-->
Receptor
PDB id Resolution Class Description Source Keywords
4R08 2.4 Å NON-ENZYME: SIGNAL_HORMONE CRYSTAL STRUCTURE OF HUMAN TLR8 IN COMPLEX WITH SSRNA40 HOMO SAPIENS LEUCINE RICH REPEAT GLYCOSYLATION INNATE IMMUNITY RNA RECRNA RECEPTOR RNA BINDING ANTIVIRAL BINDING ANTITUMOR DRUBINDING IMMUNE SYSTEM
Ref.: TOLL-LIKE RECEPTOR 8 SENSES DEGRADATION PRODUCTS OF SINGLE-STRANDED RNA. NAT.STRUCT.MOL.BIOL. V. 22 109 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
URI D:901;
C:902;
B:901;
A:901;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
Kd = 55 uM
244.201 C9 H12 N2 O6 C1=CN...
NAG A:912;
C:913;
D:913;
D:914;
B:914;
A:908;
D:909;
B:908;
A:911;
B:912;
B:913;
D:912;
C:909;
B:911;
A:913;
C:914;
C:912;
A:914;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
221.208 C8 H15 N O6 CC(=O...
NAG BMA NAG A:906;
Invalid;
none;
submit data n/a n/a n/a n/a
UCG B:915;
D:902;
C:901;
A:915;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
731.351 C19 H24 N7 O18 P3 c1nc2...
NAG NAG BMA B:905;
C:903;
D:903;
D:906;
C:906;
B:902;
A:902;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
submit data
570.545 n/a O=C(N...
NAG NAG B:909;
C:910;
D:910;
A:909;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
submit data
408.404 n/a O=C(N...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5WYZ 2.3 Å NON-ENZYME: SIGNAL_HORMONE CRYSTAL STRUCTURE OF HUMAN TLR8 IN COMPLEX WITH CU-CPT9B HOMO SAPIENS IMMUNE SYSTEM
Ref.: SMALL-MOLECULE INHIBITION OF TLR8 THROUGH STABILIZA ITS RESTING STATE NAT. CHEM. BIOL. V. 14 58 2018
Members (14)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 286 families.
1 4QBZ - D80 C14 H15 N3 O CCCCc1nc2c....
2 5WYZ Kd = 21 nM 7VF C16 H13 N O2 Cc1cc(ccc1....
3 4R07 Kd = 55 uM URI C9 H12 N2 O6 C1=CN(C(=O....
4 3W3J - C09 C13 H14 N4 O CCOCc1[nH]....
5 4QC0 - XG1 C14 H16 N4 CCCCn1cc2c....
6 3WN4 - D87 C15 H16 N2 O CCCCc1cc2c....
7 3W3K - L07 C13 H13 N3 S CCCc1nc2c(....
8 5AWB - M0A C22 H25 N5 CCCCc1nc2c....
9 4R08 Kd = 55 uM URI C9 H12 N2 O6 C1=CN(C(=O....
10 3W3L - RX8 C17 H22 N4 O2 CCOCc1nc2c....
11 5WYX Kd = 0.22 uM CU8 C14 H12 N4 O Cc1cccc(c1....
12 3W3N - RX8 C17 H22 N4 O2 CCOCc1nc2c....
13 4R0A Kd = 55 uM URI C9 H12 N2 O6 C1=CN(C(=O....
14 5AWD - IDQ C22 H25 N5 CCCCc1nc2c....
70% Homology Family (14)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 209 families.
1 4QBZ - D80 C14 H15 N3 O CCCCc1nc2c....
2 5WYZ Kd = 21 nM 7VF C16 H13 N O2 Cc1cc(ccc1....
3 4R07 Kd = 55 uM URI C9 H12 N2 O6 C1=CN(C(=O....
4 3W3J - C09 C13 H14 N4 O CCOCc1[nH]....
5 4QC0 - XG1 C14 H16 N4 CCCCn1cc2c....
6 3WN4 - D87 C15 H16 N2 O CCCCc1cc2c....
7 3W3K - L07 C13 H13 N3 S CCCc1nc2c(....
8 5AWB - M0A C22 H25 N5 CCCCc1nc2c....
9 4R08 Kd = 55 uM URI C9 H12 N2 O6 C1=CN(C(=O....
10 3W3L - RX8 C17 H22 N4 O2 CCOCc1nc2c....
11 5WYX Kd = 0.22 uM CU8 C14 H12 N4 O Cc1cccc(c1....
12 3W3N - RX8 C17 H22 N4 O2 CCOCc1nc2c....
13 4R0A Kd = 55 uM URI C9 H12 N2 O6 C1=CN(C(=O....
