Receptor
PDB id Resolution Class Description Source Keywords
3VTC 1.5 Å NON-ENZYME: SIGNAL_HORMONE CRYSTAL STRUCTURE OF RAT VITAMIN D RECEPTOR BOUND TO A PARTI 26-ADAMANTYL-23-YNE-19-NORVITAMMIN D ADTK3 RATTUS NORVEGICUS TRANSCRIPTION HORMONE RECEPTOR
Ref.: COMBINATION OF TRIPLE BOND AND ADAMANTANE RING ON T VITAMIN D SIDE CHAIN PRODUCED PARTIAL AGONISTS FOR RECEPTOR. J.MED.CHEM. 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
EDO A:501;
 Invalid;
 none;
 submit data
62.068 C2 H6 O2 C(CO)...
TK3 A:500;
 Valid;
 none;
 ic50 = 13 nM
532.796 C36 H52 O3 C[C@H...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3VRV 1.9 Å NON-ENZYME: SIGNAL_HORMONE VDR LIGAND BINDING DOMAIN IN COMPLEX WITH 2-METHYLIDENE-26,2 DIMETHYL-19,24-DINOR-1ALPHA,25-DIHYDROXYVITAMIN D3 RATTUS NORVEGICUS NUCLEAR HORMONE RECEPTOR TRANSCRIPTION VITAMIN D3 VDRE RFACTORS NUCLEAR
Ref.: BUTYL POCKET FORMATION IN THE VITAMIN D RECEPTOR ST AFFECTS THE AGONISTIC OR ANTAGONISTIC BEHAVIOR OF L J.MED.CHEM. V. 55 4373 2012
Members (50)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 289 families.
1 2ZMI ic50 = 3 nM TT2 C35 H52 O3 C[C@@H](C=....
2 3VT6 - 5YI C28 H44 O4 S CCC(CC)(CS....
3 3W0I - O11 C26 H38 O5 CCC(CC)(c1....
4 3VT9 - YI4 C31 H50 O4 C[C@H](CCC....
5 6JEZ - YSV C27 H44 O3 C[C@H](CCC....
6 3VT5 - YI2 C28 H44 O4 S CCC(CC)(CS....
7 2ZLA - VDB C28 H46 O5 S CCC(CC)(CS....
8 2ZLC - VDX C27 H44 O3 C[C@H](CCC....
9 3VT7 - VDX C27 H44 O3 C[C@H](CCC....
10 2ZFX - YR3 C28 H42 O5 CCC(CC)(c1....
11 3VJT ic50 = 4.1 uM 10R C17 H42 B10 O4 [BH]1234[B....
12 3WT5 ic50 = 0.29 nM YA1 C31 H52 O3 CCCC[C@H](....
13 5XPM ic50 = 23 nM 8C0 C36 H54 O4 CCCC[C@@H]....
14 4YNK - YW2 C34 H44 O3 C[C@]12CCC....
15 5B41 - YSV C27 H44 O3 C[C@H](CCC....
16 3W0H - W12 C28 H42 O5 CCCC(CCC)(....
17 6K5O - D0O C25 H42 O5 S C[C@H](CCC....
18 3W0G - W07 C24 H34 O5 CC(C)(C)[C....
19 3VTB ic50 = 0.5 nM TKA C35 H50 O3 C[C@H](CC#....
20 5XZF ic50 = 0.24 nM 8J0 C35 H50 O3 C[C@H](CC#....
21 5B5B ic50 = 0.43 nM AKX C39 H52 O3 C[C@H](CCC....
22 5XPO ic50 = 84 nM 8BL C31 H42 O4 C[C@H](CCC....
23 5ZWI ic50 = 2.3 nM 9KX C27 H38 O3 C/C=C/C=C/....
24 3VT8 - YI3 C30 H52 O3 CCCC[C@@H]....
25 3W0J - T08 C26 H38 O5 Cc1cc(ccc1....
26 3VT4 - 5YI C28 H44 O4 S CCC(CC)(CS....
27 3VJS ic50 = 0.64 uM 10S C17 H42 B10 O4 [BH]1234[B....
28 3W5T - LHP C27 H44 O4 CCC(=O)O[C....
29 3VRU ic50 = 0.1 nM YS3 C26 H42 O3 C[C@H](CCC....
30 3AUN - YR4 C29 H44 O5 CCC(CC)(c1....
31 2ZMH - NYA C34 H50 O3 C[C@H](C=C....
32 5AWJ ic50 = 0.21 nM YSL C30 H50 O3 CCCCCC[C@@....
