Receptor
PDB id Resolution Class Description Source Keywords
4P8O 2.4 Å EC: 5.99.1.3 S. AUREUS GYRASE BOUND TO AN AMINOBENZIMIDAZOLE UREA INHIBIT STAPHYLOCOCCUS AUREUS ANTIBACTERIAL GRAM-POSITIVE GYRASE TOPOISOMERASE STAPHYLAUREUS ISOMERASE
Ref.: SECOND-GENERATION ANTIBACTERIAL BENZIMIDAZOLE UREAS DISCOVERY OF A PRECLINICAL CANDIDATE WITH REDUCED M LIABILITY. J.MED.CHEM. V. 57 8792 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
883 A:301;
B:301;
Valid;
Valid;
none;
none;
submit data
377.375 C19 H16 F N7 O CCNC(...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4P8O 2.4 Å EC: 5.99.1.3 S. AUREUS GYRASE BOUND TO AN AMINOBENZIMIDAZOLE UREA INHIBIT STAPHYLOCOCCUS AUREUS ANTIBACTERIAL GRAM-POSITIVE GYRASE TOPOISOMERASE STAPHYLAUREUS ISOMERASE
Ref.: SECOND-GENERATION ANTIBACTERIAL BENZIMIDAZOLE UREAS DISCOVERY OF A PRECLINICAL CANDIDATE WITH REDUCED M LIABILITY. J.MED.CHEM. V. 57 8792 2014
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 14 families.
1 4P8O - 883 C19 H16 F N7 O CCNC(=O)Nc....
70% Homology Family (15)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 11 families.
1 5D7D - 57X C17 H15 N5 O S CCCN1c2c(c....
2 5CTY ic50 = 0.265 uM 55H C14 H9 N5 O S c1cc(cnc1)....
3 5D7R ic50 = 0.013 uM 57Y C19 H16 N4 O4 S CCCc1c(ccc....
4 5CTW - 55D C9 H12 N2 O2 S CCCC(=O)Nc....
5 5CTU - 54X C10 H6 N2 O S2 c1cc(sc1)c....
6 3U2D - 08B C16 H18 Br N5 O3 Cc1c(cc([n....
7 5CTX ic50 = 1.32 uM 55G C20 H13 N5 O S c1ccc(cc1)....
8 3TTZ ic50 = 0.004 uM 07N C15 H15 Cl2 F N4 O3 S Cc1c(c(c([....
9 5D6Q ic50 = 5.8 uM 57V C17 H17 N5 O S CCNC(=O)Nc....
10 3U2K - 087 C17 H18 Cl3 N5 O2 Cc1c(c(c([....
11 5D6P ic50 = 2.5 uM 57U C11 H14 N4 O2 S CCNC(=O)Nc....
12 5D7C ic50 = 0.14 uM 57W C20 H18 N6 O CCNC(=O)Nc....
13 5CPH - EVO C14 H10 N2 O c1ccc2c(c1....
14 4P8O - 883 C19 H16 F N7 O CCNC(=O)Nc....
15 4B6C ic50 = 0.69 uM B5U C27 H34 N6 O2 Cc1ccc(cc1....
50% Homology Family (15)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 5D7D - 57X C17 H15 N5 O S CCCN1c2c(c....
2 5CTY ic50 = 0.265 uM 55H C14 H9 N5 O S c1cc(cnc1)....
3 5D7R ic50 = 0.013 uM 57Y C19 H16 N4 O4 S CCCc1c(ccc....
4 3U2D - 08B C16 H18 Br N5 O3 Cc1c(cc([n....
5 4GEE Ki < 1 nM 0WT C17 H18 Cl N7 O CCc1c(c2c(....
6 4GGL Ki < 1 nM CJC C19 H19 Cl N8 O S CCc1c(c2c(....
7 4HXW Ki = 2 nM 1A0 C19 H19 Cl N8 S CCc1c(c2c(....
8 4GFN Ki = 5 nM SUY C17 H18 Cl N7 S CCc1c(c2c(....
9 4HZ0 - 1AV C13 H9 N7 S c1cc(cnc1)....
10 4P8O - 883 C19 H16 F N7 O CCNC(=O)Nc....
11 5MMO - 9JG C22 H21 N5 O3 CCNC(=O)Nc....
12 1S14 - NOV C31 H36 N2 O11 Cc1c(ccc2c....
