Receptor
PDB id Resolution Class Description Source Keywords
3WN4 1.81 Å NON-ENZYME: SIGNAL_HORMONE CRYSTAL STRUCTURE OF HUMAN TLR8 IN COMPLEX WITH DS-877 HOMO SAPIENS LEUCINE RICH REPEAT RNA GLYCOSYLATION INNATE IMMUNITY RNRECOGNITION SSRNAR STRUCTURE-BASED LIGAND DESIGN TLR8-SPAGONIST VACCINE ADJUVANTS ANTIVIRAL-ANTITUMOR DRUG BINDINSYSTEM
Ref.: STRUCTURE-BASED DESIGN OF NOVEL HUMAN TOLL-LIKE REC AGONISTS. CHEMMEDCHEM 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
NAG A:920;
A:904;
A:915;
A:903;
A:902;
A:910;
A:916;
A:921;
A:911;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
none;
none;
none;
none;
 submit data
221.208 C8 H15 N O6 CC(=O...
D87 A:901;
 Valid;
 none;
 submit data
240.3 C15 H16 N2 O CCCCc...
NAG NAG BMA C:1;
D:1;
 Invalid;
Invalid;
 none;
none;
 submit data
570.545 n/a O=C(N...
NAG NAG BMA MAN MAN B:1;
 Invalid;
 none;
 submit data
n/a n/a
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 (15)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 289 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 6ZJZ ic50 = 120 nM QLH C16 H15 F3 N4 c1cc2c(ccc....
7 3WN4 - D87 C15 H16 N2 O CCCCc1cc2c....
8 3W3K - L07 C13 H13 N3 S CCCc1nc2c(....
9 5AWB - M0A C22 H25 N5 CCCCc1nc2c....
10 4R08 Kd = 55 uM URI C9 H12 N2 O6 C1=CN(C(=O....
11 3W3L - RX8 C17 H22 N4 O2 CCOCc1nc2c....
12 5WYX Kd = 0.22 uM CU8 C14 H12 N4 O Cc1cccc(c1....
13 3W3N - RX8 C17 H22 N4 O2 CCOCc1nc2c....
14 4R0A Kd = 55 uM URI C9 H12 N2 O6 C1=CN(C(=O....
15 5AWD - IDQ C22 H25 N5 CCCCc1nc2c....
70% Homology Family (15)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 214 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 6ZJZ ic50 = 120 nM QLH C16 H15 F3 N4 c1cc2c(ccc....
7 3WN4 - D87 C15 H16 N2 O CCCCc1cc2c....
8 3W3K - L07 C13 H13 N3 S CCCc1nc2c(....
9 5AWB - M0A C22 H25 N5 CCCCc1nc2c....
10 4R08 Kd = 55 uM URI C9 H12 N2 O6 C1=CN(C(=O....
11 3W3L - RX8 C17 H22 N4 O2 CCOCc1nc2c....
12 5WYX Kd = 0.22 uM CU8 C14 H12 N4 O Cc1cccc(c1....
13 3W3N - RX8 C17 H22 N4 O2 CCOCc1nc2c....
14 4R0A Kd = 55 uM URI C9 H12 N2 O6 C1=CN(C(=O....
15 5AWD - IDQ C22 H25 N5 CCCCc1nc2c....
50% Homology Family (17)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 181 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 6ZJZ ic50 = 120 nM QLH C16 H15 F3 N4 c1cc2c(ccc....
7 3WN4 - D87 C15 H16 N2 O CCCCc1cc2c....
8 3W3K - L07 C13 H13 N3 S CCCc1nc2c(....
9 5AWB - M0A C22 H25 N5 CCCCc1nc2c....
10 4R08 Kd = 55 uM URI C9 H12 N2 O6 C1=CN(C(=O....
11 3W3L - RX8 C17 H22 N4 O2 CCOCc1nc2c....
12 5WYX Kd = 0.22 uM CU8 C14 H12 N4 O Cc1cccc(c1....
13 3W3N - RX8 C17 H22 N4 O2 CCOCc1nc2c....
14 4R0A Kd = 55 uM URI C9 H12 N2 O6 C1=CN(C(=O....
15 5AWD - IDQ C22 H25 N5 CCCCc1nc2c....
16 5GMF Kd = 1 uM GMP C10 H13 N5 O5 c1nc2c(n1[....
