Receptor
PDB id Resolution Class Description Source Keywords
5UL5 2.2 Å EC: 3.1.1.64 CRYSTAL STRUCTURE OF RPE65 IN COMPLEX WITH MB-004 AND PALMIT BOS TAURUS RETINOID ISOMERASE NON-HEME IRON ENZYME INHIBITOR ISOMERAISOMERASE-ISOMERASE INHIBITOR COMPLEX
Ref.: RATIONAL TUNING OF VISUAL CYCLE MODULATOR PHARMACOD J. PHARMACOL. EXP. THER. V. 362 131 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
8D7 B:603;
A:603;
 Valid;
Valid;
 none;
none;
 ic50 = 106 nM
279.418 C17 H29 N O2 CCCC(...
NA B:605;
A:604;
 Part of Protein;
Part of Protein;
 none;
none;
 submit data
22.99 Na [Na+]
PLM A:602;
B:602;
 Valid;
Valid;
 none;
none;
 submit data
256.424 C16 H32 O2 CCCCC...
FE2 B:601;
A:601;
 Part of Protein;
Part of Protein;
 none;
none;
 submit data
55.845 Fe [Fe+2...
PG6 A:605;
B:604;
 Invalid;
Invalid;
 none;
none;
 submit data
266.331 C12 H26 O6 COCCO...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5UL5 2.2 Å EC: 3.1.1.64 CRYSTAL STRUCTURE OF RPE65 IN COMPLEX WITH MB-004 AND PALMIT BOS TAURUS RETINOID ISOMERASE NON-HEME IRON ENZYME INHIBITOR ISOMERAISOMERASE-ISOMERASE INHIBITOR COMPLEX
Ref.: RATIONAL TUNING OF VISUAL CYCLE MODULATOR PHARMACOD J. PHARMACOL. EXP. THER. V. 362 131 2017
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 4RSC ic50 = 232 nM A3V C16 H25 N O2 c1cc(cc(c1....
2 5UL5 ic50 = 106 nM 8D7 C17 H29 N O2 CCCC(CCC)C....
3 5ULG ic50 = 189 nM 8E4 C16 H27 N O3 CCC[C@@H](....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 4RSC ic50 = 232 nM A3V C16 H25 N O2 c1cc(cc(c1....
2 5UL5 ic50 = 106 nM 8D7 C17 H29 N O2 CCCC(CCC)C....
3 5ULG ic50 = 189 nM 8E4 C16 H27 N O3 CCC[C@@H](....
50% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 4RSC ic50 = 232 nM A3V C16 H25 N O2 c1cc(cc(c1....
2 5UL5 ic50 = 106 nM 8D7 C17 H29 N O2 CCCC(CCC)C....
3 5ULG ic50 = 189 nM 8E4 C16 H27 N O3 CCC[C@@H](....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: 8D7; Similar ligands found: 4
No: Ligand ECFP6 Tc MDL keys Tc
1 8D7 1 1
2 8E4 0.886792 0.926829
3 A6V 0.5 0.77551
4 A3V 0.492537 0.829268
Ligand no: 2; 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: 8D7; Similar ligands found: 0
No: Ligand Similarity coefficient
Ligand no: 2; 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 : 5UL5; Ligand: 8D7; 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: 5ul5.bio1) has 36 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5UL5; 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: 5ul5.bio1) has 36 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 5UL5; 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: 3) in the query (biounit: 5ul5.bio1) has 36 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 5UL5; Ligand: 8D7; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 5ul5.bio1) has 36 residues
No: Leader PDB Ligand Sequence Similarity
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