13 4B6C ic50 = 0.69 uM B5U C27 H34 N6 O2 Cc1ccc(cc1....
14 4MBC - 28G C21 H24 N6 O3 S C=CCNC(=O)....
15 4LPB ic50 < 10 nM 1YP C19 H14 F3 N7 O3 S CCNC(=O)Nc....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 883; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 883 1 1
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4P8O; Ligand: 883; Similar sites found: 48
This union binding pocket(no: 1) in the query (biounit: 4p8o.bio2) has 15 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4WN5 MVC 0.02354 0.40266 None
2 5Y3N 8MF 0.002135 0.42614 3.20856
3 1QKQ MAN 0.0001252 0.5078 3.52113
4 2IOR ADP 0.0008277 0.46064 3.74332
5 5XDT ZI7 0.01394 0.4201 3.74332
6 3A0T ADP 0.004168 0.43508 3.94737
7 5WSY 7UC 0.01027 0.4025 4.04624
8 3E85 BSU 0.04938 0.40329 4.43038
9 1QY8 RDI 0.0001002 0.51006 4.81283
10 2O1V ADP 0.0004369 0.47074 4.81283
11 4BIX ADP 0.003023 0.42312 4.81283
12 2GFD RDA 0.00008782 0.41356 4.81283
13 3PE2 E1B 0.04173 0.41155 4.81283
14 4BUY F37 0.03435 0.40235 5
15 5F5R ANP 0.00265 0.43051 5.34759
16 1OVD FMN 0.04884 0.4017 5.34759
17 1OVD ORO 0.04884 0.4017 5.34759
18 4B7P 9UN 0.000021 0.59032 5.88235
19 3NMQ 7PP 0.00217 0.44248 5.88235
20 3K60 ADP 0.001156 0.44021 5.88235
21 4GID 0GH 0.04466 0.43408 5.88235
22 4ZL4 4PK 0.02238 0.4095 5.88235
23 5DQ8 FLF 0.03073 0.40608 5.88235
24 3E3U NVC 0.01481 0.40187 5.88235
25 3L9R L9R 0.03264 0.41111 6.12245
26 1YC4 43P 0.00003382 0.49651 6.41711
27 2PNC CLU 0.009584 0.41604 6.41711
28 4COL DTP 0.01313 0.4065 6.41711
29 4XCL AGS 0.000084 0.43215 6.95187
30 4FFG 0U8 0.01112 0.4097 7.48663
31 4WOE ADP 0.01474 0.40139 7.48663
32 3ND6 ATP 0.04398 0.4001 7.60234
33 5MW4 5JU 0.03045 0.41071 8.02139
34 1MJT ITU 0.01155 0.40322 8.02139
35 5IDM ANP 0.0001112 0.51045 8.93855
36 4I5I NAD 0.02107 0.41217 11.7647
37 1GKZ ADP 0.0001862 0.50184 12.2995
38 1ZNY GDP 0.005699 0.40814 12.2995
39 3H4L ANP 0.0001945 0.41491 13.369
40 3D36 ADP 0.001971 0.45118 13.9037
41 5EYP GDP 0.03222 0.40258 14.2012
42 4XIZ LPP 0.03139 0.40787 15.7143
43 1ID0 ANP 0.0006684 0.43995 15.7895
44 4L2I FAD 0.01936 0.42218 17.1123
45 4L2I NAD 0.0276 0.42218 17.1123
46 2ZKJ ADP 0.00006426 0.55676 19.2513
47 2XCM ADP 0.0001057 0.50619 20.6522
48 1I58 ADP 0.0001775 0.45149 21.3904
Pocket No.: 2; Query (leader) PDB : 4P8O; Ligand: 883; Similar sites found: 9
This union binding pocket(no: 2) in the query (biounit: 4p8o.bio1) has 15 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1FKB RAP 0.0368 0.40196 None
2 1IZE IVA VAL VAL STA ALA STA 0.009219 0.42486 2.13904
3 2GBB CIT 0.01372 0.40097 5.12821
4 3EFV NAD 0.03066 0.40494 7.14286
5 1KGI T4A 0.01278 0.41766 9.44882
6 1WKR IVA VAL VAL STA ALA STA 0.005666 0.4339 9.62567
7 5JFL NAD 0.03712 0.40059 12.2995
8 1VLH PNS 0.02005 0.40119 13.2948
9 1BXO PP7 0.008695 0.43831 13.369
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