Receptor
PDB id Resolution Class Description Source Keywords
5R8F 1.41 Å NON-ENZYME: OTHER PANDDA ANALYSIS GROUP DEPOSITION INTERLEUKIN-1 BETA -- FRAGM Z2377835233 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...
K3Y A:203;
 Valid;
 none;
 submit data
208.26 C10 H16 N4 O Cn1cc...
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: K3Y; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 K3Y 1 1
Similar Ligands (3D)
Ligand no: 1; Ligand: K3Y; Similar ligands found: 172
No: Ligand Similarity coefficient
1 1Z8 0.9476
2 BPS 0.9469
3 QZ8 0.9381
4 W8G 0.9374
5 1FF 0.9365
6 MOK 0.9347
7 25O 0.9309
8 T2D 0.9295
9 A9O 0.9285
10 ACE PHE 0.9262
11 M4B 0.9253
12 B4O 0.9230
13 6J9 0.9208
14 SQP 0.9208
15 JR2 0.9207
16 OSB 0.9207
17 BQ5 0.9182
18 BPY 0.9160
19 B2T 0.9158
20 61O 0.9152
21 49O 0.9124
22 49N 0.9123
23 F69 0.9113
24 AM1 0.9109
25 8WZ 0.9108
26 6PB 0.9096
27 TT4 0.9093
28 A9P 0.9084
29 692 0.9076
30 3B4 0.9075
31 XFE 0.9069
32 A1Y 0.9066
33 M1Z 0.9041
34 7I2 0.9018
35 BZE 0.9013
36 1XA 0.9012
37 AY4 0.9011
38 2LX 0.8979
39 5VJ 0.8977
40 M3E 0.8973
41 TQU 0.8967
42 RUY 0.8962
43 JUO 0.8958
44 MUR 0.8952
45 89J 0.8946
46 AIN 0.8942
47 9X5 0.8940
48 X11 0.8937
49 GV9 0.8933
50 ZME 0.8923
51 BCK 0.8920
52 AX3 0.8917
53 90J 0.8916
54 ALN 0.8906
55 M02 0.8898
56 512 0.8887
57 96R 0.8886
58 XZ8 0.8879
59 SQ7 0.8879
60 0GY 0.8876
61 5OF 0.8871
62 AVO 0.8870
63 5E4 0.8868
64 SQ4 0.8854
65 XDK 0.8850
66 TLF 0.8845
67 CH9 0.8842
68 2GD 0.8841
69 MXD 0.8838
70 A3K 0.8829
71 6J3 0.8828
72 SLC 0.8818
73 SYR 0.8816
74 NQM 0.8814
75 ID8 0.8812
76 E35 0.8811
77 1WC 0.8810
78 DIF 0.8810
79 M5H 0.8807
80 ONR 0.8796
81 7ZL 0.8795
82 XQI 0.8791
83 HLD 0.8788
84 DNC 0.8788
85 X0W 0.8783
86 AKD 0.8782
87 9F8 0.8781
88 0GZ 0.8772
89 BY5 0.8772
90 5VL 0.8771
91 ABJ 0.8770
92 WUB 0.8769
93 8NX 0.8768
94 7ME 0.8768
95 4ME 0.8763
96 SLY 0.8762
97 2D3 0.8760
98 ELH 0.8756
99 KFN 0.8756
100 T6Z 0.8753
101 2KU 0.8752
102 43U 0.8752
103 WOE 0.8748
104 OKM 0.8746
105 6DP 0.8745
106 KYA 0.8741
107 H70 0.8741
108 QMS 0.8740
109 9UG 0.8740
110 54X 0.8740
111 CKU 0.8739
112 256 0.8732
113 LJ3 0.8731
114 4OG 0.8729
115 MPK 0.8726
116 FA6 0.8725
117 A3Q 0.8724
118 2C0 0.8724
119 TRP 0.8719
120 O2Y 0.8712
121 CR1 0.8712
122 55D 0.8712
123 PRZ 0.8708
124 ORO 0.8703
125 LL1 0.8696
126 K2P 0.8695
127 V6F 0.8692
128 P9I 0.8690
129 M3Q 0.8690
130 F12 0.8679
131 4NO 0.8679
132 XQK 0.8668
133 87L 0.8667
134 EGR 0.8665
135 D1X 0.8665
136 IPT 0.8661
137 X6P 0.8661
138 3CR 0.8658
139 7FF 0.8657
140 36Z 0.8656
141 3Y7 0.8656
142 AED 0.8653
143 78P 0.8652
144 DHK 0.8649
145 DOR 0.8643
146 KF5 0.8630
147 KW8 0.8627
148 HQJ 0.8627
149 AYS 0.8613
150 HNL 0.8612
151 VXX 0.8607
152 WVV 0.8604
153 DI6 0.8602
154 JMS 0.8601
155 5P3 0.8600
156 S7B 0.8599
157 KED 0.8596
158 CFA 0.8595
159 NPA 0.8585
160 K80 0.8585
161 HNQ 0.8581
162 ZYV 0.8581
163 YTX 0.8579
164 4A1 0.8573
165 3YQ 0.8568
166 OX2 0.8567
167 K3Q 0.8562
168 H05 0.8561
169 67Y 0.8555
170 AUV 0.8553
171 VM1 0.8524
172 KDM 0.8522
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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