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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 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 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 (17)
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 5Z9P - AX7 C7 H7 N3 c1ccc2c(c1....
13 5D7C ic50 = 0.14 uM 57W C20 H18 N6 O CCNC(=O)Nc....
14 5CPH - EVO C14 H10 N2 O c1ccc2c(c1....
15 4P8O - 883 C19 H16 F N7 O CCNC(=O)Nc....
16 4B6C ic50 = 0.69 uM B5U C27 H34 N6 O2 Cc1ccc(cc1....
17 4BAE ic50 = 3 nM RWX C19 H21 Br Cl N7 O4 S Cc1c(c(c([....
50% Homology Family (50)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4URL ic50 = 500 nM XAM C44 H60 Cl2 N4 O14 Cc1c(c(c([....
2 5CTW - 55D C9 H12 N2 O2 S CCCC(=O)Nc....
3 5CTU - 54X C10 H6 N2 O S2 c1cc(sc1)c....
4 3U2D - 08B C16 H18 Br N5 O3 Cc1c(cc([n....
5 5CTX ic50 = 1.32 uM 55G C20 H13 N5 O S c1ccc(cc1)....
6 3TTZ ic50 = 0.004 uM 07N C15 H15 Cl2 F N4 O3 S Cc1c(c(c([....
7 5D6Q ic50 = 5.8 uM 57V C17 H17 N5 O S CCNC(=O)Nc....
8 3U2K - 087 C17 H18 Cl3 N5 O2 Cc1c(c(c([....
9 5D6P ic50 = 2.5 uM 57U C11 H14 N4 O2 S CCNC(=O)Nc....
10 5Z9P - AX7 C7 H7 N3 c1ccc2c(c1....
11 5D7C ic50 = 0.14 uM 57W C20 H18 N6 O CCNC(=O)Nc....
12 5CPH - EVO C14 H10 N2 O c1ccc2c(c1....
13 4WUB - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
14 4PRX - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
15 4XTJ - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
16 1EI1 - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
17 4PU9 - ADP BEF n/a n/a
18 4WUC - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
19 4PRV - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
20 4WUD - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
21 4ZVI Kd = 0.47 uM 4S4 C14 H11 Br2 N3 O4 c1cc(ccc1C....
22 1S16 - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
23 4URN - NOV C31 H36 N2 O11 Cc1c(ccc2c....
24 4HY1 Ki = 2 nM 19X C20 H19 Cl N6 O S CCc1c(c2c(....
25 4HYM Ki = 6 nM CJC C19 H19 Cl N8 O S CCc1c(c2c(....
26 4HXW Ki = 2 nM 1A0 C19 H19 Cl N8 S CCc1c(c2c(....
27 4GFN Ki = 5 nM SUY C17 H18 Cl N7 S CCc1c(c2c(....
28 4P8O - 883 C19 H16 F N7 O CCNC(=O)Nc....
29 1KIJ - NOV C31 H36 N2 O11 Cc1c(ccc2c....
30 4B6C ic50 = 0.69 uM B5U C27 H34 N6 O2 Cc1ccc(cc1....
31 4EMV ic50 = 0.005 uM 0R9 C20 H15 F3 N6 O3 CCNC(=O)c1....
32 4MB9 - 28F C18 H20 N6 O3 S CCNC(=O)Nc....
33 4MBC - 28G C21 H24 N6 O3 S C=CCNC(=O)....
34 4LPB ic50 < 10 nM 1YP C19 H14 F3 N7 O3 S CCNC(=O)Nc....
35 4MOT - 2B7 C20 H23 N5 O2 S CC(C)CCN1c....
36 4EM7 ic50 = 7.7 uM 0RA C16 H14 N2 O2 c1cc(cc(c1....
37 5Z9Q - HX4 C9 H9 N3 c1ccc(cc1)....
38 5Z4H - AX7 C7 H7 N3 c1ccc2c(c1....
39 5Z9L - 8H8 C7 H4 F N O c1cc(c(cc1....
40 5Z9E - AX7 C7 H7 N3 c1ccc2c(c1....
41 1KZN Kd = 1.2 nM CBN C35 H37 Cl N2 O11 Cc1ccc([nH....
42 1AJ6 Kd = 1.2 uM NOV C31 H36 N2 O11 Cc1c(ccc2c....
43 5Z9B - AX7 C7 H7 N3 c1ccc2c(c1....
44 5MMO - 9JG C22 H21 N5 O3 CCNC(=O)Nc....
45 5Z4O - HX8 C12 H10 O2 c1ccc(cc1)....
46 5MMP ic50 = 0.03 uM G3Z C22 H20 N6 O CCNC(=O)Nc....
47 4DUH Kd = 6.6 uM RLI C17 H16 N4 O3 S2 CCC(=O)Nc1....
48 5MMN ic50 = 0.125 uM O54 C19 H20 N4 O CCNC(=O)Nc....
49 5Z9F - AX7 C7 H7 N3 c1ccc2c(c1....
50 4BAE ic50 = 3 nM RWX C19 H21 Br Cl N7 O4 S Cc1c(c(c([....
