Receptor
PDB id Resolution Class Description Source Keywords
1RJK 1.99 Å NON-ENZYME: SIGNAL_HORMONE CRYSTAL STRUCTURE OF THE RAT VITAMIN D RECEPTOR LIGAND BINDI COMPLEXED WITH 2MD AND A SYNTHETIC PEPTIDE CONTAINING THE ND RIP 205 RATTUS NORVEGICUS NUCLEAR RECEPTOR-SUPERAGONIST COMPLEX NUCLEAR RECEPTOR-COACINTERACTIONS HORMONE-GROWTH FACTOR RECEPTOR COMPLEX
Ref.: MOLECULAR STRUCTURE OF THE RAT VITAMIN D RECEPTOR L BINDING DOMAIN COMPLEXED WITH 2-CARBON-SUBSTITUTED D(3) HORMONE ANALOGUES AND A LXXLL-CONTAINING COACT PEPTIDE BIOCHEMISTRY V. 43 4101 2004
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
VDZ A:500;
 Valid;
 none;
 submit data
416.636 C27 H44 O3 C[C@@...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2O4J 1.74 Å NON-ENZYME: SIGNAL_HORMONE CRYSTAL STRUCTURE OF RAT VITAMIN D RECEPTOR LIGAND BINDING D COMPLEXED WITH VITIII 17-20Z AND THE NR2 BOX OF DRIP 205 RATTUS NORVEGICUS NUCLEAR RECEPTOR-LIGAND COMPLEX HORMONE-GROWTH FACTOR RECEPCOMPLEX
Ref.: NEW ANALOGS OF 2-METHYLENE-19-NOR-(20S)-1,25-DIHYDROXYVITAMIN D(3) CONFORMATIONALLY RESTRICTED SIDE CHAINS: EVALUATION BIOLOGICAL ACTIVITY AND STRUCTURAL DETERMINATION OF VDR-BOUND CONFORMATIONS. ARCH.BIOCHEM.BIOPHYS. V. 460 161 2007
Members (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 289 families.
1 1RJK - VDZ C27 H44 O3 C[C@@H](CC....
2 2O4J Ki = 0.08 nM VD4 C27 H42 O3 C/C(=C/1CC....
3 1RKG - VD1 C23 H36 O2 CC[C@H](C)....
4 1RK3 Kd = 0.37 nM VDX C27 H44 O3 C[C@H](CCC....
5 2O4R Ki = 0.4 nM VD5 C27 H42 O3 C/C(=C1/CC....
6 1RKH - VD2 C27 H46 O3 CC1[C@@H](....
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: VDZ; Similar ligands found: 46
No: Ligand ECFP6 Tc MDL keys Tc
1 VDZ 1 1
2 YSV 1 1
3 YS3 0.831169 0.97561
4 YS2 0.818182 0.909091
5 YSD 0.756098 0.928571
6 VD2 0.756098 0.97561
7 AKX 0.747253 0.930233
8 VD1 0.717949 0.904762
9 VDY 0.694118 0.926829
10 VDX 0.674157 1
11 8BL 0.652632 0.909091
12 YA1 0.648352 0.97619
13 8BO 0.645833 0.888889
14 9RO 0.645833 0.888889
15 MVD 0.641304 1
16 C33 0.608247 0.97619
17 O1C 0.602041 0.931818
18 C3O 0.59596 0.891304
19 OCC 0.584158 0.87234
20 TKA 0.581633 0.906977
21 YSL 0.578947 0.888889
22 YA2 0.57732 0.952381
23 YS5 0.57732 0.952381
24 TK3 0.558824 0.906977
25 NYA 0.541667 0.904762
26 9KX 0.536842 0.904762
27 VD3 0.532609 0.853659
28 TEY 0.531532 0.621212
29 TT2 0.529412 0.928571
30 TX5 0.526882 0.904762
31 9N9 0.520408 0.883721
32 MI4 0.504762 0.928571
33 8C9 0.5 0.888889
34 H97 0.5 0.851064
35 G72 0.5 0.851064
36 BIV 0.494949 1
37 8C0 0.486486 0.869565
38 M7E 0.477064 0.672414
39 YI4 0.466019 0.909091
40 YI3 0.460784 0.952381
41 VD4 0.459184 1
42 VD5 0.459184 1
43 ZNE 0.438596 0.754717
44 YW2 0.433962 0.840909
45 7ZU 0.403846 0.951219
46 TEJ 0.40367 0.847826
Similar Ligands (3D)
Ligand no: 1; Ligand: VDZ; Similar ligands found: 9
No: Ligand Similarity coefficient
1 2MV 0.8937
2 COV 0.8898
3 23R 0.8896
4 KH1 0.8866
5 0CO 0.8820
6 AYT 0.8774
7 EB1 0.8627
8 CA9 0.8603
9 91W 0.8545
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2O4J; Ligand: VD4; 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: 2o4j.bio2) has 28 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 2O4J; Ligand: VD4; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 2o4j.bio2) has 28 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 2O4J; Ligand: VD4; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 2o4j.bio1) has 28 residues
No: Leader PDB Ligand Sequence Similarity
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