Receptor
PDB id Resolution Class Description Source Keywords
5R8D 1.47 Å NON-ENZYME: OTHER PANDDA ANALYSIS GROUP DEPOSITION INTERLEUKIN-1 BETA -- FRAGM Z1745658474 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...
S7J A:203;
 Valid;
 none;
 submit data
191.111 C6 H4 F3 N3 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: S7J; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 S7J 1 1
Similar Ligands (3D)
Ligand no: 1; Ligand: S7J; Similar ligands found: 478
No: Ligand Similarity coefficient
1 3AE 0.9977
2 FBF 0.9951
3 4NZ 0.9813
4 4NB 0.9715
5 LR5 0.9699
6 LQ2 0.9671
7 SNO 0.9649
8 RNO 0.9640
9 36E 0.9624
10 AM4 0.9621
11 4BZ 0.9589
12 4CM 0.9554
13 M4S 0.9543
14 12T 0.9540
15 AMH 0.9538
16 4JC 0.9529
17 L14 0.9511
18 PNZ 0.9486
19 BZ2 0.9449
20 Z13 0.9448
21 BPN 0.9444
22 E5X 0.9441
23 ICB 0.9418
24 ANN 0.9413
25 SAN 0.9399
26 ESX 0.9366
27 ESP 0.9364
28 KBZ 0.9361
29 6FZ 0.9360
30 MSR 0.9356
31 S0E 0.9349
32 TSU 0.9336
33 0HN 0.9319
34 1F1 0.9318
35 6NT 0.9315
36 4WL 0.9312
37 JAW 0.9294
38 QBP 0.9292
39 SNU 0.9290
40 AMS 0.9290
41 K4V 0.9272
42 TZF 0.9271
43 F4E 0.9269
44 HHI 0.9263
45 FCR 0.9260
46 6NI 0.9254
47 9ZE 0.9252
48 4BY 0.9248
49 GJP 0.9246
50 2ZM 0.9243
51 SKF 0.9243
52 AAS 0.9242
53 3A9 0.9240
54 AES 0.9236
55 0JD 0.9229
56 4BL 0.9227
57 4P5 0.9221
58 5NI 0.9220
59 AN3 0.9219
60 5LA 0.9219
61 152 0.9218
62 428 0.9217
63 15N 0.9207
64 27B 0.9203
65 8ZE 0.9202
66 X0V 0.9195
67 3ZB 0.9194
68 E1T 0.9194
69 BZ3 0.9192
70 SN4 0.9186
71 3VS 0.9186
72 0HO 0.9180
73 4NM 0.9178
74 2HU 0.9174
75 6KT 0.9173
76 4ZA 0.9172
77 SSC 0.9162
78 3NY 0.9153
79 EXD 0.9147
80 SLS 0.9144
81 2BX 0.9137
82 I3E 0.9131
83 4FH 0.9131
84 ABI 0.9129
85 HIS 0.9128
86 DVQ 0.9127
87 PPY 0.9121
88 PHB 0.9121
89 VC3 0.9117
90 A7N 0.9113
91 UNJ 0.9111
92 4RU 0.9109
93 N2I 0.9106
94 EUE 0.9104
95 2HC 0.9099
96 N91 0.9097
97 8WO 0.9096
98 YZM 0.9095
99 XIY 0.9093
100 A7H 0.9086
101 4NS 0.9083
102 1FD 0.9082
103 HNT 0.9080
104 CWJ 0.9076
105 EVF 0.9074
106 IFP 0.9066
107 BQ2 0.9053
108 259 0.9051
109 NPO 0.9047
110 TCA 0.9046
111 HBD 0.9045
112 F4K 0.9044
113 ATX 0.9042
114 JDN 0.9041
115 ESI 0.9040
116 BHQ 0.9038
117 4MB 0.9038
118 N1E 0.9037
119 RYV 0.9037
120 1M2 0.9034
121 4NP 0.9031
122 MAJ 0.9030
123 363 0.9030
124 PAB 0.9028
125 TYL 0.9028
126 2BG 0.9026
127 9FL 0.9025
128 J6W 0.9023
129 F02 0.9023
130 1HN 0.9021
131 E7S 0.9019
132 9CA 0.9019
133 HDH 0.9017
134 5GT 0.9009
135 4LW 0.9004
136 TMG 0.9003
137 XCG 0.9002
138 NAG 0.8999
139 GO2 0.8996
140 EKZ 0.8996
141 PZM 0.8995
142 GNM 0.8993
143 X0U 0.8992
144 6FB 0.8991