33 3W5R - LOA C26 H42 O4 C[C@H](CCC....
34 2ZL9 - VDA C28 H46 O5 S CCC(CC)(CS....
35 5XZH ic50 = 3.13 nM 8J3 C35 H50 O3 C[C@H](CC#....
36 3VRW ic50 = 0.41 nM YS5 C32 H54 O3 CCCC[C@@H]....
37 3VT3 - VDX C27 H44 O3 C[C@H](CCC....
38 3VRT ic50 = 2.7 nM YS2 C24 H38 O3 C[C@H](CCC....
39 3VTC ic50 = 13 nM TK3 C36 H52 O3 C[C@H](CC#....
40 3AFR - ICJ C31 H52 O3 CCCC[C@@H]....
41 3WT6 ic50 = 0.29 nM YA1 C31 H52 O3 CCCC[C@H](....
42 5XPN ic50 = 102 nM 9RO C32 H46 O4 C[C@H](CCC....
43 5ZWH ic50 = 1.9 nM 9N9 C27 H36 O3 C/C=C/C#CC....
44 2ZXN - JC1 C28 H46 O3 CCCC[C@@H]....
45 3A2H - TEJ C27 H38 O4 C[C@@H](C[....
46 3W5P - 4OA C24 H40 O3 C[C@H](CCC....
47 3WT7 ic50 = 1.79 nM YA2 C32 H54 O3 CCCC[C@H](....
48 3VRV ic50 = 0.029 nM YSD C28 H46 O3 CCC(CC)(CC....
49 3W5Q - 3KL C24 H38 O3 C[C@H](CCC....
50 2ZMJ ic50 = 30 nM MI4 C36 H54 O3 C[C@@H](C=....
70% Homology Family (56)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 214 families.
1 2ZMI ic50 = 3 nM TT2 C35 H52 O3 C[C@@H](C=....
2 3VT6 - 5YI C28 H44 O4 S CCC(CC)(CS....
3 3W0I - O11 C26 H38 O5 CCC(CC)(c1....
4 3VT9 - YI4 C31 H50 O4 C[C@H](CCC....
5 6JEZ - YSV C27 H44 O3 C[C@H](CCC....
6 3VT5 - YI2 C28 H44 O4 S CCC(CC)(CS....
7 2ZLA - VDB C28 H46 O5 S CCC(CC)(CS....
8 2ZLC - VDX C27 H44 O3 C[C@H](CCC....
9 3VT7 - VDX C27 H44 O3 C[C@H](CCC....
10 2ZFX - YR3 C28 H42 O5 CCC(CC)(c1....
11 3VJT ic50 = 4.1 uM 10R C17 H42 B10 O4 [BH]1234[B....
12 3WT5 ic50 = 0.29 nM YA1 C31 H52 O3 CCCC[C@H](....
13 5XPM ic50 = 23 nM 8C0 C36 H54 O4 CCCC[C@@H]....
14 4YNK - YW2 C34 H44 O3 C[C@]12CCC....
15 5B41 - YSV C27 H44 O3 C[C@H](CCC....
16 3W0H - W12 C28 H42 O5 CCCC(CCC)(....
17 6K5O - D0O C25 H42 O5 S C[C@H](CCC....
18 3W0G - W07 C24 H34 O5 CC(C)(C)[C....
19 3VTB ic50 = 0.5 nM TKA C35 H50 O3 C[C@H](CC#....
20 5XZF ic50 = 0.24 nM 8J0 C35 H50 O3 C[C@H](CC#....
21 5B5B ic50 = 0.43 nM AKX C39 H52 O3 C[C@H](CCC....
22 5XPO ic50 = 84 nM 8BL C31 H42 O4 C[C@H](CCC....
23 5ZWI ic50 = 2.3 nM 9KX C27 H38 O3 C/C=C/C=C/....
24 3VT8 - YI3 C30 H52 O3 CCCC[C@@H]....
25 3W0J - T08 C26 H38 O5 Cc1cc(ccc1....
26 3VT4 - 5YI C28 H44 O4 S CCC(CC)(CS....
27 3VJS ic50 = 0.64 uM 10S C17 H42 B10 O4 [BH]1234[B....
28 3W5T - LHP C27 H44 O4 CCC(=O)O[C....
29 3VRU ic50 = 0.1 nM YS3 C26 H42 O3 C[C@H](CCC....
30 3AUN - YR4 C29 H44 O5 CCC(CC)(c1....
31 2ZMH - NYA C34 H50 O3 C[C@H](C=C....
