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 263 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 196 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 171 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: 42
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) Sequence Similarity
1 3B6C SDN 0.002558 0.46014 3.4188
2 3IX9 MTX 0.003958 0.42336 3.68421
3 5AZC PGT 0.03453 0.40338 3.71901
4 2FDW D3G 0.02503 0.40426 3.87324
5 4MNS 2AX 0.005433 0.42216 4.40252
6 5B4B LP5 0.002238 0.41963 5.3719
7 3LLI FAD 0.005702 0.40021 5.3719
8 1TMX HGX 0.005612 0.40637 5.6338
9 4M73 SAH 0.01009 0.40107 5.6338
10 3V78 ET 0.01896 0.40265 5.76923
11 4XPL ACO 0.008006 0.40952 6.74847
12 4LWU 20U 0.00407 0.43073 7.05882
13 5DCH 1YO 0.01917 0.41695 8.33333
14 3KP6 SAL 0.01721 0.41688 11.9205
15 3RV5 DXC 0.03754 0.40058 12.3596
16 5IF4 6AK 0.008862 0.40345 12.5786
17 2XKO AKG 0.009041 0.43263 14.6067
18 4OAS 2SW 0.002416 0.44143 16.6667
19 3QCP FAD 0.002093 0.41628 17.3913
20 3BQD DAY 0.001795 0.40542 26.0331
21 1TV5 N8E 0.001976 0.47713 30.4348
22 5HCV 60R 0.0002486 0.46817 34.7107
23 2A3I C0R 0.001302 0.4117 34.7107
24 2XXP DSL 0.003444 0.44435 34.7826
25 1M13 HYF 0.00005396 0.48909 35.5372
26 4DK7 0KS 0.0001792 0.47904 36.0324
27 1DB1 VDX 0.0006299 0.44653 37.4517
28 3DCT 064 0.00007235 0.47314 39.5745
29 3OKI OKI 0.005032 0.41165 40.3433
30 5ICK FEZ 0.00008843 0.49259 40.6114
31 3RUU 37G 0.00008321 0.4763 40.6114
32 2I0G I0G 0.003082 0.43463 40.9091
33 1YYE 196 0.00008238 0.42335 40.9091
34 1U3R 338 0.0001661 0.42599 41.0788
35 1FCZ 156 0.00111 0.42201 41.7021
36 5AAV GW5 0.00001004 0.54767 41.7355
37 4OIV XX9 0.006545 0.41112 42.0354
38 2QE4 JJ3 0.0002108 0.4865 42.1488
39 2BJ4 OHT 0.0002962 0.42767 42.1488
40 1YMT DR9 0.0005316 0.44356 46.281
41 1ZDT PEF 0.0003884 0.44744 47.3029
42 2LBD REA 0.002296 0.41304 48.6891
Pocket No.: 2; Query (leader) PDB : 1RDT; Ligand: L79; Similar sites found: 77
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) Sequence Similarity
1 4RJD TFP 0.02303 0.40478 None
2 2PFC PLM 0.01376 0.40301 None
3 1UVC STE 0.00393 0.42083 2.1978
4 2Q8H TF4 0.002197 0.45409 2.46479
5 5DEY 59T 0.01659 0.41394 2.47934
6 5CSD ACD 0.00529 0.4251 3.14465
7 4NKW PLO 0.002664 0.41186 3.52113
8 4UCC ZKW 0.04154 0.41289 3.86266
9 4R29 SAM 0.01123 0.41124 4.01786
10 4JMO JAF 0.01391 0.4109 4.5
11 5UC9 MYR 0.01032 0.41737 4.86726
12 3B9Z CO2 0.00895 0.43083 4.95868
