Receptor
PDB id Resolution Class Description Source Keywords
7A78 1.72 Å NON-ENZYME: SIGNAL_HORMONE CRYSTAL STRUCTURE OF RXR BETA LBD IN COMPLEXES WITH PALMITIC GRIP-1 PEPTIDE HOMO SAPIENS RXRB STEROID HORMONE RECEPTOR INHIBITOR LIPID BINDING FASTRUCTURAL GENOMICS CONSORTIUM SGC DNA BINDING PROTEIN
Ref.: COMPREHENSIVE SET OF TERTIARY COMPLEX STRUCTURES AN PALMITIC ACID BINDING PROVIDE MOLECULAR INSIGHTS IN DESIGN FOR RXR ISOFORMS. INT J MOL SCI V. 21 2020
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
EDO A:607;
A:605;
A:603;
A:604;
A:606;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
 submit data
62.068 C2 H6 O2 C(CO)...
CL A:602;
 Invalid;
 none;
 submit data
35.453 Cl [Cl-]
PLM A:601;
 Valid;
 none;
 submit data
256.424 C16 H32 O2 CCCCC...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
7A78 1.72 Å NON-ENZYME: SIGNAL_HORMONE CRYSTAL STRUCTURE OF RXR BETA LBD IN COMPLEXES WITH PALMITIC GRIP-1 PEPTIDE HOMO SAPIENS RXRB STEROID HORMONE RECEPTOR INHIBITOR LIPID BINDING FASTRUCTURAL GENOMICS CONSORTIUM SGC DNA BINDING PROTEIN
Ref.: COMPREHENSIVE SET OF TERTIARY COMPLEX STRUCTURES AN PALMITIC ACID BINDING PROVIDE MOLECULAR INSIGHTS IN DESIGN FOR RXR ISOFORMS. INT J MOL SCI V. 21 2020
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 289 families.
1 7A78 - PLM C16 H32 O2 CCCCCCCCCC....
70% Homology Family (34)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 266 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 6STI - 754 C26 H36 O3 CCCOc1cc2c....
14 3E94 - TBY C12 H27 Sn CCCC[Sn](C....
15 4POJ Kd = 8 nM 2VP C21 H24 O2 Cc1ccc2c(c....
16 4K6I - 9RA C24 H28 O2 Cc1cc2c(cc....
17 2P1V - 5TN C26 H32 O4 CCCOc1cc2c....
18 7A77 - PLM C16 H32 O2 CCCCCCCCCC....
19 4ZSH Kd = 90 nM 4XW C20 H36 O2 C[C@H]1CC=....
20 3KWY - T9T C18 H15 Sn c1ccc(cc1)....
21 4RME Kd = 9 nM 3T2 C24 H36 O2 CC(C)CCC1=....
22 1MZN - BM6 C24 H27 O4 CC1(CCC(c2....
23 1MVC - BM6 C24 H27 O4 CC1(CCC(c2....
24 5LYQ - 7BE C26 H30 O4 CC1(CCC(c2....
25 7A78 - PLM C16 H32 O2 CCCCCCCCCC....
26 1XIU - 9CR C20 H28 O2 CC1=C(C(CC....
27 7A79 - PLM C16 H32 O2 CCCCCCCCCC....
28 4M8E Kd = 13 nM 29V C21 H26 O2 C[C@H]1CC/....
29 3OZJ - BGV C17 H20 O5 C[C@@H]1C[....
30 5MK4 - I5W C22 H18 O3 Cc1ccc(cc1....
31 5EC9 - 5LO C26 H30 O3 CC1(CCC(c2....
32 3OAP Kd = 14 nM 9CR C20 H28 O2 CC1=C(C(CC....
33 4M8H Kd = 25 nM R4M C21 H26 O2 C[C@@H]1CC....
34 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 220 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 6STI - 754 C26 H36 O3 CCCOc1cc2c....
14 3E94 - TBY C12 H27 Sn CCCC[Sn](C....
15 4POJ Kd = 8 nM 2VP C21 H24 O2 Cc1ccc2c(c....
