Receptor
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
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
YSD A:501;
Valid;
none;
ic50 = 0.029 nM
430.663 C28 H46 O3 CCC(C...
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 (48)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 286 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 3VT5 - YI2 C28 H44 O4 S CCC(CC)(CS....
6 2ZLA - VDB C28 H46 O5 S CCC(CC)(CS....
7 2ZLC - VDX C27 H44 O3 C[C@H](CCC....
8 3VT7 - VDX C27 H44 O3 C[C@H](CCC....
9 2ZFX - YR3 C28 H42 O5 CCC(CC)(c1....
10 3VJT ic50 = 4.1 uM 10R C17 H42 B10 O4 [BH]1234[B....
11 3WT5 ic50 = 0.29 nM YA1 C31 H52 O3 CCCC[C@H](....
12 5XPM ic50 = 23 nM 8C0 C36 H54 O4 CCCC[C@@H]....
13 4YNK - YW2 C34 H44 O3 C[C@]12CCC....
14 5B41 - YSV C27 H44 O3 C[C@H](CCC....
15 3W0H - W12 C28 H42 O5 CCCC(CCC)(....
16 3W0G - W07 C24 H34 O5 CC(C)(C)[C....
17 3VTB ic50 = 0.5 nM TKA C35 H50 O3 C[C@H](CC#....
18 5XZF ic50 = 0.24 nM 8J0 C35 H50 O3 C[C@H](CC#....
19 5B5B ic50 = 0.43 nM AKX C39 H52 O3 C[C@H](CCC....
20 5XPO ic50 = 84 nM 8BL C31 H42 O4 C[C@H](CCC....
21 5ZWI ic50 = 2.3 nM 9KX C27 H38 O3 C/C=C/C=C/....
22 3VT8 - YI3 C30 H52 O3 CCCC[C@@H]....
23 3W0J - T08 C26 H38 O5 Cc1cc(ccc1....
24 3VT4 - 5YI C28 H44 O4 S CCC(CC)(CS....
25 3VJS ic50 = 0.64 uM 10S C17 H42 B10 O4 [BH]1234[B....
26 3W5T - LHP C27 H44 O4 CCC(=O)O[C....
27 3VRU ic50 = 0.1 nM YS3 C26 H42 O3 C[C@H](CCC....
28 3AUN - YR4 C29 H44 O5 CCC(CC)(c1....
29 2ZMH - NYA C34 H50 O3 C[C@H](C=C....
30 5AWJ ic50 = 0.21 nM YSL C30 H50 O3 CCCCCC[C@@....
31 3W5R - LOA C26 H42 O4 C[C@H](CCC....
32 2ZL9 - VDA C28 H46 O5 S CCC(CC)(CS....
33 5XZH ic50 = 3.13 nM 8J3 C35 H50 O3 C[C@H](CC#....
34 3VRW ic50 = 0.41 nM YS5 C32 H54 O3 CCCC[C@@H]....
35 3VT3 - VDX C27 H44 O3 C[C@H](CCC....
36 3VRT ic50 = 2.7 nM YS2 C24 H38 O3 C[C@H](CCC....
37 3VTC ic50 = 13 nM TK3 C36 H52 O3 C[C@H](CC#....
38 3AFR - ICJ C31 H52 O3 CCCC[C@@H]....
39 3WT6 ic50 = 0.29 nM YA1 C31 H52 O3 CCCC[C@H](....
40 5XPN ic50 = 102 nM 9RO C32 H46 O4 C[C@H](CCC....
41 5ZWH ic50 = 1.9 nM 9N9 C27 H36 O3 C/C=C/C#CC....
42 2ZXN - JC1 C28 H46 O3 CCCC[C@@H]....
43 3A2H - TEJ C27 H38 O4 C[C@@H](C[....
44 3W5P - 4OA C24 H40 O3 C[C@H](CCC....
45 3WT7 ic50 = 1.79 nM YA2 C32 H54 O3 CCCC[C@H](....
46 3VRV ic50 = 0.029 nM YSD C28 H46 O3 CCC(CC)(CC....
47 3W5Q - 3KL C24 H38 O3 C[C@H](CCC....
48 2ZMJ ic50 = 30 nM MI4 C36 H54 O3 C[C@@H](C=....
70% Homology Family (54)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 209 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 3VT5 - YI2 C28 H44 O4 S CCC(CC)(CS....
6 2ZLA - VDB C28 H46 O5 S CCC(CC)(CS....
7 2ZLC - VDX C27 H44 O3 C[C@H](CCC....
8 3VT7 - VDX C27 H44 O3 C[C@H](CCC....
9 2ZFX - YR3 C28 H42 O5 CCC(CC)(c1....
10 3VJT ic50 = 4.1 uM 10R C17 H42 B10 O4 [BH]1234[B....
11 3WT5 ic50 = 0.29 nM YA1 C31 H52 O3 CCCC[C@H](....
12 5XPM ic50 = 23 nM 8C0 C36 H54 O4 CCCC[C@@H]....
13 4YNK - YW2 C34 H44 O3 C[C@]12CCC....
14 5B41 - YSV C27 H44 O3 C[C@H](CCC....
