Receptor
PDB id Resolution Class Description Source Keywords
1db1 1.8 Å NON-ENZYME: TRANSCRIPT_TRANSLATE CRYSTAL STRUCTURE OF THE NUCLEAR RECEPTOR FOR VITAMIN D COMP VITAMIN D HOMO SAPIENS COMPLEX GENE REGULATION
Ref.: THE CRYSTAL STRUCTURE OF THE NUCLEAR RECEPTOR FOR V BOUND TO ITS NATURAL LIGAND. MOL.CELL V. 5 173 2000
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
VDX A:428;
Valid;
none;
Kd = 0.55 nM
416.636 C27 H44 O3 C[C@H...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1DB1 1.8 Å NON-ENZYME: TRANSCRIPT_TRANSLATE CRYSTAL STRUCTURE OF THE NUCLEAR RECEPTOR FOR VITAMIN D COMP VITAMIN D HOMO SAPIENS COMPLEX GENE REGULATION
Ref.: THE CRYSTAL STRUCTURE OF THE NUCLEAR RECEPTOR FOR V BOUND TO ITS NATURAL LIGAND. MOL.CELL V. 5 173 2000
Members (31)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 308 families.
1 3A3Z - 2MV C29 H46 O4 C[C@H]1[C@....
2 1IE8 - KH1 C29 H48 O4 CCC(CC)(CC....
3 2HAS - C3O C30 H50 O4 CCCO[C@H]1....
4 1S0Z - EB1 C30 H46 O3 CCC(CC)(C=....
5 3AZ1 - DS2 C27 H38 O5 CCC(CC)(c1....
6 1IE9 - VDX C27 H44 O3 C[C@H](CCC....
7 2HAM - C33 C30 H50 O3 CCC[C@H]1[....
8 2HB8 - MVD C28 H46 O3 C[C@H]1[C@....
9 3CS4 - COV C28 H44 O4 C[C@]12CCC....
10 1S19 - MC9 C27 H40 O3 C[C@H](C=C....
11 3M7R - VDX C27 H44 O3 C[C@H](CCC....
12 3A40 - 23R C29 H46 O4 C[C@H]1[C@....
13 3AUR - CA9 C27 H42 O3 C[C@H]1[C@....
14 3KPZ - ZNE C28 H41 N O3 S C[C@H](CCC....
15 1TXI - TX5 C26 H40 O3 C[C@H](CC#....
16 1DB1 Kd = 0.55 nM VDX C27 H44 O3 C[C@H](CCC....
17 4G2I - 0VQ C25 H26 F6 O3 CC/C(=CC=C....
18 3CS6 - 0CO C28 H44 O4 C[C@]12CCC....
19 3AZ2 - DS3 C30 H44 O5 CCC(CC)(c1....
20 3AZ3 - DS6 C31 H46 O5 CCC(CC)(c1....
21 5YT2 - 90O C29 H48 O4 C[C@H](CCC....
22 5GIE Kd = 769.2 nM VDP C37 H53 N O4 C[C@H](C[C....
23 2HB7 - O1C C30 H50 O4 C[C@H](CCC....
24 3VHW - VHW C34 H50 O7 CCC1(CC/C(....
25 2HAR - OCC C30 H50 O5 C[C@H](CCC....
26 5GID Kd = 769.2 nM VDP C37 H53 N O4 C[C@H](C[C....
27 3TKC - FMV C28 H40 O4 C[C@H](c1c....
28 4ITE - TEY C30 H48 N4 O3 C[C@H](CCC....
29 5GIC Kd = 330.9 nM DLC C35 H51 N O4 C[C@H]1/C(....
30 3P8X - ZYD C27 H44 O3 CC(C)(CCCC....
31 5YSY - 90L C29 H48 O4 C[C@H](CCC....
70% Homology Family (32)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 266 families.
1 4Q0A Kd = 0.33 uM 4OA C24 H40 O3 C[C@H](CCC....
2 3A3Z - 2MV C29 H46 O4 C[C@H]1[C@....
3 1IE8 - KH1 C29 H48 O4 CCC(CC)(CC....
4 2HAS - C3O C30 H50 O4 CCCO[C@H]1....
5 1S0Z - EB1 C30 H46 O3 CCC(CC)(C=....
6 3AZ1 - DS2 C27 H38 O5 CCC(CC)(c1....
7 1IE9 - VDX C27 H44 O3 C[C@H](CCC....
8 2HAM - C33 C30 H50 O3 CCC[C@H]1[....
9 2HB8 - MVD C28 H46 O3 C[C@H]1[C@....
10 3CS4 - COV C28 H44 O4 C[C@]12CCC....
11 1S19 - MC9 C27 H40 O3 C[C@H](C=C....
12 3M7R - VDX C27 H44 O3 C[C@H](CCC....
13 3A40 - 23R C29 H46 O4 C[C@H]1[C@....
14 3AUR - CA9 C27 H42 O3 C[C@H]1[C@....
15 3KPZ - ZNE C28 H41 N O3 S C[C@H](CCC....
16 1TXI - TX5 C26 H40 O3 C[C@H](CC#....
