Receptor
PDB id Resolution Class Description Source Keywords
1S19 2.1 Å NON-ENZYME: TRANSCRIPT_TRANSLATE CRYSTAL STRUCTURE OF VDR LIGAND BINDING DOMAIN COMPLEXED TO CALCIPOTRIOL. HOMO SAPIENS NUCLEAR RECEPTOR TRANSCRIPTION REGULATION ALPHA-HELICAL SAGENE REGULATION
Ref.: CRYSTAL STRUCTURES OF THE VITAMIN D NUCLEAR RECEPTO LIGANDED WITH THE VITAMIN D SIDE CHAIN ANALOGUES CALCIPOTRIOL AND SEOCALCITOL, RECEPTOR AGONISTS OF IMPORTANCE. INSIGHTS INTO A STRUCTURAL BASIS FOR TH SWITCHING OF CALCIPOTRIOL TO A RECEPTOR ANTAGO
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MC9 A:500;
Valid;
none;
submit data
412.605 C27 H40 O3 C[C@H...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1DB1 1.8 Å NON-ENZYME: TRANSCRIPT_TRANSLATE CRYSTAL STRUCTURE OF THE NUCLEAR RECEPTOR FOR VITAMIN D COMP VITAMIN D HOMO SAPIENS COMPLEX GENE REGULATION
Ref.: THE CRYSTAL STRUCTURE OF THE NUCLEAR RECEPTOR FOR V BOUND TO ITS NATURAL LIGAND. MOL.CELL V. 5 173 2000
Members (31)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 291 families.
1 3A3Z - 2MV C29 H46 O4 C[C@H]1[C@....
2 1IE8 - KH1 C29 H48 O4 CCC(CC)(CC....
3 2HAS - C3O C30 H50 O4 CCCO[C@H]1....
4 1S0Z - EB1 C30 H46 O3 CCC(CC)(C=....
5 3AZ1 - DS2 C27 H38 O5 CCC(CC)(c1....
6 1IE9 - VDX C27 H44 O3 C[C@H](CCC....
7 2HAM - C33 C30 H50 O3 CCC[C@H]1[....
8 2HB8 - MVD C28 H46 O3 C[C@H]1[C@....
9 3CS4 - COV C28 H44 O4 C[C@]12CCC....
10 1S19 - MC9 C27 H40 O3 C[C@H](C=C....
11 3M7R - VDX C27 H44 O3 C[C@H](CCC....
12 3A40 - 23R C29 H46 O4 C[C@H]1[C@....
13 3AUR - CA9 C27 H42 O3 C[C@H]1[C@....
14 3KPZ - ZNE C28 H41 N O3 S C[C@H](CCC....
15 1TXI - TX5 C27 H40 O3 C[C@H](CC#....
16 1DB1 Kd = 0.55 nM VDX C27 H44 O3 C[C@H](CCC....
17 4G2I - 0VQ C25 H26 F6 O3 CC/C(=CC=C....
18 3CS6 - 0CO C28 H44 O4 C[C@]12CCC....
19 3AZ2 - DS3 C30 H44 O5 CCC(CC)(c1....
20 3AZ3 - DS6 C31 H46 O5 CCC(CC)(c1....
21 5YT2 - 90O C29 H48 O4 C[C@H](CCC....
22 5GIE Kd = 769.2 nM VDP C37 H53 N O4 C[C@H](C[C....
23 2HB7 - O1C C30 H50 O4 C[C@H](CCC....
24 3VHW - VHW C34 H50 O7 CCC1(CC/C(....
25 2HAR - OCC C30 H50 O5 C[C@H](CCC....
26 5GID Kd = 769.2 nM VDP C37 H53 N O4 C[C@H](C[C....
27 3TKC - FMV C28 H40 O4 C[C@H](c1c....
28 4ITE - TEY C30 H48 N4 O3 C[C@H](CCC....
29 5GIC Kd = 330.9 nM DLC C35 H51 N O4 C[C@H]1/C(....
30 3P8X - ZYD C27 H44 O3 CC(C)(CCCC....
31 5YSY - 90L C29 H48 O4 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 247 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 C27 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 (42)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 209 families.
1 4Q0A Kd = 0.33 uM 4OA C24 H40 O3 C[C@H](CCC....
2 4X1F Ki = 11.5 uM 3WF C20 H24 O2 C[C@]12CC[....
3 5M24 - 9CR C20 H28 O2 CC1=C(C(CC....
4 1FCY Kd = 3 nM 564 C26 H26 O3 CC1(CCC(c2....
5 3A3Z - 2MV C29 H46 O4 C[C@H]1[C@....
