Receptor
PDB id Resolution Class Description Source Keywords
5R86 1.5 Å NON-ENZYME: OTHER PANDDA ANALYSIS GROUP DEPOSITION INTERLEUKIN-1 BETA -- FRAGM Z943693514 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...
GT4 A:203;
 Valid;
 none;
 submit data
181.189 C9 H11 N O3 COCC(...
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: GT4; Similar ligands found: 3
No: Ligand ECFP6 Tc MDL keys Tc
1 GT4 1 1
2 TYL 0.5 0.631579
3 N0E 0.461538 0.642857
Similar Ligands (3D)
Ligand no: 1; Ligand: GT4; Similar ligands found: 280
No: Ligand Similarity coefficient
1 TYR 0.9673
2 ENO 0.9652
3 HC4 0.9652
4 E3X 0.9633
5 PH3 0.9622
6 92G 0.9549
7 36M 0.9539
8 B1J 0.9510
9 4HB 0.9478
10 S7S 0.9470
11 DTY 0.9446
12 CXH 0.9441
13 0NX 0.9440
14 PPY 0.9431
15 JCZ 0.9426
16 GVY 0.9390
17 XCG 0.9374
18 D3G 0.9370
19 5OO 0.9366
20 TYC 0.9335
21 DAH 0.9325
22 H4E 0.9315
23 SOJ 0.9312
24 JAH 0.9308
25 36Y 0.9308
26 6SD 0.9307
27 DHC 0.9303
28 MSR 0.9298
29 4LW 0.9286
30 CPZ 0.9273
31 C82 0.9263
32 A7H 0.9261
33 5VU 0.9253
34 6ZX 0.9250
35 EN1 0.9247
36 9R5 0.9246
37 HFA 0.9246
38 4BF 0.9243
39 TYE 0.9237
40 TCA 0.9235
41 PBN 0.9231
42 PFF 0.9229
43 FMQ 0.9209
44 PHE 0.9203
45 HX4 0.9195
46 L03 0.9186
47 I3E 0.9173
48 S0W 0.9172
49 HNL 0.9169
50 56D 0.9169
51 BNL 0.9168
52 3H2 0.9163
53 CK2 0.9163
54 J9N 0.9158
55 XDK 0.9156
56 PBA 0.9154
57 B40 0.9148
58 1A7 0.9147
59 I2E 0.9139
60 HNH 0.9138
61 KMY 0.9136
62 P81 0.9132
63 G14 0.9128
64 2QC 0.9123
65 IS2 0.9118
66 X48 0.9110
67 PUE 0.9106
68 BPW 0.9103
69 JMG 0.9098
70 HIS 0.9096
71 J1K 0.9093
72 492 0.9093
73 R9J 0.9090
74 4LV 0.9087
75 TZF 0.9086
76 ODK 0.9085
77 BRH 0.9083
78 XDE 0.9083
79 AOT 0.9081
80 OHJ 0.9075
81 OTR 0.9072
82 1L5 0.9068
83 EYV 0.9068
84 D8Q 0.9064
85 6P3 0.9064
86 HPP 0.9063
87 VC3 0.9055
88 0K7 0.9053
89 B41 0.9053
90 HNK 0.9052
91 5O6 0.9046
92 N9J 0.9046
93 JGB 0.9045
94 PHI 0.9043
95 SWX 0.9043
96 2FX 0.9038
97 FCD 0.9038
98 FZM 0.9037
99 HWD 0.9035
100 K7M 0.9034
101 E0O 0.9031
102 M78 0.9027
103 A5E 0.9026
104 80G 0.9025
105 Y4L 0.9023
106 K80 0.9016
107 L15 0.9015
108 LR8 0.9014
109 YZM 0.9008
110 KTJ 0.9000
111 NFA 0.8994
112 IYR 0.8990
113 XIZ 0.8990
114 HJH 0.8989
115 ZZA 0.8987
116 TT4 0.8975
117 DPN 0.8968
118 3VQ 0.8968
119 MMS 0.8963
120 HL4 0.8957
121 9FG 0.8956
122 50C 0.8954
123 4FP 0.8954
124 7O4 0.8941
125 8YH 0.8938
126 4Z3 0.8937
127 28A 0.8925
128 YPN 0.8922
