Receptor
PDB id Resolution Class Description Source Keywords
2HAM 1.9 Å NON-ENZYME: TRANSCRIPT_TRANSLATE CRYSTAL STRUCTURE OF VDR LBD COMPLEXED TO 2ALPHA-PROPYL-CALC HOMO SAPIENS ALPHA-HELICAL SANDWICH GENE REGULATION
Ref.: PROBING A WATER CHANNEL NEAR THE A-RING OF RECEPTOR 1ALPHA,25-DIHYDROXYVITAMIN D3 WITH SELECTED 2ALPHA-SUBSTITUTED ANALOGUES J.MED.CHEM. V. 49 5199 2006
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
C33 A:1001;
 Valid;
 none;
 submit data
458.716 C30 H50 O3 CCC[C...
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: C33; Similar ligands found: 35
No: Ligand ECFP6 Tc MDL keys Tc
1 C33 1 1
2 O1C 0.857143 0.911111
3 TEY 0.76699 0.61194
4 C3O 0.734694 0.913043
5 MVD 0.734043 0.97619
6 OCC 0.669903 0.854167
7 VDX 0.659794 0.97619
8 VDY 0.642105 0.904762
9 VDZ 0.608247 0.97619
10 VD2 0.608247 0.952381
11 YSV 0.608247 0.97619
12 VD3 0.514852 0.833333
13 YS3 0.5 0.952381
14 BIV 0.495327 0.97619
15 YS2 0.490196 0.888889
16 M7E 0.478632 0.661017
17 AKX 0.474138 0.909091
18 YSD 0.471698 0.952381
19 ZNE 0.442623 0.740741
20 VD1 0.431373 0.928571
21 JC1 0.429825 0.911111
22 YA1 0.421053 1
23 8BL 0.420168 0.888889
24 VHW 0.415385 0.788462
25 YI3 0.412281 0.97619
26 KH1 0.411765 0.911111
27 7ZU 0.410714 0.928571
28 TEJ 0.410256 0.829787
29 91W 0.408696 0.847826
30 8BO 0.404959 0.869565
31 9RO 0.404959 0.869565
32 EB1 0.403361 0.952381
33 8J0 0.401639 0.886364
34 8J3 0.401639 0.886364
35 TX5 0.4 0.883721
Similar Ligands (3D)
Ligand no: 1; Ligand: C33; Similar ligands found: 11
No: Ligand Similarity coefficient
1 2MV 0.9163
2 23R 0.9022
3 COV 0.8951
4 0CO 0.8826
5 MC9 0.8804
6 VD4 0.8762
7 FMV 0.8685
8 YI4 0.8649
9 AYT 0.8626
10 90O 0.8622
11 CA9 0.8576
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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