Receptor
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
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...
JGY A:203;
 Valid;
 none;
 submit data
209.245 C10 H15 N3 O2 Cn1cc...
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: JGY; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 JGY 1 1
2 S8P 0.564516 0.763636
Similar Ligands (3D)
Ligand no: 1; Ligand: JGY; Similar ligands found: 282
No: Ligand Similarity coefficient
1 5TO 0.9597
2 6C5 0.9512
3 6C9 0.9460
4 6C8 0.9446
5 NFZ 0.9385
6 OJD 0.9358
7 P93 0.9356
8 MKN 0.9345
9 4AU 0.9314
10 HLP 0.9277
11 PIQ 0.9270
12 JF5 0.9268
13 GHQ 0.9260
14 RDV 0.9258
15 HAR 0.9242
16 68B 0.9238
17 0ON 0.9238
18 11X 0.9237
19 XI7 0.9201
20 LVP 0.9195
21 9JT 0.9191
22 S7D 0.9183
23 536 0.9178
24 M4N 0.9172
25 FZ3 0.9156
26 C4E 0.9151
27 BSA 0.9148
28 BZM 0.9139
29 5B2 0.9134
30 9JH 0.9131
31 5F8 0.9131
32 HWH 0.9125
33 6C4 0.9123
34 0DF 0.9122
35 RK4 0.9116
36 6FR 0.9111
37 0QA 0.9101
38 4Z0 0.9100
39 0UL 0.9099
40 F40 0.9095
41 LR2 0.9094
42 1HP 0.9090
43 2UD 0.9088
44 6FG 0.9087
45 TRP 0.9077
46 IOP 0.9071
47 5E5 0.9070
48 1XS 0.9066
49 1FE 0.9053
50 0K7 0.9043
51 F91 0.9038
52 D25 0.9032
53 47V 0.9030
54 FCW 0.9028
55 6DQ 0.9026
56 ZZA 0.9018
57 4Z9 0.9016
58 NAL 0.9007
59 L1T 0.8997
60 VM1 0.8994
61 Z70 0.8993
62 LZ5 0.8986
63 JMG 0.8979
64 HPX 0.8978
65 S0F 0.8977
66 KYN 0.8970
67 1PS 0.8968
68 DBE 0.8966
69 BZQ 0.8965
70 JSX 0.8965
71 6MW 0.8962
72 5WN 0.8958
73 CUQ 0.8957
74 8CC 0.8954
75 HH6 0.8953
76 AJ1 0.8945
77 LL1 0.8944
78 D4G 0.8940
79 3IP 0.8939
80 LTN 0.8939
81 27K 0.8938
82 A9B 0.8934
83 AZY 0.8932
84 S0B 0.8932
85 A8K 0.8931
86 LIG 0.8928
87 7ZO 0.8927
88 PZX 0.8925
89 CBE 0.8921
90 OGY 0.8918
91 22T 0.8914
92 SOJ 0.8914
93 SU9 0.8912
94 JCZ 0.8906
95 7VY 0.8905
96 5R9 0.8900
97 2JX 0.8898
98 RE4 0.8895
99 N9M 0.8895
100 363 0.8891
101 BB4 0.8891
102 H35 0.8885
103 2LW 0.8883
104 D26 0.8881
105 4RG 0.8877
106 SNJ 0.8874
107 DTR 0.8874
108 BL0 0.8874
109 P4L 0.8872
110 ASE 0.8870
111 E8U 0.8870
112 52F 0.8869
113 DAH 0.8861
114 GVA 0.8855
115 3IB 0.8853
116 G14 0.8849
117 2P3 0.8848
118 2O8 0.8844
119 AC2 0.8842
120 0MB 0.8839
121 L2K 0.8839
122 MD6 0.8834
123 PHQ DAL 0.8834
124 DI9 0.8832
125 GGG 0.8829
126 3VQ 0.8827
127 BGK 0.8826
128 LFQ 0.8826
129 KLE 0.8821
130 P7V 0.8818
131 4NS 0.8816
132 5WK 0.8811
133 2QU 0.8811