145 KTW 0.8991
146 DZA 0.8988
147 JB8 0.8983
148 KMY 0.8981
149 QMR 0.8981
150 PBZ 0.8980
151 4SX 0.8973
152 BNL 0.8970
153 657 0.8966
154 ST2 0.8966
155 CPZ 0.8966
156 2O6 0.8964
157 4JQ 0.8963
158 1IT 0.8960
159 1L5 0.8959
160 F9Y 0.8958
161 ZEC 0.8956
162 2A9 0.8955
163 7O4 0.8955
164 94W 0.8949
165 826 0.8947
166 4I8 0.8942
167 P72 0.8942
168 AA 0.8941
169 HA5 0.8941
170 A5P 0.8940
171 XIZ 0.8936
172 HX4 0.8931
173 2QC 0.8931
174 AZM 0.8927
175 IAC 0.8925
176 AAN 0.8923
177 N4E 0.8923
178 OTR 0.8921
179 5XC 0.8921
180 PO6 0.8919
181 BZJ 0.8918
182 MQN 0.8917
183 KDV 0.8912
184 DHI 0.8911
185 DOB 0.8909
186 BHA 0.8907
187 3VX 0.8905
188 BVA 0.8902
189 ODO 0.8902
190 FBB 0.8899
191 PIY 0.8897
192 A5Q 0.8895
193 PIM 0.8892
194 0BP 0.8891
195 FA0 0.8889
196 CH9 0.8889
197 QIV 0.8889
198 9R5 0.8888
199 9FE 0.8888
200 54Z 0.8885
201 ANF 0.8884
202 IWT 0.8878
203 717 0.8878
204 6RQ 0.8878
205 3XR 0.8878
206 P9E 0.8878
207 3HG 0.8876
208 R9Y 0.8876
209 DHC 0.8875
210 N2M 0.8873
211 DHB 0.8872
212 MAH 0.8872
213 1Y6 0.8872
214 4M0 0.8869
215 FZM 0.8868
216 4FA 0.8868
217 J9N 0.8863
218 K2T 0.8861
219 3R4 0.8860
220 1VK 0.8857
221 0FN 0.8856
222 PNP 0.8856
223 4MA 0.8856
224 FHC 0.8856
225 FQX 0.8856
226 M3H 0.8855
227 THA 0.8851
228 7VP 0.8851
229 4JE 0.8850
230 1SA 0.8850
231 5NU 0.8848
232 UFV 0.8847
233 3PF 0.8845
234 HC4 0.8845
235 H42 0.8845
236 GF4 0.8843
237 Y3L 0.8842
238 5CU 0.8839
239 3PG 0.8836
240 D48 0.8835
241 ZYX 0.8835
242 URO 0.8834
243 K3D 0.8833
244 KTJ 0.8833
245 PJW 0.8833
246 56D 0.8833
247 J9Q 0.8833
248 RP3 0.8831
249 1X4 0.8831
250 549 0.8830
251 A5E 0.8828
252 15E 0.8828
253 AC6 0.8825
254 HFA 0.8820
255 3W8 0.8817
256 FUD 0.8816
257 5QY 0.8815
258 ET2 0.8814
259 OQC 0.8814
260 Z82 0.8813
261 7MW 0.8812
262 8XL 0.8812
263 5OB 0.8810
264 PHE 0.8808
265 N3W 0.8805
266 IHB 0.8803
267 4NC 0.8799
268 NF3 0.8798
269 DXP 0.8797
270 CSN 0.8791
271 P80 0.8791
272 PQK 0.8790
273 HHH 0.8787
274 SW7 0.8782
275 DE5 0.8782
276 FHB 0.8781
277 9NB 0.8779
278 IOS 0.8779
279 C53 0.8778
280 0TU 0.8778
281 TGX 0.8778
282 CHB 0.8777
283 P9P 0.8775
284 EN1 0.8774
285 1A7 0.8774
286 2FY 0.8774
287 MPV 0.8773
288 ST3 0.8771
289 E4P 0.8771
290 535 0.8770
291 LR8 0.8763
292 36Y 0.8763
293 MS9 0.8761
294 AKG 0.8759
295 92G 0.8759
296 AOT 0.8758
297 4A3 0.8758
298 KYA 0.8758
299 V1T 0.8758
300 3VQ 0.8757
301 5GV 0.8756
302 RA7 0.8756
303 6TZ 0.8755
304 H5B 0.8754
305 GF1 0.8753
306 449 0.8753
307 INO 0.8753
308 9FH 0.8751
309 4XF 0.8750
310 4YO 0.8748
311 GVY 0.8746
312 2FX 0.8745
313 R20 0.8744
314 N8Y 0.8743
