Receptor
PDB id Resolution Class Description Source Keywords
5R8M 1.39 Å NON-ENZYME: OTHER PANDDA ANALYSIS GROUP DEPOSITION INTERLEUKIN-1 BETA -- FRAGM Z1818332938 IN COMPLEX WITH INTERLEUKIN-1 BETA HOMO SAPIENS IL-1 BETA SIGNALING PROTEIN SGC - DIAMOND I04-1 FRAGMENT SPANDDA XCHEMEXPLORER
Ref.: MINING THE PDB FOR TRACTABLE CASES WHERE X-RAY CRYSTALLOGRAPHY COMBINED WITH FRAGMENT SCREENS CAN TO SYSTEMATICALLY DESIGN PROTEIN-PROTEIN INHIBITORS TEST CASES ILLUSTRATED BY IL1 BETA-IL1R AND P38 ALP COMPLEXES. J.MED.CHEM. V. 63
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SO4 A:201;
A:202;
 Invalid;
Invalid;
 none;
none;
 submit data
96.063 O4 S [O-]S...
S8G A:203;
 Valid;
 none;
 submit data
224.223 C9 H15 F3 N2 O C1C[C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5R8Q 1.23 Å NON-ENZYME: OTHER PANDDA ANALYSIS GROUP DEPOSITION INTERLEUKIN-1 BETA -- FRAGM Z2643472210 IN COMPLEX WITH INTERLEUKIN-1 BETA HOMO SAPIENS IL-1 BETA SIGNALING PROTEIN SGC - DIAMOND I04-1 FRAGMENT SPANDDA XCHEMEXPLORER
Ref.: MINING THE PDB FOR TRACTABLE CASES WHERE X-RAY CRYSTALLOGRAPHY COMBINED WITH FRAGMENT SCREENS CAN TO SYSTEMATICALLY DESIGN PROTEIN-PROTEIN INHIBITORS TEST CASES ILLUSTRATED BY IL1 BETA-IL1R AND P38 ALP COMPLEXES. J.MED.CHEM. V. 63
Members (22)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1610 families.
1 5R8J - S8D C10 H20 N2 O2 CCNC(=O)CN....
2 5R85 - S7A C7 H11 F3 N2 O C1CN(CCN1)....
3 5R8Q - JGY C10 H15 N3 O2 Cn1ccc(n1)....
4 5R8C - M25 C10 H14 N2 O3 S CC(=O)NCCc....
5 5R8N - S8J C11 H13 N5 O2 CCOc1cccc(....
6 5R8D - S7J C6 H4 F3 N3 O c1c(cnc(n1....
7 5R8O - S8P C10 H14 N2 O2 S Cc1cc(ns1)....
8 5R8A - S7G C11 H14 N2 O CC(=O)N[C@....
9 5R8B - K34 C5 H4 N4 S c1csc(n1)c....
10 5R8I - A7N C10 H15 N O CCOc1ccc(c....
11 5R8H - T91 C14 H19 N3 O CC(C)(C)C(....
12 5R8M - S8G C9 H15 F3 N2 O C1C[C@H](C....
13 5R89 - S7D C10 H15 N3 O2 C[C@H]1CN(....
14 5R8E - S7S C7 H13 N5 O CCCC(=O)Nc....
15 5R8G - S7V C12 H17 N O2 c1ccc(cc1)....
16 5R8K - S8D C10 H20 N2 O2 CCNC(=O)CN....
17 5R8F - K3Y C10 H16 N4 O Cn1cc(c(n1....
18 5R8L - NY4 C12 H16 N2 O C[C@@H](c1....
19 5R88 - LWA C12 H14 N2 O3 c1cc(ccc1C....
20 5R86 - GT4 C9 H11 N O3 COCC(=O)Nc....
21 5R8P - S8V C8 H15 N O C1COC[C@@H....
22 5R87 - K0G C12 H11 N3 O c1ccc(cc1)....
70% Homology Family (22)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1331 families.
