Receptor
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
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...
LNY A:1003;
Valid;
none;
ic50 = 0.5 uM
330.355 C17 H14 O5 S c1cc(...
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 (11)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 11 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 5HN0 - LNN C14 H12 O3 c1ccc(cc1)....
8 5HMW - LNW C16 H14 O4 c1ccc(cc1)....
9 5F3Z Kd = 29 uM 5V5 C13 H12 O3 S COc1ccc(cc....
10 5F3T Kd = 210 uM 5UH C15 H14 O3 COc1ccc(cc....
11 5HMX - LNX C14 H12 O4 S c1cc(sc1)c....
70% Homology Family (14)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 5K5M - 68T C23 H21 N O7 S2 COc1cccc(c....
2 4HDG - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
3 4HDH - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
4 3VWS Kd = 225 uM VWS C16 H12 Cl N O5 S Cc1c(c2cc(....
5 5HMZ - LNZ C17 H17 N O5 S2 Cc1cc(c(cc....
6 5HMY ic50 = 0.5 uM LNY C17 H14 O5 S c1cc(sc1C#....
7 5I3Q - 68E C25 H20 N2 O5 S2 Cc1cc(c(cc....
8 5F41 Kd = 67 uM 5V6 C13 H12 O3 S COc1ccc(cc....
9 5I3P - 68T C23 H21 N O7 S2 COc1cccc(c....
10 5HN0 - LNN C14 H12 O3 c1ccc(cc1)....
11 5HMW - LNW C16 H14 O4 c1ccc(cc1)....
12 5F3Z Kd = 29 uM 5V5 C13 H12 O3 S COc1ccc(cc....
13 5F3T Kd = 210 uM 5UH C15 H14 O3 COc1ccc(cc....
14 5HMX - LNX C14 H12 O4 S c1cc(sc1)c....
50% Homology Family (18)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 5K5M - 68T C23 H21 N O7 S2 COc1cccc(c....
2 4HDG - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
3 4HDH - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
4 3VWS Kd = 225 uM VWS C16 H12 Cl N O5 S Cc1c(c2cc(....
5 5HMZ - LNZ C17 H17 N O5 S2 Cc1cc(c(cc....
6 5HMY ic50 = 0.5 uM LNY C17 H14 O5 S c1cc(sc1C#....
7 5I3Q - 68E C25 H20 N2 O5 S2 Cc1cc(c(cc....
8 5F41 Kd = 67 uM 5V6 C13 H12 O3 S COc1ccc(cc....
9 5I3P - 68T C23 H21 N O7 S2 COc1cccc(c....
10 5HN0 - LNN C14 H12 O3 c1ccc(cc1)....
11 5HMW - LNW C16 H14 O4 c1ccc(cc1)....
12 5F3Z Kd = 29 uM 5V5 C13 H12 O3 S COc1ccc(cc....
13 5F3T Kd = 210 uM 5UH C15 H14 O3 COc1ccc(cc....
14 5HMX - LNX C14 H12 O4 S c1cc(sc1)c....
15 4V0Q - SAH C14 H20 N6 O5 S c1nc(c2c(n....
16 5JJR ic50 = 0.016 uM 68E C25 H20 N2 O5 S2 Cc1cc(c(cc....
17 4V0R - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
18 5JJS ic50 = 0.048 uM 6L2 C23 H27 N O7 S2 COc1cc(c(c....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: LNY; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 LNY 1 1
2 LNX 0.433333 0.83871
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5HMY; Ligand: LNY; Similar sites found: 8
This union binding pocket(no: 1) in the query (biounit: 5hmy.bio1) has 42 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5FJJ MAN 0.01897 0.42546 2.3622
2 4G86 BNT 0.0285 0.42153 2.46479
3 3K8L CEY 0.02187 0.42048 3.77953
4 1P4V GLY 0.04833 0.40814 4.0678
5 2R5A MLZ 0.02383 0.41335 4.90566
6 5DCH 1YO 0.02206 0.42832 7.29167
7 5TDC NMM ILE PHE SER 0.03316 0.42006 9.21053
8 4FFG 0U8 0.01427 0.43672 11.1789
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