Receptor
PDB id Resolution Class Description Source Keywords
2HC4 2.2 Å EC: 2.3.1.48 CRYSTAL STRUCTURE OF THE LBD OF VDR OF DANIO RERIO IN COMPLEX WITH CALCITRIOL DANIO RERIO ALPHA HELICAL SANDWICH GENE REGULATION
Ref.: ADAPTABILITY OF THE VITAMIN D NUCLEAR RECEPTOR TO THE SYNTHETIC LIGAND GEMINI: REMODELLING THE LBP WITH ONE SIDE CHAIN ROTATION J.STEROID BIOCHEM.MOL.BIOL. V. 103 235 2007
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
VDX A:525;
Valid;
none;
submit data
416.636 C27 H44 O3 C[C@H...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5E7V 2.4 Å EC: 2.3.1.48 POTENT VITAMIN D RECEPTOR AGONIST DANIO RERIO TRANSCRIPTION VITAMIN D NUCLEAR RECEPTOR VDR LIGAND BINDI
Ref.: CARBORANE-BASED DESIGN OF A POTENT VITAMIN D RECEPT AGONIST. CHEM SCI V. 7 1033 2016
Members (11)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 64 families.
1 4G1Z - 0VP C31 H40 O4 CCCc1cc(cc....
2 4RUJ - VDX C27 H44 O3 C[C@H](CCC....
3 5NKY - 91W C28 H44 O4 C[C@@H]([C....
4 6FOD ic50 = 7.11 nM E05 C26 H38 O3 CC/C(=CC=C....
5 6FO8 ic50 = 18.4 nM DZT C30 H46 O3 CCCCCC/C(=....
6 5OW9 - AYT C27 H44 O2 CC(C)CCC[C....
7 5E7V ic50 = 2.9 nM M7E C26 H37 B10 O2 B1234B567B....
8 5OW7 - AYK C26 H41 N O3 CC(C)NC(=O....
9 5OWD - B0B C27 H42 O2 CC(=CCC[C@....
10 2HC4 - VDX C27 H44 O3 C[C@H](CCC....
11 4G2H - 0VQ C25 H26 F6 O3 CC/C(=CC=C....
70% Homology Family (17)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 35 families.
1 4G1Z - 0VP C31 H40 O4 CCCc1cc(cc....
2 4RUJ - VDX C27 H44 O3 C[C@H](CCC....
3 5NKY - 91W C28 H44 O4 C[C@@H]([C....
4 6FOD ic50 = 7.11 nM E05 C26 H38 O3 CC/C(=CC=C....
5 6FO8 ic50 = 18.4 nM DZT C30 H46 O3 CCCCCC/C(=....
6 5OW9 - AYT C27 H44 O2 CC(C)CCC[C....
7 5E7V ic50 = 2.9 nM M7E C26 H37 B10 O2 B1234B567B....
8 5OW7 - AYK C26 H41 N O3 CC(C)NC(=O....
9 5OWD - B0B C27 H42 O2 CC(=CCC[C@....
10 2HC4 - VDX C27 H44 O3 C[C@H](CCC....
11 4G2H - 0VQ C25 H26 F6 O3 CC/C(=CC=C....
12 4FHH ic50 = 35 nM 0U3 C27 H39 N O5 CCC(CC)(c1....
13 4IA1 - BIV C32 H54 O4 C[C@]12CCC....
14 3O1E - H97 C31 H44 F6 O4 C[C@]12CCC....
15 4FHI ic50 = 100 nM 0S4 C27 H39 N O5 CCC(CC)(c1....
16 3O1D - G72 C31 H44 F6 O4 C[C@]12CCC....
17 5LGA ic50 = 0.23 nM 6VH C32 H40 F6 O4 C[C@]12CCC....
50% Homology Family (19)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 25 families.
1 4G1Z - 0VP C31 H40 O4 CCCc1cc(cc....
2 4RUJ - VDX C27 H44 O3 C[C@H](CCC....
3 5NKY - 91W C28 H44 O4 C[C@@H]([C....
