Receptor
PDB id Resolution Class Description Source Keywords
5F41 2 Å EC: 2.7.7.48 DENGUE SEROTYPE 3 RNA-DEPENDENT RNA POLYMERASE BOUND TO FD-8 DENGUE VIRUS 3 INHIBITOR RDRP DENGUE VIRUS TRANSFERASE
Ref.: A CONSERVED POCKET IN THE DENGUE VIRUS POLYMERASE I THROUGH FRAGMENT-BASED SCREENING J.BIOL.CHEM. V. 291 8541 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...
5V6 A:1003;
 Valid;
 none;
 Kd = 67 uM
248.298 C13 H12 O3 S COc1c...
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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: 5V6; Similar ligands found: 4
No: Ligand ECFP6 Tc MDL keys Tc
1 5V6 1 1
2 5UH 0.625 0.806452
3 5V5 0.532258 0.967742
4 YTX 0.431034 0.69697
Similar Ligands (3D)
Ligand no: 1; Ligand: 5V6; Similar ligands found: 45
No: Ligand Similarity coefficient
1 LNN 0.9392
2 AED 0.9154
3 EYM 0.9150
4 HA6 0.9094
5 LF5 0.9020
6 CX4 0.8983
7 C09 0.8982
8 LJW 0.8965
9 EYA 0.8965
10 5WS 0.8958
11 L07 0.8954
12 AO6 0.8934
13 MUX 0.8929
14 P83 0.8928
15 XG1 0.8908
16 3C5 0.8894
17 D80 0.8894
18 4XY 0.8890
19 9F8 0.8887
20 C1F 0.8815
21 9XZ 0.8805
22 ROL 0.8800
23 W22 0.8793
24 77X 0.8781
25 5KN 0.8748
26 020 0.8742
27 HKK 0.8740
28 JAA 0.8725
29 018 0.8701
30 1CE 0.8694
31 OKM 0.8683
32 LP8 0.8683
33 EY2 0.8681
34 AH3 0.8658
35 KFN 0.8649
36 C8O 0.8641
37 3S6 0.8612
38 ASG 0.8600
39 GG5 0.8595
40 7M6 0.8594
41 6NZ 0.8559
42 O82 0.8552
43 MN9 0.8541
44 2LX 0.8526
45 4UB 0.8525
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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