14 5AWD - IDQ C22 H25 N5 CCCCc1nc2c....
50% Homology Family (16)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 174 families.
1 4QBZ - D80 C14 H15 N3 O CCCCc1nc2c....
2 5WYZ Kd = 21 nM 7VF C16 H13 N O2 Cc1cc(ccc1....
3 4R07 Kd = 55 uM URI C9 H12 N2 O6 C1=CN(C(=O....
4 3W3J - C09 C13 H14 N4 O CCOCc1[nH]....
5 4QC0 - XG1 C14 H16 N4 CCCCn1cc2c....
6 3WN4 - D87 C15 H16 N2 O CCCCc1cc2c....
7 3W3K - L07 C13 H13 N3 S CCCc1nc2c(....
8 5AWB - M0A C22 H25 N5 CCCCc1nc2c....
9 4R08 Kd = 55 uM URI C9 H12 N2 O6 C1=CN(C(=O....
10 3W3L - RX8 C17 H22 N4 O2 CCOCc1nc2c....
11 5WYX Kd = 0.22 uM CU8 C14 H12 N4 O Cc1cccc(c1....
12 3W3N - RX8 C17 H22 N4 O2 CCOCc1nc2c....
13 4R0A Kd = 55 uM URI C9 H12 N2 O6 C1=CN(C(=O....
14 5AWD - IDQ C22 H25 N5 CCCCc1nc2c....
15 5GMF Kd = 1 uM GMP C10 H13 N5 O5 c1nc2c(n1[....
16 5GMH Kd = 0.49 uM RX8 C17 H22 N4 O2 CCOCc1nc2c....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: URI; Similar ligands found: 91
No: Ligand ECFP6 Tc MDL keys Tc
1 URI 1 1
2 CJB 0.895833 0.949153
3 DKX 0.709091 0.857143
4 2TU 0.666667 0.888889
5 U5P 0.661017 0.848485
6 U 0.661017 0.848485
7 U4S 0.65 0.833333
8 U3P 0.644068 0.833333
9 UA3 0.644068 0.833333
10 U3S 0.629032 0.833333
11 U2S 0.629032 0.848485
12 UDP 0.625 0.863636
13 44P 0.603175 0.826087
14 UPU 0.6 0.863636
15 UTP 0.597015 0.863636
16 U2P 0.590164 0.848485
17 UDP UDP 0.575758 0.861538
18 2KH 0.565217 0.838235
19 UUA 0.561404 0.864407
20 ZEB 0.553571 0.966102
21 GDU 0.552632 0.865672
22 UPG 0.552632 0.865672
23 660 0.552632 0.852941
24 URM 0.552632 0.852941
25 GUD 0.552632 0.865672
26 UFM 0.552632 0.865672
27 UNP 0.549296 0.838235
28 Y6W 0.545455 0.816901
29 N3E 0.544118 0.835821
30 DHZ 0.534483 0.966102
31 U2F 0.531646 0.816901
32 UPF 0.531646 0.816901
33 UMF 0.53125 0.757143
34 U1S 0.527027 0.8
35 BRD 0.525424 0.915254
36 UVC 0.515625 0.782609
37 UFG 0.5125 0.816901
38 DUR 0.508475 0.903226
39 CTN 0.5 0.919355
40 5UD 0.5 0.920635
41 AR3 0.5 0.919355
42 UPP 0.5 0.838235
43 UDH 0.5 0.794521
44 URD 0.491525 0.881356
45 CTD 0.491525 0.9
46 CSQ 0.488372 0.780822
47 UDM 0.488372 0.84058
48 CSV 0.488372 0.780822
49 3UC 0.488095 0.816901
50 U U 0.481481 0.823529
51 UD1 0.477273 0.852941
52 UD2 0.477273 0.852941
53 UAD 0.47561 0.838235
54 UDX 0.47561 0.838235
55 USQ 0.464286 0.730769
56 UGA 0.464286 0.850746
57 UGB 0.464286 0.850746
58 GPQ 0.460317 0.875
59 G3N 0.458824 0.814286
60 PUP 0.457831 0.811594
61 GPK 0.453125 0.875
62 GPU 0.446154 0.875
63 6SY 0.43662 0.80597
64 0YQ 0.435897 0.835821
65 EPZ 0.428571 0.84058
66 U U U U 0.426829 0.808824
67 UM3 0.426471 0.782609
68 D1M 0.426471 0.903226
69 12V 0.425532 0.828571
70 HWU 0.425532 0.828571
71 D1J 0.424658 0.848485
72 EPU 0.424242 0.828571
73 EEB 0.424242 0.828571
74 A U 0.424242 0.76
75 UTP U U U 0.421687 0.818182
