Receptor
PDB id Resolution Class Description Source Keywords
1M13 2.15 Å EC: 2.3.1.48 CRYSTAL STRUCTURE OF THE HUMAN PREGANE X RECEPTOR LIGAND BINDING DOMAIN IN COMPLEX WITH HYPERFORIN, A CONSTITUENT O F ST. JOHN'S WORT HOMO SAPIENS NUCLEAR RECEPTOR LIGAND BINDING DOMAIN PROTEIN-LIGAND COMPLEX TRANSCRIPTION
Ref.: 2.1 A CRYSTAL STRUCTURE OF HUMAN PXR IN COMPLEX WITH THE ST. JOHN'S WORT COMPOUND HYPERFORIN BIOCHEMISTRY V. 42 1430 2003
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
HYF A:435;
Valid;
none;
Kd = 27 nM
536.785 C35 H52 O4 CC(C)...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4X1F 2 Å EC: 2.3.1.48 CRYSTAL STRUCTURE OF THE HPXR-LBD IN COMPLEX WITH THE SYNTHE ESTROGEN 17ALPHA-ETHINYLESTRADIOL HOMO SAPIENS NUCLEAR RECEPTOR HORMONE RECEPTOR PREGNANE X RECEPTOR ESTGENE REGULATION
Ref.: SYNERGISTIC ACTIVATION OF HUMAN PREGNANE X RECEPTOR BINARY COCKTAILS OF PHARMACEUTICAL AND ENVIRONMENTA COMPOUNDS. NAT COMMUN V. 6 8089 2015
Members (11)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 64 families.
1 6DUP - HCJ C20 H15 F3 N2 O3 c1cc(cc(c1....
2 6P2B - NQD C27 H38 O4 Cc1cc(cc2c....
3 4XHD - 40U C23 H33 Cl N2 O3 CC(C)[C@H]....
4 6XP9 - QCG C29 H30 F N3 O4 Cc1c(cc(c2....
5 3HVL - SRL C24 H42 O7 P2 CCOP(=O)(C....
6 1M13 Kd = 27 nM HYF C35 H52 O4 CC(C)C(=O)....
7 6HTY ic50 = 1242 nM GRH C21 H19 Cl N2 O4 S C[C@H](c1c....
8 4X1G Kd = 11.5 uM 3WF C20 H24 O2 C[C@]12CC[....
9 6TFI - N6H C22 H24 Cl N3 O4 CC1(CN(CCO....
10 6NX1 - L7D C20 H17 F7 O3 S c1cc(ccc1C....
11 4X1F Kd = 10.8 nM 3WF C20 H24 O2 C[C@]12CC[....
70% Homology Family (11)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 35 families.
1 6DUP - HCJ C20 H15 F3 N2 O3 c1cc(cc(c1....
2 6P2B - NQD C27 H38 O4 Cc1cc(cc2c....
3 4XHD - 40U C23 H33 Cl N2 O3 CC(C)[C@H]....
4 6XP9 - QCG C29 H30 F N3 O4 Cc1c(cc(c2....
5 3HVL - SRL C24 H42 O7 P2 CCOP(=O)(C....
6 1M13 Kd = 27 nM HYF C35 H52 O4 CC(C)C(=O)....
7 6HTY ic50 = 1242 nM GRH C21 H19 Cl N2 O4 S C[C@H](c1c....
8 4X1G Kd = 11.5 uM 3WF C20 H24 O2 C[C@]12CC[....
9 6TFI - N6H C22 H24 Cl N3 O4 CC1(CN(CCO....
10 6NX1 - L7D C20 H17 F7 O3 S c1cc(ccc1C....
11 4X1F Kd = 10.8 nM 3WF C20 H24 O2 C[C@]12CC[....
50% Homology Family (10)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 25 families.
1 6DUP - HCJ C20 H15 F3 N2 O3 c1cc(cc(c1....
2 6P2B - NQD C27 H38 O4 Cc1cc(cc2c....
3 4XHD - 40U C23 H33 Cl N2 O3 CC(C)[C@H]....
4 6XP9 - QCG C29 H30 F N3 O4 Cc1c(cc(c2....
5 3HVL - SRL C24 H42 O7 P2 CCOP(=O)(C....
6 1M13 Kd = 27 nM HYF C35 H52 O4 CC(C)C(=O)....
7 6HTY ic50 = 1242 nM GRH C21 H19 Cl N2 O4 S C[C@H](c1c....
8 4X1G Kd = 11.5 uM 3WF C20 H24 O2 C[C@]12CC[....
9 6TFI - N6H C22 H24 Cl N3 O4 CC1(CN(CCO....
10 6NX1 - L7D C20 H17 F7 O3 S c1cc(ccc1C....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: HYF; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 HYF 1 1
Similar Ligands (3D)
Ligand no: 1; Ligand: HYF; 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 : 4X1F; Ligand: 3WF; Similar sites found with APoc: 2
This union binding pocket(no: 1) in the query (biounit: 4x1f.bio1) has 36 residues
No: Leader PDB Ligand Sequence Similarity
1 6LM1 D10 5.40541
2 6LM1 OCT 5.40541
Pocket No.: 2; Query (leader) PDB : 4X1F; Ligand: 3WF; 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: 4x1f.bio1) has 36 residues
No: Leader PDB Ligand Sequence Similarity
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