15 3W0H - W12 C28 H42 O5 CCCC(CCC)(....
16 3W0G - W07 C24 H34 O5 CC(C)(C)[C....
17 3VTB ic50 = 0.5 nM TKA C35 H50 O3 C[C@H](CC#....
18 5XZF ic50 = 0.24 nM 8J0 C35 H50 O3 C[C@H](CC#....
19 5B5B ic50 = 0.43 nM AKX C39 H52 O3 C[C@H](CCC....
20 5XPO ic50 = 84 nM 8BL C31 H42 O4 C[C@H](CCC....
21 5ZWI ic50 = 2.3 nM 9KX C27 H38 O3 C/C=C/C=C/....
22 3VT8 - YI3 C30 H52 O3 CCCC[C@@H]....
23 3W0J - T08 C26 H38 O5 Cc1cc(ccc1....
24 3VT4 - 5YI C28 H44 O4 S CCC(CC)(CS....
25 3VJS ic50 = 0.64 uM 10S C17 H42 B10 O4 [BH]1234[B....
26 3W5T - LHP C27 H44 O4 CCC(=O)O[C....
27 3VRU ic50 = 0.1 nM YS3 C26 H42 O3 C[C@H](CCC....
28 3AUN - YR4 C29 H44 O5 CCC(CC)(c1....
29 2ZMH - NYA C34 H50 O3 C[C@H](C=C....
30 5AWJ ic50 = 0.21 nM YSL C30 H50 O3 CCCCCC[C@@....
31 3W5R - LOA C26 H42 O4 C[C@H](CCC....
32 2ZL9 - VDA C28 H46 O5 S CCC(CC)(CS....
33 5XZH ic50 = 3.13 nM 8J3 C35 H50 O3 C[C@H](CC#....
34 3VRW ic50 = 0.41 nM YS5 C32 H54 O3 CCCC[C@@H]....
35 3VT3 - VDX C27 H44 O3 C[C@H](CCC....
36 3VRT ic50 = 2.7 nM YS2 C24 H38 O3 C[C@H](CCC....
37 3VTC ic50 = 13 nM TK3 C36 H52 O3 C[C@H](CC#....
38 3AFR - ICJ C31 H52 O3 CCCC[C@@H]....
39 3WT6 ic50 = 0.29 nM YA1 C31 H52 O3 CCCC[C@H](....
40 5XPN ic50 = 102 nM 9RO C32 H46 O4 C[C@H](CCC....
41 5ZWH ic50 = 1.9 nM 9N9 C27 H36 O3 C/C=C/C#CC....
42 2ZXN - JC1 C28 H46 O3 CCCC[C@@H]....
43 3A2H - TEJ C27 H38 O4 C[C@@H](C[....
44 3W5P - 4OA C24 H40 O3 C[C@H](CCC....
45 3WT7 ic50 = 1.79 nM YA2 C32 H54 O3 CCCC[C@H](....
46 3VRV ic50 = 0.029 nM YSD C28 H46 O3 CCC(CC)(CC....
47 3W5Q - 3KL C24 H38 O3 C[C@H](CCC....
48 2ZMJ ic50 = 30 nM MI4 C36 H54 O3 C[C@@H](C=....
49 1RJK - VDZ C27 H44 O3 C[C@@H](CC....
50 2O4J Ki = 0.08 nM VD4 C27 H42 O3 C/C(=C/1CC....
51 1RKG - VD1 C23 H36 O2 CC[C@H](C)....
52 1RK3 Kd = 0.37 nM VDX C27 H44 O3 C[C@H](CCC....
53 2O4R Kd = 0.4 nM VD5 C27 H42 O3 C/C(=C1/CC....
54 1RKH - VD2 C27 H46 O3 CC1[C@@H](....
50% Homology Family (54)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 174 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 3VT5 - YI2 C28 H44 O4 S CCC(CC)(CS....
6 2ZLA - VDB C28 H46 O5 S CCC(CC)(CS....
7 2ZLC - VDX C27 H44 O3 C[C@H](CCC....
8 3VT7 - VDX C27 H44 O3 C[C@H](CCC....
9 2ZFX - YR3 C28 H42 O5 CCC(CC)(c1....
10 3VJT ic50 = 4.1 uM 10R C17 H42 B10 O4 [BH]1234[B....
11 3WT5 ic50 = 0.29 nM YA1 C31 H52 O3 CCCC[C@H](....
12 5XPM ic50 = 23 nM 8C0 C36 H54 O4 CCCC[C@@H]....
13 4YNK - YW2 C34 H44 O3 C[C@]12CCC....
14 5B41 - YSV C27 H44 O3 C[C@H](CCC....
15 3W0H - W12 C28 H42 O5 CCCC(CCC)(....
16 3W0G - W07 C24 H34 O5 CC(C)(C)[C....
17 3VTB ic50 = 0.5 nM TKA C35 H50 O3 C[C@H](CC#....
18 5XZF ic50 = 0.24 nM 8J0 C35 H50 O3 C[C@H](CC#....
19 5B5B ic50 = 0.43 nM AKX C39 H52 O3 C[C@H](CCC....