1 5R8J - S8D C10 H20 N2 O2 CCNC(=O)CN....
2 5R85 - S7A C7 H11 F3 N2 O C1CN(CCN1)....
3 5R8Q - JGY C10 H15 N3 O2 Cn1ccc(n1)....
4 5R8C - M25 C10 H14 N2 O3 S CC(=O)NCCc....
5 5R8N - S8J C11 H13 N5 O2 CCOc1cccc(....
6 5R8D - S7J C6 H4 F3 N3 O c1c(cnc(n1....
7 5R8O - S8P C10 H14 N2 O2 S Cc1cc(ns1)....
8 5R8A - S7G C11 H14 N2 O CC(=O)N[C@....
9 5R8B - K34 C5 H4 N4 S c1csc(n1)c....
10 5R8I - A7N C10 H15 N O CCOc1ccc(c....
11 5R8H - T91 C14 H19 N3 O CC(C)(C)C(....
12 5R8M - S8G C9 H15 F3 N2 O C1C[C@H](C....
13 5R89 - S7D C10 H15 N3 O2 C[C@H]1CN(....
14 5R8E - S7S C7 H13 N5 O CCCC(=O)Nc....
15 5R8G - S7V C12 H17 N O2 c1ccc(cc1)....
16 5R8K - S8D C10 H20 N2 O2 CCNC(=O)CN....
17 5R8F - K3Y C10 H16 N4 O Cn1cc(c(n1....
18 5R8L - NY4 C12 H16 N2 O C[C@@H](c1....
19 5R88 - LWA C12 H14 N2 O3 c1cc(ccc1C....
20 5R86 - GT4 C9 H11 N O3 COCC(=O)Nc....
21 5R8P - S8V C8 H15 N O C1COC[C@@H....
22 5R87 - K0G C12 H11 N3 O c1ccc(cc1)....
50% Homology Family (22)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1144 families.
1 5R8J - S8D C10 H20 N2 O2 CCNC(=O)CN....
2 5R85 - S7A C7 H11 F3 N2 O C1CN(CCN1)....
3 5R8Q - JGY C10 H15 N3 O2 Cn1ccc(n1)....
4 5R8C - M25 C10 H14 N2 O3 S CC(=O)NCCc....
5 5R8N - S8J C11 H13 N5 O2 CCOc1cccc(....
6 5R8D - S7J C6 H4 F3 N3 O c1c(cnc(n1....
7 5R8O - S8P C10 H14 N2 O2 S Cc1cc(ns1)....
8 5R8A - S7G C11 H14 N2 O CC(=O)N[C@....
9 5R8B - K34 C5 H4 N4 S c1csc(n1)c....
10 5R8I - A7N C10 H15 N O CCOc1ccc(c....
11 5R8H - T91 C14 H19 N3 O CC(C)(C)C(....
12 5R8M - S8G C9 H15 F3 N2 O C1C[C@H](C....
13 5R89 - S7D C10 H15 N3 O2 C[C@H]1CN(....
14 5R8E - S7S C7 H13 N5 O CCCC(=O)Nc....
15 5R8G - S7V C12 H17 N O2 c1ccc(cc1)....
16 5R8K - S8D C10 H20 N2 O2 CCNC(=O)CN....
17 5R8F - K3Y C10 H16 N4 O Cn1cc(c(n1....
18 5R8L - NY4 C12 H16 N2 O C[C@@H](c1....
19 5R88 - LWA C12 H14 N2 O3 c1cc(ccc1C....
20 5R86 - GT4 C9 H11 N O3 COCC(=O)Nc....
21 5R8P - S8V C8 H15 N O C1COC[C@@H....
