Receptor
PDB id Resolution Class Description Source Keywords
4Q0A 1.9 Å NON-ENZYME: SIGNAL_HORMONE VITAMIN D RECEPTOR COMPLEX WITH LITHOCHOLIC ACID DANIO RERIO ALPHA-HELICAL SANDWICH TRANSCRIPTION FACTOR CALCITRIOL BINBINDING NUCLEUS GENE REGULATION
Ref.: STRUCTURAL INSIGHTS INTO THE MOLECULAR MECHANISM OF D RECEPTOR ACTIVATION BY LITHOCHOLIC ACID INVOLVING MODE OF LIGAND RECOGNITION. J.MED.CHEM. V. 57 4710 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
4OA C:501;
C:502;
Valid;
Valid;
none;
none;
Kd = 0.33 uM
376.573 C24 H40 O3 C[C@H...
GLY HIS LYS ILE LEU HIS ARG LEU LEU GLN D:687;
Valid;
none;
submit data
1216.5 n/a O=C([...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4Q0A 1.9 Å NON-ENZYME: SIGNAL_HORMONE VITAMIN D RECEPTOR COMPLEX WITH LITHOCHOLIC ACID DANIO RERIO ALPHA-HELICAL SANDWICH TRANSCRIPTION FACTOR CALCITRIOL BINBINDING NUCLEUS GENE REGULATION
Ref.: STRUCTURAL INSIGHTS INTO THE MOLECULAR MECHANISM OF D RECEPTOR ACTIVATION BY LITHOCHOLIC ACID INVOLVING MODE OF LIGAND RECOGNITION. J.MED.CHEM. V. 57 4710 2014
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 289 families.
1 4Q0A Kd = 0.33 uM 4OA C24 H40 O3 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: 4OA; Similar ligands found: 15
No: Ligand ECFP6 Tc MDL keys Tc
1 4OA 1 1
2 LOA 0.691358 0.894737
3 D0O 0.682927 0.618182
4 LHP 0.674699 0.871795
5 3KL 0.634146 0.918919
6 DXC 0.619048 0.972222
7 JN3 0.609756 0.972222
8 AON 0.52 0.833333
9 AOM 0.52 0.833333
10 CHO 0.479167 0.7
11 CHD 0.478261 0.972222
12 CHC 0.478261 0.945946
13 UZ9 0.443396 0.692308
14 AOI 0.423529 0.861111
15 AOX 0.423529 0.861111
Ligand no: 2; Ligand: GLY HIS LYS ILE LEU HIS ARG LEU LEU GLN; Similar ligands found: 111
No: Ligand ECFP6 Tc MDL keys Tc
1 GLY HIS LYS ILE LEU HIS ARG LEU LEU GLN 1 1
2 HIS LYS ILE LEU HIS ARG LEU LEU GLN ASP 0.719697 0.966667
3 HIS LYS ILE LEU HIS ARG LEU LEU GLN GLU 0.708955 0.983051
4 LYS ILE LEU HIS ARG LEU LEU GLN ASP 0.69697 0.95
5 LYS ILE LEU HIS ARG LEU LEU GLN ASP SER 0.657143 0.904762
6 ALA ILE LEU HIS ARG LEU LEU GLN 0.645669 0.915254
7 ILE LEU GLY LYS PHE LEU HIS ARG LEU 0.608696 0.983333
8 ARG ILE ILE PRO ARG HIS LEU GLN LEU 0.589041 0.878788
9 ILE LEU MET GLU HIS ILE HIS LYS LEU 0.577778 0.84127
10 ARG ARG LYS TRP ARG ARG TRP HIS LEU 0.557143 0.888889
11 ARG ARG LYS TRP CIR ARG TRP HIS LEU 0.541667 0.875
12 GLU LYS VAL HIS VAL GLN 0.539062 0.847458
13 ILE ARG LYS ILE LEU PHE LEU ASP GLY ILE 0.530612 0.822581
14 ALA LYS PHE ARG HIS ASP 0.529851 0.885246
15 ARG HIS ARG MLY VAL LEU ARG ASP ASN 0.527778 0.811594
16 ILE LEU ALA LYS PHE LEU HIS ARG LEU 0.527397 0.916667
17 ARG ARG LEU LEU ARG GLY HIS ASN GLN TYR 0.527027 0.850746
18 SER HIS LYS ILE ASP ASN LEU ASP 0.524823 0.8
19 LYS ARG TRP ILE ILE LEU GLY LEU ASN LYS 0.522293 0.936508
20 GLU LEU LYS ARG LYS MET ILE TYR MET 0.520548 0.75
21 ALA LYS ARG HIS ARG LYS VAL LEU ARG ASP 0.517986 0.898305
22 SER GLU LEU GLU ILE LYS ARG TYR 0.51773 0.75
