Receptor
PDB id Resolution Class Description Source Keywords
6LD2 1.4 Å EC: 2.1.1.56 ZIKA NS5 POLYMERASE DOMAIN ZIKA VIRUS (ISOLATE ZIKV/HUMAN/FRENCH POLYNESIA/10087PF/2013) ZIKA POLYMERASE NS5 RDRP RNA DEPDENDANT RNA POLYMERASE TRAN
Ref.: NON-NUCLEOSIDE INHIBITORS OF ZIKA VIRUS RNA-DEPENDE POLYMERASE. J.VIROL. V. 94 2020
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ZN A:902;
A:901;
 Part of Protein;
Part of Protein;
 none;
none;
 submit data
65.409 Zn [Zn+2...
KY3 A:903;
 Valid;
 none;
 ic50 = 246.6 uM
270.345 C13 H18 O4 S CO[C@...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6LD3 2.3 Å EC: 2.1.1.56 ZIKA NS5 POLYMERASE DOMAIN ZIKA VIRUS (ISOLATE ZIKV/HUMAN/FRENCH POLYNESIA/10087PF/2013) ZIKA POLYMERASE NS5 RDRP RNA DEPDENDANT RNA POLYMERASE TRAN
Ref.: NON-NUCLEOSIDE INHIBITORS OF ZIKA VIRUS RNA-DEPENDE POLYMERASE. J.VIROL. V. 94 2020
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 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[....
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: KY3; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 KY3 1 1
Similar Ligands (3D)
Ligand no: 1; Ligand: KY3; Similar ligands found: 49
No: Ligand Similarity coefficient
1 B56 0.8997
2 96U 0.8993
3 CB1 0.8983
4 B61 0.8891
5 EV2 0.8829
6 JY4 0.8814
7 TQU 0.8803
8 5V7 0.8784
9 64E 0.8782
10 96R 0.8780
11 M3F 0.8745
12 AC2 0.8744
13 DXK 0.8734
14 MIL 0.8725
15 GHM 0.8721
16 H2B 0.8713
17 WUB 0.8709
18 4AB 0.8688
19 BIO 0.8686
20 AMR 0.8684
21 NBG 0.8676
22 5NN 0.8672
23 4VS 0.8671
24 GDL 0.8667
25 92O 0.8655
26 QR2 0.8653
27 9H2 0.8644
28 2AN 0.8632
29 HHS 0.8629
30 CR1 0.8625
31 LZB 0.8620
32 LFQ 0.8617
33 64F 0.8615
34 KF5 0.8614
35 EAE 0.8612
36 SYR 0.8612
37 GA2 0.8608
38 0FK 0.8603
39 DX7 0.8596
40 H4B 0.8589
41 DX2 0.8588
42 64C 0.8586
43 5B2 0.8582
44 TR4 0.8553
45 UQ1 0.8553
46 8MO 0.8545
47 5V5 0.8535
48 25O 0.8518
49 JAK 0.8509
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6LD3; Ligand: G8O FB2; 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: 6ld3.bio1) has 19 residues
No: Leader PDB Ligand Sequence Similarity
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