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 with APoc: 84
This union binding pocket(no: 1) in the query (biounit: 4b6c.bio2) has 21 residues
No: Leader PDB Ligand Sequence Similarity
1 3KO0 TFP None
2 5NNT DPV None
3 2VWA PTY None
4 1G27 BB1 None
5 5UC4 83S 1.02041
6 5F5R ANP 2.04082
7 5Y3N 8MF 2.04082
8 3AQT RCO 2.04082
9 5DQW ADP 2.04082
10 3EHH ADP 2.55102
11 1LT3 GAL BGC 2.55102
12 1ZPD CIT 2.55102
13 6BR8 PGV 2.55102
14 1LTI GAL 2.60417
15 1LTT GAL BGC 2.7027
16 1Q3A NGH 3.0303
17 5XJD 87L 3.06122
18 4M3P HCS 3.06122
19 5U97 PIT 3.06122
20 3C88 ARG ARG GLY CYS NH2 3.06122
21 4EOX 0S5 3.06122
22 3G5N PB2 3.06122
23 3K60 ADP 3.57143
24 2C2A ADP 3.57143
25 5LX9 OLB 3.57143
26 4GCZ ADP 3.57143
27 1ZED PNP 3.57143
28 3UA1 08Y 3.57143
29 1C9K 5GP 3.88889
30 3O01 DXC 4.08163
31 1BGQ RDC 4.08163
32 1R6N 434 4.08163
33 3KC1 2T6 4.45104
34 2GBB CIT 4.48718
35 4WGF HX2 4.59184
36 3KP6 SAL 4.63576
37 1I58 ADP 4.7619
38 1I58 ACP 4.7619
39 1GKZ ADP 5.10204
40 2GWH PCI 5.10204
41 3UWB BB2 5.19481
42 4DR9 BB2 5.20833
43 3EHG ATP 5.46875
44 2OWZ CIT 5.61225
45 4MNS 2AX 5.66038
46 5UGW GSH 5.71429
47 1XMY ROL 5.77889
48 1TID ATP 5.88235
49 1LQY BB2 6.52174
50 3G5K BB2 6.55738
51 3N29 NSD 6.63265
52 3F8C HT1 7.14286
53 1GJW GLC 7.14286
54 1TH8 ADP 7.58621
55 4B7P 9UN 7.65306
56 2YI0 YI0 7.65306
57 1YC4 43P 7.65306
58 3CV2 COA 7.65306
59 5IDM ANP 7.82123
60 5JF2 SF7 9.69388
61 2GFD RDA 10.2041
62 6D28 NEC 10.2041
63 2O1V ADP 10.2041
64 5MTE BB2 10.219
65 4XCL AGS 10.7143
66 5MZI FYK 10.7143
67 1Q1Y BB2 10.9948
68 3H4L ANP 11.7347
69 4RJD TFP 12.1212
70 1ID0 ANP 12.5
71 5C9J DAO 12.7551
72 5OF9 ANP 12.7551
73 1KUK PCA LYS TRP 12.7551
74 3D36 ADP 13.2653
75 5J6A P46 14.2857
76 4BIX ADP 14.2857
77 3FS1 ALA ALA LEU ALA ALA LEU LEU ALA ALA 14.7959
78 1B63 ANP 14.7959
79 2ZKJ ADP 14.7959
80 2XCM ADP 14.8649
81 1Y8O ADP 17.1875
82 1FBL HTA 18.8776
83 2Q8G AZX 20.4082
84 2IOR ADP 25.5102
Pocket No.: 2; Query (leader) PDB : 4B6C; Ligand: B5U; Similar sites found with APoc: 42
This union binding pocket(no: 2) in the query (biounit: 4b6c.bio1) has 19 residues
No: Leader PDB Ligand Sequence Similarity
1 4WG0 CHD None
2 3RV5 DXC None
3 2BYC FMN None
4 2HI4 BHF 2.04082
5 3Q2H QHF 2.55102
6 4P6X HCY 2.55102
7 2QEH SRO 2.75862
8 5EY0 GTP 3.06122
9 5AOG IAC 3.57143
10 3O5N BR0 3.57143
11 3CH6 311 3.57143
12 3CH6 NAP 3.57143
13 4QWT ACD 3.57143
14 4URG C2E 3.59281
15 5I8F ML1 3.63636
16 4IVG ANP 4.59184
17 4IPE ANP 4.59184
18 2FLI DX5 4.59184
19 5IM3 DTP 6.12245
20 5UC1 486 6.12245
21 3PE2 E1B 7.14286
22 5B4B LP5 7.14286
23 2QZT PLM 7.20721
24 4R3U 5AD 7.65306
25 3PMD 11A 7.84314
26 3LGS SAH 8.16327
27 4BKS X6C 8.65385
28 1JQ3 AAT 8.67347
29 2OBF F83 9.18367
30 2OBF SAH 9.18367
31 1NHZ 486 9.69388
32 5M67 ADE 9.69388
33 5M67 NAD 9.69388
34 2OKL BB2 10.2703
35 4OIV XX9 10.7143
36 5J32 IPM 11.7347
37 5X7Q GLC GLC 12.2449
38 5C9J STE 12.7551
39 4GKV NAD 13.2653
40 5DQY BEZ 17.1429
41 5URY PAM 19.863
42 4POJ 2VP 38.4615
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