Receptor
PDB id Resolution Class Description Source Keywords
5F3Z 2 Å EC: 2.7.7.48 DENGUE SEROTYPE 3 RNA-DEPENDENT RNA POLYMERASE BOUND TO PC-7 DENGUE VIRUS 3 RDRP INHIBITOR DENGUE 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
5V5 A:1003;
 Valid;
 none;
 Kd = 29 uM
248.298 C13 H12 O3 S COc1c...
ZN A:1002;
A:1001;
 Part of Protein;
Part of Protein;
 none;
none;
 submit data
65.409 Zn [Zn+2...
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: 5V5; Similar ligands found: 6
No: Ligand ECFP6 Tc MDL keys Tc
1 5V5 1 1
2 5UH 0.559322 0.78125
3 5V6 0.532258 0.967742
4 G8O 0.516667 0.8
5 LNX 0.416667 0.628571
6 YTX 0.4 0.676471
Similar Ligands (3D)
Ligand no: 1; Ligand: 5V5; Similar ligands found: 56
No: Ligand Similarity coefficient
1 LNN 0.9409
2 AED 0.9359
3 LF5 0.9198
4 EYM 0.9150
5 LJW 0.9131
6 HA6 0.9062
7 C09 0.8969
8 4XY 0.8949
9 CX4 0.8939
10 EYA 0.8937
11 AO6 0.8929
12 L07 0.8919
13 3C5 0.8918
14 XG1 0.8911
15 P83 0.8903
16 5WS 0.8898
17 MUX 0.8877
18 D80 0.8862
19 5KN 0.8859
20 60L 0.8848
21 9F8 0.8839
22 HKK 0.8832
23 W22 0.8814
24 C1F 0.8794
25 77X 0.8787
26 ROL 0.8777
27 020 0.8747
28 9XZ 0.8746
29 1CE 0.8730
30 JAA 0.8723
31 018 0.8717
32 VKE 0.8716
33 78P 0.8701
34 KFN 0.8695
35 CSN 0.8694
36 OKM 0.8681
37 67Y 0.8676
38 EY2 0.8669
39 LP8 0.8658
40 BOQ 0.8650
41 7M6 0.8628
42 I46 0.8620
43 AH3 0.8615
44 D87 0.8609
45 O82 0.8595
46 C8O 0.8594
47 29B 0.8590
48 LFQ 0.8580
49 GG5 0.8560
50 ASG 0.8558
51 QVK 0.8556
52 5RM 0.8554
53 V2Z 0.8552
54 KY3 0.8535
55 EYY 0.8529
56 2GE 0.8519
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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