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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 with APoc: 43
This union binding pocket(no: 1) in the query (biounit: 5hmy.bio1) has 42 residues
No: Leader PDB Ligand Sequence Similarity
1 4WG0 CHD None
2 3MMR ABH 1.93705
3 5FJJ MAN 2.3622
4 4G86 BNT 2.46479
5 5X80 SAL 2.5
6 2WCI GSH 2.96296
7 1QB7 ADE 2.9661
8 2J5V PCA 2.99728
9 2R68 SUP 3.00601
10 5Z21 OXM 3.07263
11 1A5Z FBP 3.1348
12 1BCJ NGA 3.24675
13 1MID LAP 3.2967
14 4L80 OXL 3.44828
15 2ZL4 ALA ALA ALA ALA 3.57143
16 5Y02 HBX 3.73832
17 2BCG GER 3.75276
18 4JWK CTN 4.14508
19 2AEB ABH 4.34783
20 4RM0 FUC NDG GAL 4.43038
21 4USI AKG 4.54545
22 2DT9 THR 4.79042
23 2R5A MLZ 4.90566
24 4XZ9 G3P 4.93274
25 3R7F CP 4.93421
26 4AP9 1PS 5.47264
27 3AB4 THR 5.61798
28 1D8C GLV 6.14173
29 1P7T PYR 6.45669
30 4DE2 DN3 6.46388
31 4QDI ATP 6.77966
32 5GVR LMR 6.83761
33 5YIZ EF2 7.20721
34 5YJ1 6EL 7.20721
35 5YJ0 EF2 7.20721
36 5DCH 1YO 7.29167
37 2ZX2 RAM 7.69231
38 5H4S RAM 7.74648
39 5X2N ALA 8.75576
40 5TDC NMM ILE PHE SER 9.21053
41 1UPF URF 9.375
42 4FFG 0U8 11.1789
43 5G3L SIA 22.2222
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