Receptor
PDB id Resolution Class Description Source Keywords
5R8I 1.47 Å NON-ENZYME: OTHER PANDDA ANALYSIS GROUP DEPOSITION INTERLEUKIN-1 BETA -- FRAGM Z210803634 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...
A7N A:203;
 Valid;
 none;
 submit data
165.232 C10 H15 N O CCOc1...
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: A7N; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 A7N 1 1
Similar Ligands (3D)
Ligand no: 1; Ligand: A7N; Similar ligands found: 493
No: Ligand Similarity coefficient
1 RNO 0.9674
2 4NM 0.9672
3 6KT 0.9650
4 5LA 0.9647
5 AMH 0.9643
6 AES 0.9641
7 ANN 0.9630
8 PNZ 0.9617
9 SNO 0.9610
10 BPN 0.9533
11 ZYX 0.9520
12 4JE 0.9518
13 Z13 0.9502
14 SN4 0.9499
15 3W8 0.9486
16 PZM 0.9468
17 L14 0.9443
18 259 0.9441
19 4JC 0.9440
20 86L 0.9436
21 I3E 0.9434
22 4NB 0.9433
23 S0E 0.9425
24 DVQ 0.9421
25 M4S 0.9420
26 LQ2 0.9414
27 A7H 0.9372
28 3ZB 0.9367
29 428 0.9343
30 KBZ 0.9340
31 9NB 0.9331
32 N4E 0.9330
33 K4V 0.9329
34 94W 0.9324
35 4BZ 0.9322
36 2FX 0.9317
37 EUE 0.9316
38 F4K 0.9315
39 Z82 0.9315
40 UNJ 0.9313
41 YI6 0.9293
42 4BY 0.9289
43 1F1 0.9288
44 QIV 0.9271
45 ST3 0.9268
46 ICB 0.9266
47 3W3 0.9265
48 J6W 0.9264
49 K82 0.9261
50 3W6 0.9259
51 5XC 0.9259
52 CWJ 0.9255
53 FBF 0.9253
54 K3D 0.9252
55 PFL 0.9251
56 E5X 0.9250
57 12T 0.9241
58 4FA 0.9239
59 6NI 0.9239
60 4I8 0.9236
61 GO2 0.9226
62 4CM 0.9225
63 4MB 0.9219
64 YRL 0.9208
65 8WO 0.9205
66 P9E 0.9203
67 HC4 0.9203
68 6NT 0.9202
69 1M2 0.9199
70 0HO 0.9199
71 4NZ 0.9196
72 JAW 0.9193
73 0JD 0.9190
74 3VS 0.9189
75 JDN 0.9188
76 5NI 0.9182
77 PHB 0.9181
78 AEF 0.9179
79 8ZE 0.9176
80 AZM 0.9173
81 AAN 0.9173
82 PBZ 0.9168
83 NAG 0.9167
84 E7S 0.9164
85 X0U 0.9164
86 SKF 0.9162
87 JB8 0.9162
88 XIY 0.9160
89 0HN 0.9157
90 LR5 0.9156
91 3A9 0.9156
92 CPZ 0.9154
93 2QC 0.9153
94 AM4 0.9153
95 DHR 0.9151
96 TYL 0.9150
97 F4E 0.9150
98 4NP 0.9149
99 NPO 0.9147
100 2O8 0.9147
101 3AE 0.9147
102 J9N 0.9145
103 HBD 0.9144
104 PAB 0.9141
105 OHJ 0.9134
106 36Y 0.9134
107 BZ2 0.9133
108 5GU 0.9132
109 9R5 0.9126
110 4YO 0.9121
111 TSU 0.9121
112 N2I 0.9120
113 S7J 0.9113
114 2A9 0.9113
115 4NS 0.9110
116 F02 0.9109
117 2ZM 0.9105
118 LDP 0.9105
119 DZA 0.9101
120 7MW 0.9100
121 PNP 0.9100
122 OTR 0.9100
123 IWT 0.9100
124 ESX 0.9099
125 UA5 0.9099
126 8NB 0.9097
127 MAJ 0.9097
128 ES2 0.9096
129 XCG 0.9096
130 7O4 0.9095
131 4WL 0.9090
132 MSR 0.9090
133 3R4 0.9086
134 3NY 0.9085
135 15N 0.9084
136 Y3L 0.9084
137 SSC 0.9080
138 KDV 0.9079
139 2BX 0.9078
140 1Y6 0.9077
141 VD9 0.9069
142 AC6 0.9064
143 VC3 0.9058
144 W81 0.9057
145 DE5 0.9057
146 IAC 0.9056
147 C53 0.9053
148 4J8 0.9051
149 BZ3 0.9050