16 4K6I - 9RA C24 H28 O2 Cc1cc2c(cc....
17 2P1V - 5TN C26 H32 O4 CCCOc1cc2c....
18 7A77 - PLM C16 H32 O2 CCCCCCCCCC....
19 4ZSH Kd = 90 nM 4XW C20 H36 O2 C[C@H]1CC=....
20 3KWY - T9T C18 H15 Sn c1ccc(cc1)....
21 4RME Kd = 9 nM 3T2 C24 H36 O2 CC(C)CCC1=....
22 7A78 - PLM C16 H32 O2 CCCCCCCCCC....
23 1XIU - 9CR C20 H28 O2 CC1=C(C(CC....
24 7A79 - PLM C16 H32 O2 CCCCCCCCCC....
25 4M8E Kd = 13 nM 29V C21 H26 O2 C[C@H]1CC/....
26 3OZJ - BGV C17 H20 O5 C[C@@H]1C[....
27 5MK4 - I5W C22 H18 O3 Cc1ccc(cc1....
28 5EC9 - 5LO C26 H30 O3 CC1(CCC(c2....
29 3OAP Kd = 14 nM 9CR C20 H28 O2 CC1=C(C(CC....
30 1PZL - MYR C14 H28 O2 CCCCCCCCCC....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: PLM; Similar ligands found: 64
No: Ligand ECFP6 Tc MDL keys Tc
1 PLM 1 1
2 STE 1 1
3 MYR 1 1
4 TDA 1 1
5 F23 1 1
6 DAO 1 1
7 X90 1 1
8 DCR 1 1
9 KNA 1 1
10 11A 1 1
11 EW8 1 1
12 F15 1 1
13 DKA 1 1
14 OCA 0.956522 1
15 SHV 0.833333 0.952381
16 KTC 0.793103 0.875
17 AZ1 0.73913 0.64
18 6NA 0.72 0.904762
19 ELA 0.71875 0.954545
20 NER 0.71875 0.954545
21 OLA 0.71875 0.954545
22 PAM 0.666667 0.954545
23 VCA 0.666667 0.954545
24 PML 0.625 0.6
25 3LA 0.606061 0.8
26 LEA 0.6 0.809524
27 MYZ 0.588235 0.909091
28 12H 0.586207 0.615385
29 ODD 0.567568 0.913043
30 BRC 0.566667 0.666667
31 14V 0.555556 0.740741
32 M12 0.545455 0.869565
33 14U 0.542857 0.703704
34 EOD 0.538462 0.7
35 EIC 0.538462 0.913043
36 BMJ 0.5 0.954545
37 BNV 0.5 0.954545
38 D0G 0.5 0.954545
39 BUA 0.48 0.666667
40 RCL 0.468085 0.84
41 FTT 0.459459 0.807692
42 56S 0.459459 0.653846
43 HXD 0.459459 0.807692
44 T4T 0.459459 0.8
45 ODT 0.452381 0.782609
46 3X1 0.444444 0.818182
47 LNL 0.44186 0.826087
48 9J6 0.441176 0.666667
49 OOA 0.441176 0.76
50 CUY 0.435897 0.68
51 CNS 0.435897 0.68
52 6UL 0.435897 0.68
53 5UF 0.432432 0.807692
54 243 0.428571 0.807692
55 EKG 0.418605 0.606061
56 GYM 0.418605 0.606061
57 1QW 0.418605 0.606061
58 OC9 0.413793 0.75
59 PL3 0.413793 0.75
60 F09 0.413793 0.75
61 DE1 0.413793 0.75
62 1DO 0.413793 0.75
63 O8N 0.413793 0.75
64 T25 0.403846 0.677419
Similar Ligands (3D)
Ligand no: 1; Ligand: PLM; Similar ligands found: 6
No: Ligand Similarity coefficient
1 16A 0.9171
2 O4B 0.9104
3 SP5 0.8963
4 EPA 0.8948
5 SSV 0.8891
6 ACA ACA 0.8666
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 7A78; Ligand: PLM; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 7a78.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 7A78; Ligand: PLM; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 7a78.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
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