Receptor
PDB id Resolution Class Description Source Keywords
5R8P 1.53 Å NON-ENZYME: OTHER PANDDA ANALYSIS GROUP DEPOSITION INTERLEUKIN-1 BETA -- FRAGM Z818727262 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...
S8V A:203;
 Valid;
 none;
 submit data
141.211 C8 H15 N O C1COC...
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: S8V; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 S8V 1 1
Similar Ligands (3D)
Ligand no: 1; Ligand: S8V; Similar ligands found: 494
No: Ligand Similarity coefficient
1 TCA 0.9847
2 PBA 0.9702
3 XIZ 0.9673
4 URO 0.9671
5 HCI 0.9631
6 CFI 0.9616
7 PO6 0.9583
8 AKG 0.9568
9 GOJ 0.9553
10 HIS 0.9550
11 ISZ 0.9513
12 268 0.9507
13 PPY 0.9501
14 BNF 0.9496
15 NIZ 0.9496
16 HC4 0.9478
17 FK8 0.9474
18 264 0.9462
19 ZBT 0.9461
20 PRA 0.9452
21 0L1 0.9447
22 OOG 0.9440
23 8OZ 0.9427
24 O45 0.9425
25 173 0.9423
26 OGA 0.9416
27 4HP 0.9387
28 FAN 0.9382
29 HX4 0.9379
30 R9M 0.9376
31 4LV 0.9372
32 MXN 0.9371
33 4TB 0.9371
34 J0Z 0.9371
35 MNN 0.9367
36 GUA 0.9366
37 M45 0.9365
38 5XC 0.9361
39 P81 0.9358
40 258 0.9353
41 3YP 0.9350
42 PEL 0.9341
43 KQY 0.9340
44 GLU 0.9339
45 PEA 0.9334
46 HSO 0.9327
47 PBN 0.9326
48 4LW 0.9326
49 NYL 0.9325
50 TIH 0.9322
51 CXP 0.9314
52 7C3 0.9308
53 4WL 0.9308
54 LYS 0.9301
55 PIM 0.9298
56 ESX 0.9297
57 P80 0.9297
58 ORN 0.9293
59 ACA 0.9291
60 CCU 0.9291
61 HY1 0.9290
62 MR1 0.9290
63 3OL 0.9288
64 SHV 0.9288
65 TPA 0.9287
66 ESP 0.9284
67 3H2 0.9281
68 1L5 0.9280
69 Q9Z 0.9279
70 CEE 0.9272
71 N6C 0.9268
72 NLE 0.9267
73 OEG 0.9266
74 K7M 0.9263
75 DHI 0.9262
76 PAC 0.9260
77 MES 0.9255
78 N4B 0.9249
79 RMN 0.9241
80 FEH 0.9240
81 SHO 0.9226
82 DE5 0.9226
83 VKC 0.9226
84 URP 0.9222
85 BZ2 0.9220
86 XBT 0.9220
87 DHY 0.9220
88 YZM 0.9218
89 DLY 0.9217
90 6NT 0.9217
91 PHU 0.9215
92 5NI 0.9214
93 RP3 0.9212
94 2FM 0.9211
95 SSB 0.9209
96 RBJ 0.9209
97 I1E 0.9208
98 LSQ 0.9208
99 LT1 0.9206
100 N9J 0.9206
101 1DJ 0.9201
102 1X4 0.9199
103 J9N 0.9197
104 DAV 0.9197
105 BHO 0.9196
106 FBJ 0.9195
107 PHE 0.9192
108 PMF 0.9192
109 LVD 0.9191
110 3HP 0.9187
111 2IT 0.9187
112 3HG 0.9180
113 AEF 0.9179
114 263 0.9175
115 EYV 0.9173
116 S7A 0.9171
117 717 0.9171
118 GRO 0.9170
119 AG2 0.9170
120 1BN 0.9169
121 KMT 0.9169
122 ONH 0.9166
123 AL0 0.9166
124 HDH 0.9166
125 1F1 0.9165
126 TYL 0.9164
127 9ON 0.9163
128 OTR 0.9163
129 HPP 0.9163
130 GLN 0.9162
131 B85 0.9162
132 SMN 0.9161
133 GPJ 0.9161
134 2BG 0.9160
135 M6H 0.9159
136 4ZA 0.9158
137 HPN 0.9153
138 6NA 0.9151
139 LMR 0.9151
140 92K 0.9150
141 SLZ 0.9147
142 MED 0.9146
143 5XA 0.9145
144 650 0.9144
145 16D 0.9144
146 AHN 0.9144
147 98J 0.9141
148 AEG 0.9138
149 GVA 0.9138
