Receptor
PDB id Resolution Class Description Source Keywords
5R85 1.44 Å NON-ENZYME: OTHER PANDDA ANALYSIS GROUP DEPOSITION INTERLEUKIN-1 BETA -- FRAGM Z1262246195 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...
S7A A:203;
 Valid;
 none;
 submit data
196.17 C7 H11 F3 N2 O C1CN(...
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: S7A; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 S7A 1 1
2 BZP 0.4 0.686275
Similar Ligands (3D)
Ligand no: 1; Ligand: S7A; Similar ligands found: 381
No: Ligand Similarity coefficient
1 IOS 0.9417
2 1L5 0.9399
3 IWT 0.9314
4 36E 0.9305
5 2O6 0.9296
6 PHE 0.9287
7 YZM 0.9286
8 TCA 0.9283
9 EYV 0.9281
10 LVD 0.9274
11 EVF 0.9257
12 5LD 0.9251
13 CLT 0.9250
14 BZ2 0.9250
15 PPY 0.9238
16 AOT 0.9233
17 MAJ 0.9223
18 HCI 0.9215
19 CXP 0.9205
20 DPN 0.9201
21 NVU 0.9191
22 FK8 0.9187
23 S0E 0.9184
24 0JD 0.9183
25 173 0.9177
26 ICB 0.9175
27 RP3 0.9172
28 IAC 0.9171
29 6FZ 0.9171
30 S8V 0.9171
31 N9J 0.9169
32 HFA 0.9163
33 Z13 0.9158
34 4WL 0.9158
35 MES 0.9155
36 15N 0.9151
37 1X4 0.9150
38 4LV 0.9150
39 RA7 0.9147
40 PO6 0.9147
41 TZP 0.9146
42 XIZ 0.9143
43 HIS 0.9143
44 0HN 0.9140
45 ZON 0.9137
46 YIE 0.9136
47 RP5 0.9134
48 EXD 0.9130
49 5WZ 0.9121
50 NFA 0.9121
51 M45 0.9118
52 5GT 0.9113
53 6NT 0.9111
54 3NY 0.9111
55 1PS 0.9105
56 L22 0.9093
57 DHI 0.9093
58 3A9 0.9090
59 1BN 0.9088
60 BNL 0.9084
61 TT4 0.9075
62 6KT 0.9072
63 7UC 0.9070
64 1A7 0.9068
65 5NI 0.9067
66 FOM 0.9065
67 1F1 0.9064
68 0HO 0.9063
69 F98 0.9058
70 TZM 0.9055
71 ENO 0.9055
72 LR5 0.9054
73 4ZA 0.9054
74 MSR 0.9051
75 0NX 0.9048
76 5DL 0.9045
77 TSR 0.9044
78 R20 0.9042
79 HHI 0.9041
80 MQB 0.9041
81 3QO 0.9040
82 HNM 0.9037
83 2C2 0.9035
84 1VK 0.9035
85 DEW 0.9031
86 3AE 0.9029
87 JZA 0.9026
88 4TB 0.9025
89 FBF 0.9023
90 6J5 0.9020
91 P81 0.9019
92 2ZM 0.9015
93 E4P 0.9014
94 61M 0.9011
95 AZM 0.9011
96 JFM 0.9010
97 GWM 0.9007
98 CSN 0.9001
99 EUE 0.9000
100 PPT 0.8997
101 8U3 0.8996
102 TYR 0.8984
103 PJW 0.8983
104 TMG 0.8982
105 P7Y 0.8976
106 HX4 0.8976
107 RLG 0.8974
108 3ZB 0.8973
109 6NI 0.8970
110 SHI 0.8968
111 KMH 0.8968
112 OIA 0.8968
113 YIP 0.8964
114 4P5 0.8964
115 GLR 0.8964
116 E1P 0.8963
117 PUE 0.8962
118 HQJ 0.8962
119 Q06 0.8959
120 J0Z 0.8957
121 SEP 0.8956
122 PBA 0.8956
123 PRO GLY 0.8955
124 9FL 0.8954
125 OGA 0.8953
126 4LW 0.8953
127 DXG 0.8953
128 BNF 0.8949
129 RMN 0.8948
130 FHC 0.8947
131 IOP 0.8946
132 M74 0.8944
133 N1E 0.8943
134 5XC 0.8942
135 TRP 0.8941
136 RNO 0.8938
137 J9N 0.8930
138 SKF 0.8928
139 GAE 0.8927
140 9FE 0.8926
141 GZ2 0.8925
142 56D 0.8924
143 N2I 0.8924
144 795 0.8923
145 9ZE 0.8921
146 ABI 0.8919
147 SNO 0.8916
148 R9M 0.8914
149 4HP 0.8914
150 3PG 0.8913
151 5XB 0.8912
152 DHY 0.8912
153 TYL 0.8906
154 X0V 0.8905
155 F4E 0.8905
156 DAH 0.8905
157 AKG 0.8905
158 3HG 0.8902
159 41K 0.8902
160 DZA 0.8901
161 152 0.8899
162 P4F 0.8891
163 SNU 0.8891
164 TZF 0.8889
165 XI7 0.8889
166 YOF 0.8888
167 AHN 0.8888
168 HSX 0.8888
169 IVL 0.8887
170 M5E 0.8887
171 SLS 0.8884
172 BQ2 0.8882
173 HA5 0.8880
174 6HO 0.8876
175 HNL 0.8873
176 Q04 0.8873
177 AEG 0.8871
178 4NZ 0.8869
179 TIH 0.8868
180 M3H 0.8868