22 5R87 - K0G C12 H11 N3 O c1ccc(cc1)....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: S8G; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 S8G 1 1
Similar Ligands (3D)
Ligand no: 1; Ligand: S8G; Similar ligands found: 279
No: Ligand Similarity coefficient
1 1PS 0.9256
2 NK5 0.9247
3 DX5 0.9238
4 3XH 0.9231
5 JFM 0.9189
6 5WN 0.9189
7 LZ5 0.9189
8 RDV 0.9148
9 PA5 0.9136
10 XI7 0.9136
11 S7D 0.9129
12 NFZ 0.9119
13 6HO 0.9100
14 2FX 0.9066
15 FER 0.9055
16 JMG 0.9043
17 GGG 0.9041
18 IOP 0.9040
19 QIV 0.9032
20 ONZ 0.9023
21 G14 0.9023
22 5TO 0.9022
23 DTE 0.9012
24 3N1 0.9006
25 CTE 0.9001
26 3VQ 0.8998
27 6FG 0.8994
28 P1J 0.8989
29 IAC 0.8981
30 TRP 0.8975
31 ZZA 0.8973
32 VFJ 0.8970
33 D8Q 0.8966
34 F6R 0.8962
35 JOV 0.8961
36 Q4G 0.8957
37 D1G 0.8956
38 EYV 0.8956
39 MD6 0.8955
40 4BX 0.8953
41 TJM 0.8952
42 6C9 0.8952
43 D9Z 0.8950
44 FHV 0.8949
45 1XS 0.8947
46 GO2 0.8941
47 HBI 0.8940
48 A5P 0.8940
49 PNP 0.8939
50 DT7 0.8931
51 A5Q 0.8931
52 G6P 0.8931
53 PUE 0.8928
54 4NP 0.8927
55 1HR 0.8926
56 HSA 0.8926
57 EYJ 0.8925
58 H4B 0.8919
59 CG 0.8918
60 RSV 0.8917
61 DHC 0.8912
62 9BF 0.8909
63 LVD 0.8908
64 EV2 0.8907
65 ODK 0.8906
66 AOY 0.8906
67 6MW 0.8906
68 NPX 0.8905
69 S6P 0.8902
70 QH3 0.8902
71 DTR 0.8899
72 6C8 0.8894
73 TZP 0.8894
74 4MB 0.8892
75 I2E 0.8890
76 5ER 0.8889
77 22T 0.8888
78 68B 0.8888
79 BG6 0.8884
80 NAL 0.8884
81 S8P 0.8879
82 2J3 0.8878
83 4FE 0.8878
84 7PJ 0.8876
85 R5P 0.8876
86 1AE 0.8873
87 G6Q 0.8860
88 ARG 0.8858
89 1AJ 0.8858
90 0F3 0.8857
91 YIP 0.8856
92 5C1 0.8854
93 PAN 0.8852
94 M4N 0.8851
95 S7P 0.8848
96 GZ2 0.8848
97 DAH 0.8846
98 RB7 0.8845
99 4NS 0.8844
100 8CC 0.8843
101 0ON 0.8841
102 SB9 0.8839
103 STV 0.8838
104 4AU 0.8838
105 AGP 0.8835
106 5PV 0.8835
107 6C5 0.8835
108 7O4 0.8834
109 EYY 0.8833
110 G30 0.8833
111 VFM 0.8833
112 ASE 0.8827
113 PLP 0.8826
114 11X 0.8824
115 J38 0.8824
116 HWH 0.8824
117 FCD 0.8820
118 P93 0.8819
119 BIO 0.8818
120 96Z 0.8816
121 FC2 0.8815
122 M83 0.8813
123 ZYQ 0.8811
124 LTN 0.8811
125 B5A 0.8811
126 4TB 0.8808
127 YE6 0.8806
128 KYN 0.8806
129 XEV 0.8805
130 QKU 0.8805
131 ZEA 0.8804
132 4ZD 0.8804
133 VFG 0.8801
134 RA7 0.8800
135 37E 0.8798
136 TMG 0.8797
137 EUH 0.8795
138 JXK 0.8794
139 RGP 0.8794
140 5B2 0.8793
141 H35 0.8789
142 SB7 0.8787
143 JGY 0.8786
