Receptor
PDB id Resolution Class Description Source Keywords
5R8L 1.56 Å NON-ENZYME: OTHER PANDDA ANALYSIS GROUP DEPOSITION INTERLEUKIN-1 BETA -- FRAGM Z1891773393 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...
NY4 A:203;
 Valid;
 none;
 submit data
204.268 C12 H16 N2 O C[C@@...
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: NY4; Similar ligands found: 3
No: Ligand ECFP6 Tc MDL keys Tc
1 NY4 1 1
2 20N 0.568182 0.851852
3 Y27 0.5 0.638889
Similar Ligands (3D)
Ligand no: 1; Ligand: NY4; Similar ligands found: 226
No: Ligand Similarity coefficient
1 1EB 0.9658
2 9NB 0.9546
3 TID 0.9446
4 IS2 0.9424
5 LO1 0.9393
6 6SD 0.9355
7 JA5 0.9328
8 7N8 0.9262
9 J1K 0.9253
10 PQM 0.9251
11 6P3 0.9242
12 KLS 0.9226
13 A5Q 0.9226
14 RYV 0.9220
15 3VS 0.9206
16 NFZ 0.9205
17 K3D 0.9182
18 4FC 0.9174
19 PQS 0.9157
20 S0D 0.9150
21 7FU 0.9149
22 4I8 0.9148
23 G1L 0.9147
24 L4K 0.9140
25 0UL 0.9139
26 VC3 0.9118
27 LWA 0.9112
28 AJG 0.9110
29 RYY 0.9105
30 DVK 0.9105
31 5O6 0.9104
32 LR8 0.9103
33 4UM 0.9099
34 HNT 0.9099
35 FYR 0.9097
36 JCZ 0.9094
37 VFJ 0.9080
38 Y3L 0.9080
39 JMG 0.9080
40 8V8 0.9078
41 BIH 0.9073
42 4CF 0.9073
43 EZL 0.9070
44 KLE 0.9068
45 BC5 0.9061
46 K4V 0.9058
47 4FE 0.9052
48 7EH 0.9048
49 4NP 0.9047
50 XCG 0.9046
51 80G 0.9046
52 M28 0.9045
53 GVY 0.9042
54 ENO 0.9042
55 E3X 0.9041
56 NDD 0.9036
57 3O5 0.9036
58 72D 0.9028
59 A7H 0.9027
60 JBZ 0.9016
61 3W3 0.9015
62 B1J 0.9013
63 K82 0.9010
64 M25 0.9000
65 VFG 0.8999
66 4AF 0.8998
67 SQG 0.8996
68 RCV 0.8992
69 F4K 0.8984
70 2PK 0.8982
71 D9Z 0.8981
72 VFM 0.8979
73 0F3 0.8979
74 A98 0.8976
75 OLU 0.8975
76 RSV 0.8973
77 I3E 0.8969
78 N4E 0.8968
79 S7S 0.8966
80 NPS 0.8964
81 397 0.8963
82 FZM 0.8961
83 1FE 0.8960
84 U55 0.8956
85 VGS 0.8955
86 TMG 0.8950
87 QIV 0.8949
88 QBP 0.8946
89 GJG 0.8945
90 2JX 0.8945
91 2P3 0.8945
92 5TT 0.8934
93 JAH 0.8928
94 PIQ 0.8926
95 72E 0.8924
96 1BW 0.8922
97 WA1 0.8920
98 NPX 0.8919
99 HC4 0.8914
100 EP1 0.8913
101 2PV 0.8910
102 833 0.8907
103 5SJ 0.8905
104 M5A 0.8902
105 4MB 0.8900
106 2D2 0.8891
107 EES 0.8891
108 SJK 0.8889
109 GB5 0.8888
110 TYR 0.8885
111 2QC 0.8882
112 PNP 0.8881
113 2FX 0.8881
114 SWX 0.8877
115 363 0.8875
116 CT0 0.8871
117 B15 0.8870
118 7MW 0.8870
119 D26 0.8861
120 M78 0.8859
121 PH3 0.8859
122 LZ4 0.8859
123 AD6 0.8858
124 WV7 0.8858
125 ERZ 0.8853
126 P4T 0.8852
127 BFL 0.8850
128 ZTW 0.8848
129 8CC 0.8845
130 3VQ 0.8840
131 LC1 0.8827
132 L03 0.8824
133 4HB 0.8823
134 I2E 0.8822
135 8NB 0.8821
136 6KT 0.8820
137 FCW 0.8820
138 T1N 0.8820
139 0OK 0.8815
140 4Z1 0.8814
141 DAH 0.8814
142 M4N 0.8805
143 1HP 0.8804
144 BVS 0.8803
145 PTB 0.8802
146 A9B 0.8800
147 613 0.8799
148 OQC 0.8798
149 4BX 0.8796
150 2O8 0.8796
151 P81 0.8795
152 0DF 0.8793
153 G2V 0.8787
154 0NJ 0.8787
155 BQ2 0.8785
156 BX4 0.8782
157 SNV 0.8777
158 FT6 0.8777
159 5H6 0.8774
160 C5F 0.8772
161 S0W 0.8772
162 CX6 0.8767
163 CXH 0.8765
164 5VU 0.8756
165 K7H 0.8755
166 FMQ 0.8753
167 REG 0.8748
168 5GV 0.8745
169 MKN 0.8738
170 YZ9 0.8737
171 5OR 0.8736
172 RKY 0.8733
173 STX 0.8732
174 NAL 0.8728
175 ZSP 0.8728
176 GO2 0.8725
177 EE8 0.8724
178 S62 0.8719
179 3W8 0.8716
180 D25 0.8711
181 0NX 0.8705
182 250 0.8699
183 7KE 0.8697
184 7G0 0.8695
185 P7V 0.8695
186 AJ1 0.8694
187 II4 0.8689
188 8YH 0.8687
189 DHC 0.8686
190 RZ0 0.8685
191 H75 0.8684
192 5OO 0.8682
193 S45 0.8681
194 FMH 0.8680
195 EQW 0.8677
196 54E 0.8675
197 A6Z 0.8674
198 6T5 0.8671
199 ODK 0.8671
200 7EL 0.8666
201 OHJ 0.8664
202 88L 0.8654
203 RA7 0.8652
204 8EU 0.8644
205 ESJ 0.8639
206 C82 0.8630
207 SJR 0.8629
208 AWE 0.8627
209 8D6 0.8626
210 NK5 0.8626
211 EZ1 0.8620
212 3VX 0.8617
213 ZEC 0.8613
214 2L1 0.8609
215 C0V 0.8609
216 6MW 0.8598
217 AZM 0.8594
218 6PG 0.8592
219 GB4 0.8591
220 6C8 0.8586
221 LIG 0.8563
222 5SP 0.8563
223 UA5 0.8560
224 AP6 0.8558
225 NEO 0.8520
226 Z3R 0.8516
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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