ligand: 570; Similar sites found: 123
This union binding pocket(no: 1) in the query (biounit: 1rdt.bio1) has 26 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc)
1 1FM9 570 3.207e-17 0.989
2 3G9E RO7 0.0000000000001618 0.84646
3 3KDU NKS 0.000000000004657 0.80321
4 3KDU NKS 0.000000000004657 0.80321
5 3KDU NKS 0.00000000001229 0.77836
6 1K7L 544 0.000000000006915 0.73783
7 3FEI CTM 0.0000000001319 0.72976
8 1K7L 544 0.00000000001273 0.7277
9 1K7L 544 0.00000000002639 0.71517
10 2PRG BRL 0.0000000000008668 0.7115
11 1K7L 544 0.0000000001075 0.70633
12 2P54 735 0.00000000007441 0.69789
13 3ET1 ET1 0.0000000001518 0.63826
14 3H0A D30 0.00000001032 0.63247
15 3ET1 ET1 0.000000000455 0.63234
16 3B1M KRC 0.000000000006557 0.60572
17 2P4Y C03 0.000000000000233 0.57584
18 3GZ9 D32 0.0000000008537 0.56432
19 2HFP NSI 0.0000006184 0.54889
20 3UUA 0CZ 0.00004662 0.53553
21 2B1Z 17M 0.00001127 0.51349
22 3BEJ MUF 0.00001837 0.48528
23 1M13 HYF 0.00005507 0.48175
24 4DK7 0KS 0.0001792 0.47904
25 3UU7 2OH 0.001374 0.4777
26 1TV5 N8E 0.001976 0.47713
27 1NRL SRL 0.0002235 0.47481
28 3UUA 0CZ 0.0005012 0.47363
29 3UUA 0CZ 0.0005012 0.47363
30 3PLZ 470 0.0001402 0.47354
31 3DCT 064 0.00007235 0.47314
32 1NRL SRL 0.0002111 0.47125
33 1NRL SRL 0.0002111 0.47125
34 2QE4 JJ3 0.0003397 0.4668
35 1RL4 BL5 0.004703 0.46317
36 3UU7 2OH 0.002475 0.46088
37 3UU7 2OH 0.002475 0.46088
38 3B6C SDN 0.002558 0.46014
39 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 0.005729 0.45657
40 3TDC 0EU 0.001042 0.45565
41 3VHU SNL 0.0002704 0.45407
42 3RUU 37G 0.00008321 0.45203
43 4M8E 29V 0.0006436 0.45031
44 4I67 G G G RPC 0.002691 0.44849
45 1RL4 BL5 0.01038 0.44808
46 1DB1 VDX 0.0006299 0.44653
47 1ZDT PEF 0.0003527 0.44561
48 3KMR EQN 0.001028 0.44555
49 1YUC EPH 0.0006233 0.44383
50 1YMT DR9 0.0005316 0.44356
51 1NF8 BOG 0.007877 0.44347
52 1YUC EPH 0.0005179 0.44239
53 1YUC EPH 0.0005179 0.44239
54 4OAS 2SW 0.002416 0.44143
55 3IPQ 965 0.00009851 0.44078
56 3B9Z CO2 0.01502 0.43937
57 3PLZ 470 0.00009819 0.43666
58 2CB8 MYA 0.009015 0.43486
59 2I0G I0G 0.003082 0.43463
60 1XVB 3BR 0.005167 0.43446
61 3F33 PFL 0.009451 0.43291
62 2XKO AKG 0.009041 0.43263
63 4LWU 20U 0.00407 0.43073
64 2E2R 2OH 0.001754 0.43067
65 4POJ 2VP 0.0006812 0.43003
66 2Q8H TF4 0.01074 0.42965
67 1ZDU P3A 0.00105 0.42833
68 1U3R 338 0.0005571 0.42814
69 2BJ4 OHT 0.0002962 0.42767
70 3W54 RNB 0.004859 0.4271
71 3I6B KDO 0.01113 0.42686
72 3I6B KDO 0.01113 0.42686
73 3KV4 OGA 0.01183 0.42677
74 2VWA PTY 0.01698 0.42622
75 1FCY 564 0.001107 0.42573
76 2QA8 GEN 0.00007598 0.42518
77 1PZL MYR 0.003884 0.42373
78 3IX9 MTX 0.003958 0.42336
79 1YYE 196 0.00008238 0.42335
80 4DM8 REA 0.000666 0.42313
81 3IX9 MTX 0.007497 0.4222
82 4OAS 2SW 0.0035 0.42204
83 1FCZ 156 0.00111 0.42201
84 3UUD EST 0.000096 0.42201
85 2XEM SSV 0.00922 0.42199
