Receptor
PDB id Resolution Class Description Source Keywords
5owd 2.15 Å EC: 2.3.1.48 VITAMIN D RECEPTOR COMPLEX DANIO RERIO NUCLEAR RECEPTOR VITAMIN D COMPLEX TRANSCRIPTION
Ref.: INVESTIGATION OF 20S-HYDROXYVITAMIN D3 ANALOGS AND ALPHA-OH DERIVATIVES AS POTENT VITAMIN D RECEPTOR A WITH ANTI-INFLAMMATORY ACTIVITIES. SCI REP V. 8 1478 2018
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
B0B A:4000;
 Valid;
 none;
 submit data
398.621 C27 H42 O2 CC(=C...
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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: B0B; Similar ligands found: 5
No: Ligand ECFP6 Tc MDL keys Tc
1 B0B 1 1
2 AYT 0.738095 1
3 AYK 0.652174 0.72549
4 VDY 0.520833 1
5 VD3 0.489583 0.921053
Similar Ligands (3D)
Ligand no: 1; Ligand: B0B; Similar ligands found: 15
No: Ligand Similarity coefficient
1 TEJ 0.9204
2 VDX 0.9141
3 MC9 0.9005
4 FMV 0.8986
5 COV 0.8945
6 2MV 0.8917
7 YSV 0.8842
8 0CO 0.8839
9 MVD 0.8834
10 VD2 0.8827
11 91W 0.8776
12 23R 0.8768
13 9KX 0.8750
14 VD4 0.8654
15 JC1 0.8538
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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