Receptor
PDB id Resolution Class Description Source Keywords
5R8E 1.35 Å NON-ENZYME: OTHER PANDDA ANALYSIS GROUP DEPOSITION INTERLEUKIN-1 BETA -- FRAGM Z57475877 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...
S7S A:203;
 Valid;
 none;
 submit data
183.211 C7 H13 N5 O CCCC(...
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: S7S; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 S7S 1 1
Similar Ligands (3D)
Ligand no: 1; Ligand: S7S; Similar ligands found: 380
No: Ligand Similarity coefficient
1 GT4 0.9470
2 36M 0.9445
3 6SD 0.9345
4 RCV 0.9319
5 B1J 0.9313
6 TYR 0.9309
7 HC4 0.9305
8 L03 0.9294
9 VFJ 0.9280
10 Y3L 0.9276
11 D3G 0.9265
12 J1K 0.9262
13 AJG 0.9262
14 E3X 0.9261
15 N7I 0.9260
16 5O6 0.9248
17 KLS 0.9242
18 J6W 0.9236
19 0NX 0.9227
20 GLY GLY GLY 0.9225
21 GVY 0.9223
22 80G 0.9221
23 2PV 0.9213
24 I3E 0.9198
25 P80 0.9184
26 ENO 0.9166
27 5FL 0.9144
28 TYE 0.9141
29 P81 0.9138
30 A7H 0.9133
31 JMG 0.9130
32 5H6 0.9127
33 CIY 0.9126
34 CXH 0.9112
35 NFZ 0.9105
36 FER 0.9104
37 492 0.9104
38 4I8 0.9102
39 K7H 0.9100
40 YPN 0.9098
41 4UM 0.9097
42 3ZB 0.9095
43 14W 0.9094
44 2PK 0.9090
45 4FE 0.9089
46 VFG 0.9086
47 GB5 0.9079
48 FZM 0.9075
49 A98 0.9075
50 JCZ 0.9073
51 DVQ 0.9071
52 D2G 0.9065
53 OQC 0.9065
54 ALE 0.9065
55 EN1 0.9065
56 LO1 0.9064
57 J9N 0.9057
58 CK2 0.9053
59 6ZX 0.9051
60 HIC 0.9049
61 G14 0.9048
62 HPP 0.9047
63 7MW 0.9046
64 PH3 0.9046
65 QIV 0.9044
66 A5H 0.9044
67 F90 0.9039
68 4YZ 0.9038
69 5TT 0.9038
70 4BY 0.9035
71 OHJ 0.9034
72 5TO 0.9034
73 JAH 0.9033
74 9BF 0.9030
75 PHE 0.9024
76 3N1 0.9023
77 IS2 0.9023
78 6P3 0.9022
79 0K7 0.9022
80 F4K 0.9020
81 AJ1 0.9020
82 1EB 0.9019
83 6L6 0.9011
84 ZEC 0.9011
85 A5E 0.9007
86 VXX 0.9005
87 0LO 0.9002
88 TJM 0.8998
89 YI6 0.8997
90 HNT 0.8994
91 PPT 0.8992
92 IWT 0.8989
93 JBZ 0.8989
94 795 0.8987
95 Y4L 0.8986
96 PUE 0.8986
97 IOP 0.8985
98 3XH 0.8983
99 64Z 0.8983
100 60L 0.8982
101 2D2 0.8981
102 5F8 0.8981
103 GJK 0.8978
104 1XS 0.8976
105 TRP 0.8975
106 C9M 0.8972
107 K3D 0.8972
108 JA5 0.8969
109 TYL 0.8967
110 NY4 0.8966
111 CWJ 0.8962
112 4HB 0.8962
113 E7S 0.8958
114 1FE 0.8957
115 9NB 0.8956
116 BVS 0.8956
117 6Q3 0.8951
118 A9B 0.8947
119 DHC 0.8946
120 6KT 0.8942
121 7FU 0.8942
122 5OO 0.8940
123 7VP 0.8939
124 069 0.8939
125 JOV 0.8937
126 PRL 0.8935
127 FMQ 0.8934
128 549 0.8934
129 MPV 0.8930
130 SNU 0.8927
131 HX4 0.8926
132 C4E 0.8926
133 5TZ 0.8924
134 FXY 0.8924
135 EWG 0.8922
136 RYV 0.8922
137 K82 0.8922
138 ZZA 0.8919
139 F4E 0.8915
140 EQW 0.8915
141 GOE 0.8910
142 V2Z 0.8910
143 VM1 0.8909
144 4FF 0.8906
145 LSQ 0.8905
146 3VX 0.8904
147 RYY 0.8903
148 S0D 0.8903
149 XDE 0.8902
150 A29 0.8901
151 LVD 0.8901
152 SX2 0.8900
153 3R4 0.8898
154 856 0.8897
155 7O4 0.8894
156 94W 0.8894
157 ET0 0.8889
158 FF2 0.8887
159 ODK 0.8887
160 PBN 0.8886
161 D8Q 0.8885
162 XDK 0.8884
163 H4E 0.8881
164 EUE 0.8880
165 3C5 0.8879
166 N91 0.8876
167 4V2 0.8875
168 X6W 0.8873
169 0OO 0.8871
170 RD4 0.8870
171 BGU 0.8868
172 D1G 0.8866
173 L22 0.8863
174 S60 0.8863
175 613 0.8862
176 Z70 0.8862
177 M78 0.8862
178 4Z3 0.8858
179 VFM 0.8858
