Receptor
PDB id Resolution Class Description Source Keywords
5HN0 2.05 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...
LNN A:1003;
Valid;
none;
submit data
228.243 C14 H12 O3 c1ccc...
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: LNN; Similar ligands found: 7
No: Ligand ECFP6 Tc MDL keys Tc
1 LNN 1 1
2 5UH 0.555556 0.851852
3 DHY 0.468085 0.75
4 3C4 0.44898 0.75
5 YTX 0.433962 0.724138
6 LNW 0.423077 0.666667
7 3HP 0.4 0.76
Similar Ligands (3D)
Ligand no: 1; Ligand: LNN; Similar ligands found: 81
No: Ligand Similarity coefficient
1 AED 0.9463
2 5V5 0.9409
3 3C5 0.9395
4 5V6 0.9392
5 60L 0.9304
6 77X 0.9230
7 D1G 0.9200
8 V2Z 0.9160
9 HKK 0.9120
10 6NZ 0.9106
11 UN3 0.9102
12 9XZ 0.9059
13 69W 0.9059
14 5F8 0.9059
15 5KN 0.9047
16 1ER 0.9019
17 EV2 0.9001
18 2GE 0.8997
19 0LO 0.8973
20 D2G 0.8971
21 F63 0.8969
22 5FL 0.8968
23 FX5 0.8960
24 JSX 0.8959
25 CX4 0.8938
26 AUV 0.8933
27 S1D 0.8930
28 E42 0.8928
29 MIL 0.8927
30 VBC 0.8925
31 U7E 0.8916
32 MMJ 0.8886
33 LFQ 0.8882
34 TCR 0.8864
35 Q4G 0.8850
36 X6W 0.8849
37 FZ6 0.8837
38 LEL 0.8830
39 L5D 0.8827
40 IQQ 0.8820
41 1CE 0.8817
42 49P 0.8817
43 TR4 0.8806
44 8RK 0.8797
45 L98 0.8794
46 KCH 0.8793
47 K4T 0.8778
48 C09 0.8776
49 L1T 0.8774
50 XG1 0.8760
51 JHY 0.8756
52 5TZ 0.8750
53 BQ5 0.8750
54 L07 0.8733
55 KWQ 0.8728
56 SU9 0.8723
57 JF5 0.8719
58 5P3 0.8710
59 5C1 0.8707
60 EYM 0.8703
61 A9B 0.8695
62 FZ0 0.8693
63 HHB 0.8691
64 0K7 0.8686
65 LF5 0.8684
66 KWB 0.8672
67 4AU 0.8672
68 S46 0.8667
69 7G2 0.8656
70 D3G 0.8655
71 90M 0.8634
72 K6N 0.8633
73 RI2 0.8624
74 ROL 0.8611
75 K6B 0.8595
76 KWH 0.8586
77 G6Q 0.8580
78 S2X 0.8564
79 EYA 0.8557
80 AJ1 0.8557
81 ET0 0.8517
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
APoc FAQ
Feedback