76 UD7 0.419355 0.826087
77 HP7 0.419355 0.838235
78 G U34 0.415842 0.7125
79 G U 0.415842 0.721519
80 MJZ 0.414894 0.814286
81 5AE 0.412698 0.887097
82 F5G 0.410526 0.826087
83 F5P 0.410526 0.814286
84 UD4 0.410526 0.814286
85 DU 0.408451 0.771429
86 UMP 0.408451 0.771429
87 UP5 0.408163 0.76
88 DDU 0.403226 0.793651
89 IUG 0.402062 0.721519
90 4TC 0.4 0.74026
91 DUS 0.4 0.701299
Ligand no: 2; Ligand: UCG; Similar ligands found: 50
No: Ligand ECFP6 Tc MDL keys Tc
1 UCG 1 1
2 GPX 0.632479 0.910256
3 U2G 0.607692 0.95
4 G U 0.544118 0.9375
5 CG2 0.517986 0.95
6 A G U U 0.509554 0.925926
7 APU 0.507246 0.911392
8 G U34 0.5 0.925926
9 GPC 0.493056 0.915663
10 A G U 0.487179 0.925926
11 G G G RPC 0.472222 0.936709
12 GPG 0.469697 0.901235
13 PUP 0.46875 0.777778
14 G4P 0.461538 0.923077
15 G 0.459016 0.923077
16 5GP 0.459016 0.923077
17 G3D 0.457364 0.923077
18 UPU 0.455285 0.797468
19 G C 0.452055 0.9375
20 A G C C 0.450331 0.949367
21 0O2 0.447761 0.923077
22 G C C C 0.43871 0.962025
23 UPA 0.4375 0.876543
24 2GP 0.430894 0.898734
25 3GP 0.430894 0.910256
26 GDP 0.429688 0.911392
27 GNH 0.426357 0.9
28 G G G C 0.424837 0.95
29 GSP 0.424242 0.86747
30 SGP 0.424 0.819277
31 P2G 0.424 0.873418
32 GP3 0.421875 0.9125
33 GTP 0.419847 0.911392
34 G2R 0.419118 0.878049
35 Y9Z 0.414286 0.827586
36 GDD 0.414286 0.901235
37 GDC 0.414286 0.901235
38 GKE 0.414286 0.901235
39 GMV 0.409091 0.888889
40 GAV 0.407407 0.878049
41 G1R 0.406015 0.9
42 GCP 0.406015 0.888889
43 DGP 0.404762 0.876543
44 DG 0.404762 0.876543
45 9GM 0.402985 0.888889
46 GNP 0.402985 0.888889
47 G2P 0.402985 0.878049
48 JB2 0.402778 0.901235
49 U A 0.402597 0.9
50 3PD UM3 0.4 0.902439
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5WYZ; Ligand: 7VF; Similar sites found with APoc: 33
This union binding pocket(no: 1) in the query (biounit: 5wyz.bio1) has 84 residues
No: Leader PDB Ligand Sequence Similarity
1 2CXG GLC GLC 1.74927
2 2X24 X24 2.01765
3 3WW2 SF9 2.34375
4 2INV FRU FRU 2.43902
5 4XWM CBI 2.49633
6 2ZX2 RAM 2.5641
7 1K7T NAG GAL 2.68817
8 3G5N PB2 3.15126
9 2YN4 39J 3.81356
10 5W75 SUC 3.82653
11 3MA0 XYP 3.83387
12 5F90 LMR 3.84615
13 1QH9 LAC 3.87931
14 2JIG PD2 4.01786
15 3K0T BGC 4.1958
16 3CL7 HYN 4.22078
17 3MMH SME 4.79042
18 4CNK MEU 5.6266
19 2Z49 AMG 6.01852
20 2Z48 NGA 6.01852
21 2Z48 A2G 6.01852
22 4Y4V DAL 6.19469
23 5H4S RAM 6.33803
24 2ZSC BTN 6.38298
25 3A06 NDP 7.27497
26 4AML GYU 7.60234
27 1NX4 AKG 9.15751
28 2WDQ TEO 9.66387
29 5D6T NGA 10.6618
30 1WBI BTN 11.6279
31 4NZ6 DGL 11.8211
32 1GG6 APL 14.433
33 3HCH RSM 20.5479
Pocket No.: 2; Query (leader) PDB : 5WYZ; Ligand: 7VF; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 5wyz.bio1) has 84 residues
No: Leader PDB Ligand Sequence Similarity
APoc FAQ
Feedback