134 BVS 0.8806
135 TBJ 0.8804
136 RKV 0.8802
137 AHN 0.8801
138 DE7 0.8797
139 NK5 0.8797
140 MUX 0.8796
141 KPV 0.8796
142 8YH 0.8794
143 EMU 0.8793
144 MGB 0.8793
145 ENG 0.8792
146 C82 0.8791
147 7EH 0.8790
148 B5A 0.8788
149 STV 0.8787
150 B41 0.8787
151 S8G 0.8786
152 D53 0.8784
153 4TB 0.8782
154 DXK 0.8778
155 7PS 0.8777
156 TJM 0.8773
157 5DS 0.8768
158 QIV 0.8767
159 TCR 0.8763
160 DHC 0.8763
161 39Z 0.8762
162 7L4 0.8762
163 OA1 0.8758
164 3D3 0.8756
165 3VW 0.8756
166 7O4 0.8755
167 DTE 0.8755
168 EQW 0.8754
169 5PV 0.8751
170 OLU 0.8750
171 MFY 0.8749
172 GG8 0.8749
173 6J5 0.8746
174 A6W 0.8744
175 2FX 0.8743
176 YE6 0.8743
177 2L1 0.8742
178 0OM 0.8737
179 6H2 0.8736
180 4MB 0.8736
181 J1K 0.8735
182 4NP 0.8734
183 PNP 0.8730
184 5O6 0.8730
185 1HR 0.8729
186 FZ0 0.8728
187 3XH 0.8728
188 245 0.8723
189 S7G 0.8721
190 A51 0.8718
191 0XR 0.8717
192 4ZD 0.8715
193 TPM 0.8715
194 SVG 0.8713
195 1AJ 0.8713
196 WCU 0.8712
197 SJR 0.8709
198 WA2 0.8706
199 IYR 0.8704
200 FCD 0.8704
201 YOF 0.8703
202 PUE 0.8694
203 833 0.8689
204 7N8 0.8688
205 J4K 0.8686
206 ZIP 0.8685
207 G6Q 0.8684
208 D1G 0.8683
209 657 0.8682
210 PPN 0.8682
211 S1D 0.8681
212 6N4 0.8680
213 M28 0.8673
214 EWG 0.8673
215 P2L 0.8673
216 2D2 0.8673
217 5VU 0.8673
218 1AE 0.8672
219 VFG 0.8671
220 0OP 0.8669
221 X2M 0.8668
222 EYV 0.8665
223 AX5 0.8664
224 SCE 0.8662
225 1Q4 0.8661
226 VBC 0.8658
227 YE7 0.8657
228 49P 0.8656
229 CX4 0.8654
230 60L 0.8651
231 AMR 0.8650
232 4YZ 0.8650
233 0A1 0.8650
234 ALY 0.8649
235 58X 0.8649
236 M83 0.8645
237 AVO 0.8645
238 AOY 0.8644
239 ODK 0.8642
240 AGP 0.8640
241 EGV 0.8635
242 JX7 0.8633
243 Y3L 0.8633
244 D1Y 0.8623
245 S7P 0.8622
246 7MW 0.8619
247 35K 0.8615
248 0SY 0.8613
249 ML1 0.8612
250 D2G 0.8610
251 PLP 0.8602
252 ZRK 0.8602
253 0V8 0.8601
254 FC2 0.8600
255 FWD 0.8596
256 3C5 0.8594
257 00G 0.8593
258 RKY 0.8590
259 M3L 0.8588
260 0LO 0.8587
261 TMG 0.8586
262 AJG 0.8586
263 I2E 0.8586
264 28B 0.8584
265 J38 0.8584
266 IQQ 0.8582
267 5WS 0.8579
268 GNW 0.8578
269 8CV 0.8576
270 1OS 0.8572
271 UN3 0.8570
272 GO2 0.8570
273 JKK 0.8568
274 GRQ 0.8568
275 5LD 0.8564
276 GZ2 0.8562
277 L03 0.8553
278 L5D 0.8529
279 BQ2 0.8527
280 0NX 0.8523
281 4I8 0.8523
282 ALA PHE 0.8511
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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