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
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
Members (12)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 263 families.
1 4QBZ - D80 C14 H15 N3 O CCCCc1nc2c....
2 4R07 Kd = 55 uM URI C9 H12 N2 O6 C1=CN(C(=O....
3 3W3J - C09 C13 H14 N4 O CCOCc1[nH]....
4 4QC0 - XG1 C14 H16 N4 CCCCn1cc2c....
5 3WN4 - D87 C15 H16 N2 O CCCCc1cc2c....
6 3W3K - L07 C13 H13 N3 S CCCc1nc2c(....
7 5AWB - M0A C22 H25 N5 CCCCc1nc2c....
8 4R08 Kd = 55 uM URI C9 H12 N2 O6 C1=CN(C(=O....
9 3W3L - RX8 C17 H22 N4 O2 CCOCc1nc2c....
10 3W3N - RX8 C17 H22 N4 O2 CCOCc1nc2c....
11 4R0A Kd = 55 uM URI C9 H12 N2 O6 C1=CN(C(=O....
12 5AWD - IDQ C22 H25 N5 CCCCc1nc2c....
70% Homology Family (12)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 196 families.
1 4QBZ - D80 C14 H15 N3 O CCCCc1nc2c....
2 4R07 Kd = 55 uM URI C9 H12 N2 O6 C1=CN(C(=O....
3 3W3J - C09 C13 H14 N4 O CCOCc1[nH]....
4 4QC0 - XG1 C14 H16 N4 CCCCn1cc2c....
5 3WN4 - D87 C15 H16 N2 O CCCCc1cc2c....
6 3W3K - L07 C13 H13 N3 S CCCc1nc2c(....
7 5AWB - M0A C22 H25 N5 CCCCc1nc2c....
8 4R08 Kd = 55 uM URI C9 H12 N2 O6 C1=CN(C(=O....
9 3W3L - RX8 C17 H22 N4 O2 CCOCc1nc2c....
10 3W3N - RX8 C17 H22 N4 O2 CCOCc1nc2c....
11 4R0A Kd = 55 uM URI C9 H12 N2 O6 C1=CN(C(=O....
12 5AWD - IDQ C22 H25 N5 CCCCc1nc2c....
50% Homology Family (14)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 171 families.
1 4QBZ - D80 C14 H15 N3 O CCCCc1nc2c....
2 4R07 Kd = 55 uM URI C9 H12 N2 O6 C1=CN(C(=O....
3 3W3J - C09 C13 H14 N4 O CCOCc1[nH]....
4 4QC0 - XG1 C14 H16 N4 CCCCn1cc2c....
5 3WN4 - D87 C15 H16 N2 O CCCCc1cc2c....
6 3W3K - L07 C13 H13 N3 S CCCc1nc2c(....
7 5AWB - M0A C22 H25 N5 CCCCc1nc2c....
8 4R08 Kd = 55 uM URI C9 H12 N2 O6 C1=CN(C(=O....
9 3W3L - RX8 C17 H22 N4 O2 CCOCc1nc2c....
10 3W3N - RX8 C17 H22 N4 O2 CCOCc1nc2c....
11 4R0A Kd = 55 uM URI C9 H12 N2 O6 C1=CN(C(=O....
12 5AWD - IDQ C22 H25 N5 CCCCc1nc2c....
13 5GMF Kd = 1 uM GMP C10 H13 N5 O5 c1nc2c(n1[....
14 5GMH Kd = 0.49 uM RX8 C17 H22 N4 O2 CCOCc1nc2c....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: URI; Similar ligands found: 90
No: Ligand ECFP6 Tc MDL keys Tc
1 U 1 1
2 URI 1 1
3 CJB 0.895833 0.949153
4 DKX 0.709091 0.857143
5 2TU 0.666667 0.888889
6 U5P 0.661017 0.848485
7 U4S 0.65 0.833333
8 UA3 0.644068 0.833333
9 U3P 0.644068 0.833333
10 U2S 0.629032 0.848485
11 U3S 0.629032 0.833333
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 UFM 0.552632 0.865672
23 URM 0.552632 0.852941
24 GUD 0.552632 0.865672
25 UPG 0.552632 0.865672
26 660 0.552632 0.852941
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 UDP GAL 0.531646 0.865672
32 U2F 0.531646 0.816901
33 UPF 0.531646 0.816901
34 UMF 0.53125 0.757143
35 U1S 0.527027 0.8
36 BRD 0.525424 0.915254
37 UVC 0.515625 0.782609
38 UFG 0.5125 0.816901
39 DUR 0.508475 0.903226
40 AR3 0.5 0.919355
41 UDH 0.5 0.794521
42 CTN 0.5 0.919355
43 UPP 0.5 0.838235
44 5UD 0.5 0.920635
45 CTD 0.491525 0.9
46 URD 0.491525 0.881356
47 CSV 0.488372 0.780822
48 CSQ 0.488372 0.780822
49 UDM 0.488372 0.84058
50 3UC 0.488095 0.816901
51 U U 0.481481 0.823529
52 UD1 0.477273 0.852941
53 UD2 0.477273 0.852941
54 UAD 0.47561 0.838235
55 UDX 0.47561 0.838235
56 USQ 0.464286 0.730769
57 UGB 0.464286 0.850746
58 UGA 0.464286 0.850746
59 GPQ 0.460317 0.875
60 G3N 0.458824 0.814286
61 PUP 0.457831 0.811594
62 GPK 0.453125 0.875
63 GPU 0.446154 0.875
64 6SY 0.43662 0.80597
65 0YQ 0.435897 0.835821
66 EPZ 0.428571 0.84058
67 CH 0.428571 0.811594
68 U U U U 0.426829 0.808824
69 D1M 0.426471 0.903226
70 UM3 0.426471 0.782609
71 12V 0.425532 0.828571
72 HWU 0.425532 0.828571
73 D1J 0.424658 0.848485
74 EPU 0.424242 0.828571
75 EEB 0.424242 0.828571
76 A U 0.424242 0.76
77 UTP U U U 0.421687 0.818182