150 4ZD 0.9135
151 MLT 0.9134
152 TZL 0.9133
153 M3P 0.9130
154 ICB 0.9129
155 3QO 0.9128
156 9RW 0.9126
157 GJZ 0.9124
158 0VT 0.9123
159 EVF 0.9123
160 SYM 0.9119
161 MLZ 0.9118
162 P7Y 0.9117
163 S2G 0.9114
164 PRO GLY 0.9113
165 K34 0.9111
166 MET 0.9111
167 M4T 0.9109
168 3LR 0.9108
169 9YT 0.9106
170 CLT 0.9106
171 I4B 0.9105
172 TYR 0.9103
173 NM2 0.9099
174 CXF 0.9097
175 DPN 0.9097
176 SPA 0.9097
177 OCT 0.9096
178 LDP 0.9095
179 KMH 0.9094
180 OKG 0.9091
181 CCD 0.9090
182 HSM 0.9089
183 13P 0.9087
184 B40 0.9084
185 DGL 0.9084
186 Q02 0.9084
187 6FZ 0.9082
188 QY9 0.9081
189 HFA 0.9080
190 7UC 0.9078
191 A3M 0.9077
192 ASP 0.9077
193 J9T 0.9075
194 PG0 0.9074
195 BNL 0.9074
196 HGA 0.9072
197 3QM 0.9072
198 3PG 0.9072
199 7BC 0.9071
200 LYN 0.9071
201 URS 0.9070
202 MHN 0.9065
203 2FT 0.9064
204 FBM 0.9062
205 5XB 0.9062
206 RJY 0.9060
207 F4E 0.9058
208 11C 0.9057
209 7OD 0.9055
210 GGL 0.9054
211 GPF 0.9052
212 ALA ALA 0.9050
213 3S5 0.9048
214 MUC 0.9047
215 ARG 0.9046
216 YPN 0.9046
217 GVM 0.9045
218 NF3 0.9045
219 HTX 0.9044
220 AHC 0.9042
221 152 0.9041
222 K6V 0.9039
223 4LR 0.9032
224 QMP 0.9030
225 DIR 0.9029
226 5WZ 0.9028
227 6XA 0.9028
228 JDN 0.9027
229 MPV 0.9026
230 F9P 0.9025
231 2HG 0.9023
232 54D 0.9021
233 MSL 0.9021
234 JB8 0.9020
235 DHS 0.9020
236 ENW 0.9020
237 9X6 0.9018
238 DHC 0.9016
239 UN1 0.9013
240 MF3 0.9011
241 G3H 0.9011
242 MAH 0.9010
243 PIY 0.9008
244 HPS 0.9007
245 M3H 0.9005
246 AT3 0.9004
247 M5E 0.9004
248 GO2 0.9003
249 CUW 0.9003
250 RNS 0.9003
251 AE3 0.9003
252 4P5 0.9002
253 HPV 0.9001
254 GLR 0.9001
255 HF2 0.9001
256 36E 0.9000
257 SD4 0.8999
258 YRL 0.8999
259 4VY 0.8998
260 23J 0.8997
261 4FA 0.8995
262 LNR 0.8995
263 MSR 0.8995
264 BCU 0.8995
265 NCT 0.8994
266 IP8 0.8994
267 HHH 0.8991
268 KTA 0.8990
269 PH3 0.8988
270 XIY 0.8985
271 IWT 0.8978
272 CPZ 0.8978
273 2FX 0.8968
274 Q03 0.8967
275 HL4 0.8967
276 TEG 0.8966
277 NM3 0.8965
278 SNU 0.8964
279 PML 0.8963
280 SYC 0.8962
281 PEP 0.8955
282 GGB 0.8953
283 NFA 0.8953
284 MEQ 0.8950
285 269 0.8949
286 QFJ 0.8947
287 3C4 0.8944
288 DZA 0.8944
289 8EW 0.8943
290 DAL DAL 0.8943
291 ZGL 0.8942
292 PGH 0.8940
293 AOT 0.8939
294 FUM 0.8939
295 M74 0.8938
296 S0W 0.8937
297 PC 0.8937
298 8U3 0.8936
299 HHI 0.8936
300 FOM 0.8931
301 XDK 0.8931
302 F98 0.8927
303 261 0.8927
304 RSO 0.8926
305 BPW 0.8926
306 1GP 0.8925
307 ALE 0.8925
308 GWM 0.8924
309 61M 0.8922
310 GP9 0.8922
311 7VP 0.8919
312 GLY GLY 0.8918
313 2LP 0.8918
314 LUQ 0.8916
315 B3U 0.8914
316 ONL 0.8911
317 PPT 0.8910
318 OCA 0.8909
319 DXG 0.8905
320 IVL 0.8904
321 JX7 0.8903
322 2HC 0.8901
323 ENO 0.8901
324 7WG 0.8901
325 011 0.8899