150 4MA 0.9048
151 88L 0.9041
152 YPN 0.9040
153 80G 0.9039
154 9ZE 0.9038
155 3VX 0.9038
156 PSJ 0.9038
157 HDH 0.9036
158 ABI 0.9036
159 ESP 0.9034
160 RYV 0.9033
161 BL0 0.9032
162 MR1 0.9032
163 FBB 0.9031
164 LLH 0.9030
165 6FB 0.9026
166 ZEC 0.9025
167 JBZ 0.9024
168 6FZ 0.9023
169 4BL 0.9020
170 SAN 0.9020
171 TYR 0.9008
172 0F3 0.9008
173 1P8 0.9002
174 KMY 0.8999
175 3XR 0.8999
176 657 0.8997
177 1L5 0.8997
178 FUD 0.8996
179 AMS 0.8995
180 7FU 0.8994
181 OOG 0.8993
182 LPK 0.8992
183 OQC 0.8992
184 A5E 0.8990
185 TMG 0.8989
186 C2B 0.8989
187 SNU 0.8988
188 4JQ 0.8988
189 VFG 0.8985
190 4ZA 0.8985
191 PPY 0.8985
192 4JL 0.8982
193 HNT 0.8980
194 EVF 0.8977
195 4TU 0.8977
196 3DM 0.8977
197 5OB 0.8976
198 GJP 0.8976
199 AOS 0.8975
200 717 0.8975
201 N1E 0.8974
202 DJN 0.8971
203 MS9 0.8971
204 N91 0.8971
205 F9Y 0.8969
206 QBP 0.8967
207 K2T 0.8966
208 2BG 0.8965
209 EYV 0.8957
210 3UF 0.8954
211 IPB 0.8954
212 P72 0.8954
213 4P5 0.8949
214 TGX 0.8948
215 FCR 0.8946
216 ZHA 0.8939
217 NFM 0.8938
218 AAS 0.8937
219 549 0.8936
220 HBA 0.8935
221 36E 0.8931
222 RB5 0.8929
223 4RU 0.8929
224 BPW 0.8928
225 TAG 0.8928
226 RA7 0.8927
227 OW4 0.8926
228 VGD 0.8924
229 0NX 0.8924
230 E4P 0.8924
231 OVP 0.8924
232 7VP 0.8921
233 5VM 0.8921
234 1FD 0.8920
235 HHH 0.8916
236 BQ2 0.8915
237 HX4 0.8915
238 2FY 0.8914
239 4AA 0.8913
240 4VP 0.8913
241 KLS 0.8911
242 EZ1 0.8909
243 OW7 0.8908
244 I2E 0.8905
245 92G 0.8904
246 15E 0.8904
247 SWX 0.8902
248 ODO 0.8902
249 REL 0.8902
250 36R 0.8901
251 P81 0.8900
252 NGA 0.8899
253 FA0 0.8899
254 KJU 0.8899
255 DOB 0.8899
256 MD6 0.8898
257 A98 0.8898
258 DHC 0.8894
259 IBP 0.8893
260 SLS 0.8892
261 SOR 0.8892
262 TZF 0.8891
263 FBS 0.8891
264 EE8 0.8891
265 STX 0.8891
266 C1M 0.8890
267 492 0.8887
268 OVM 0.8887
269 ST2 0.8884
270 CUW 0.8880
271 A5P 0.8879
272 CLW 0.8879
273 0TU 0.8878
274 4M0 0.8877
275 36M 0.8877
276 6SD 0.8876
277 363 0.8875
278 DHB 0.8873
279 ONH 0.8872
280 NOK 0.8872
281 M1T 0.8870
282 JA5 0.8868
283 BBK 0.8868
284 DA4 0.8868
285 6N4 0.8866
286 E1T 0.8866
287 5GT 0.8865
288 9FL 0.8858
289 AEG 0.8857
290 BCU 0.8852
291 ET2 0.8852
292 BHA 0.8849
293 NDG 0.8849
294 FBA 0.8847
295 MQN 0.8847
296 FOC 0.8841
297 GWM 0.8838
298 CIY 0.8835
299 GLY GLY GLY 0.8834
300 PH3 0.8834
301 JA8 0.8833
302 GXY 0.8832
303 HMH 0.8830
304 27B 0.8829
305 PHE 0.8823
306 RBL 0.8822
307 GDL 0.8821
308 FF2 0.8819
309 5NU 0.8818
310 G14 0.8818
311 MZM 0.8817
312 174 0.8817
313 J1K 0.8815
314 ZZT 0.8811
315 PPT 0.8810
316 8H8 0.8810
317 4NC 0.8808
318 A2G 0.8806
319 H42 0.8803
320 1EB 0.8803
321 HHR 0.8801
322 MAH 0.8801
323 PPN 0.8801
324 6ZX 0.8801
