Receptor
PDB id Resolution Class Description Source Keywords
5R8H 1.5 Å NON-ENZYME: OTHER PANDDA ANALYSIS GROUP DEPOSITION INTERLEUKIN-1 BETA -- FRAGM Z111716368 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...
T91 A:203;
 Valid;
 Atoms found LESS than expected: % Diff = 0.389;
 submit data
245.32 C14 H19 N3 O CC(C)...
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: T91; Similar ligands found: 4
No: Ligand ECFP6 Tc MDL keys Tc
1 T91 1 1
2 B95 0.527778 0.603175
3 AWN 0.434211 0.6
4 B5E 0.402299 0.614035
Similar Ligands (3D)
Ligand no: 1; Ligand: T91; Similar ligands found: 0
No: Ligand Similarity coefficient
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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