23 ALA LYS ARG HIS ARG MLY VAL LEU ARG ASP 0.513699 0.791045
24 THR SER ARG HIS LYS ALY LEU MET ALA 0.513514 0.774648
25 ALA LEU PRO HIS ALA ILE LEU ARG LEU 0.513158 0.876923
26 ALA LYS ARG HIS ARG MLZ VAL LEU ARG ASP 0.51049 0.828125
27 GLU LEU ASN ARG LYS MET ILE TYR MET 0.509804 0.742857
28 GLY ARG PHE ALA ALA ALA ILE ALA LYS 0.50365 0.833333
29 ILE LEU ALA LYS PHE LEU HIS GLU LEU 0.503497 0.883333
30 LYS GLY GLY ALA ALY ARG HIS ARG 0.503448 0.887097
31 ARG ARG ARG TRP HIS ARG TRP ARG LEU 0.5 0.873016
32 ARG HIS ARG MLZ VAL LEU ARG ASP ASN TYR 0.496855 0.802817
33 ILE LEU ALA LYS PHE LEU HIS THR LEU 0.493151 0.8
34 GLY ALA ARG ALA HIS SER SER 0.492424 0.80303
35 ALA ARG LYS ILE ASP ASN LEU ASP 0.489051 0.806452
36 LYS SER HIS GLN GLU 0.488372 0.734375
37 HIS LYS LEU VAL GLN LEU LEU THR THR THR 0.485507 0.784615
38 LYS ARG TRP ILE ILE MET GLY LEU ASN LYS 0.48503 0.880597
39 GLY LYS ILE SER LYS HIS TRP THR GLY ILE 0.484472 0.779412
40 ARG HIS ARG MLY VAL LEU ARG ASP TYR 0.483871 0.780822
41 SER ILE ILE GLN PHE GLU HIS LEU 0.482517 0.784615
42 GLY ASN PHE LEU GLN SER ARG 0.482014 0.742424
43 ARG HIS LYS ALY LEU MET PHE LYS 0.480263 0.830769
44 ILE GLU GLU ALA LEU GLN ILE ILE HIS SER 0.475862 0.806452
45 SER ARG LYS ILE ASP ASN LEU ASP 0.475177 0.769231
46 GLY GLY ARG LYS LYS TYR LYS LEU 0.459854 0.796875
47 GLY GLY LYS LYS LYS TYR ARG LEU 0.459854 0.796875
48 GLY GLY LYS LYS ARG TYR LYS LEU 0.459854 0.796875
49 LEU PRO PHE GLU LEU ARG GLY HIS LEU VAL 0.45509 0.878788
50 LYS HIS LYS 0.452991 0.779661
51 GLY HIS ARG PRO NH2 0.451128 0.784615
52 GLY HIS ARG PRO 0.451128 0.815385
53 ALA ARG LYS LEU ASP 0.45082 0.783333
54 GLU LEU ARG ARG LYS MET MET TYR MET 0.448276 0.724638
55 ARG ARG GLU VAL HIS THR TYR TYR 0.448052 0.797101
56 ARG ARG LEU ILE PHE NH2 0.44697 0.737705
57 ARG ARG ILE TYR ASP LEU ILE GLU LEU 0.446667 0.757576
58 3BY PRO LYS ARG ILE ALA 0.445205 0.757143
59 PHE ALA GLY LEU ARG GLN ALA VAL THR GLN 0.441176 0.71875
60 ILE LEU LYS GLU PRO VAL HIS GLY VAL 0.440994 0.815385
61 ARG PRO LYS ARG ILE ALA 0.440559 0.787879
62 GLY VAL TYR ASP GLY ARG GLU HIS THR VAL 0.438272 0.823529
63 SER SER THR ARG GLY ILE SER GLN LEU TRP 0.436364 0.823529
64 TYR GLU LEU ASP GLU LYS PHE ASP ARG LEU 0.434211 0.761194
65 TYR PRO LYS ARG ILE ALA 0.434211 0.771429
66 ARG LEU GLN ARG ARG ARG GLU THR GLN VAL 0.433824 0.707692
67 LEU GLY GLY ALA LYS GLN ARG GLY ASP VAL 0.433824 0.783333
68 HIS MET THR GLU VAL VAL ARG HIS CYS 0.433121 0.811594
69 SER GLU ILE GLU PHE ALA ARG LEU 0.432432 0.738462
70 ACE ARG HIS LYS ALY MCM 0.432258 0.701299
71 ARG HIS LYS FDL 0.431373 0.710526
72 GLU LEU LYS TPO GLU ARG TYR 0.431373 0.675676
73 GLN PHE LYS ASP ASN VAL ILE LEU LEU 0.430464 0.714286
74 ILE GLN GLN SER ILE GLU ARG ILE 0.42963 0.71875
75 PHE ASN GLU LEU SER HIS LEU 0.427481 0.75
76 SER HIS PRO ARG PRO ILE ARG VAL 0.426752 0.802817
77 GLN ILE LYS VAL ARG VAL ASP MET VAL 0.424658 0.75
