Receptor
PDB id Resolution Class Description Source Keywords
5R8A 1.47 Å NON-ENZYME: OTHER PANDDA ANALYSIS GROUP DEPOSITION INTERLEUKIN-1 BETA -- FRAGM Z1492796719 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
S7G A:203;
 Valid;
 none;
 submit data
190.242 C11 H14 N2 O CC(=O...
SO4 A:201;
A:202;
 Invalid;
Invalid;
 none;
none;
 submit data
96.063 O4 S [O-]S...
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: S7G; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 S7G 1 1
Similar Ligands (3D)
Ligand no: 1; Ligand: S7G; Similar ligands found: 349
No: Ligand Similarity coefficient
1 EYV 0.9561
2 2FX 0.9509
3 TMG 0.9491
4 EV2 0.9464
5 SYE 0.9448
6 IOP 0.9384
7 NAG 0.9382
8 DHC 0.9326
9 H4B 0.9325
10 PHE 0.9308
11 IAC 0.9296
12 EYY 0.9276
13 ICB 0.9269
14 TRP 0.9266
15 4Z9 0.9264
16 657 0.9263
17 NAL 0.9246
18 EUH 0.9234
19 4NP 0.9234
20 M78 0.9232
21 2P3 0.9230
22 A7H 0.9229
23 TSS 0.9228
24 KLS 0.9228
25 8ZE 0.9221
26 IOS 0.9220
27 PPY 0.9220
28 MD6 0.9216
29 EYJ 0.9201
30 5GT 0.9195
31 3VW 0.9179
32 8XL 0.9168
33 DEW 0.9165
34 MQB 0.9161
35 IQ5 0.9160
36 GNR 0.9156
37 BZQ 0.9155
38 DJN 0.9155
39 PLP 0.9148
40 AMR 0.9146
41 RD4 0.9142
42 M5H 0.9138
43 JXK 0.9137
44 I2E 0.9136
45 LVD 0.9125
46 ARP 0.9123
47 9R5 0.9117
48 61M 0.9117
49 15N 0.9113
50 DHY 0.9112
51 6MW 0.9105
52 GO8 0.9102
53 3XH 0.9101
54 9BF 0.9099
55 3C4 0.9098
56 4NS 0.9093
57 BHS 0.9092
58 YI6 0.9092
59 SKF 0.9088
60 0FR 0.9085
61 HLP 0.9085
62 R9Y 0.9084
63 92P 0.9074
64 N1E 0.9065
65 2UD 0.9064
66 0QA 0.9064
67 DTR 0.9063
68 APS 0.9062
69 JFM 0.9057
70 ALE 0.9053
71 327 0.9053
72 XI7 0.9051
73 PMP 0.9045
74 6N4 0.9044
75 LL2 0.9043
76 36M 0.9043
77 4WF 0.9042
78 LDP 0.9040
79 P80 0.9039
80 SRO 0.9038
81 YE6 0.9037
82 FPL 0.9034
83 1PS 0.9034
84 848 0.9034
85 11X 0.9031
86 NPA 0.9023
87 TSR 0.9022
88 B41 0.9019
89 M3Q 0.9017
90 MR1 0.9017
91 MZM 0.9016
92 HBI 0.9015
93 KYN 0.9010
94 CTE 0.9009
95 7MX 0.9008
96 0JD 0.9006
97 4BX 0.9003
98 PQZ 0.9003
99 MJ5 0.8990
100 S7D 0.8989
101 B5A 0.8987
102 5WN 0.8985
103 M4E 0.8985
104 NDG 0.8985
105 BL0 0.8982
106 TYR 0.8980
107 BM3 0.8979
108 LTN 0.8978
109 K4V 0.8977
110 1L5 0.8975
111 30G 0.8972
112 ITW 0.8966
113 BGP 0.8964
114 YZM 0.8957
115 3TC 0.8956
116 S8A 0.8956
117 S0W 0.8954
118 42J 0.8954
119 5TO 0.8953
120 C4E 0.8953
121 JY2 0.8953
122 QMS 0.8951
123 3EB 0.8951
124 ENO 0.8948
125 6C5 0.8945
126 1OH 0.8943
127 R7T 0.8941
128 NLA 0.8940
129 27K 0.8940
130 6VD 0.8937
131 FCW 0.8936
132 3D3 0.8933
133 2K8 0.8931
134 CH8 0.8930
135 BB4 0.8930
136 AHC 0.8930
137 3XR 0.8930
138 XDE 0.8925
139 G6P 0.8924
140 YOF 0.8923
141 78U 0.8921
142 YIE 0.8920
143 NGA 0.8914
144 GDL 0.8914
145 YIH 0.8914
146 5O5 0.8914
147 3SU 0.8913
148 OA1 0.8911
149 535 0.8911
150 NVU 0.8909
151 22T 0.8908
152 0J5 0.8908
153 C0W 0.8906
154 PLR 0.8906
155 ZON 0.8905
156 9UL 0.8905
157 AAN 0.8902
158 D2G 0.8900
159 CSN 0.8900
160 TZP 0.8900
161 3IB 0.8900
162 CFA 0.8896