144 0K7 0.8784
145 4AF 0.8783
146 92O 0.8780
147 S0D 0.8773
148 KF5 0.8773
149 IQQ 0.8773
150 L5D 0.8771
151 E9S 0.8771
152 OLU 0.8768
153 NIY 0.8768
154 BVS 0.8766
155 6C4 0.8765
156 EAE 0.8765
157 MPP 0.8764
158 PLR 0.8761
159 IBP 0.8761
160 AX5 0.8761
161 AZM 0.8761
162 MUX 0.8759
163 LR2 0.8759
164 K48 0.8756
165 TCR 0.8756
166 M7P 0.8754
167 PTR 0.8753
168 XCG 0.8753
169 NPS 0.8750
170 3VX 0.8750
171 EQA 0.8747
172 2P3 0.8746
173 BB4 0.8742
174 SYE 0.8742
175 ZIP 0.8742
176 ITW 0.8741
177 4G2 0.8740
178 363 0.8738
179 1ER 0.8734
180 4OG 0.8732
181 6J5 0.8732
182 5F8 0.8728
183 GNR 0.8726
184 PQT 0.8726
185 C0W 0.8724
186 GOE 0.8723
187 3IP 0.8723
188 5H6 0.8722
189 657 0.8721
190 RK4 0.8719
191 MP5 0.8718
192 2L1 0.8716
193 MKN 0.8713
194 KLS 0.8713
195 GZV 0.8709
196 Y3L 0.8709
197 FY8 0.8708
198 Q5M 0.8707
199 KLV 0.8706
200 PIQ 0.8704
201 5O6 0.8701
202 ZHA 0.8701
203 Q9T 0.8700
204 N9J 0.8700
205 DG6 0.8697
206 0NX 0.8690
207 2JX 0.8690
208 NWD 0.8689
209 3GZ 0.8689
210 S0A 0.8689
211 LJ4 0.8686
212 MUK 0.8685
213 T03 0.8680
214 0FR 0.8676
215 YOF 0.8675
216 3IB 0.8673
217 GJK 0.8669
218 KPV 0.8668
219 4CN 0.8663
220 9JT 0.8662
221 GG8 0.8662
222 ZEC 0.8660
223 FT6 0.8660
224 HNT 0.8659
225 C4E 0.8657
226 JCZ 0.8651
227 HC4 0.8646
228 KMY 0.8645
229 5VU 0.8644
230 P7V 0.8642
231 OJD 0.8642
232 6L6 0.8635
233 2O8 0.8633
234 M2E 0.8633
235 7AP 0.8630
236 HPP 0.8630
237 8YH 0.8630
238 IS2 0.8627
239 PW5 0.8626
240 4FF 0.8623
241 3VS 0.8623
242 LPA 0.8623
243 5OO 0.8623
244 ASP SER 0.8622
245 A51 0.8622
246 FYR 0.8621
247 DER 0.8617
248 BQ2 0.8616
249 NEO 0.8615
250 5AD 0.8614
251 7EH 0.8612
252 VGS 0.8603
253 KWV 0.8602
254 4ZF 0.8601
255 CIR 0.8600
256 ZRK 0.8597
257 BWD 0.8595
258 T1N 0.8589
259 0OO 0.8584
260 WV7 0.8583
261 LOT 0.8578
262 EGV 0.8577
263 KLE 0.8570
264 47V 0.8567
265 FWD 0.8566
266 H2B 0.8565
267 5E5 0.8563
268 XRS 0.8560
269 8EU 0.8557
270 F90 0.8556
271 8D6 0.8555
272 AJ1 0.8552
273 2QU 0.8551
274 848 0.8546
275 A9B 0.8544
276 W23 0.8542
277 5WK 0.8537
278 EMU 0.8520
279 4Z1 0.8517
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5R8Q; Ligand: JGY; 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: 5r8q.bio1) has 15 residues
No: Leader PDB Ligand Sequence Similarity
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