Receptor
PDB id Resolution Class Description Source Keywords
5R8G 1.43 Å NON-ENZYME: OTHER PANDDA ANALYSIS GROUP DEPOSITION INTERLEUKIN-1 BETA -- FRAGM Z1259086950 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...
S7V A:203;
 Valid;
 none;
 submit data
207.269 C12 H17 N O2 c1ccc...
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: S7V; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 S7V 1 1
Similar Ligands (3D)
Ligand no: 1; Ligand: S7V; Similar ligands found: 193
No: Ligand Similarity coefficient
1 0OO 0.9656
2 531 0.9437
3 536 0.9337
4 F63 0.9337
5 C0H 0.9316
6 VJJ 0.9295
7 HHV 0.9278
8 0A9 0.9197
9 N1Y 0.9188
10 OJD 0.9154
11 SZ7 0.9151
12 TZM 0.9149
13 EXG 0.9148
14 7ZL 0.9137
15 TH4 0.9135
16 HLP 0.9133
17 3D8 0.9123
18 9VQ 0.9116
19 ZMG 0.9106
20 C4E 0.9104
21 AX4 0.9098
22 MUK 0.9091
23 KLS 0.9086
24 11X 0.9085
25 54F 0.9084
26 EVO 0.9084
27 AX5 0.9081
28 JM2 0.9063
29 5TT 0.9060
30 1PS 0.9057
31 RK4 0.9052
32 4GU 0.9046
33 0UL 0.9043
34 TYR 0.9029
35 GNW 0.9016
36 4FP 0.9013
37 9JT 0.9012
38 FNA 0.9010
39 92O 0.9004
40 0OL 0.9003
41 FY8 0.8964
42 BZQ 0.8964
43 AOY 0.8957
44 HO6 0.8956
45 A18 0.8956
46 H35 0.8956
47 WCU 0.8949
48 8CV 0.8938
49 9PL 0.8937
50 QME 0.8932
51 3AK 0.8931
52 RCV 0.8917
53 H4B 0.8914
54 NFZ 0.8913
55 JF5 0.8911
56 AHL 0.8908
57 12R 0.8906
58 KLE 0.8904
59 3VR 0.8903
60 14W 0.8902
61 BDJ 0.8900
62 3QO 0.8899
63 848 0.8897
64 TYP 0.8897
65 DAH 0.8891
66 FCW 0.8887
67 JM7 0.8883
68 PQS 0.8881
69 HA6 0.8877
70 3VW 0.8874
71 A6Z 0.8873
72 VIO 0.8870
73 M5P 0.8866
74 2D2 0.8865
75 M5E 0.8865
76 PTB 0.8863
77 ENO 0.8863
78 5PV 0.8861
79 M2E 0.8856
80 3N1 0.8854
81 0OM 0.8851
82 JAH 0.8850
83 ZEZ 0.8841
84 0FR 0.8833
85 3CX 0.8829
86 PQM 0.8824
87 S7D 0.8822
88 E9S 0.8811
89 KWB 0.8810
90 E9P 0.8810
91 4AF 0.8810
92 50Q 0.8809
93 RQD 0.8805
94 5TO 0.8803
95 ZRK 0.8802
96 MMS 0.8800
97 X48 0.8789
98 DTY 0.8788
99 S7S 0.8785
100 TIA 0.8784
101 2KJ 0.8779
102 F4K 0.8778
103 FHV 0.8777
104 4VT 0.8776
105 H2B 0.8776
106 108 0.8776
107 BC3 0.8771
108 HX8 0.8771
109 PFF 0.8768
110 LR8 0.8768
111 PW1 0.8763
112 ZSP 0.8763
113 6C5 0.8761
114 AEY 0.8758
115 BHS 0.8758
116 API 0.8757
117 OLU 0.8752
118 F9W 0.8751
119 HBI 0.8751
120 8D6 0.8748
121 AX8 0.8743
122 CTN 0.8741
123 IM4 0.8736
124 P2L 0.8735
125 HC4 0.8729
126 HXY 0.8728
127 0NX 0.8720
128 5O6 0.8717
129 SJK 0.8715
130 94X 0.8715
131 6P3 0.8709
132 SX3 0.8709
133 XYP XIF 0.8701
134 6C4 0.8699
135 1KJ 0.8696
136 AJG 0.8694
137 14N 0.8691
138 3IP 0.8688
139 YOF 0.8686
140 5VU 0.8684
141 4RG 0.8683
142 C1E 0.8683
143 W1G 0.8682
144 EMU 0.8679
145 PCS 0.8677
146 EIP 0.8674
147 4AB 0.8670
148 4KJ 0.8669
149 JA5 0.8668
150 S0A 0.8666
151 RSV 0.8665
152 68B 0.8662
153 I2E 0.8660
154 MXD 0.8656
155 LR2 0.8655
156 GT4 0.8655
157 DNB 0.8654
158 9X3 0.8653
159 ZIP 0.8652
160 TOH 0.8651
161 6DQ 0.8650
162 TYC 0.8647
163 RVE 0.8647
164 9FH 0.8645
165 5RP 0.8643
166 M77 0.8639
167 0ON 0.8637
168 RDV 0.8630
169 FUZ 0.8627
170 BIO 0.8626
171 XIF XYP 0.8625
172 JMG 0.8616
173 3AR 0.8606
174 4CF 0.8600
175 N2Y 0.8599
176 C82 0.8591
177 VC3 0.8590
178 SB7 0.8588
179 AMJ 0.8585
180 F40 0.8585
181 M4N 0.8581
182 7L4 0.8575
183 EAT 0.8571
184 HNM 0.8570
185 3VX 0.8570
186 2LT 0.8567
187 XYP XYP 0.8564
188 4P8 0.8562
189 M02 0.8562
190 X2M 0.8555
191 RDY 0.8554
192 CU0 0.8531
193 2L2 0.8528
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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