Receptor
PDB id Resolution Class Description Source Keywords
3W0I 1.9 Å NON-ENZYME: SIGNAL_HORMONE CRYSTAL STRUCTURE OF RAT VDR LIGAND BINDING DOMAIN IN COMPLE NOVEL NONSECOSTEROIDAL LIGANDS RATTUS NORVEGICUS GENE REGULATION TRANSCRIPTION
Ref.: STRUCTURAL BASIS FOR VITAMIN D RECEPTOR AGONISM BY NON-SECOSTEROIDAL LIGANDS. FEBS LETT. V. 587 957 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
O11 A:501;
Valid;
none;
submit data
430.577 C26 H38 O5 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: O11; Similar ligands found: 5
No: Ligand ECFP6 Tc MDL keys Tc
1 O11 1 1
2 W12 0.773585 0.857143
3 W07 0.72549 0.972222
4 YR3 0.476923 0.923077
5 T08 0.402985 0.897436
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
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