4 6FOD ic50 = 7.11 nM E05 C26 H38 O3 CC/C(=CC=C....
5 6FO8 ic50 = 18.4 nM DZT C30 H46 O3 CCCCCC/C(=....
6 5OW9 - AYT C27 H44 O2 CC(C)CCC[C....
7 5E7V ic50 = 2.9 nM M7E C26 H37 B10 O2 B1234B567B....
8 5OW7 - AYK C26 H41 N O3 CC(C)NC(=O....
9 5OWD - B0B C27 H42 O2 CC(=CCC[C@....
10 2HC4 - VDX C27 H44 O3 C[C@H](CCC....
11 4G2H - 0VQ C25 H26 F6 O3 CC/C(=CC=C....
12 4FHH ic50 = 35 nM 0U3 C27 H39 N O5 CCC(CC)(c1....
13 4IA1 - BIV C32 H54 O4 C[C@]12CCC....
14 3O1E - H97 C31 H44 F6 O4 C[C@]12CCC....
15 4FHI ic50 = 100 nM 0S4 C27 H39 N O5 CCC(CC)(c1....
16 3O1D - G72 C31 H44 F6 O4 C[C@]12CCC....
17 5LGA ic50 = 0.23 nM 6VH C32 H40 F6 O4 C[C@]12CCC....
18 5A86 - D7E C18 H17 Cl F3 N3 O2 S CCn1c2cc(c....
19 1NRL - SRL C24 H42 O7 P2 CCOP(=O)(C....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: VDX; Similar ligands found: 48
No: Ligand ECFP6 Tc MDL keys Tc
1 VDX 1 1
2 BIV 0.758621 1
3 MVD 0.714286 1
4 VDY 0.712644 0.926829
5 M7E 0.693878 0.672414
6 VDZ 0.674157 1
7 YSV 0.674157 1
8 C33 0.659794 0.97619
9 ZNE 0.656863 0.754717
10 VD2 0.655556 0.97561
11 O1C 0.653061 0.931818
12 C3O 0.646465 0.891304
13 7ZU 0.641304 0.951219
14 OCC 0.633663 0.87234
15 TEJ 0.628866 0.847826
16 JC1 0.625 0.888889
17 MC9 0.623656 0.904762
18 91W 0.614583 0.866667
19 KH1 0.61 0.888889
20 8J3 0.607843 0.906977
21 8J0 0.607843 0.906977
22 EB1 0.6 0.928571
23 FMV 0.58 0.829787
24 TEY 0.576577 0.621212
25 ICJ 0.572816 0.97619
26 6VH 0.567308 0.833333
27 YS3 0.553191 0.97561
28 VD3 0.553191 0.853659
29 YS2 0.542553 0.909091
30 VDP 0.520661 0.634921
31 AKX 0.518519 0.930233
32 YSD 0.50505 0.928571
33 ZYD 0.50505 1
34 0CO 0.5 0.851064
35 COV 0.5 0.851064
36 VD1 0.463158 0.904762
37 TX5 0.455446 0.904762
38 8BL 0.446429 0.909091
39 8BO 0.442478 0.888889
40 9RO 0.442478 0.888889
41 G72 0.4375 0.851064
42 H97 0.4375 0.851064
43 YA1 0.435185 0.97619
44 YI3 0.425926 0.952381
45 AYT 0.419048 0.926829
46 YI4 0.405405 0.909091
47 TKA 0.403509 0.906977
48 TK3 0.401709 0.906977
Similar Ligands (3D)
Ligand no: 1; Ligand: VDX; Similar ligands found: 9
No: Ligand Similarity coefficient
1 VD4 0.9544
2 2MV 0.9456
3 23R 0.9333
4 B0B 0.9141
5 AYK 0.9083
6 CA9 0.8970
7 VD5 0.8944
8 E05 0.8839
9 9KX 0.8607
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5E7V; Ligand: M7E; 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: 5e7v.bio1) has 30 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5E7V; Ligand: M7E; 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: 5e7v.bio1) has 30 residues
No: Leader PDB Ligand Sequence Similarity
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