Receptor
PDB id Resolution Class Description Source Keywords
5R89 1.65 Å NON-ENZYME: OTHER PANDDA ANALYSIS GROUP DEPOSITION INTERLEUKIN-1 BETA -- FRAGM Z217038356 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...
S7D A:203;
 Valid;
 none;
 submit data
209.245 C10 H15 N3 O2 C[C@H...
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: S7D; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 S7D 1 1
Similar Ligands (3D)
Ligand no: 1; Ligand: S7D; Similar ligands found: 384
No: Ligand Similarity coefficient
1 YIP 0.9523
2 3XH 0.9493
3 FZM 0.9342
4 XCG 0.9318
5 KLS 0.9313
6 S0D 0.9299
7 EXG 0.9278
8 TMG 0.9262
9 RE4 0.9247
10 RCV 0.9239
11 CUQ 0.9232
12 FPL 0.9228
13 0OP 0.9224
14 68B 0.9219
15 FER 0.9216
16 AX5 0.9206
17 QME 0.9202
18 XI7 0.9200
19 YIH 0.9199
20 JGY 0.9183
21 GNW 0.9154
22 V15 0.9148
23 A51 0.9143
24 5O5 0.9139
25 S8G 0.9129
26 BVS 0.9125
27 HLP 0.9118
28 2PV 0.9112
29 DA3 0.9108
30 C4E 0.9105
31 I2E 0.9105
32 363 0.9104
33 NK5 0.9090
34 EQA 0.9090
35 DHC 0.9090
36 39Z 0.9087
37 VJJ 0.9086
38 H7S 0.9085
39 EV2 0.9082
40 DY8 0.9080
41 H35 0.9078
42 BZM 0.9075
43 OJD 0.9073
44 6J5 0.9073
45 JAH 0.9069
46 3VW 0.9064
47 BB4 0.9062
48 DAH 0.9056
49 GOE 0.9054
50 3IL 0.9051
51 B5A 0.9050
52 MIL 0.9046
53 5B2 0.9046
54 EGV 0.9044
55 6SD 0.9042
56 7ZL 0.9042
57 6L6 0.9038
58 ARG 0.9037
59 11X 0.9031
60 6C4 0.9029
61 FHV 0.9027
62 AMR 0.9027
63 5AD 0.9024
64 NIY 0.9024
65 2L2 0.9019
66 KWB 0.9019
67 92O 0.9017
68 FY8 0.9016
69 6DQ 0.9013
70 833 0.9012
71 2FX 0.9011
72 0QA 0.9010
73 IAC 0.9005
74 TRP 0.9005
75 KPV 0.9002
76 GGB 0.9000
77 D8Y 0.8999
78 E8U 0.8997
79 J4K 0.8996
80 M5E 0.8995
81 S7G 0.8989
82 S98 0.8987
83 LR2 0.8986
84 VC3 0.8986
85 MJW 0.8985
86 P80 0.8979
87 TJM 0.8977
88 0OK 0.8976
89 2PK 0.8976
90 3D8 0.8967
91 3IP 0.8966
92 5WN 0.8964
93 5WK 0.8961
94 LVD 0.8959
95 4BX 0.8958
96 SRO 0.8956
97 PRO GLY 0.8956
98 3AK 0.8956
99 2P3 0.8955
100 6P3 0.8953
101 D4G 0.8953
102 7VY 0.8950
103 9JT 0.8949
104 4FF 0.8949
105 4OG 0.8946
106 ASE 0.8945
107 A6Z 0.8944
108 CBE 0.8942
109 4Z9 0.8939
110 3D3 0.8939
111 Y0V 0.8938
112 6FG 0.8934
113 FNA 0.8930
114 6MW 0.8928
115 2M7 0.8927
116 GZ2 0.8927
117 LZ5 0.8926
118 HBI 0.8926
119 IOS 0.8924
120 C82 0.8923
121 7MW 0.8923
122 8CC 0.8922
123 0ON 0.8921
124 MMS 0.8920
125 A5Q 0.8920
126 12R 0.8919
127 Y3L 0.8916
128 H75 0.8912
129 M4N 0.8909
130 TPM 0.8908
131 AC2 0.8906
132 GHQ 0.8904
133 7EH 0.8902
134 SZ7 0.8901
135 WCU 0.8898
136 RK4 0.8898
137 ZIP 0.8898
138 ITW 0.8897
139 D9Z 0.8897
140 IYR 0.8897
141 9UL 0.8891
142 K48 0.8891
143 D8Q 0.8891
144 1PS 0.8890
145 AVO 0.8889
146 FCW 0.8885
147 RKV 0.8885
148 RNK 0.8884
149 KF5 0.8881
150 JOV 0.8879
151 IEE 0.8879
152 9FH 0.8878
153 NAL 0.8877
154 9VQ 0.8874
155 X2M 0.8873
156 22T 0.8873
157 K7H 0.8872
158 H4B 0.8871
159 YTZ 0.8869
160 OLU 0.8867
161 QBP 0.8866
162 A4V 0.8863
163 CC5 0.8863
164 FWD 0.8862
165 5TO 0.8860
166 3IB 0.8860
167 DBS 0.8858
168 0NX 0.8858
169 6C5 0.8857
170 2JX 0.8857
171 IOP 0.8854
172 F02 0.8853
173 3D1 0.8851
174 7O4 0.8849
175 4FP 0.8848
176 JMG 0.8848
177 5E5 0.8847
178 0UL 0.8846
179 FF2 0.8845
180 FT6 0.8844
181 DXK 0.8843
182 ZHA 0.8842