326 0LH 0.8898
327 EN1 0.8898
328 GVG 0.8897
329 NVU 0.8893
330 G3P 0.8890
331 SIN 0.8889
332 3BU 0.8889
333 DGN 0.8886
334 CCE 0.8885
335 A29 0.8883
336 BHU 0.8881
337 56D 0.8880
338 NNH 0.8874
339 IXW 0.8873
340 L22 0.8870
341 SAF 0.8869
342 RNT 0.8866
343 DHM 0.8865
344 COI 0.8863
345 1PS 0.8862
346 CHH 0.8860
347 R67 0.8860
348 JZ7 0.8858
349 6ZX 0.8856
350 HSX 0.8855
351 P58 0.8853
352 B09 0.8853
353 LEU 0.8851
354 OHP 0.8851
355 KPA 0.8849
356 S2P 0.8847
357 BHH 0.8847
358 ODO 0.8842
359 XLS 0.8841
360 1SH 0.8841
361 TSS 0.8840
362 CIR 0.8839
363 TZP 0.8837
364 ILO 0.8835
365 3OM 0.8834
366 S24 0.8834
367 EOU 0.8825
368 HIC 0.8824
369 PGA 0.8823
370 RAT 0.8821
371 O8Y 0.8811
372 KDG 0.8809
373 SEP 0.8808
374 TYE 0.8807
375 36M 0.8805
376 GZL 0.8805
377 64Z 0.8804
378 IAC 0.8804
379 4SX 0.8804
380 BHL 0.8802
381 DEZ 0.8798
382 GLO 0.8798
383 42J 0.8797
384 MQB 0.8793
385 MSE 0.8789
386 MHO 0.8787
387 7N0 0.8786
388 DHR 0.8786
389 RUJ 0.8785
390 AMS 0.8785
391 HE4 0.8784
392 F06 0.8783
393 RP5 0.8782
394 MTL 0.8777
395 C82 0.8777
396 LPK 0.8774
397 129 0.8774
398 PZM 0.8773
399 SHI 0.8772
400 XYL 0.8772
401 DAR 0.8767
402 CS2 0.8767
403 8GL 0.8765
404 SOR 0.8764
405 M44 0.8760
406 TZE 0.8757
407 AX3 0.8756
408 BSX 0.8756
409 ENV 0.8752
410 SAN 0.8749
411 NFM 0.8749
412 RA7 0.8748
413 YIE 0.8747
414 FUD 0.8746
415 TZM 0.8745
416 RUY 0.8745
417 RTK 0.8744
418 NSD 0.8742
419 TSR 0.8730
420 H4E 0.8729
421 NSB 0.8728
422 41K 0.8726
423 GCO 0.8724
424 49F 0.8719
425 FHC 0.8717
426 PAH 0.8717
427 8SZ 0.8713
428 RB5 0.8710
429 7MU 0.8707
430 0BP 0.8704
431 CFA 0.8703
432 LEA 0.8703
433 DEE 0.8702
434 HL5 0.8702
435 BRH 0.8695
436 CYX 0.8692
437 6HO 0.8691
438 3SL 0.8691
439 XUL 0.8691
440 PSE 0.8690
441 PRY 0.8689
442 SME 0.8687
443 YIV 0.8683
444 4TP 0.8681
445 PZI 0.8680
446 KPC 0.8676
447 NLP 0.8671
448 ABU 0.8666
449 DTY 0.8665
450 AMH 0.8665
451 LL2 0.8663
452 9GB 0.8662
453 MZT 0.8658
454 DII 0.8656
455 IOS 0.8653
456 SHF 0.8652
457 E4P 0.8650
458 LFC 0.8649
459 JF6 0.8644
460 JYD 0.8644
461 ABF 0.8643
462 3VW 0.8642
463 TAG 0.8638
464 DI6 0.8634
465 JZ4 0.8630
466 JFJ 0.8629
467 Z70 0.8629
468 1FD 0.8624
469 4MV 0.8617
470 YTX 0.8613
471 DEW 0.8612
472 HP6 0.8611
473 A09 0.8607
474 4XF 0.8606
475 3CR 0.8605
476 2JJ 0.8605
477 B3M 0.8598
478 492 0.8593
479 I2E 0.8591
480 HXY 0.8590
481 3PP 0.8577
482 F90 0.8576
483 JZA 0.8572
484 B41 0.8568
485 MPH 0.8564
486 795 0.8554
487 M6W 0.8538
488 FOC 0.8533
489 I3E 0.8522
490 NPI 0.8520
491 XDE 0.8515
492 1LN 0.8514
493 1KA 0.8512
494 QDK 0.8510
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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