Receptor
PDB id Resolution Class Description Source Keywords
5R8C 1.54 Å NON-ENZYME: OTHER PANDDA ANALYSIS GROUP DEPOSITION INTERLEUKIN-1 BETA -- FRAGM Z30857828 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...
M25 A:203;
 Valid;
 none;
 submit data
242.295 C10 H14 N2 O3 S CC(=O...
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: M25; Similar ligands found: 16
No: Ligand ECFP6 Tc MDL keys Tc
1 M25 1 1
2 TG4 0.545455 0.796875
3 9E8 0.508772 0.738462
4 4JE 0.5 0.703704
5 R21 0.5 0.710145
6 M28 0.488889 0.706897
7 ZYX 0.487805 0.865385
8 S2O 0.465116 0.75
9 M29 0.46 0.688525
10 L4K 0.446809 0.714286
11 CQS 0.441176 0.644737
12 4JC 0.428571 0.698113
13 42G 0.416667 0.728571
14 B15 0.402778 0.671233
15 9HK 0.4 0.6
16 D7A 0.4 0.769231
Similar Ligands (3D)
Ligand no: 1; Ligand: M25; Similar ligands found: 116
No: Ligand Similarity coefficient
1 3O5 0.9595
2 5RD 0.9577
3 RYY 0.9484
4 RYJ 0.9395
5 FQV 0.9394
6 3UF 0.9394
7 FQY 0.9386
8 EZ1 0.9351
9 VD9 0.9329
10 RZ0 0.9281
11 U55 0.9240
12 LZ4 0.9227
13 TFM 0.9200
14 R7T 0.9184
15 3W6 0.9182
16 3W3 0.9175
17 RPN 0.9148
18 RYV 0.9121
19 LEG 0.9120
20 109 0.9081
21 J1K 0.9067
22 QTD 0.9059
23 7N8 0.9059
24 G8V 0.9055
25 9JH 0.9022
26 TEF 0.9016
27 JL7 0.9002
28 NY4 0.9000
29 6DH 0.8999
30 RZ5 0.8996
31 DVK 0.8989
32 4AF 0.8984
33 EZL 0.8974
34 EYY 0.8973
35 SAB 0.8971
36 8V8 0.8965
37 AD6 0.8962
38 4WA 0.8956
39 KOH 0.8951
40 250 0.8947
41 EP1 0.8943
42 856 0.8943
43 S6I 0.8941
44 1EB 0.8930
45 GJG 0.8916
46 SJR 0.8912
47 HMZ 0.8911
48 EPE 0.8887
49 LC1 0.8879
50 7O8 0.8870
51 4CF 0.8867
52 WW3 0.8861
53 PTR 0.8851
54 8EU 0.8846
55 5UN 0.8845
56 3VR 0.8845
57 3NM 0.8843
58 9VQ 0.8842
59 PPN 0.8840
60 3G3 0.8837
61 QTJ 0.8834
62 BC5 0.8831
63 RYX 0.8830
64 00G 0.8830
65 F91 0.8830
66 Y27 0.8829
67 C0V 0.8824
68 5UM 0.8818
69 JW8 0.8806
70 TFQ 0.8777
71 SQG 0.8775
72 EYJ 0.8758
73 HPK 0.8740
74 4BX 0.8727
75 3W1 0.8724
76 SZA 0.8723
77 35K 0.8719
78 REG 0.8715
79 BXS 0.8715
80 F6W 0.8701
81 E90 0.8701
82 BP5 0.8700
83 CT0 0.8689
84 WDT 0.8689
85 QTK 0.8689
86 JW2 0.8682
87 JVD 0.8677
88 BSA 0.8675
89 20N 0.8669
90 D8W 0.8664
91 Q86 0.8662
92 RPI 0.8659
93 ESJ 0.8650
94 AES 0.8650
95 TPD 0.8635
96 HPX 0.8631
97 5UF 0.8623
98 L8N 0.8619
99 8YH 0.8606
100 E9P 0.8604
101 J4K 0.8600
102 CWP 0.8599
103 BZM 0.8597
104 VFJ 0.8595
105 Z13 0.8590
106 TBJ 0.8588
107 5M2 0.8586
108 HDI 0.8583
109 3CX 0.8578
110 BVS 0.8577
111 0QA 0.8576
112 EFR 0.8562
113 6IP 0.8557
114 6N4 0.8554
115 BOW 0.8551
116 HRS 0.8535
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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