Receptor
PDB id Resolution Class Description Source Keywords
5R8K 1.47 Å NON-ENZYME: OTHER PANDDA ANALYSIS GROUP DEPOSITION INTERLEUKIN-1 BETA -- FRAGM Z355728146 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...
S8D A:203;
 Valid;
 none;
 submit data
200.278 C10 H20 N2 O2 CCNC(...
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: S8D; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 S8D 1 1
Similar Ligands (3D)
Ligand no: 1; Ligand: S8D; Similar ligands found: 202
No: Ligand Similarity coefficient
1 ALE 0.9482
2 N7I 0.9363
3 CIY 0.9317
4 1QP 0.9282
5 TRP 0.9240
6 EGR 0.9209
7 GJK 0.9200
8 FER 0.9195
9 JPQ 0.9186
10 HL4 0.9186
11 9F8 0.9159
12 BDI 0.9158
13 A7K 0.9128
14 7ZL 0.9107
15 H4E 0.9099
16 ETV 0.9098
17 THM 0.9097
18 TLM 0.9094
19 XQI 0.9090
20 DHC 0.9085
21 IOP 0.9083
22 ZME 0.9083
23 23J 0.9074
24 7MX 0.9067
25 3EB 0.9065
26 AMR 0.9055
27 SQV 0.9054
28 E35 0.9045
29 H7Y 0.9042
30 67Y 0.9040
31 8GK 0.9040
32 PQT 0.9034
33 2LY 0.9010
34 QUB 0.9009
35 6Q3 0.9008
36 C9M 0.9000
37 55D 0.9000
38 ZEA 0.8999
39 I2E 0.8983
40 SRO 0.8982
41 LNR 0.8978
42 9BF 0.8975
43 DUR 0.8969
44 SBK 0.8955
45 MD6 0.8955
46 SYR 0.8943
47 NHT 0.8933
48 SLY 0.8931
49 FF2 0.8927
50 ARG 0.8927
51 GZ2 0.8924
52 DAH 0.8924
53 DXK 0.8918
54 3TC 0.8916
55 PPY 0.8913
56 NIY 0.8910
57 NB1 0.8906
58 SNV 0.8902
59 IAC 0.8899
60 D8Q 0.8898
61 Q5M 0.8897
62 E1P 0.8897
63 C2Y 0.8891
64 M6Z 0.8889
65 92P 0.8888
66 NGT 0.8884
67 VXX 0.8883
68 4ME 0.8881
69 4A1 0.8881
70 GC3 0.8878
71 PW1 0.8875
72 1A7 0.8875
73 78U 0.8875
74 263 0.8871
75 AOJ 0.8870
76 TL5 0.8865
77 DCZ 0.8865
78 ONZ 0.8864
79 AC2 0.8856
80 GO8 0.8855
81 KYN 0.8854
82 TYR 0.8853
83 UFV 0.8853
84 6J9 0.8852
85 54F 0.8851
86 TZM 0.8846
87 CK2 0.8842
88 KWB 0.8837
89 C0H 0.8834
90 XYH 0.8832
91 IQU 0.8826
92 LTN 0.8825
93 M4E 0.8824
94 NVU 0.8824
95 B21 0.8820
96 M5H 0.8814
97 SNY 0.8813
98 7CT 0.8813
99 EOL 0.8812
100 ZIP 0.8809
101 LDP 0.8806
102 12R 0.8804
103 TSS 0.8804
104 JTH 0.8785
105 BPY 0.8784
106 61M 0.8780
107 PF1 0.8772
108 C4L 0.8769
109 JRB 0.8769
110 ELH 0.8767
111 ET0 0.8767
112 3XH 0.8765
113 H7S 0.8764
114 JD7 0.8758
115 A6H 0.8757
116 HVE 0.8754
117 28S 0.8752
118 FC2 0.8752
119 BB4 0.8752
120 SBI 0.8746
121 W8G 0.8744
122 M01 0.8743
123 3IL 0.8737
124 M02 0.8737
125 JAA 0.8737
126 AX3 0.8734
127 HPT 0.8731
128 CKU 0.8731
129 R9G 0.8721
130 QBM 0.8721
131 LL2 0.8720
132 H35 0.8718
133 LLG 0.8715
134 5WN 0.8712
135 2KU 0.8705
136 8MP 0.8700
137 9UL 0.8698
138 069 0.8698
139 F52 0.8694
140 3IB 0.8688
141 BK9 0.8676
142 EQW 0.8674
143 MMS 0.8670
144 NFZ 0.8666
145 6HP 0.8665
146 4Z3 0.8664
147 2UD 0.8661
148 C53 0.8661
149 JYW 0.8659
150 GRX 0.8658
151 NPA 0.8654
152 5ER 0.8651
153 C4E 0.8648
154 KTA 0.8647
155 0OP 0.8647
156 TQU 0.8646
157 8WT 0.8646
158 NZ9 0.8645
159 1HR 0.8643
160 YE6 0.8639
161 TJM 0.8637
162 7BX 0.8632
163 CFA 0.8631
164 FUZ 0.8630
165 GCO 0.8628
166 ML1 0.8628
167 JND 0.8626
168 FCD 0.8626
169 CXH 0.8626
170 36M 0.8625
171 FNA 0.8621
172 A29 0.8621
173 6HO 0.8614
174 TAG 0.8613
175 B23 0.8612
176 MBP 0.8612
177 LYS 0.8602
178 B2J 0.8596
179 J9T 0.8594
180 HL6 0.8592
181 7OD 0.8590
182 RUG 0.8588
183 JXK 0.8585
184 O2Y 0.8584
185 512 0.8584
186 42J 0.8578
187 3GZ 0.8577
188 AYS 0.8574
189 I59 0.8567
190 SOL 0.8567
191 SAF 0.8563
192 AS3 0.8562
193 A9P 0.8561
194 2LT 0.8554
195 ABF 0.8545
196 7ZC 0.8542
197 49O 0.8539
198 1XS 0.8522
199 CK1 0.8520
200 NNH 0.8517
201 HWH 0.8517
202 MHK 0.8512
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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