6 1IE8 - KH1 C29 H48 O4 CCC(CC)(CC....
7 2HAS - C3O C30 H50 O4 CCCO[C@H]1....
8 1S0Z - EB1 C30 H46 O3 CCC(CC)(C=....
9 3AZ1 - DS2 C27 H38 O5 CCC(CC)(c1....
10 1IE9 - VDX C27 H44 O3 C[C@H](CCC....
11 2HAM - C33 C30 H50 O3 CCC[C@H]1[....
12 2HB8 - MVD C28 H46 O3 C[C@H]1[C@....
13 3CS4 - COV C28 H44 O4 C[C@]12CCC....
14 1S19 - MC9 C27 H40 O3 C[C@H](C=C....
15 3M7R - VDX C27 H44 O3 C[C@H](CCC....
16 3A40 - 23R C29 H46 O4 C[C@H]1[C@....
17 3AUR - CA9 C27 H42 O3 C[C@H]1[C@....
18 3KPZ - ZNE C28 H41 N O3 S C[C@H](CCC....
19 1TXI - TX5 C27 H40 O3 C[C@H](CC#....
20 1DB1 Kd = 0.55 nM VDX C27 H44 O3 C[C@H](CCC....
21 4G2I - 0VQ C25 H26 F6 O3 CC/C(=CC=C....
22 3CS6 - 0CO C28 H44 O4 C[C@]12CCC....
23 3AZ2 - DS3 C30 H44 O5 CCC(CC)(c1....
24 3AZ3 - DS6 C31 H46 O5 CCC(CC)(c1....
25 5YT2 - 90O C29 H48 O4 C[C@H](CCC....
26 5GIE Kd = 769.2 nM VDP C37 H53 N O4 C[C@H](C[C....
27 2HB7 - O1C C30 H50 O4 C[C@H](CCC....
28 3VHW - VHW C34 H50 O7 CCC1(CC/C(....
29 2HAR - OCC C30 H50 O5 C[C@H](CCC....
30 5GID Kd = 769.2 nM VDP C37 H53 N O4 C[C@H](C[C....
31 3TKC - FMV C28 H40 O4 C[C@H](c1c....
32 4ITE - TEY C30 H48 N4 O3 C[C@H](CCC....
33 5GIC Kd = 330.9 nM DLC C35 H51 N O4 C[C@H]1/C(....
34 3P8X - ZYD C27 H44 O3 CC(C)(CCCC....
35 5YSY - 90L C29 H48 O4 C[C@H](CCC....
36 1PQ9 - BNS C6 H6 O3 S c1ccc(cc1)....
37 4RAK Ki = 14 nM 652 C28 H29 Cl N2 O3 S CC(C)(c1cc....
38 1UPV - 444 C17 H12 F9 N O3 S c1ccc(cc1)....
39 1PQ6 - 965 C33 H31 Cl F3 N O3 c1ccc(cc1)....
40 1UPW - 444 C17 H12 F9 N O3 S c1ccc(cc1)....
41 5JY3 Ki = 12 nM 6OX C29 H28 Cl2 F2 N2 O4 S CC(C)(c1cn....
42 3KFC ic50 = 2.8 nM 61X C23 H16 F3 N O3 S CS(=O)(=O)....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: MC9; Similar ligands found: 28
No: Ligand ECFP6 Tc MDL keys Tc
1 MC9 1 1
2 7ZU 0.761905 0.95
3 EB1 0.688172 0.926829
4 VDX 0.623656 0.904762
5 BIV 0.612903 0.904762
6 TX5 0.589474 0.904762
7 91W 0.583333 0.863636
8 TEJ 0.581633 0.844444
9 JC1 0.57732 0.844444
10 ICJ 0.574257 0.883721
11 FMV 0.565657 0.826087
12 KH1 0.564356 0.844444
13 8J3 0.548077 0.904762
14 8J0 0.548077 0.904762
15 6VH 0.52381 0.791667
16 M7E 0.523364 0.666667
17 ZNE 0.522936 0.716981
18 NYA 0.485149 0.95
19 VDP 0.471545 0.603175
20 COV 0.457143 0.808511
21 0CO 0.457143 0.808511
22 MI4 0.454545 0.926829
23 TT2 0.436364 0.926829
24 MVD 0.429907 0.904762
25 VDY 0.417476 0.833333
26 ZYD 0.417476 0.904762
27 VD1 0.402062 0.902439
28 VD3 0.401961 0.761905
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1DB1; Ligand: VDX; 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: 1db1.bio1) has 52 residues
No: Leader PDB Ligand Sequence Similarity
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