Receptor
PDB id Resolution Class Description Source Keywords
5R87 1.47 Å NON-ENZYME: OTHER PANDDA ANALYSIS GROUP DEPOSITION INTERLEUKIN-1 BETA -- FRAGM Z44592329 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...
K0G A:203;
 Valid;
 none;
 submit data
213.235 C12 H11 N3 O 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: K0G; Similar ligands found: 6
No: Ligand ECFP6 Tc MDL keys Tc
1 K0G 1 1
2 BSU 0.621622 0.827586
3 M4T 0.522727 0.677419
4 0ON 0.520833 0.6875
5 245 0.471698 0.8
6 3GG 0.421053 0.666667
Similar Ligands (3D)
Ligand no: 1; Ligand: K0G; Similar ligands found: 167
No: Ligand Similarity coefficient
1 WA1 0.9954
2 ZTW 0.9589
3 CIU 0.9413
4 397 0.9338
5 D26 0.9300
6 MKN 0.9285
7 HPK 0.9269
8 KLS 0.9265
9 STL 0.9264
10 6P3 0.9247
11 LR8 0.9241
12 9EG 0.9240
13 G2V 0.9222
14 FHV 0.9202
15 D25 0.9199
16 S0B 0.9195
17 RDV 0.9183
18 6H2 0.9160
19 MR4 0.9148
20 S0D 0.9138
21 P4T 0.9120
22 9JT 0.9108
23 PIT 0.9108
24 OLU 0.9103
25 4CN 0.9087
26 S0A 0.9055
27 BMZ 0.9051
28 5OR 0.9041
29 39R 0.9032
30 1Q2 0.9031
31 HPX 0.9014
32 RF2 0.9014
33 6C8 0.9009
34 IW3 0.9003
35 EES 0.9001
36 MR5 0.8998
37 LJ2 0.8992
38 3CX 0.8982
39 L02 0.8982
40 CR4 0.8982
41 ESJ 0.8974
42 IPJ 0.8971
43 120 0.8969
44 0NJ 0.8966
45 BX4 0.8963
46 VC3 0.8963
47 801 0.8962
48 8M5 0.8950
49 124 0.8944
50 CT0 0.8938
51 83D 0.8929
52 5VU 0.8927
53 M4N 0.8926
54 LJ1 0.8917
55 REG 0.8916
56 8V8 0.8915
57 5TT 0.8915
58 5TO 0.8913
59 A51 0.8909
60 U13 0.8902
61 BVB 0.8894
62 0MB 0.8890
63 WG8 0.8886
64 7EH 0.8880
65 6FG 0.8878
66 7FZ 0.8874
67 LR2 0.8867
68 72D 0.8865
69 TID 0.8862
70 122 0.8858
71 AZB 0.8856
72 C0V 0.8846
73 IW5 0.8844
74 0UL 0.8843
75 135 0.8837
76 4P9 0.8833
77 PQM 0.8832
78 AD6 0.8823
79 L2K 0.8819
80 4ZF 0.8818
81 BXS 0.8817
82 AOY 0.8817
83 F18 0.8815
84 68C 0.8814
85 ZRK 0.8814
86 IJ6 0.8813
87 LJ5 0.8810
88 BC5 0.8800
89 F5N 0.8796
90 0XR 0.8795
91 TEF 0.8791
92 LZ4 0.8790
93 HCC 0.8783
94 MR6 0.8782
95 3VQ 0.8782
96 2OX 0.8781
97 3K1 0.8781
98 4FC 0.8777
99 JMG 0.8773
100 ZUF 0.8771
101 1EB 0.8770
102 A9B 0.8765
103 3VS 0.8764
104 A6W 0.8764
105 CDX 0.8764
106 PQS 0.8755
107 C4E 0.8747
108 IIH 0.8744
109 47V 0.8741
110 23M 0.8740
111 S45 0.8740
112 5TU 0.8739
113 4BX 0.8738
114 MI2 0.8736
115 UAY 0.8730
116 121 0.8728
117 1Q1 0.8725
118 WCU 0.8722
119 D8B 0.8721
120 AP6 0.8715
121 KLE 0.8711
122 FBC 0.8705
123 LIG 0.8704
124 MJW 0.8703
125 PIQ 0.8703
126 0SY 0.8696
127 A8D 0.8691
128 1V8 0.8688
129 4AU 0.8684
130 LWA 0.8684
131 LPA 0.8680
132 RE2 0.8677
133 0DF 0.8677
134 Z3R 0.8676
135 833 0.8675
136 2M7 0.8670
137 IW4 0.8666
138 HRG 0.8663
139 1OT 0.8661
140 1HP 0.8659
141 789 0.8659
142 U55 0.8658
143 47X 0.8653
144 A5Q 0.8647
145 7G0 0.8647
146 DZ3 0.8645
147 802 0.8642
148 6BK 0.8636
149 IDZ 0.8632
150 NFZ 0.8621
151 6C5 0.8618
152 1XS 0.8614
153 J84 0.8612
154 6C4 0.8606
155 5H6 0.8606
156 CX5 0.8592
157 ZRL 0.8591
158 4UM 0.8588
159 0K7 0.8584
160 M28 0.8573
161 6DQ 0.8571
162 JL7 0.8567
163 205 0.8545
164 246 0.8542
165 A26 0.8542
166 TFQ 0.8539
167 BFL 0.8536
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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