Receptor
PDB id Resolution Class Description Source Keywords
5R88 1.48 Å NON-ENZYME: OTHER PANDDA ANALYSIS GROUP DEPOSITION INTERLEUKIN-1 BETA -- FRAGM Z1545313172 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...
LWA A:203;
 Valid;
 none;
 submit data
234.251 C12 H14 N2 O3 c1cc(...
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: LWA; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 LWA 1 1
Similar Ligands (3D)
Ligand no: 1; Ligand: LWA; Similar ligands found: 166
No: Ligand Similarity coefficient
1 1EB 0.9595
2 135 0.9285
3 J2N 0.9252
4 CT0 0.9251
5 C0V 0.9207
6 IS2 0.9190
7 4FC 0.9151
8 J3B 0.9138
9 J1K 0.9115
10 NY4 0.9112
11 14N 0.9104
12 A8D 0.9094
13 AZB 0.9085
14 WF4 0.9078
15 20N 0.9076
16 BXS 0.9062
17 5VU 0.9055
18 N5B 0.9041
19 JMM 0.9040
20 G2V 0.9038
21 G1L 0.9007
22 JCQ 0.9004
23 72H 0.9000
24 ZTW 0.8988
25 3K1 0.8987
26 4UM 0.8979
27 GF7 0.8970
28 EP1 0.8965
29 T1N 0.8959
30 0NJ 0.8958
31 RYJ 0.8946
32 A26 0.8945
33 TFX 0.8940
34 7N8 0.8938
35 613 0.8935
36 TID 0.8927
37 5S9 0.8904
38 6P3 0.8904
39 SJR 0.8903
40 397 0.8899
41 FMH 0.8898
42 VGV 0.8896
43 D26 0.8896
44 WDW 0.8896
45 4ZF 0.8890
46 Y27 0.8885
47 ESJ 0.8882
48 6SD 0.8878
49 1R5 0.8867
50 AV7 0.8863
51 250 0.8862
52 245 0.8855
53 GJG 0.8843
54 BIH 0.8841
55 124 0.8838
56 ZUF 0.8831
57 S6I 0.8827
58 246 0.8826
59 BOS 0.8822
60 NFZ 0.8821
61 K97 0.8821
62 7EH 0.8821
63 VFJ 0.8815
64 5ER 0.8812
65 M83 0.8811
66 S45 0.8810
67 BBP 0.8802
68 LEG 0.8797
69 P7V 0.8793
70 NDD 0.8792
71 120 0.8789
72 2PV 0.8789
73 IPJ 0.8789
74 L2K 0.8788
75 5M2 0.8786
76 7KE 0.8782
77 RYY 0.8782
78 5TU 0.8778
79 J2W 0.8773
80 BMZ 0.8773
81 WA1 0.8773
82 L4K 0.8771
83 2PK 0.8770
84 LC1 0.8769
85 HNT 0.8767
86 BSU 0.8762
87 27F 0.8761
88 ENY 0.8760
89 2JP 0.8755
90 K3D 0.8752
91 08C 0.8749
92 CR4 0.8749
93 1Q1 0.8747
94 801 0.8744
95 6H2 0.8742
96 TEF 0.8742
97 LO1 0.8736
98 29F 0.8735
99 121 0.8735
100 122 0.8734
101 EZL 0.8732
102 1XS 0.8729
103 WLH 0.8729
104 23M 0.8727
105 STL 0.8725
106 HDI 0.8716
107 5O6 0.8708
108 D64 0.8705
109 1V8 0.8705
110 4CN 0.8699
111 06R 0.8698
112 OJM 0.8695
113 NEU 0.8693
114 PQM 0.8690
115 OLU 0.8684
116 K0G 0.8684
117 MBT 0.8677
118 EES 0.8673
119 E92 0.8661
120 PJK 0.8660
121 D25 0.8659
122 9JT 0.8657
123 AP6 0.8655
124 HPX 0.8650
125 4AF 0.8649
126 TPM 0.8648
127 MI2 0.8645
128 2OX 0.8636
129 4ZW 0.8636
130 8V8 0.8634
131 MRE 0.8634
132 U4J 0.8632
133 HAU 0.8626
134 KLS 0.8626
135 E98 0.8624
136 22M 0.8614
137 A63 0.8614
138 E6Q 0.8613
139 DFL 0.8613
140 F18 0.8609
141 9EG 0.8607
142 5SJ 0.8600
143 X2L 0.8595
144 N08 0.8595
145 M16 0.8593
146 0UL 0.8589
147 S0D 0.8589
148 GEN 0.8588
149 K3T 0.8584
150 1V0 0.8583
151 S7S 0.8582
152 PIQ 0.8580
153 HRD 0.8580
154 C4E 0.8577
155 IPO 0.8576
156 JVB 0.8571
157 PW8 0.8562
158 25F 0.8562
159 0DF 0.8550
160 WCU 0.8550
161 0XR 0.8546
162 1FE 0.8543
163 7G2 0.8532
164 FTK 0.8525
165 J84 0.8516
166 FJR 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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