181 ATX 0.8866
182 EN1 0.8866
183 TYE 0.8866
184 M3Q 0.8858
185 ISA 0.8856
186 9BF 0.8856
187 657 0.8854
188 PGH 0.8851
189 4V2 0.8849
190 0A9 0.8847
191 S2P 0.8843
192 NM3 0.8840
193 PMF 0.8840
194 4I8 0.8839
195 7O4 0.8837
196 DI6 0.8835
197 GLU 0.8834
198 LGT 0.8834
199 JOV 0.8832
200 M6H 0.8830
201 JB8 0.8829
202 GLN 0.8826
203 0OL 0.8825
204 DTY 0.8823
205 GVM 0.8820
206 Q03 0.8819
207 LTT 0.8818
208 HXY 0.8816
209 BCU 0.8815
210 A3M 0.8813
211 HL4 0.8810
212 4NS 0.8808
213 9SE 0.8806
214 K80 0.8805
215 2UB 0.8804
216 AT3 0.8802
217 FIX 0.8801
218 HPP 0.8801
219 CCE 0.8801
220 13P 0.8800
221 RJY 0.8797
222 33S 0.8791
223 1FD 0.8791
224 BZQ 0.8790
225 I2E 0.8788
226 PSE 0.8787
227 P80 0.8783
228 3C4 0.8783
229 0QW 0.8782
230 PC 0.8781
231 4BF 0.8779
232 PHI 0.8779
233 3CR 0.8779
234 DDU 0.8779
235 2FX 0.8778
236 OOG 0.8775
237 E5X 0.8775
238 QMS 0.8775
239 N2M 0.8774
240 S0W 0.8774
241 SB7 0.8773
242 DTR 0.8772
243 B41 0.8772
244 JAW 0.8772
245 2IT 0.8772
246 DNF 0.8770
247 EXR 0.8769
248 MNP 0.8767
249 7BC 0.8765
250 JF2 0.8764
251 TIU 0.8763
252 J4K 0.8758
253 DIR 0.8758
254 BRH 0.8757
255 ABF 0.8755
256 MSL 0.8750
257 9RH 0.8749
258 SOR 0.8749
259 LUQ 0.8749
260 PAU 0.8749
261 HNK 0.8749
262 K7M 0.8748
263 ZIQ 0.8747
264 HJH 0.8747
265 SOJ 0.8746
266 LPK 0.8746
267 CS2 0.8742
268 P9E 0.8742
269 MP5 0.8742
270 6DP 0.8742
271 AMQ 0.8741
272 G3H 0.8738
273 PFF 0.8736
274 AHC 0.8734
275 3VW 0.8734
276 0BP 0.8734
277 PLP 0.8732
278 GNW 0.8731
279 CCB 0.8730
280 RQD 0.8729
281 MMS 0.8724
282 URO 0.8723
283 KDG 0.8721
284 7MW 0.8720
285 FUD 0.8719
286 R9J 0.8717
287 2HG 0.8714
288 4FH 0.8714
289 LX1 0.8714
290 QUS 0.8712
291 UN1 0.8712
292 DHS 0.8710
293 GLO 0.8710
294 ARP 0.8710
295 APS 0.8709
296 NAG 0.8709
297 B3U 0.8707
298 3S5 0.8706
299 LL2 0.8705
300 AAN 0.8703
301 C0H 0.8702
302 HPS 0.8699
303 IYR 0.8698
304 HBU 0.8696
305 GCO 0.8695
306 NCT 0.8694
307 QMR 0.8692
308 2JJ 0.8690
309 XYH 0.8689
310 S2G 0.8684
311 8XL 0.8681
312 HHH 0.8679
313 GRF 0.8679
314 UA5 0.8677
315 9CA 0.8676
316 C1M 0.8676
317 1IT 0.8673
318 7OD 0.8673
319 0L1 0.8671
320 T03 0.8669
321 DER 0.8668
322 9UL 0.8665
323 SRO 0.8665
324 CLU 0.8665
325 11X 0.8662
326 DXP 0.8661
327 Q9Z 0.8659
328 2HC 0.8656
329 TOH 0.8654
330 VNL 0.8648
331 L14 0.8648
332 AN3 0.8645
333 GLY GLY GLY 0.8644
334 4SX 0.8640
335 3QM 0.8638
336 A5P 0.8635
337 API 0.8635
338 SYC 0.8634
339 BZS 0.8634
340 M6P 0.8634
341 4OG 0.8633
342 HX8 0.8632
343 SD4 0.8631
344 MAH 0.8628
345 5RP 0.8626
346 X1P 0.8625
347 TPO 0.8624
348 SOL 0.8623
349 30G 0.8613
350 G6P 0.8613
351 PSJ 0.8612
352 EQW 0.8606
353 268 0.8605
354 HMS 0.8605
355 S24 0.8603
356 3LR 0.8600
357 TAG 0.8600
358 HWD 0.8596
359 HJ7 0.8594
360 TYC 0.8590
361 9R5 0.8589
362 REL 0.8588
363 E0O 0.8587
364 XXG 0.8583
365 88L 0.8578
366 TSS 0.8577
367 IPD 0.8577
368 7UZ 0.8573
369 C5A 0.8571
370 PLR 0.8570
371 BL0 0.8563
372 XIY 0.8562
373 JG8 0.8560
374 E1T 0.8560
375 4BL 0.8557
376 QMP 0.8553
377 ESX 0.8550
378 M5H 0.8530
379 KPC 0.8529
380 SG3 0.8524
381 BGP 0.8514
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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