163 X6P 0.8886
164 3QO 0.8886
165 JF1 0.8884
166 EXG 0.8884
167 CLU 0.8882
168 X1P 0.8881
169 5LD 0.8881
170 CX4 0.8880
171 GZV 0.8877
172 57O 0.8875
173 NFM 0.8874
174 A2G 0.8874
175 HCI 0.8873
176 PBN 0.8870
177 PZP 0.8869
178 MP5 0.8868
179 MMS 0.8865
180 MNP 0.8862
181 4MB 0.8859
182 GC2 0.8859
183 N9J 0.8857
184 6J5 0.8855
185 ZIP 0.8853
186 FK8 0.8853
187 J4K 0.8851
188 4TB 0.8850
189 PPT 0.8846
190 1A7 0.8845
191 2HC 0.8844
192 G1P 0.8842
193 MUX 0.8841
194 ISC 0.8840
195 HPP 0.8840
196 0QW 0.8840
197 AHN 0.8831
198 3IP 0.8831
199 S24 0.8829
200 H35 0.8828
201 9F8 0.8824
202 3D8 0.8824
203 TZM 0.8822
204 D1G 0.8820
205 GHQ 0.8818
206 GCO 0.8816
207 28S 0.8816
208 M5E 0.8815
209 HHT 0.8810
210 JYT 0.8810
211 AC2 0.8804
212 A5P 0.8802
213 YIP 0.8801
214 GXG 0.8798
215 EV3 0.8797
216 1BN 0.8795
217 BG6 0.8795
218 0FN 0.8794
219 RNK 0.8790
220 1Q4 0.8790
221 F52 0.8788
222 S0F 0.8788
223 NOK 0.8786
224 PXP 0.8784
225 XQI 0.8781
226 BC3 0.8781
227 4ZD 0.8779
228 BQ2 0.8778
229 TXW 0.8776
230 EQA 0.8774
231 5DL 0.8772
232 BSA 0.8769
233 3IL 0.8768
234 PMM 0.8767
235 FT6 0.8765
236 YTX 0.8765
237 NBB 0.8765
238 5RP 0.8764
239 OMD 0.8764
240 39Z 0.8763
241 HXY 0.8762
242 96Z 0.8761
243 PYU 0.8760
244 HA6 0.8757
245 0OL 0.8757
246 MS0 0.8754
247 QUS 0.8754
248 CUW 0.8750
249 9VQ 0.8748
250 ZEA 0.8746
251 K82 0.8746
252 94W 0.8745
253 H4E 0.8741
254 5WZ 0.8741
255 5PV 0.8738
256 1SS 0.8735
257 8W9 0.8734
258 6ZX 0.8734
259 4AV 0.8732
260 GLP 0.8729
261 268 0.8729
262 GXD 0.8728
263 4AU 0.8727
264 0XR 0.8723
265 STV 0.8723
266 6HO 0.8722
267 JGY 0.8721
268 QLI 0.8719
269 ZIQ 0.8717
270 3CR 0.8715
271 8U3 0.8713
272 QJA 0.8711
273 6HP 0.8708
274 RE4 0.8708
275 22F 0.8706
276 HWD 0.8706
277 BPW 0.8701
278 3LJ 0.8700
279 QBM 0.8699
280 4R1 0.8697
281 D1Y 0.8696
282 TLM 0.8691
283 HSA 0.8687
284 56D 0.8686
285 1U7 0.8683
286 THM 0.8682
287 CHQ 0.8682
288 2OH 0.8681
289 ET0 0.8680
290 AVA 0.8678
291 3D1 0.8676
292 GNW 0.8676
293 UA5 0.8675
294 3W1 0.8675
295 HL6 0.8674
296 H48 0.8673
297 A6P 0.8672
298 S3C 0.8672
299 FUD 0.8671
300 5OF 0.8669
301 TLG 0.8668
302 SBK 0.8667
303 LSQ 0.8665
304 Q5M 0.8663
305 6L6 0.8662
306 YTZ 0.8659
307 3AK 0.8659
308 A7Q 0.8657
309 14W 0.8655
310 I4D 0.8649
311 BK9 0.8648
312 7ZC 0.8647
313 CWJ 0.8646
314 WVV 0.8645
315 NPL 0.8644
316 HCT 0.8642
317 86L 0.8639
318 VJP 0.8636
319 60L 0.8635
320 TL6 0.8628
321 CG 0.8627
322 E4P 0.8626
323 27L 0.8623
324 RLG 0.8620
325 NEU 0.8619
326 X0T 0.8619
327 PRA 0.8609
328 QTG 0.8598
329 6Q3 0.8598
330 8GK 0.8597
331 X04 0.8597
332 4FP 0.8596
333 ODO 0.8593
334 6FG 0.8591
335 BZM 0.8587
336 O45 0.8584
337 CUQ 0.8584
338 MDR 0.8573
339 EF0 0.8569
340 AUV 0.8567
341 9W5 0.8566
342 8YH 0.8565
343 1AJ 0.8556
344 MPP 0.8553
345 F6R 0.8544
346 JHY 0.8544
347 YO5 0.8527
348 M6R 0.8523
349 GOE 0.8519
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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