Receptor
PDB id Resolution Class Description Source Keywords
6EUZ 1.95 Å NON-ENZYME: TRANSCRIPT_TRANSLATE THE TRANSCRIPTIONAL REGULATOR PRFA FROM LISTERIA MONOCYTOGEN COMPLEX WITH A RING-FUSED 2-PYRIDONE (MK37) LISTERIA MONOCYTOGENES TRANSCRIPTION REGULATOR DNA BINDING 2-PYRIDONE DRUG DESIGLISTERIA MONOCYTOGENES DNA BINDING PROTEIN
Ref.: STRUCTURE-BASED DESIGN OF INHIBITORS TARGETING PRFA MASTER VIRULENCE REGULATOR OF LISTERIA MONOCYTOGENE J. MED. CHEM. V. 61 4165 2018
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
NA B:303;
A:303;
 Part of Protein;
Part of Protein;
 none;
none;
 submit data
22.99 Na [Na+]
IPA B:302;
A:301;
A:302;
 Invalid;
Invalid;
Invalid;
 none;
none;
none;
 submit data
60.095 C3 H8 O CC(C)...
C8Q B:301;
 Valid;
 none;
 ic50 = 65.6 uM
367.418 C20 H17 N O4 S COC1=...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5F1R 2.25 Å NON-ENZYME: TRANSCRIPT_TRANSLATE THE TRANSCRIPTIONAL REGULATOR PRFA FROM LISTERIA MONOCYTOGEN COMPLEX WITH A RING-FUSED 2-PYRIDONE (C10) LISTERIA MONOCYTOGENES SEROVAR 1/2A (SATCC BAA-679 / EGD-E) DNA BINDING PROTEIN PRFA 2-PYRIDONES VIRULENCE
Ref.: ATTENUATING LISTERIA MONOCYTOGENES VIRULENCE BY TAR THE REGULATORY PROTEIN PRFA. CELL CHEM BIOL V. 23 404 2016
Members (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 308 families.
1 5LRR - GSH C10 H17 N3 O6 S C(CC(=O)N[....
2 6EXM ic50 = 3 uM QQH C19 H23 N2 O3 S Cc1cccc(c1....
3 6EUT - BY8 C23 H21 N O3 S Cc1ccc(c2c....
4 6EV0 ic50 = 1.8 uM BYK C21 H21 N2 O3 S C[NH+](C)C....
5 6EXL ic50 = 1.5 uM C2Q C22 H23 N2 O3 S Cc1ccc(c2c....
6 6EXK ic50 = 1.5 uM C2Q C22 H23 N2 O3 S Cc1ccc(c2c....
7 6EUZ ic50 = 65.6 uM C8Q C20 H17 N O4 S COC1=C2N([....
8 2BGC - DTU C4 H10 O2 S2 C([C@H]([C....
9 5F1R Kd = 1 uM 42O C22 H19 N O3 S c1ccc2c(c1....
70% Homology Family (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 266 families.
1 5LRR - GSH C10 H17 N3 O6 S C(CC(=O)N[....
2 6EXM ic50 = 3 uM QQH C19 H23 N2 O3 S Cc1cccc(c1....
3 6EUT - BY8 C23 H21 N O3 S Cc1ccc(c2c....
4 6EV0 ic50 = 1.8 uM BYK C21 H21 N2 O3 S C[NH+](C)C....
5 6EXL ic50 = 1.5 uM C2Q C22 H23 N2 O3 S Cc1ccc(c2c....
6 6EXK ic50 = 1.5 uM C2Q C22 H23 N2 O3 S Cc1ccc(c2c....
7 6EUZ ic50 = 65.6 uM C8Q C20 H17 N O4 S COC1=C2N([....
8 2BGC - DTU C4 H10 O2 S2 C([C@H]([C....
9 5F1R Kd = 1 uM 42O C22 H19 N O3 S c1ccc2c(c1....
50% Homology Family (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 220 families.
1 5LRR - GSH C10 H17 N3 O6 S C(CC(=O)N[....
2 6EXM ic50 = 3 uM QQH C19 H23 N2 O3 S Cc1cccc(c1....
3 6EUT - BY8 C23 H21 N O3 S Cc1ccc(c2c....
4 6EV0 ic50 = 1.8 uM BYK C21 H21 N2 O3 S C[NH+](C)C....
5 6EXL ic50 = 1.5 uM C2Q C22 H23 N2 O3 S Cc1ccc(c2c....
6 6EXK ic50 = 1.5 uM C2Q C22 H23 N2 O3 S Cc1ccc(c2c....
7 6EUZ ic50 = 65.6 uM C8Q C20 H17 N O4 S COC1=C2N([....
8 2BGC - DTU C4 H10 O2 S2 C([C@H]([C....
9 5F1R Kd = 1 uM 42O C22 H19 N O3 S c1ccc2c(c1....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: C8Q; Similar ligands found: 10
No: Ligand ECFP6 Tc MDL keys Tc
1 C8Q 1 1
2 BYK 0.674419 0.80597
3 C8N 0.674419 0.80597
4 42O 0.662791 0.85
5 BY8 0.484211 0.866667
6 C2Q 0.46875 0.80597
7 XC2 0.461538 0.708333
8 EC2 0.451923 0.8
9 QQH 0.40404 0.768116
10 EC5 0.401869 0.637681
Similar Ligands (3D)
Ligand no: 1; Ligand: C8Q; Similar ligands found: 1
No: Ligand Similarity coefficient
1 V50 0.8650
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5F1R; Ligand: 42O; 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: 5f1r.bio1) has 40 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5F1R; Ligand: 42O; 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: 5f1r.bio1) has 57 residues
No: Leader PDB Ligand Sequence Similarity
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