20 5XPO ic50 = 84 nM 8BL C31 H42 O4 C[C@H](CCC....
21 5ZWI ic50 = 2.3 nM 9KX C27 H38 O3 C/C=C/C=C/....
22 3VT8 - YI3 C30 H52 O3 CCCC[C@@H]....
23 3W0J - T08 C26 H38 O5 Cc1cc(ccc1....
24 3VT4 - 5YI C28 H44 O4 S CCC(CC)(CS....
25 3VJS ic50 = 0.64 uM 10S C17 H42 B10 O4 [BH]1234[B....
26 3W5T - LHP C27 H44 O4 CCC(=O)O[C....
27 3VRU ic50 = 0.1 nM YS3 C26 H42 O3 C[C@H](CCC....
28 3AUN - YR4 C29 H44 O5 CCC(CC)(c1....
29 2ZMH - NYA C34 H50 O3 C[C@H](C=C....
30 5AWJ ic50 = 0.21 nM YSL C30 H50 O3 CCCCCC[C@@....
31 3W5R - LOA C26 H42 O4 C[C@H](CCC....
32 2ZL9 - VDA C28 H46 O5 S CCC(CC)(CS....
33 5XZH ic50 = 3.13 nM 8J3 C35 H50 O3 C[C@H](CC#....
34 3VRW ic50 = 0.41 nM YS5 C32 H54 O3 CCCC[C@@H]....
35 3VT3 - VDX C27 H44 O3 C[C@H](CCC....
36 3VRT ic50 = 2.7 nM YS2 C24 H38 O3 C[C@H](CCC....
37 3VTC ic50 = 13 nM TK3 C36 H52 O3 C[C@H](CC#....
38 3AFR - ICJ C31 H52 O3 CCCC[C@@H]....
39 3WT6 ic50 = 0.29 nM YA1 C31 H52 O3 CCCC[C@H](....
40 5XPN ic50 = 102 nM 9RO C32 H46 O4 C[C@H](CCC....
41 5ZWH ic50 = 1.9 nM 9N9 C27 H36 O3 C/C=C/C#CC....
42 2ZXN - JC1 C28 H46 O3 CCCC[C@@H]....
43 3A2H - TEJ C27 H38 O4 C[C@@H](C[....
44 3W5P - 4OA C24 H40 O3 C[C@H](CCC....
45 3WT7 ic50 = 1.79 nM YA2 C32 H54 O3 CCCC[C@H](....
46 3VRV ic50 = 0.029 nM YSD C28 H46 O3 CCC(CC)(CC....
47 3W5Q - 3KL C24 H38 O3 C[C@H](CCC....
48 2ZMJ ic50 = 30 nM MI4 C36 H54 O3 C[C@@H](C=....
49 1RJK - VDZ C27 H44 O3 C[C@@H](CC....
50 2O4J Ki = 0.08 nM VD4 C27 H42 O3 C/C(=C/1CC....
51 1RKG - VD1 C23 H36 O2 CC[C@H](C)....
52 1RK3 Kd = 0.37 nM VDX C27 H44 O3 C[C@H](CCC....
53 2O4R Kd = 0.4 nM VD5 C27 H42 O3 C/C(=C1/CC....
54 1RKH - VD2 C27 H46 O3 CC1[C@@H](....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: YSD; Similar ligands found: 45
No: Ligand ECFP6 Tc MDL keys Tc
1 YSD 1 1
2 YS3 0.831169 0.951219
3 VDZ 0.756098 0.928571
4 YSV 0.756098 0.928571
5 YS2 0.75 0.886364
6 VD1 0.74026 0.975
7 AKX 0.673684 0.906977
8 YA2 0.62766 0.97561
9 YS5 0.62766 0.97561
10 YA1 0.612903 0.952381
11 9RO 0.612245 0.866667
12 8BO 0.612245 0.866667
13 8BL 0.602041 0.886364
14 TKA 0.581633 0.928571
15 YSL 0.578947 0.909091
16 TK3 0.574257 0.928571
17 VD2 0.565217 0.904762
18 NYA 0.541667 0.926829
19 9KX 0.536842 0.926829
20 TT2 0.529412 0.951219
21 9N9 0.520408 0.904762
22 VDY 0.515789 0.857143
23 VDX 0.50505 0.928571
24 MI4 0.504762 0.951219
25 8C9 0.5 0.909091
26 8C0 0.5 0.888889
27 VD3 0.484211 0.785714
28 MVD 0.480392 0.928571
29 C33 0.471698 0.952381
30 C3O 0.462963 0.869565
31 O1C 0.453704 0.866667
32 TX5 0.446602 0.928571
33 KH1 0.444444 0.909091
34 OCC 0.441441 0.8125
35 M7E 0.424779 0.655172
36 EB1 0.422018 1
37 YW2 0.420561 0.860465
38 H97 0.418182 0.791667
39 G72 0.418182 0.791667
40 TEJ 0.416667 0.866667
41 VD4 0.415842 0.928571
42 VD5 0.415842 0.928571
43 ZNE 0.413793 0.735849
44 BIV 0.409524 0.928571
45 7ZU 0.403846 0.926829
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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