325 CXH 0.8800
326 SJK 0.8800
327 TID 0.8800
328 152 0.8800
329 PRO GLY 0.8799
330 1SA 0.8799
331 BZJ 0.8798
332 826 0.8797
333 PH2 0.8797
334 CFA 0.8796
335 NF3 0.8795
336 K6V 0.8794
337 HBO 0.8793
338 5CU 0.8792
339 SW7 0.8792
340 2HU 0.8792
341 L1O 0.8791
342 GVY 0.8790
343 ZZA 0.8787
344 5GV 0.8786
345 HMU 0.8784
346 PRL 0.8784
347 SSB 0.8781
348 HRM 0.8780
349 XRG 0.8779
350 3HG 0.8779
351 GF4 0.8777
352 268 0.8776
353 1HN 0.8774
354 4JM 0.8774
355 FER 0.8773
356 IQ5 0.8773
357 HNE 0.8773
358 KMH 0.8770
359 PUE 0.8767
360 EFF 0.8763
361 ATX 0.8761
362 LO1 0.8761
363 AHC 0.8759
364 2F6 0.8758
365 0FN 0.8758
366 PO6 0.8758
367 9FH 0.8756
368 H8N 0.8753
369 ODK 0.8752
370 1A5 0.8748
371 TXW 0.8746
372 6P3 0.8745
373 LNR 0.8745
374 PKU 0.8744
375 TYE 0.8743
376 IOP 0.8743
377 LGT 0.8742
378 X0V 0.8742
379 3C4 0.8741
380 HJ7 0.8738
381 RD4 0.8735
382 24B 0.8735
383 MP5 0.8733
384 EN1 0.8732
385 PRF 0.8732
386 4FE 0.8727
387 4VY 0.8727
388 B15 0.8726
389 B1J 0.8725
390 M78 0.8724
391 9FE 0.8723
392 8NX 0.8722
393 M28 0.8721
394 FYU 0.8720
395 AJ1 0.8720
396 8XL 0.8716
397 CS2 0.8714
398 FZM 0.8714
399 L15 0.8712
400 M4E 0.8711
401 1Z6 0.8710
402 MTL 0.8708
403 5O6 0.8708
404 54Z 0.8707
405 DEW 0.8705
406 GLO 0.8705
407 HIC 0.8704
408 JAH 0.8703
409 HX3 0.8700
410 6RQ 0.8700
411 KOJ 0.8699
412 EZL 0.8696
413 TH7 0.8695
414 YZM 0.8695
415 XUL 0.8694
416 5WZ 0.8693
417 NSP 0.8692
418 K7H 0.8692
419 RKV 0.8691
420 VFM 0.8689
421 5SP 0.8687
422 HA5 0.8685
423 L99 0.8683
424 4AF 0.8683
425 EKZ 0.8679
426 S7S 0.8678
427 E3X 0.8676
428 5H6 0.8673
429 4SX 0.8671
430 LFC 0.8668
431 DVK 0.8661
432 XAZ 0.8661
433 61M 0.8660
434 NYL 0.8658
435 3VQ 0.8655
436 5RP 0.8653
437 X1R 0.8649
438 3QV 0.8647
439 5OO 0.8646
440 KYA 0.8645
441 THA 0.8645
442 6L6 0.8645
443 8V8 0.8643
444 ALE 0.8640
445 ENO 0.8639
446 HNL 0.8636
447 HNK 0.8636
448 8TX 0.8633
449 EF0 0.8631
450 5TT 0.8630
451 IFP 0.8628
452 B41 0.8628
453 KTJ 0.8627
454 PCS 0.8622
455 1X4 0.8619
456 54E 0.8614
457 2HQ 0.8613
458 GZQ 0.8612
459 JMG 0.8609
460 4FS 0.8609
461 A5Q 0.8603
462 LR8 0.8603
463 S0W 0.8600
464 AN3 0.8600
465 2HC 0.8600
466 DAH 0.8599
467 MKN 0.8598
468 5JQ 0.8598
469 PFF 0.8592
470 HNH 0.8588
471 EUH 0.8584
472 R5P 0.8583
473 R52 0.8578
474 OCA 0.8577
475 03V 0.8577
476 4BF 0.8573
477 9CA 0.8573
478 R1P 0.8568
479 1FE 0.8568
480 RBJ 0.8566
481 7UC 0.8566
482 COU 0.8558
483 GOJ 0.8553
484 11S 0.8553
485 IV2 0.8552
486 1IT 0.8545
487 2K8 0.8544
488 FTV 0.8540
489 3XH 0.8540
490 RYY 0.8536
491 75K 0.8533
492 KDG 0.8533
493 FK1 0.8524
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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