86 3UUD EST 0.00009797 0.42187
87 3UUD EST 0.00009797 0.42187
88 1FM4 DXC 0.005737 0.42113
89 3HYW DCQ 0.01188 0.4208
90 1ZDT PEF 0.001135 0.42053
91 4FGC PQ0 0.01633 0.42041
92 2QQC AG2 0.01736 0.41985
93 4QJR PIZ 0.001167 0.4198
94 2QZO KN1 0.0003971 0.41931
95 1DKF BMS 0.001087 0.41711
96 3W54 RNB 0.005498 0.41691
97 3KP6 SAL 0.01721 0.41688
98 4DOL PLM 0.005562 0.41668
99 3QCP FAD 0.002093 0.41628
100 4UYF 73B 0.01642 0.41548
101 2XN5 FUN 0.01272 0.41504
102 3TL1 JRO 0.01936 0.41425
103 2GIU FBR 0.002459 0.41346
104 4R29 SAM 0.01472 0.41189
105 2A3I C0R 0.001302 0.4117
106 3OKI OKI 0.005032 0.41165
107 1FM9 9CR 0.001057 0.41067
108 1RL4 BRR 0.0198 0.40947
109 4R29 SAM 0.01663 0.40926
110 4HW3 19G 0.001028 0.40783
111 3F8C HT1 0.03537 0.40738
112 1OSH FEX 0.0003951 0.40732
113 1TMX HGX 0.005612 0.40637
114 3BQD DAY 0.001795 0.40542
115 2FDW D3G 0.02503 0.40426
116 2HI4 BHF 0.01081 0.40361
117 3V78 ET 0.01896 0.40265
118 1YUC EPH 0.004385 0.40178
119 2VWA PTY 0.04843 0.4011
120 4M73 SAH 0.01009 0.40107
121 3RV5 DXC 0.03754 0.40058
122 3IX9 MTX 0.01491 0.40057
123 3KO0 TFP 0.0362 0.40035
Pocket No.: 2; Query (leader) PDB : 1RDT; Ligand: L79; Similar sites found: 140
This union binding pocket(no: 2) in the query (biounit: 1rdt.bio1) has 22 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc)
1 4POJ 2VP 0.000000000000003997 0.93059
2 4M8E 29V 0.00000000000001033 0.89898
3 1FM9 9CR 0.00000000000003231 0.87812
4 3H0A 9RA 0.00000000000002154 0.86847
5 1XIU REA 0.0000000000002308 0.80758
6 1FBY REA 0.000000000003026 0.73655
7 1DKF OLA 0.00000000009719 0.67882
8 1PZL MYR 0.000000007835 0.66813
9 2B1Z 17M 0.00000001038 0.6681
10 2I0G I0G 0.0000001141 0.65541
11 2E2R 2OH 0.0000001118 0.63306
12 3PLZ 470 0.00000009514 0.63219
13 2QZO KN1 0.00000001583 0.62889
14 2GIU FBR 0.00000005727 0.6281
15 3FS1 MYR 0.000000004954 0.62759
16 1U3R 338 0.00000005649 0.62018
17 2QE4 JJ3 0.0000003677 0.61845
18 3UU7 2OH 0.000001609 0.6164
19 3UU7 2OH 0.000001609 0.6164
20 3UUA 0CZ 0.0000004536 0.60633
21 3UUA 0CZ 0.0000004536 0.60633
22 3VHU SNL 0.00000001352 0.60524
23 2BJ4 OHT 0.0000001718 0.59372
24 2QA8 GEN 0.00000002825 0.58961
25 3UUD EST 0.00000004714 0.58322
26 1YYE 196 0.0000000455 0.58207
27 3UUD EST 0.00000005858 0.57986
28 3UUD EST 0.00000005858 0.57986
29 3UU7 2OH 0.00001273 0.57403
30 2A3I C0R 0.0000005877 0.57396
31 1HG4 LPP 0.000002413 0.55968
32 1YUC EPH 0.000003282 0.55384
33 1YUC EPH 0.000003282 0.55384
34 1YUC EPH 0.000004492 0.55384
35 3UUA 0CZ 0.00001306 0.55351
36 3BQD DAY 0.000001848 0.5528
37 1HG4 LPP 0.000003806 0.55104
38 3PLZ 470 0.000001015 0.54583
39 1YUC EPH 0.000008397 0.53181
40 3RV5 DXC 0.00001872 0.53173
41 1G2N EPH 0.00001764 0.51571
42 1YMT DR9 0.00003639 0.51008
43 1DKF BMS 0.0000238 0.50789
44 1ZDU P3A 0.00004207 0.50354
45 1UO5 PIH 0.0005325 0.4993