315 RHU 0.8742
316 IPB 0.8742
317 JWB 0.8742
318 D5X 0.8739
319 HCI 0.8737
320 BP7 0.8736
321 PFL 0.8735
322 4FS 0.8735
323 I2E 0.8735
324 ODK 0.8735
325 97T 0.8734
326 L22 0.8734
327 FBS 0.8731
328 03V 0.8731
329 8NX 0.8730
330 PH3 0.8728
331 68A 0.8726
332 0W1 0.8726
333 HIC 0.8726
334 ES5 0.8726
335 ANC 0.8725
336 JLZ 0.8725
337 MR1 0.8724
338 QSB 0.8723
339 LLH 0.8723
340 PH2 0.8722
341 JB5 0.8722
342 AX7 0.8722
343 M45 0.8721
344 CCU 0.8721
345 8NB 0.8719
346 5XB 0.8718
347 61M 0.8717
348 ZYR 0.8716
349 COU 0.8715
350 P81 0.8715
351 4AA 0.8714
352 13P 0.8713
353 JG8 0.8713
354 SYV 0.8710
355 86L 0.8707
356 2K8 0.8707
357 5RO 0.8706
358 HQJ 0.8706
359 VGD 0.8705
360 344 0.8704
361 JBZ 0.8704
362 2AQ 0.8703
363 BPY 0.8703
364 ES2 0.8702
365 8HC 0.8700
366 6QF 0.8699
367 TYR 0.8699
368 C1M 0.8699
369 MYJ 0.8698
370 L99 0.8698
371 NDG 0.8697
372 QMP 0.8697
373 4J8 0.8696
374 0FK 0.8694
375 TT4 0.8692
376 A29 0.8692
377 KYN 0.8690
378 L5V 0.8690
379 1A5 0.8689
380 HNL 0.8688
381 HNK 0.8688
382 5VL 0.8687
383 5GU 0.8686
384 8W9 0.8686
385 DNA 0.8684
386 FF2 0.8683
387 YRL 0.8683
388 92K 0.8683
389 36R 0.8682
390 CLW 0.8681
391 NGA 0.8681
392 174 0.8680
393 KJU 0.8678
394 1P8 0.8677
395 E0O 0.8677
396 G3E 0.8677
397 NNO 0.8676
398 DEZ 0.8675
399 BDP 0.8672
400 J5I 0.8668
401 TWO 0.8665
402 FDR 0.8664
403 KW8 0.8663
404 KMH 0.8663
405 PRL 0.8661
406 ABV 0.8660
407 OCH 0.8659
408 S2G 0.8658
409 AEF 0.8656
410 BBK 0.8655
411 4V2 0.8654
412 PEY 0.8651
413 TTL 0.8650
414 LNR 0.8650
415 30G 0.8649
416 XDK 0.8648
417 3QV 0.8645
418 NCT 0.8641
419 MZT 0.8639
420 9TW 0.8638
421 ENO 0.8637
422 NFA 0.8635
423 SE2 0.8633
424 4LV 0.8631
425 5VM 0.8631
426 G3P 0.8630
427 MTL 0.8628
428 HBA 0.8627
429 80G 0.8627
430 1Z6 0.8623
431 5TY 0.8622
432 DDU 0.8622
433 BEA 0.8621
434 DHR 0.8619
435 3DM 0.8618
436 DHY 0.8617
437 P92 0.8616
438 2F6 0.8614
439 HG3 0.8614
440 E79 0.8613
441 CIT 0.8609
442 DER 0.8608
443 12Q 0.8607
444 2MI 0.8606
445 UA5 0.8606
446 JP2 0.8604
447 B62 0.8603
448 93K 0.8601
449 HHS 0.8598
450 DX3 0.8598
451 TIH 0.8598
452 1DV 0.8593
453 JAE 0.8592
454 4HP 0.8592
455 JA8 0.8589
456 FLC 0.8588
457 NM2 0.8584
458 MD6 0.8580
459 SEP 0.8576
460 P7Y 0.8575
461 CTL 0.8574
462 1OS 0.8571
463 E7Z 0.8569
464 ALE 0.8568
465 173 0.8565
466 ARP 0.8561
467 HSO 0.8556
468 3PO 0.8554
469 GLN 0.8552
470 GHM 0.8551
471 44V 0.8549
472 3HM 0.8544
473 G3H 0.8538
474 0F9 0.8537
475 ZHA 0.8533
476 3VW 0.8523
477 2HO 0.8520
478 DRG 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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