13 5B4B LP5 0.007181 0.41068 5.3719
14 3WYJ H78 0.03037 0.40868 5.78512
15 5A89 ADP 0.01628 0.40679 6.41026
16 3KU0 ADE 0.02673 0.40592 6.61157
17 4P3H 25G 0.002037 0.41724 6.73575
18 5V4R MGT 0.02514 0.4066 6.79012
19 2ZCQ B65 0.02408 0.40067 7.39437
20 4RW3 TDA 0.01446 0.43973 8
21 3HUJ AGH 0.02693 0.40088 8.08081
22 4MC3 28U 0.01574 0.41261 8.09249
23 3BPX SAL 0.02682 0.40313 8.10811
24 5BVT PAM 0.00597 0.40166 8.20895
25 3G4Q MCH 0.01457 0.40181 8.21918
26 2OCI TYC 0.01774 0.41118 8.66142
27 3TL1 JRO 0.01406 0.41513 8.80503
28 1UO5 PIH 0.0005325 0.4993 8.82353
29 2QZZ EMF 0.01715 0.40385 9.85915
30 2QZZ NAP 0.01787 0.40205 9.85915
31 1NF8 BOG 0.01398 0.42116 10.1449
32 3KP6 SAL 0.005875 0.43452 11.9205
33 3RV5 DXC 0.00001872 0.53173 12.3596
34 1XVB 3BR 0.004535 0.43039 14.7059
35 2A1L PCW 0.01787 0.40671 16
36 1DTL BEP 0.007391 0.41583 16.1491
37 3ANP DAO 0.006409 0.40709 16.1765
38 3KO0 TFP 0.02565 0.40468 16.8317
39 2JAP J01 0.01289 0.41255 17.3913
40 4QEK GLC 0.01602 0.4115 17.3913
41 3HYW DCQ 0.005383 0.44149 21.7391
42 2Y69 CHD 0.007789 0.43565 24
43 3BQD DAY 0.000001848 0.5528 26.0331
44 1JGS SAL 0.02599 0.41541 26.087
45 2QCX PF1 0.008456 0.42767 30.4348
46 3G5N PB2 0.01043 0.42481 30.4348
47 1TV5 N8E 0.01716 0.41513 30.4348
48 3R9V DXC 0.01249 0.41061 32
49 2Z77 NCA 0.01919 0.40818 32
50 3GYT DL4 0.004809 0.41089 32.2314
51 3WBG 2AN 0.00309 0.42515 32.6797
52 5HCV 60R 0.00000004916 0.6167 34.7107
53 2A3I C0R 0.0000005877 0.57396 34.7107
54 1QV1 CZH 0.01118 0.40085 34.7826
55 1M13 HYF 0.004198 0.42365 35.5372
56 2VWA PTY 0.02241 0.41031 36
57 4DK7 0KS 0.003178 0.41686 36.0324
58 1DB1 VDX 0.001906 0.44024 37.4517
59 3DCT 064 0.0003583 0.46131 39.5745
60 5ICK FEZ 0.0005735 0.449 40.6114
61 3RUU 37G 0.0002122 0.42047 40.6114
62 2I0G I0G 0.0000001141 0.65541 40.9091
63 1YYE 196 0.0000000455 0.58207 40.9091
64 1U3R 338 0.000000004693 0.64082 41.0788
65 1FCZ 156 0.00009098 0.48506 41.7021
66 5AAV GW5 0.000002408 0.59803 41.7355
67 4OIV XX9 0.01135 0.41208 42.0354
68 2QE4 JJ3 0.0000005676 0.62403 42.1488
69 2BJ4 OHT 0.0000001718 0.59372 42.1488
70 5OCA 9QZ 0.004958 0.45588 44
71 1YMT DR9 0.00003639 0.51008 46.281
72 1ZDT PEF 0.00008806 0.49145 47.3029
73 4IGH FMN 0.04662 0.40012 48
74 4IGH 1EA 0.04662 0.40012 48
75 4IGH ORO 0.04662 0.40012 48
76 1N83 CLR 0.002205 0.42717 48.5185
77 2LBD REA 0.0001611 0.47632 48.6891
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