46 1YP0 PEF 0.00004675 0.49535
47 3KMR EQN 0.00006083 0.49108
48 3KDU NKS 0.0002578 0.48585
49 1FCZ 156 0.00009098 0.48506
50 1XAP TTB 0.00006681 0.48421
51 1FCY 564 0.0001213 0.48166
52 3KDU NKS 0.0005505 0.47441
53 3KDU NKS 0.0005505 0.47441
54 3G9E RO7 0.0003609 0.47393
55 4DM8 REA 0.0001681 0.46947
56 1ZDT PEF 0.00002356 0.46538
57 3DCT 064 0.0003583 0.46131
58 1ZDT PEF 0.00007199 0.45653
59 2Q8H TF4 0.002197 0.45409
60 4DM8 REA 0.0004757 0.45224
61 3BEJ MUF 0.0006204 0.44731
62 4QJR PIZ 0.0001365 0.44158
63 3HYW DCQ 0.005383 0.44149
64 1DB1 VDX 0.001906 0.44024
65 2Y69 CHD 0.007789 0.43565
66 3KP6 SAL 0.005875 0.43452
67 2VWA PTY 0.007368 0.43196
68 3B9Z CO2 0.00895 0.43083
69 1XVB 3BR 0.004535 0.43039
70 1YFX 4AA 0.007091 0.43038
71 3HYW DCQ 0.008522 0.4296
72 1OSV CHC 0.001015 0.42939
73 1FM9 570 0.003002 0.42879
74 2QCX PF1 0.008456 0.42767
75 1N83 CLR 0.002205 0.42717
76 3WBG 2AN 0.00309 0.42515
77 3G5N PB2 0.01043 0.42481
78 3KO0 TFP 0.005216 0.42345
79 3TL1 JRO 0.01015 0.42239
80 1M13 HYF 0.00349 0.42164
81 1NF8 BOG 0.01398 0.42116
82 3F33 PFL 0.02815 0.42096
83 1UVC STE 0.00393 0.42083
84 3RUU 37G 0.0002122 0.42047
85 1OSV CHC 0.001754 0.41988
86 3KO0 TFP 0.006169 0.41938
87 3ET1 ET1 0.001864 0.41876
88 4R29 SAM 0.008298 0.41764
89 4P3H 25G 0.002037 0.41724
90 4P3H 25G 0.002037 0.41724
91 3KO0 TFP 0.006824 0.4169
92 4DK7 0KS 0.003178 0.41686
93 3IPQ 965 0.0002185 0.41646
94 1DTL BEP 0.007391 0.41583
95 1JGS SAL 0.02599 0.41541
96 3TL1 JRO 0.01406 0.41513
97 1TV5 N8E 0.01716 0.41513
98 2PRG BRL 0.001801 0.41469
99 3HYW DCQ 0.01188 0.41431
100 3WBG 2AN 0.005423 0.4141
101 1N4H REA 0.003929 0.41298
102 4MC3 28U 0.01574 0.41261
103 2JAP J01 0.01289 0.41255
104 4NKW PLO 0.002074 0.41153
105 4QEK GLC 0.01602 0.4115
106 4R29 SAM 0.01123 0.41124
107 2OCI TYC 0.01774 0.41118
108 4JMO JAF 0.01391 0.4109
109 3GYT DL4 0.004809 0.41089
110 4R29 SAM 0.01143 0.41087
111 3R9V DXC 0.01249 0.41061
112 4NKW PLO 0.002183 0.41056
113 2VWA PTY 0.02241 0.41031
114 3RV5 DXC 0.001312 0.40979
115 2Z77 NCA 0.01919 0.40818
116 2Z77 NCA 0.01919 0.40818
117 3ANP DAO 0.006409 0.40709
118 2A1L PCW 0.01787 0.40671
119 3KU0 ADE 0.02673 0.40592
120 3HUJ AGH 0.02375 0.40503
121 3KO0 TFP 0.02565 0.40468
122 2VWA PTY 0.02757 0.40431
123 3KO0 TFP 0.0261 0.40426
124 2QZZ EMF 0.01715 0.40385
125 2QZZ EMF 0.01715 0.40385
126 1XN0 ROL 0.01947 0.40358
127 3BPX SAL 0.02682 0.40313
128 2PFC PLM 0.01376 0.40301
129 1FO3 KIF 0.02457 0.40265
130 2QZZ NAP 0.01787 0.40205
131 2QZZ NAP 0.01787 0.40205
132 4ORM FMN 0.0408 0.40181
133 4ORM ORO 0.0408 0.40181
134 3G4Q MCH 0.01457 0.40181
135 3F8C HT1 0.03281 0.40128
136 3HUJ AGH 0.02693 0.40088
137 1QV1 CZH 0.01118 0.40085
138 2ZCQ B65 0.02408 0.40067
139 3R9V DXC 0.03061 0.40065
140 1XN0 ROL 0.02292 0.40002
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