32 5AWJ ic50 = 0.21 nM YSL C30 H50 O3 CCCCCC[C@@....
33 3W5R - LOA C26 H42 O4 C[C@H](CCC....
34 2ZL9 - VDA C28 H46 O5 S CCC(CC)(CS....
35 5XZH ic50 = 3.13 nM 8J3 C35 H50 O3 C[C@H](CC#....
36 3VRW ic50 = 0.41 nM YS5 C32 H54 O3 CCCC[C@@H]....
37 3VT3 - VDX C27 H44 O3 C[C@H](CCC....
38 3VRT ic50 = 2.7 nM YS2 C24 H38 O3 C[C@H](CCC....
39 3VTC ic50 = 13 nM TK3 C36 H52 O3 C[C@H](CC#....
40 3AFR - ICJ C31 H52 O3 CCCC[C@@H]....
41 3WT6 ic50 = 0.29 nM YA1 C31 H52 O3 CCCC[C@H](....
42 5XPN ic50 = 102 nM 9RO C32 H46 O4 C[C@H](CCC....
43 5ZWH ic50 = 1.9 nM 9N9 C27 H36 O3 C/C=C/C#CC....
44 2ZXN - JC1 C28 H46 O3 CCCC[C@@H]....
45 3A2H - TEJ C27 H38 O4 C[C@@H](C[....
46 3W5P - 4OA C24 H40 O3 C[C@H](CCC....
47 3WT7 ic50 = 1.79 nM YA2 C32 H54 O3 CCCC[C@H](....
48 3VRV ic50 = 0.029 nM YSD C28 H46 O3 CCC(CC)(CC....
49 3W5Q - 3KL C24 H38 O3 C[C@H](CCC....
50 2ZMJ ic50 = 30 nM MI4 C36 H54 O3 C[C@@H](C=....
51 1RJK - VDZ C27 H44 O3 C[C@@H](CC....
52 2O4J Ki = 0.08 nM VD4 C27 H42 O3 C/C(=C/1CC....
53 1RKG - VD1 C23 H36 O2 CC[C@H](C)....
54 1RK3 Kd = 0.37 nM VDX C27 H44 O3 C[C@H](CCC....
55 2O4R Ki = 0.4 nM VD5 C27 H42 O3 C/C(=C1/CC....
56 1RKH - VD2 C27 H46 O3 CC1[C@@H](....
50% Homology Family (56)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 181 families.
1 2ZMI ic50 = 3 nM TT2 C35 H52 O3 C[C@@H](C=....
2 3VT6 - 5YI C28 H44 O4 S CCC(CC)(CS....
3 3W0I - O11 C26 H38 O5 CCC(CC)(c1....
4 3VT9 - YI4 C31 H50 O4 C[C@H](CCC....
5 6JEZ - YSV C27 H44 O3 C[C@H](CCC....
6 3VT5 - YI2 C28 H44 O4 S CCC(CC)(CS....
7 2ZLA - VDB C28 H46 O5 S CCC(CC)(CS....
8 2ZLC - VDX C27 H44 O3 C[C@H](CCC....
9 3VT7 - VDX C27 H44 O3 C[C@H](CCC....
10 2ZFX - YR3 C28 H42 O5 CCC(CC)(c1....
11 3VJT ic50 = 4.1 uM 10R C17 H42 B10 O4 [BH]1234[B....
12 3WT5 ic50 = 0.29 nM YA1 C31 H52 O3 CCCC[C@H](....
13 5XPM ic50 = 23 nM 8C0 C36 H54 O4 CCCC[C@@H]....
14 4YNK - YW2 C34 H44 O3 C[C@]12CCC....
15 5B41 - YSV C27 H44 O3 C[C@H](CCC....
16 3W0H - W12 C28 H42 O5 CCCC(CCC)(....
17 6K5O - D0O C25 H42 O5 S C[C@H](CCC....
18 3W0G - W07 C24 H34 O5 CC(C)(C)[C....
19 3VTB ic50 = 0.5 nM TKA C35 H50 O3 C[C@H](CC#....
20 5XZF ic50 = 0.24 nM 8J0 C35 H50 O3 C[C@H](CC#....
21 5B5B ic50 = 0.43 nM AKX C39 H52 O3 C[C@H](CCC....
22 5XPO ic50 = 84 nM 8BL C31 H42 O4 C[C@H](CCC....
23 5ZWI ic50 = 2.3 nM 9KX C27 H38 O3 C/C=C/C=C/....
24 3VT8 - YI3 C30 H52 O3 CCCC[C@@H]....
