Receptor
PDB id Resolution Class Description Source Keywords
5lrr 2.17 Å NON-ENZYME: TRANSCRIPT_TRANSLATE THE TRANSCRIPTIONAL REGULATOR PRFA FROM LISTERIA MONOCYTOGEN COMPLEX WITH GLUTATHIONE LISTERIA MONOCYTOGENES TRANSCRIPTION REGULATOR DNA BINDING ACTIVATION GLUTATHIONLISTERIA MONOCYTOGENES TRANSCRIPTION DNA BINDING PROTEIN
Ref.: STRUCTURAL BASIS FOR GLUTATHIONE-MEDIATED ACTIVATIO VIRULENCE REGULATORY PROTEIN PRFA IN LISTERIA. PROC. NATL. ACAD. SCI. V. 113 14733 2016 U.S.A.
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
NA E:302;
A:302;
D:302;
H:302;
F:302;
 Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
 none;
none;
none;
none;
none;
 submit data
22.99 Na [Na+]
GSH B:301;
D:301;
H:301;
A:301;
C:301;
E:301;
G:301;
F:301;
 Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
 none;
none;
none;
none;
none;
none;
none;
none;
 submit data
307.323 C10 H17 N3 O6 S C(CC(...
PI B:302;
B:303;
A:303;
 Invalid;
Invalid;
Invalid;
 none;
none;
none;
 submit data
95.979 H O4 P OP(=O...
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: GSH; Similar ligands found: 53
No: Ligand ECFP6 Tc MDL keys Tc
1 GSH 1 1
2 HCG 0.75 0.973684
3 HGS 0.730769 0.925
4 GSM 0.690909 0.878049
5 GDS 0.672727 0.837209
6 GS8 0.672727 0.840909
7 GTS 0.672727 0.660714
8 GSF 0.660714 0.72549
9 AHE 0.649123 0.9
10 3GC 0.645833 0.918919
11 HGD 0.637931 0.837209
12 GCG 0.6 0.860465
13 KGT 0.592593 0.923077
14 TGG 0.587302 0.9
15 BWS 0.581818 0.871795
16 TS5 0.573529 0.880952
17 0HH 0.528571 0.782609
18 GSB 0.528571 0.878049
19 KSN 0.528302 0.789474
20 GSO 0.521127 0.857143
21 BOB 0.493506 0.75
22 GTB 0.493333 0.631579
23 P9H 0.486842 0.857143
24 GBI 0.486842 0.782609
25 48T 0.481013 0.8
26 L9X 0.480519 0.62069
27 GTD 0.480519 0.6
28 ESG 0.480519 0.62069
29 1R4 0.474359 0.62069
30 GIP 0.474359 0.6
31 GPS 0.468354 0.72
32 GPR 0.468354 0.72
33 GBP 0.468354 0.6
34 GAZ 0.457831 0.679245
35 GVX 0.45679 0.8
36 HFV 0.447761 0.8
37 ASV 0.446154 0.9
38 GNB 0.445783 0.6
39 W05 0.444444 0.923077
40 VB1 0.444444 0.9
41 LZ6 0.436782 0.692308
42 ACV 0.430769 0.878049
43 BCV 0.424242 0.9
44 CDH 0.424242 0.818182
45 2G2 0.42029 0.615385
46 HGA 0.42 0.622222
47 M8F 0.411765 0.837209
48 MEQ 0.411765 0.658537
49 TS4 0.410256 0.804348
50 M9F 0.405797 0.837209
51 KKA 0.4 0.894737
52 M2W 0.4 0.8
53 ACW 0.4 0.8
Similar Ligands (3D)
Ligand no: 1; Ligand: GSH; Similar ligands found: 5
No: Ligand Similarity coefficient
1 GSN 0.9495
2 MP2 0.9045
3 ALA ALA ALA ALA 0.8738
4 GGL CYW GLY 0.8570
5 DN8 0.8566
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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