Receptor
PDB id Resolution Class Description Source Keywords
4B6C 2.2 Å EC: 5.99.1.3 STRUCTURE OF THE M. SMEGMATIS GYRB ATPASE DOMAIN IN COMPLEX WITH AN AMINOPYRAZINAMIDE MYCOBACTERIUM SMEGMATIS ISOMERASE DNA TOPOISOMERASE INHIBITOR
Ref.: AMINOPYRAZINAMIDES: NOVEL AND SPECIFIC GYRB INHIBIT KILL REPLICATING AND NONREPLICATING MYCOBACTERIUM TUBERCULOSIS. ACS CHEM.BIOL. V. 8 519 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
B5U B:1256;
A:1256;
Valid;
Valid;
none;
none;
ic50 = 0.69 uM
474.598 C27 H34 N6 O2 Cc1cc...
NA A:1257;
B:1257;
Part of Protein;
Part of Protein;
none;
none;
submit data
22.99 Na [Na+]
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4B6C 2.2 Å EC: 5.99.1.3 STRUCTURE OF THE M. SMEGMATIS GYRB ATPASE DOMAIN IN COMPLEX WITH AN AMINOPYRAZINAMIDE MYCOBACTERIUM SMEGMATIS ISOMERASE DNA TOPOISOMERASE INHIBITOR
Ref.: AMINOPYRAZINAMIDES: NOVEL AND SPECIFIC GYRB INHIBIT KILL REPLICATING AND NONREPLICATING MYCOBACTERIUM TUBERCULOSIS. ACS CHEM.BIOL. V. 8 519 2013
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 14 families.
1 4B6C ic50 = 0.69 uM B5U C27 H34 N6 O2 Cc1ccc(cc1....
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: B5U; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 B5U 1 1
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4B6C; Ligand: B5U; Similar sites found: 38
This union binding pocket(no: 1) in the query (biounit: 4b6c.bio2) has 21 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2VWA PTY 0.03061 0.40209 None
2 1G27 BB1 0.006456 0.40167 None
3 5F5R ANP 0.0001396 0.50803 2.04082
4 5Y3N 8MF 0.001497 0.4517 2.04082
5 3NMQ 7PP 0.001047 0.44897 3.06122
6 3SVJ 4LI 0.007135 0.40344 3.06122
7 2C2A ADP 0.0001831 0.46159 3.57143
8 4GCZ ADP 0.0005683 0.4408 3.57143
9 3K60 ADP 0.0005748 0.40538 3.57143
10 1BGQ RDC 0.0004733 0.4639 4.08163
11 1I58 ADP 0.000019 0.4859 4.7619
12 1I58 ACP 0.0002007 0.47087 4.7619
13 1GKZ ADP 0.001678 0.42683 5.10204
14 3EHG ATP 0.007975 0.41241 5.46875
15 4MNS 2AX 0.01814 0.41267 5.66038
16 5UGW GSH 0.0006126 0.49563 5.71429
17 1TID ATP 0.00177 0.42044 5.88235
18 1LQY BB2 0.006988 0.40363 6.52174
19 3G5K BB2 0.00794 0.40852 6.55738
20 3N29 NSD 0.01057 0.42581 6.63265
21 1TH8 ADP 0.0005954 0.41503 7.58621
22 4B7P 9UN 0.000228 0.50113 7.65306
23 1YC4 43P 0.00009877 0.45186 7.65306
24 3CV2 COA 0.01382 0.41664 7.65306
25 5IDM ANP 0.001961 0.41867 7.82123
26 5JF2 SF7 0.006989 0.40018 9.69388
27 1QY8 RDI 0.0001549 0.48151 10.2041
28 2GFD RDA 0.000275 0.46895 10.2041
29 2O1V ADP 0.0001287 0.44088 10.2041
30 4XCL AGS 0.0002336 0.45518 10.7143
31 3H4L ANP 0.0001457 0.47692 11.7347
32 1ID0 ANP 0.0005531 0.42629 12.5
33 3D36 ADP 0.004527 0.4083 13.2653
34 2ZKJ ADP 0.001769 0.45279 14.7959
35 1B63 ANP 0.001158 0.41323 14.7959
36 2XCM ADP 0.001506 0.44173 14.8649
37 1Y8O ADP 0.0008846 0.40594 17.1875
38 2IOR ADP 0.0001966 0.50762 25.5102
Pocket No.: 2; Query (leader) PDB : 4B6C; Ligand: B5U; Similar sites found: 22
This union binding pocket(no: 2) in the query (biounit: 4b6c.bio1) has 19 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4WG0 CHD 0.005277 0.43814 None
2 2BYC FMN 0.007938 0.40852 None
3 2HI4 BHF 0.002166 0.41921 2.04082
4 4P6X HCY 0.009978 0.40211 2.55102
5 5AOG IAC 0.02617 0.42278 3.57143
6 3CH6 311 0.0469 0.40683 3.57143
7 3CH6 NAP 0.0469 0.40683 3.57143
8 4QWT ACD 0.0138 0.40358 3.57143
9 4IVG ANP 0.008641 0.41 4.59184
10 2FLI DX5 0.012 0.4002 4.59184
11 3PE2 E1B 0.01748 0.41725 7.14286
12 5B4B LP5 0.01287 0.40907 7.14286
13 2QZT PLM 0.01622 0.40303 7.20721
14 3LGS SAH 0.01034 0.40317 8.16327
15 2OBF F83 0.03379 0.40134 9.18367
16 1NHZ 486 0.01147 0.40274 9.69388
17 5M67 ADE 0.0462 0.40001 9.69388
18 2OKL BB2 0.006449 0.40686 10.2703
19 1Q1Y BB2 0.005041 0.40394 10.9948
20 4GKV NAD 0.02491 0.40117 13.2653
21 5DQY BEZ 0.009218 0.42255 17.1429
22 4POJ 2VP 0.008816 0.4096 38.4615
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