17 5GMH Kd = 0.49 uM RX8 C17 H22 N4 O2 CCOCc1nc2c....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: D87; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 D87 1 1
2 D80 0.442857 0.844444
Similar Ligands (3D)
Ligand no: 1; Ligand: D87; Similar ligands found: 236
No: Ligand Similarity coefficient
1 XG1 0.9798
2 C09 0.9766
3 L07 0.9556
4 IQZ 0.9244
5 2GQ 0.9227
6 QUB 0.9218
7 TXW 0.9206
8 YE7 0.9189
9 CX4 0.9143
10 9KZ 0.9135
11 52F 0.9125
12 JTF 0.9116
13 39Z 0.9113
14 WLH 0.9110
15 3AK 0.9102
16 JYE 0.9095
17 EV2 0.9091
18 6XC 0.9090
19 HA6 0.9088
20 LP8 0.9080
21 1CE 0.9078
22 MN QAY 0.9055
23 X2M 0.9039
24 EY7 0.9033
25 R4E 0.9031
26 5V7 0.9010
27 O82 0.9005
28 P83 0.9003
29 092 0.9002
30 Q5M 0.9001
31 5NN 0.9000
32 FSU 0.8996
33 NIP 0.8992
34 YZ9 0.8985
35 0FR 0.8982
36 NKI 0.8982
37 AMR 0.8975
38 EY2 0.8974
39 5ER 0.8964
40 GNR 0.8960
41 JWW 0.8953
42 4ZF 0.8946
43 GI4 0.8940
44 ET0 0.8940
45 DXK 0.8933
46 0RY 0.8933
47 EYM 0.8931
48 Z25 0.8923
49 DX2 0.8917
50 OAI 0.8916
51 SJK 0.8914
52 5XL 0.8912
53 ASE 0.8911
54 HWH 0.8909
55 1Q4 0.8906
56 22T 0.8906
57 0SX 0.8902
58 BA5 0.8902
59 7M2 0.8900
60 CKA 0.8895
61 NEO 0.8891
62 NAR 0.8890
63 2JP 0.8888
64 NIY 0.8887
65 5SJ 0.8886
66 ZEZ 0.8879
67 UN9 0.8878
68 M1D 0.8876
69 0J5 0.8871
70 6DH 0.8870
71 ZIP 0.8867
72 34L 0.8866
73 X0T 0.8865
74 2JX 0.8860
75 74Z 0.8859
76 7PJ 0.8855
77 JY2 0.8855
78 F40 0.8854
79 ZEA 0.8852
80 LI7 0.8850
81 XJ2 0.8848
82 64F 0.8841
83 RVE 0.8839
84 GI2 0.8837
85 EVO 0.8836
86 BDI 0.8835
87 1QP 0.8834
88 7M5 0.8832
89 0J2 0.8831
90 B61 0.8829
91 EYA 0.8829
92 DRG 0.8828
93 BIO 0.8827
94 3GX 0.8824
95 II4 0.8822
96 28S 0.8817
97 DDC 0.8817
98 QS4 0.8815
99 QMS 0.8814
100 GNJ 0.8809
101 PNX 0.8804
102 6DQ 0.8803
103 TCR 0.8795
104 3QI 0.8795
105 RKY 0.8793
106 GI1 0.8791
107 ZYW 0.8791
108 K7H 0.8790
109 B23 0.8790
110 TRP 0.8788
111 WUL 0.8786
112 P4L 0.8785
113 YM6 0.8785
114 WG8 0.8784
115 JXT 0.8783
116 018 0.8783
117 KU1 0.8775
118 0H5 0.8773
119 ML1 0.8770
120 7AP 0.8770
121 NEU 0.8762
122 KLV 0.8758
123 MUX 0.8757
124 1AJ 0.8751
125 IOP 0.8748
126 PMP 0.8744
127 C8O 0.8744
128 C4E 0.8743
129 H5B 0.8739
130 D5F 0.8737
131 GJW 0.8737
132 PLP 0.8737
133 H4B 0.8735
134 5WS 0.8735
135 JTA 0.8735
136 GNV 0.8734
137 HBI 0.8734
138 NYJ 0.8733
139 7L4 0.8731
140 7KE 0.8730
141 0HY 0.8726
142 3D8 0.8723
143 3L1 0.8722
144 B4L 0.8722
145 2LW 0.8721
146 GZV 0.8721
147 8RK 0.8720
148 3SU 0.8718
149 108 0.8715
150 NHT 0.8715
151 JVD 0.8714
152 1X8 0.8713
153 8Y7 0.8712
154 Z17 0.8710
155 9F8 0.8706
156 AC2 0.8706
157 H35 0.8704
158 4JV 0.8701
159 NAL 0.8700
160 5WN 0.8695
161 D2G 0.8695
162 6HP 0.8695
163 B52 0.8694
164 6ZW 0.8685
165 L1T 0.8684
166 CMG 0.8679
167 SNB 0.8677
168 A0O 0.8672
169 67Y 0.8668
170 JHY 0.8665
171 SER DNF 0.8663
172 5F1 0.8663
173 DNF SER 0.8659
174 OAL 0.8658
175 SYE 0.8656
176 G30 0.8656
177 EBB 0.8655
178 SRO 0.8654
179 H7S 0.8653
180 NAG 0.8651
181 NPL 0.8650
182 1QV 0.8650
183 2T4 0.8650
184 7VF 0.8649
185 RK4 0.8647
186 EYY 0.8646
187 QNM 0.8644
188 GNG 0.8644
189 OAQ 0.8638
190 AUE 0.8638
191 LWS 0.8638
192 0J4 0.8635
193 H2B 0.8633
194 GA2 0.8625
195 PZB 0.8624
196 LLT 0.8622
197 XFE 0.8621
198 DNA 0.8619
199 3D1 0.8618
200 AUG 0.8617
201 55D 0.8615
202 6VD 0.8614
203 78P 0.8612
204 PMM 0.8610
205 5V5 0.8609
206 UAY 0.8608
207 LDR 0.8607
208 XY2 0.8606
209 PJK 0.8603
210 8HG 0.8603
211 CL9 0.8599
212 Q9P 0.8599
213 5AV 0.8597
214 0OK 0.8590
215 C0V 0.8590
216 3UG 0.8590
217 9AP 0.8586
218 HAN 0.8586
219 AJD 0.8585
220 PW1 0.8581
221 J38 0.8578
222 FUJ 0.8574
223 WA2 0.8571
224 ADN 0.8568
225 PXP 0.8568
226 MG7 0.8558
227 VJJ 0.8556
228 8OX 0.8556
229 I2E 0.8541
230 9BF 0.8541
231 EUH 0.8536
232 VKE 0.8535
233 JPS 0.8528
234 I59 0.8526
235 IEO 0.8524
236 Q9G 0.8516
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: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 5wyz.bio1) has 86 residues
No: Leader PDB Ligand Sequence Similarity
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 86 residues
No: Leader PDB Ligand Sequence Similarity
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