Receptor
PDB id Resolution Class Description Source Keywords
3VWS 2.1 Å EC: 2.7.7.48 DENGUE SEROTYPE 3 RNA-DEPENDENT RNA POLYMERASE BOUND TO NITD DENGUE VIRUS 3 RNA-DEPENDENT RNA POLYMERASE RNA POLYMERASE VIRAL PROTEINTRANSFERASE-TRANSFERASE INHIBITOR COMPLEX
Ref.: CONFORMATIONAL FLEXIBILITY OF THE DENGUE VIRUS RNA-RNA POLYMERASE REVEALED BY A COMPLEX WITH AN INHIBI J.VIROL. V. 87 5291 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ZN A:1002;
A:1001;
 Part of Protein;
Part of Protein;
 none;
none;
 submit data
65.409 Zn [Zn+2...
VWS A:1003;
A:1004;
 Valid;
Valid;
 none;
none;
 Kd = 225 uM
365.788 C16 H12 Cl N O5 S Cc1c(...
PEG A:1005;
 Invalid;
 none;
 submit data
106.12 C4 H10 O3 C(COC...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5HMY 2.1 Å EC: 2.7.7.48 DENGUE SEROTYPE 3 RNA-DEPENDENT RNA POLYMERASE BOUND TO COMP DENGUE VIRUS 3 INHIBITOR COMPLEX POLYMERASE TRANSFERASE-TRANSFERASE INHIBICOMPLEX
Ref.: DISCOVERY OF POTENT NON-NUCLEOSIDE INHIBITORS OF DE VIRAL RNA-DEPENDENT RNA POLYMERASE FROM A FRAGMENT STRUCTURE-BASED DRUG DESIGN. J.MED.CHEM. V. 59 3935 2016
Members (13)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 3VWS Kd = 225 uM VWS C16 H12 Cl N O5 S Cc1c(c2cc(....
2 5HMZ - LNZ C17 H17 N O5 S2 Cc1cc(c(cc....
3 5HMY ic50 = 0.5 uM LNY C17 H14 O5 S c1cc(sc1C#....
4 5I3Q - 68E C25 H20 N2 O5 S2 Cc1cc(c(cc....
5 5F41 Kd = 67 uM 5V6 C13 H12 O3 S COc1ccc(cc....
6 5I3P - 68T C23 H21 N O7 S2 COc1cccc(c....
7 6H9R - 5V5 C13 H12 O3 S COc1ccc(cc....
8 5HN0 - LNN C14 H12 O3 c1ccc(cc1)....
9 6H80 - 5V5 C13 H12 O3 S COc1ccc(cc....
10 5HMW - LNW C16 H14 O4 c1ccc(cc1)....
11 5F3Z Kd = 29 uM 5V5 C13 H12 O3 S COc1ccc(cc....
12 5F3T Kd = 210 uM 5UH C15 H14 O3 COc1ccc(cc....
13 5HMX - LNX C14 H12 O4 S c1cc(sc1)c....
70% Homology Family (20)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 6LD5 ic50 = 106.6 uM G8L C9 H8 N2 O2 S c1cc2cccnc....
2 6LD3 ic50 = 43.2 uM G8O FB2 n/a n/a
3 6LD4 ic50 = 80.6 uM G8F C7 H9 N O3 S COc1cccc(c....
4 6LD2 ic50 = 246.6 uM KY3 C13 H18 O4 S CO[C@H]1C[....
5 5K5M - 68T C23 H21 N O7 S2 COc1cccc(c....
6 4HDG - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
7 4HDH - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
8 3VWS Kd = 225 uM VWS C16 H12 Cl N O5 S Cc1c(c2cc(....
9 5HMZ - LNZ C17 H17 N O5 S2 Cc1cc(c(cc....
10 5HMY ic50 = 0.5 uM LNY C17 H14 O5 S c1cc(sc1C#....
11 5I3Q - 68E C25 H20 N2 O5 S2 Cc1cc(c(cc....
12 5F41 Kd = 67 uM 5V6 C13 H12 O3 S COc1ccc(cc....
13 5I3P - 68T C23 H21 N O7 S2 COc1cccc(c....
14 6H9R - 5V5 C13 H12 O3 S COc1ccc(cc....
15 5HN0 - LNN C14 H12 O3 c1ccc(cc1)....
16 6H80 - 5V5 C13 H12 O3 S COc1ccc(cc....
17 5HMW - LNW C16 H14 O4 c1ccc(cc1)....
18 5F3Z Kd = 29 uM 5V5 C13 H12 O3 S COc1ccc(cc....
19 5F3T Kd = 210 uM 5UH C15 H14 O3 COc1ccc(cc....
20 5HMX - LNX C14 H12 O4 S c1cc(sc1)c....
50% Homology Family (25)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 6LD5 ic50 = 106.6 uM G8L C9 H8 N2 O2 S c1cc2cccnc....
2 6LD3 ic50 = 43.2 uM G8O FB2 n/a n/a
3 6LD4 ic50 = 80.6 uM G8F C7 H9 N O3 S COc1cccc(c....
4 6LD2 ic50 = 246.6 uM KY3 C13 H18 O4 S CO[C@H]1C[....
5 5K5M - 68T C23 H21 N O7 S2 COc1cccc(c....
6 4HDG - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
7 4HDH - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
8 3VWS Kd = 225 uM VWS C16 H12 Cl N O5 S Cc1c(c2cc(....
9 5HMZ - LNZ C17 H17 N O5 S2 Cc1cc(c(cc....
10 5HMY ic50 = 0.5 uM LNY C17 H14 O5 S c1cc(sc1C#....
11 5I3Q - 68E C25 H20 N2 O5 S2 Cc1cc(c(cc....
12 5F41 Kd = 67 uM 5V6 C13 H12 O3 S COc1ccc(cc....
13 5I3P - 68T C23 H21 N O7 S2 COc1cccc(c....
14 6H9R - 5V5 C13 H12 O3 S COc1ccc(cc....
15 5HN0 - LNN C14 H12 O3 c1ccc(cc1)....
16 6H80 - 5V5 C13 H12 O3 S COc1ccc(cc....
17 5HMW - LNW C16 H14 O4 c1ccc(cc1)....
18 5F3Z Kd = 29 uM 5V5 C13 H12 O3 S COc1ccc(cc....
19 5F3T Kd = 210 uM 5UH C15 H14 O3 COc1ccc(cc....
20 5HMX - LNX C14 H12 O4 S c1cc(sc1)c....
21 5ZQK - SAM C15 H22 N6 O5 S C[S@@+](CC....
22 4V0Q - SAH C14 H20 N6 O5 S c1nc(c2c(n....
23 5JJR ic50 = 0.016 uM 68E C25 H20 N2 O5 S2 Cc1cc(c(cc....
24 4V0R - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
25 5JJS ic50 = 0.048 uM 6L2 C23 H27 N O7 S2 COc1cc(c(c....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: VWS; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 VWS 1 1
Similar Ligands (3D)
Ligand no: 1; Ligand: VWS; Similar ligands found: 6
No: Ligand Similarity coefficient
1 13F 0.8900
2 P9L 0.8764
3 14X 0.8698
4 68Y 0.8662
5 0RU 0.8656
6 4A8 0.8621
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5HMY; Ligand: LNY; 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: 5hmy.bio1) has 42 residues
No: Leader PDB Ligand Sequence Similarity
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