25 3W0J - T08 C26 H38 O5 Cc1cc(ccc1....
26 3VT4 - 5YI C28 H44 O4 S CCC(CC)(CS....
27 3VJS ic50 = 0.64 uM 10S C17 H42 B10 O4 [BH]1234[B....
28 3W5T - LHP C27 H44 O4 CCC(=O)O[C....
29 3VRU ic50 = 0.1 nM YS3 C26 H42 O3 C[C@H](CCC....
30 3AUN - YR4 C29 H44 O5 CCC(CC)(c1....
31 2ZMH - NYA C34 H50 O3 C[C@H](C=C....
32 5AWJ ic50 = 0.21 nM YSL C30 H50 O3 CCCCCC[C@@....
33 3W5R - LOA C26 H42 O4 C[C@H](CCC....
34 2ZL9 - VDA C28 H46 O5 S CCC(CC)(CS....
35 5XZH ic50 = 3.13 nM 8J3 C35 H50 O3 C[C@H](CC#....
36 3VRW ic50 = 0.41 nM YS5 C32 H54 O3 CCCC[C@@H]....
37 3VT3 - VDX C27 H44 O3 C[C@H](CCC....
38 3VRT ic50 = 2.7 nM YS2 C24 H38 O3 C[C@H](CCC....
39 3VTC ic50 = 13 nM TK3 C36 H52 O3 C[C@H](CC#....
40 3AFR - ICJ C31 H52 O3 CCCC[C@@H]....
41 3WT6 ic50 = 0.29 nM YA1 C31 H52 O3 CCCC[C@H](....
42 5XPN ic50 = 102 nM 9RO C32 H46 O4 C[C@H](CCC....
43 5ZWH ic50 = 1.9 nM 9N9 C27 H36 O3 C/C=C/C#CC....
44 2ZXN - JC1 C28 H46 O3 CCCC[C@@H]....
45 3A2H - TEJ C27 H38 O4 C[C@@H](C[....
46 3W5P - 4OA C24 H40 O3 C[C@H](CCC....
47 3WT7 ic50 = 1.79 nM YA2 C32 H54 O3 CCCC[C@H](....
48 3VRV ic50 = 0.029 nM YSD C28 H46 O3 CCC(CC)(CC....
49 3W5Q - 3KL C24 H38 O3 C[C@H](CCC....
50 2ZMJ ic50 = 30 nM MI4 C36 H54 O3 C[C@@H](C=....
51 1RJK - VDZ C27 H44 O3 C[C@@H](CC....
52 2O4J Ki = 0.08 nM VD4 C27 H42 O3 C/C(=C/1CC....
53 1RKG - VD1 C23 H36 O2 CC[C@H](C)....
54 1RK3 Kd = 0.37 nM VDX C27 H44 O3 C[C@H](CCC....
55 2O4R Ki = 0.4 nM VD5 C27 H42 O3 C/C(=C1/CC....
56 1RKH - VD2 C27 H46 O3 CC1[C@@H](....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: TK3; Similar ligands found: 29
No: Ligand ECFP6 Tc MDL keys Tc
1 TK3 1 1
2 TKA 0.734694 1
3 VD1 0.602151 0.904762
4 MI4 0.601852 0.97561
5 YS3 0.591837 0.928571
6 YS2 0.581633 0.866667
7 YSD 0.574257 0.928571
8 VDZ 0.558824 0.906977
9 YSV 0.558824 0.906977
10 TX5 0.554455 0.904762
11 NYA 0.552381 0.951219
12 8J3 0.539823 1
13 8J0 0.539823 1
14 TT2 0.526786 0.97561
15 AKX 0.5 0.886364
16 YSL 0.486486 0.847826
17 YA1 0.486486 0.886364
18 8BL 0.482759 0.866667
19 9RO 0.478632 0.847826
20 8BO 0.478632 0.847826
21 YW2 0.477876 0.928571
22 9N9 0.477477 0.928571
23 YS5 0.473684 0.906977
24 YA2 0.473684 0.906977
25 9KX 0.463636 0.904762
26 VD2 0.419643 0.883721
27 8C9 0.416 0.847826
28 8C0 0.40625 0.829787
29 VDX 0.401709 0.906977
Similar Ligands (3D)
Ligand no: 1; Ligand: TK3; Similar ligands found: 0
No: Ligand Similarity coefficient
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3VRV; Ligand: YSD; 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: 3vrv.bio1) has 49 residues
No: Leader PDB Ligand Sequence Similarity
APoc FAQ
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