78 HP7 0.419355 0.838235
79 UD7 0.419355 0.826087
80 G U34 0.415842 0.7125
81 MJZ 0.414894 0.814286
82 5AE 0.412698 0.887097
83 UD4 0.410526 0.814286
84 UMP 0.408451 0.771429
85 DU 0.408451 0.771429
86 UP5 0.408163 0.76
87 DDU 0.403226 0.793651
88 IUG 0.402062 0.721519
89 4TC 0.4 0.74026
90 DUS 0.4 0.701299
Ligand no: 2; Ligand: UCG; Similar ligands found: 49
No: Ligand ECFP6 Tc MDL keys Tc
1 UCG 1 1
2 GPX 0.632479 0.910256
3 U2G 0.607692 0.95
4 CG2 0.517986 0.95
5 APU 0.507246 0.911392
6 U G A 0.503226 0.925926
7 G U34 0.5 0.925926
8 GPC 0.493056 0.915663
9 A G U 0.487179 0.925926
10 G G G RPC 0.472222 0.936709
11 GPG 0.469697 0.901235
12 PUP 0.46875 0.777778
13 OMC OMU OMG OMG U 0.4625 0.903614
14 G4P 0.461538 0.923077
15 5GP 0.459016 0.923077
16 G 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 GDC 0.414286 0.901235
37 GDD 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 DG 0.404762 0.876543
44 DGP 0.404762 0.876543
45 G2P 0.402985 0.878049
46 GNP 0.402985 0.888889
47 G G 0.402878 0.9
48 JB2 0.402778 0.901235
49 3PD UM3 0.4 0.902439
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4R08; Ligand: URI; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 4r08.bio1) has 59 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 4R08; Ligand: UCG; Similar sites found: 8
This union binding pocket(no: 2) in the query (biounit: 4r08.bio1) has 20 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5DEP UD1 0.01548 0.41295 3.10078
2 1HDR NAD 0.01789 0.44376 4.5082
3 3AGC RCC 0.01068 0.40674 5.07246
4 3VC1 GST 0.02589 0.40128 5.12821
5 4X8O AP5 0.03011 0.40169 5.14019
6 2P1O NLA 0.009984 0.41208 13.75
7 2P1O IHP 0.009984 0.41208 13.75
8 2P1M IHP 0.009722 0.40719 13.75
Pocket No.: 3; Query (leader) PDB : 4R08; Ligand: UCG; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 4r08.bio1) has 18 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 4R08; Ligand: URI; Similar sites found: 2
This union binding pocket(no: 4) in the query (biounit: 4r08.bio1) has 62 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2X1L MET 0.01379 0.43327 5.34351
2 4NZ6 DGL 0.03917 0.40891 11.8211
Pocket No.: 5; Query (leader) PDB : 4R08; Ligand: URI; Similar sites found: 13
This union binding pocket(no: 5) in the query (biounit: 4r08.bio2) has 47 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2NVA PL2 0.0184 0.40113 1.34409
2 4XV1 904 0.0158 0.41193 2.73973
3 4KQW NAP 0.01528 0.41488 2.85714
4 5JFS 6K0 0.03152 0.40327 3.57143
5 3NC9 TR3 0.02655 0.40701 4.15335
6 4L2H AR6 AR6 0.02266 0.40426 4.40252
7 3X01 AMP 0.01229 0.41199 4.58015
8 1KRH FAD 0.0109 0.40399 4.73373
9 4JSR 1NQ 0.04614 0.40299 5.26316
10 5UIU 8CG 0.01871 0.40718 5.57276
11 3A06 FOM 0.0196 0.41163 7.27497
12 3A06 NDP 0.01972 0.40942 7.27497
13 4J4H NAI 0.04433 0.40088 8.49421
Pocket No.: 6; Query (leader) PDB : 4R08; Ligand: UCG; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 4r08.bio2) has 18 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 7; Query (leader) PDB : 4R08; Ligand: UCG; Similar sites found: 9
This union binding pocket(no: 7) in the query (biounit: 4r08.bio2) has 20 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4FHD 0TT 0.001765 0.44823 3.53261
2 4FHD EEM 0.001765 0.44823 3.53261
3 4GID 0GH 0.043 0.42035 3.86598
4 5TVM PUT 0.001086 0.46561 7.05882
5 3AB4 THR 0.01683 0.40314 7.86517
6 3G08 FEE 0.01579 0.42252 11.1111
7 4X6F 3XU 0.02634 0.40093 11.4286
8 5L2J 6UL 0.04864 0.4038 12.2449
9 3VPB ADP 0.01024 0.40468 13.4752
Pocket No.: 8; Query (leader) PDB : 4R08; Ligand: URI; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 8) in the query (biounit: 4r08.bio2) has 44 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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