129 2D2 0.8917
130 ALE 0.8916
131 PQT 0.8913
132 1XS 0.8909
133 F90 0.8904
134 GWM 0.8903
135 YOF 0.8900
136 1Z6 0.8899
137 F4E 0.8897
138 LNR 0.8893
139 5H6 0.8886
140 AMR 0.8886
141 W29 0.8883
142 46P 0.8877
143 LFQ 0.8874
144 4VY 0.8874
145 RA7 0.8874
146 F4K 0.8872
147 PO6 0.8870
148 NK5 0.8869
149 4BX 0.8869
150 HSO 0.8868
151 HL6 0.8864
152 HCI 0.8864
153 BP7 0.8859
154 HIC 0.8857
155 BVS 0.8855
156 4V2 0.8855
157 CFA 0.8849
158 FTV 0.8847
159 OQC 0.8845
160 TJM 0.8842
161 1PS 0.8842
162 XI7 0.8842
163 4CF 0.8841
164 WVV 0.8840
165 27K 0.8836
166 TRP 0.8836
167 5WZ 0.8835
168 PRA 0.8835
169 2LT 0.8832
170 IWD 0.8832
171 0XR 0.8831
172 FHV 0.8829
173 9W5 0.8829
174 JSX 0.8828
175 P7Y 0.8821
176 GNW 0.8821
177 AWE 0.8821
178 2B4 0.8821
179 SB7 0.8819
180 FWD 0.8813
181 K48 0.8807
182 6J5 0.8807
183 ICB 0.8803
184 2BX 0.8800
185 BWD 0.8794
186 0BP 0.8790
187 S2P 0.8789
188 4YZ 0.8788
189 PIM 0.8786
190 61M 0.8784
191 OLU 0.8784
192 AUV 0.8783
193 A9B 0.8782
194 CWD 0.8781
195 NFM 0.8776
196 8D6 0.8771
197 RQD 0.8769
198 7MX 0.8768
199 FHC 0.8764
200 PPT 0.8757
201 SHI 0.8757
202 NAG 0.8757
203 37E 0.8752
204 3C4 0.8752
205 L1T 0.8750
206 1KN 0.8746
207 2F6 0.8746
208 9FH 0.8745
209 N9M 0.8745
210 CXP 0.8743
211 CTN 0.8736
212 TIH 0.8735
213 PIY 0.8734
214 4TB 0.8733
215 C0H 0.8728
216 QME 0.8728
217 54E 0.8726
218 S1D 0.8724
219 6FZ 0.8723
220 BNF 0.8720
221 JRB 0.8720
222 KLE 0.8719
223 URI 0.8714
224 Q04 0.8713
225 Z70 0.8713
226 TI7 0.8710
227 VM1 0.8709
228 K3D 0.8706
229 D9Z 0.8705
230 4AF 0.8703
231 1SF 0.8699
232 T2D 0.8693
233 PCS 0.8692
234 HXY 0.8691
235 88L 0.8690
236 6C5 0.8689
237 C1M 0.8689
238 X6W 0.8683
239 7OD 0.8683
240 5FL 0.8680
241 AVA 0.8671
242 M4N 0.8671
243 4HP 0.8668
244 EAT 0.8665
245 28B 0.8661
246 S7V 0.8655
247 68B 0.8653
248 KYN 0.8651
249 L13 0.8651
250 PQS 0.8650
251 PRO GLY 0.8650
252 5F8 0.8645
253 R2P 0.8645
254 3CX 0.8637
255 AMQ 0.8636
256 A4T 0.8636
257 5LD 0.8633
258 GVG 0.8633
259 VBC 0.8632
260 4FF 0.8628
261 9B3 0.8623
262 A4N 0.8622
263 MP5 0.8617
264 833 0.8615
265 5DL 0.8612
266 KDG 0.8606
267 UA5 0.8605
268 8V8 0.8604
269 3YP 0.8598
270 LDC 0.8597
271 A5Q 0.8580
272 7N8 0.8573
273 A6Z 0.8571
274 8CC 0.8568
275 STX 0.8568
276 0LO 0.8563
277 D2G 0.8561
278 L5D 0.8547
279 RUY 0.8538
280 FUD 0.8529
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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