17 1DB1 Kd = 0.55 nM VDX C27 H44 O3 C[C@H](CCC....
18 4G2I - 0VQ C25 H26 F6 O3 CC/C(=CC=C....
19 3CS6 - 0CO C28 H44 O4 C[C@]12CCC....
20 3AZ2 - DS3 C30 H44 O5 CCC(CC)(c1....
21 3AZ3 - DS6 C31 H46 O5 CCC(CC)(c1....
22 5YT2 - 90O C29 H48 O4 C[C@H](CCC....
23 5GIE Kd = 769.2 nM VDP C37 H53 N O4 C[C@H](C[C....
24 2HB7 - O1C C30 H50 O4 C[C@H](CCC....
25 3VHW - VHW C34 H50 O7 CCC1(CC/C(....
26 2HAR - OCC C30 H50 O5 C[C@H](CCC....
27 5GID Kd = 769.2 nM VDP C37 H53 N O4 C[C@H](C[C....
28 3TKC - FMV C28 H40 O4 C[C@H](c1c....
29 4ITE - TEY C30 H48 N4 O3 C[C@H](CCC....
30 5GIC Kd = 330.9 nM DLC C35 H51 N O4 C[C@H]1/C(....
31 3P8X - ZYD C27 H44 O3 CC(C)(CCCC....
32 5YSY - 90L C29 H48 O4 C[C@H](CCC....
50% Homology Family (40)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 220 families.
1 4Q0A Kd = 0.33 uM 4OA C24 H40 O3 C[C@H](CCC....
2 3A3Z - 2MV C29 H46 O4 C[C@H]1[C@....
3 1IE8 - KH1 C29 H48 O4 CCC(CC)(CC....
4 2HAS - C3O C30 H50 O4 CCCO[C@H]1....
5 1S0Z - EB1 C30 H46 O3 CCC(CC)(C=....
6 3AZ1 - DS2 C27 H38 O5 CCC(CC)(c1....
7 1IE9 - VDX C27 H44 O3 C[C@H](CCC....
8 2HAM - C33 C30 H50 O3 CCC[C@H]1[....
9 2HB8 - MVD C28 H46 O3 C[C@H]1[C@....
10 3CS4 - COV C28 H44 O4 C[C@]12CCC....
11 1S19 - MC9 C27 H40 O3 C[C@H](C=C....
12 3M7R - VDX C27 H44 O3 C[C@H](CCC....
13 3A40 - 23R C29 H46 O4 C[C@H]1[C@....
14 3AUR - CA9 C27 H42 O3 C[C@H]1[C@....
15 3KPZ - ZNE C28 H41 N O3 S C[C@H](CCC....
16 1TXI - TX5 C26 H40 O3 C[C@H](CC#....
17 1DB1 Kd = 0.55 nM VDX C27 H44 O3 C[C@H](CCC....
18 4G2I - 0VQ C25 H26 F6 O3 CC/C(=CC=C....
19 3CS6 - 0CO C28 H44 O4 C[C@]12CCC....
20 3AZ2 - DS3 C30 H44 O5 CCC(CC)(c1....
21 3AZ3 - DS6 C31 H46 O5 CCC(CC)(c1....
22 5YT2 - 90O C29 H48 O4 C[C@H](CCC....
23 5GIE Kd = 769.2 nM VDP C37 H53 N O4 C[C@H](C[C....
24 2HB7 - O1C C30 H50 O4 C[C@H](CCC....
25 3VHW - VHW C34 H50 O7 CCC1(CC/C(....
26 2HAR - OCC C30 H50 O5 C[C@H](CCC....
27 5GID Kd = 769.2 nM VDP C37 H53 N O4 C[C@H](C[C....
28 3TKC - FMV C28 H40 O4 C[C@H](c1c....
29 4ITE - TEY C30 H48 N4 O3 C[C@H](CCC....
30 1PQ9 - BNS C6 H6 O3 S c1ccc(cc1)....
31 4RAK Ki = 14 nM 652 C28 H29 Cl N2 O3 S CC(C)(c1cc....
32 6S4T Ki = 0.00000079 M KVB C32 H24 F3 N O3 c1ccc(cc1)....
33 6K9H Ki = 600 nM D40 C22 H24 N2 O3 CC(C)(C)OC....
34 1UPV - 444 C17 H12 F9 N O3 S c1ccc(cc1)....
35 1PQ6 - 965 C33 H31 Cl F3 N O3 c1ccc(cc1)....
36 6S4N Kd = 1.6 uM KUW C24 H27 Cl N4 O5 S CC(C)N1C(=....
37 1UPW - 444 C17 H12 F9 N O3 S c1ccc(cc1)....
38 5JY3 Ki = 12 nM 6OX C29 H28 Cl2 F2 N2 O4 S CC(C)(c1cn....
39 3KFC ic50 = 2.8 nM 61X C23 H16 F3 N O3 S CS(=O)(=O)....
40 6S5K Ki = 0.00000079 M KWE C28 H28 N2 O2 c1ccc(cc1)....
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 : 1DB1; Ligand: VDX; 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: 1db1.bio1) has 52 residues
No: Leader PDB Ligand Sequence Similarity
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