183 ZEA 0.8842
184 2D2 0.8839
185 MKN 0.8834
186 4AF 0.8833
187 27K 0.8832
188 G14 0.8829
189 2LT 0.8826
190 RES 0.8824
191 KLV 0.8823
192 S7V 0.8822
193 PBA 0.8820
194 SU9 0.8820
195 ILO 0.8819
196 HRM 0.8819
197 HAR 0.8818
198 1XS 0.8818
199 BSU 0.8818
200 LJ4 0.8817
201 LSQ 0.8817
202 PQS 0.8817
203 HC4 0.8817
204 Q5M 0.8817
205 KMY 0.8816
206 S7P 0.8814
207 YE6 0.8813
208 PFF 0.8812
209 531 0.8811
210 LR8 0.8811
211 ZYC 0.8806
212 AOJ 0.8805
213 ET0 0.8805
214 5GT 0.8804
215 LFQ 0.8804
216 GJK 0.8803
217 4NS 0.8803
218 JFM 0.8803
219 36M 0.8801
220 2WU 0.8800
221 X48 0.8799
222 2GQ 0.8793
223 P1J 0.8793
224 4G2 0.8791
225 CTE 0.8791
226 NFZ 0.8790
227 MUX 0.8789
228 1Q4 0.8787
229 2L1 0.8786
230 657 0.8784
231 0XR 0.8781
232 IBP 0.8778
233 613 0.8776
234 SB7 0.8775
235 AVX 0.8774
236 HSA 0.8771
237 14W 0.8771
238 96Z 0.8771
239 5C1 0.8771
240 9BF 0.8768
241 P2L 0.8766
242 EUH 0.8765
243 YOF 0.8764
244 M6H 0.8764
245 TYR 0.8763
246 MH5 0.8763
247 PLP 0.8761
248 KYN 0.8760
249 TB8 0.8758
250 LJ1 0.8756
251 LJ2 0.8755
252 ENO 0.8754
253 H2B 0.8752
254 API 0.8749
255 JVD 0.8746
256 I58 0.8746
257 N9J 0.8745
258 5F1 0.8745
259 4NP 0.8744
260 RVE 0.8743
261 G6P 0.8740
262 RA7 0.8737
263 78P 0.8735
264 M83 0.8735
265 GG8 0.8734
266 BVA 0.8732
267 3N0 0.8732
268 TSR 0.8729
269 F18 0.8727
270 RSV 0.8726
271 STL 0.8725
272 3VQ 0.8723
273 CL9 0.8719
274 1L5 0.8718
275 M5H 0.8714
276 4MB 0.8712
277 TZP 0.8712
278 GO8 0.8710
279 M3L 0.8710
280 3VX 0.8709
281 GA2 0.8708
282 5O6 0.8707
283 TU0 0.8705
284 Z70 0.8703
285 ZZA 0.8702
286 CWD 0.8702
287 4ZD 0.8702
288 5RP 0.8699
289 397 0.8698
290 L15 0.8697
291 AZY 0.8696
292 KLE 0.8694
293 4I8 0.8693
294 DTY 0.8693
295 6ZX 0.8686
296 GLY GLY GLY 0.8684
297 U13 0.8683
298 2LW 0.8680
299 L1T 0.8679
300 C53 0.8678
301 BWD 0.8677
302 GNG 0.8676
303 LXP 0.8675
304 BGP 0.8674
305 5KJ 0.8670
306 GB4 0.8664
307 SIJ 0.8663
308 EYV 0.8662
309 C0H 0.8659
310 XYP XIF 0.8657
311 6NZ 0.8656
312 AHL 0.8655
313 PLR 0.8652
314 PPN 0.8648
315 J9Y 0.8642
316 HPP 0.8640
317 A5P 0.8638
318 HXY 0.8634
319 Q4G 0.8633
320 RE2 0.8633
321 47V 0.8632
322 TBJ 0.8632
323 BVB 0.8631
324 J38 0.8630
325 4AB 0.8628
326 536 0.8626
327 SSY 0.8626
328 RDM 0.8625
329 GGG 0.8624
330 IWD 0.8624
331 B41 0.8623
332 LGT 0.8618
333 PNP 0.8618
334 37E 0.8617
335 3KJ 0.8616
336 VBC 0.8615
337 DT7 0.8613
338 8YH 0.8611
339 94X 0.8608
340 6Q3 0.8608
341 BL0 0.8607
342 PPT 0.8606
343 BHS 0.8600
344 NXB 0.8599
345 JSX 0.8596
346 GJB 0.8593
347 MDR 0.8593
348 38E 0.8592
349 848 0.8592
350 NPI 0.8592
351 5TT 0.8591
352 P81 0.8591
353 ITE 0.8589
354 K4V 0.8585
355 PRH 0.8584
356 PTB 0.8584
357 0LA 0.8581
358 S1D 0.8580
359 T03 0.8580
360 CIR 0.8579
361 NMM 0.8573
362 ZEZ 0.8571
363 CHQ 0.8570
364 ZIQ 0.8569
365 DA2 0.8567
366 NKI 0.8566
367 GB5 0.8564
368 P93 0.8563
369 N4E 0.8555
370 AVA 0.8553
371 1YO 0.8552
372 VUR 0.8550
373 LVP 0.8535
374 6NJ 0.8534
375 HO6 0.8534
376 YZ9 0.8532
377 ABH 0.8528
378 8V8 0.8525
379 0RY 0.8524
380 TH4 0.8521
381 MP5 0.8518
382 LHY 0.8512
383 0F3 0.8507
384 DIH 0.8505
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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