78 LYS GLY GLY ALA ALY ARG HIS ARG LYS ILE 0.423077 0.854839
79 LYS PRO ILE VAL VAL LEU HIS GLY TYR 0.422619 0.771429
80 LYS GLY GLY ALA ALY ARG HIS ARG LYS VAL 0.422535 0.83871
81 SER LEU ASN TYR ILE ILE LYS VAL LYS GLU 0.422078 0.666667
82 ASP ARG VAL TYR ILE HIS PRO PHE 0.419355 0.876923
83 GLU LEU PRO PRO VAL LYS ILE HIS CYS 0.418605 0.791045
84 PHE SER GLN HIS LYS THR SER TPO ILE 0.418182 0.702703
85 PRO PRO LYS ARG ILE ALA 0.416107 0.815385
86 PAC DLY DLY DAR 0.416 0.766667
87 ASN ARG LEU ILE LEU THR GLY 0.415385 0.737705
88 SER SER ILE GLU PHE ALA ARG LEU 0.414474 0.727273
89 GLY SER HIS LEU GLU VAL GLN GLY TYR TRP 0.413793 0.742857
90 ALA ARG THR MLY GLN 0.409091 0.661972
91 GLU ILE ILE ASN PHE GLU LYS LEU 0.408163 0.725806
92 ACE CSO ARG ALA THR LYS MET LEU 0.408163 0.618421
93 ARG GLN ALA SEP LEU SER ILE SER VAL 0.407895 0.638889
94 ALA ILE HIS 0.40678 0.745763
95 ACE ARG HIS ALY ALY MCM 0.406667 0.710526
96 ALA VAL TYR ASP GLY ARG GLU HIS THR VAL 0.406061 0.823529
97 SER ARG ASP HIS SER ARG THR PRO MET 0.405882 0.736842
98 SER ILE ILE ASN PHE GLU LYS LEU 0.405405 0.666667
99 LYS ALA PRO ARG ALY GLN LEU ALA THR LYS 0.404908 0.736111
100 ALA ARG THR GLU LEU TYR ARG SER LEU 0.403974 0.710145
101 ARG ARG ARG TRP ARG ARG LEU THR VAL 0.403974 0.80597
102 HIS HIS ALA SER PRO ARG LYS 0.403727 0.768116
103 TYR LEU LYS GLU PRO VAL HIS GLY VAL 0.403509 0.757143
104 THR ARG ARG GLU THR GLN LEU 0.402985 0.707692
105 GLY GLY LYS LYS LYS TYR GLN LEU 0.402878 0.703125
106 ASP GLU LEU GLU ILE LYS ALA TYR 0.402685 0.692308
107 LYS ARG LYS 0.401709 0.711864
108 VAL LYS VAL VAL ALA LYS LYS TYR ARG ASN 0.401408 0.757576
109 ARG GLY TYR LEU TYR GLN GLY LEU 0.401361 0.769231
110 ASP ALA GLU PHE ARG HIS ASP SER 0.401316 0.868852
111 ARG VAL LYS GLU LYS TYR GLN HIS LEU TRP 0.4 0.770492
Similar Ligands (3D)
Ligand no: 1; Ligand: 4OA; Similar ligands found: 9
No: Ligand Similarity coefficient
1 K2B 0.9401
2 L39 0.9061
3 5JK 0.8913
4 HCR 0.8868
5 1N7 0.8772
6 30Q 0.8749
7 3G6 0.8745
8 DL4 0.8673
9 HCY 0.8552
Ligand no: 2; Ligand: GLY HIS LYS ILE LEU HIS ARG LEU LEU GLN; 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 : 4Q0A; Ligand: 4OA; 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: 4q0a.bio1) has 13 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 4Q0A; Ligand: 4OA; 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: 4q0a.bio1) has 13 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 4Q0A; Ligand: GLY HIS LYS ILE LEU HIS ARG LEU LEU GLN; 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: 4q0a.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 4Q0A; Ligand: 4OA; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 4q0a.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 4Q0A; Ligand: 4OA; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 4q0a.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
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