180 8NB 0.8855
181 P7V 0.8847
182 J9T 0.8846
183 M4E 0.8845
184 CPZ 0.8845
185 B15 0.8845
186 49P 0.8843
187 78Y 0.8842
188 RPN 0.8841
189 EGR 0.8841
190 YTX 0.8838
191 EOU 0.8836
192 BQ2 0.8836
193 2QC 0.8836
194 SWX 0.8836
195 SJK 0.8834
196 GB4 0.8834
197 HXY 0.8831
198 KLE 0.8831
199 A6W 0.8830
200 EAE 0.8826
201 8YH 0.8826
202 NK5 0.8824
203 9R5 0.8823
204 EZL 0.8815
205 X0U 0.8815
206 AHC 0.8812
207 DE5 0.8812
208 PNZ 0.8805
209 BIK 0.8805
210 MSR 0.8802
211 HL4 0.8800
212 TYC 0.8798
213 H4B 0.8798
214 NPX 0.8797
215 VGS 0.8795
216 ZEA 0.8791
217 KMY 0.8787
218 6N4 0.8787
219 MMJ 0.8786
220 4AU 0.8786
221 S7V 0.8785
222 DVK 0.8783
223 8CC 0.8783
224 7KE 0.8783
225 U4J 0.8783
226 37Z 0.8781
227 FHV 0.8781
228 AES 0.8778
229 ZME 0.8777
230 0W1 0.8776
231 AEH 0.8774
232 AH9 0.8773
233 5VU 0.8772
234 Q4G 0.8772
235 TT4 0.8771
236 PTB 0.8771
237 PPY 0.8768
238 36Y 0.8768
239 TGX 0.8768
240 VC3 0.8766
241 RKV 0.8766
242 GLO 0.8765
243 4CF 0.8764
244 S1D 0.8763
245 L5V 0.8761
246 5F5 0.8758
247 L15 0.8757
248 GCO 0.8757
249 ERZ 0.8756
250 LGT 0.8754
251 EFF 0.8754
252 7MU 0.8754
253 TID 0.8753
254 HWH 0.8751
255 PH2 0.8749
256 3QV 0.8749
257 YRL 0.8748
258 3VQ 0.8748
259 6C8 0.8748
260 FCD 0.8743
261 8V8 0.8742
262 4BX 0.8742
263 KDG 0.8736
264 BPW 0.8734
265 363 0.8733
266 R9Y 0.8733
267 C53 0.8732
268 92P 0.8731
269 IPO 0.8727
270 3VS 0.8727
271 HQJ 0.8727
272 SZ7 0.8722
273 P9E 0.8722
274 S98 0.8721
275 28A 0.8717
276 263 0.8717
277 QBM 0.8717
278 L1T 0.8710
279 ANN 0.8709
280 5RP 0.8709
281 6FB 0.8708
282 3OL 0.8703
283 4LW 0.8700
284 M4N 0.8700
285 HBI 0.8699
286 4G2 0.8699
287 HH6 0.8696
288 EF0 0.8696
289 RNO 0.8694
290 531 0.8694
291 SOR 0.8691
292 MVH 0.8689
293 XEV 0.8688
294 N4E 0.8686
295 KTJ 0.8686
296 3OM 0.8685
297 AZM 0.8683
298 5C1 0.8682
299 GO2 0.8682
300 H2B 0.8681
301 LNR 0.8678
302 KWB 0.8678
303 A7N 0.8678
304 BHS 0.8677
305 4BZ 0.8674
306 VGD 0.8673
307 FUD 0.8672
308 SNO 0.8671
309 HL6 0.8669
310 3W8 0.8668
311 SPD 0.8668
312 SQV 0.8666
313 NPS 0.8664
314 4NM 0.8658
315 4ZF 0.8658
316 N1E 0.8658
317 N9J 0.8656
318 OJM 0.8656
319 6XA 0.8653
320 A6Z 0.8652
321 CK1 0.8647
322 ZIP 0.8643
323 0RY 0.8642
324 N5B 0.8642
325 657 0.8637
326 3SU 0.8636
327 3S9 0.8635
328 MS0 0.8634
329 HNE 0.8630
330 0FR 0.8626
331 2K8 0.8622
332 T1N 0.8619
333 4VY 0.8617
334 L99 0.8615
335 0UL 0.8612
336 M6Z 0.8608
337 NMH 0.8608
338 1Z6 0.8604
339 NWH 0.8604
340 OGA 0.8603
341 8ZE 0.8603
342 3H2 0.8602
343 LR8 0.8602
344 AHN 0.8598
345 OVM 0.8597
346 BPN 0.8596
347 M5H 0.8592
348 0OP 0.8590
349 PO6 0.8589
350 1HR 0.8589
351 0XR 0.8588
352 4YO 0.8585
353 EEK 0.8582
354 LWA 0.8582
355 6TZ 0.8580
356 LL1 0.8579
357 28B 0.8578
358 Z13 0.8578
359 D10 0.8574
360 YE6 0.8572
361 PQV 0.8570
362 VJJ 0.8568
363 LTN 0.8567
364 BTI 0.8566
365 N2I 0.8565
366 8NX 0.8562
367 428 0.8560
368 TZF 0.8556
369 2F6 0.8556
370 DTY 0.8555
371 4Z9 0.8553
372 4JQ 0.8552
373 HJD 0.8546
374 BX4 0.8540
375 OOG 0.8535
376 MPP 0.8535
377 NTU 0.8530
378 YE7 0.8530
379 TA6 0.8529
380 3N0 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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