Receptor
PDB id Resolution Class Description Source Keywords
4M3B 2 Å NON-ENZYME: TRANSCRIPT_TRANSLATE RAPID AND EFFICIENT DESIGN OF NEW INHIBITORS OF MYCOBACTERIU TUBERCULOSIS TRANSCRIPTIONAL REPRESSOR ETHR USING FRAGMENT M ERGING AND LINKING APPROACHES MYCOBACTERIUM TUBERCULOSIS HELIX-TURN-HELIX DNA BINDING PROTEIN TETR-FAMILY TRANSCRIPREGULATORY REPRESSOR INHIBITOR TRANSCRIPTION REPRESSOR-INCOMPLEX
Ref.: LIGAND EFFICIENCY DRIVEN DESIGN OF NEW INHIBITORS O MYCOBACTERIUM TUBERCULOSIS TRANSCRIPTIONAL REPRESSO USING FRAGMENT GROWING, MERGING, AND LINKING APPROA J.MED.CHEM. V. 57 4876 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
2B2 A:301;
Valid;
none;
ic50 = 0.4 uM
314.326 C14 H13 F3 N2 O S Cc1nc...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4M3B 2 Å NON-ENZYME: TRANSCRIPT_TRANSLATE RAPID AND EFFICIENT DESIGN OF NEW INHIBITORS OF MYCOBACTERIU TUBERCULOSIS TRANSCRIPTIONAL REPRESSOR ETHR USING FRAGMENT M ERGING AND LINKING APPROACHES MYCOBACTERIUM TUBERCULOSIS HELIX-TURN-HELIX DNA BINDING PROTEIN TETR-FAMILY TRANSCRIPREGULATORY REPRESSOR INHIBITOR TRANSCRIPTION REPRESSOR-INCOMPLEX
Ref.: LIGAND EFFICIENCY DRIVEN DESIGN OF NEW INHIBITORS O MYCOBACTERIUM TUBERCULOSIS TRANSCRIPTIONAL REPRESSO USING FRAGMENT GROWING, MERGING, AND LINKING APPROA J.MED.CHEM. V. 57 4876 2014
Members (66)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 308 families.
1 5J1U - P93 C10 H14 N2 O2 c1cocc1CNC....
2 5MYT - ZQC C16 H13 N3 O S2 CSc1ccc(cc....
3 3SFI ic50 = 0.4 uM 3SF C15 H17 F3 N4 O2 S c1csc(n1)c....
4 3Q0W - LL5 C16 H22 N4 O2 S CC(C)[C@@H....
5 6HO0 - GFK C19 H19 F3 N4 O3 S COc1ccc2c(....
6 4M3E ic50 = 0.56 uM 2B3 C17 H20 F3 N3 O3 S2 CCCS(=O)(=....
7 1U9N - CNS C24 H48 O2 CCCCCCCCCC....
8 5MYS ic50 = 50 uM YP6 C16 H12 F N3 O2 S c1ccnc(c1)....
9 6HOF - GJ8 C20 H18 F3 N3 O3 S2 c1ccc(cc1)....
10 5F08 Kd = 3 uM 5TG C25 H39 N3 O3 CC(C)(C)OC....
11 5MYL ic50 = 9.9 uM Q2N C16 H12 F N3 O S c1ccnc(c1)....
12 6HOA - GGN C21 H20 F3 N3 O S CCCc1cc(cc....
13 3O8G ic50 = 7.4 uM O8G C13 H14 N6 O2 S c1cc(sc1)c....
14 5F0C - 5TE C19 H28 N2 O c1cc(cc(c1....
15 6HO8 - GG8 C9 H10 F3 N O2 S c1ccc(cc1)....
16 5IOY Kd = 6 uM 6C5 C11 H20 N2 O C1CCC(C1)C....
17 5F1J Kd = 12 uM 5TO C12 H21 N O C1CCC(C1)C....
18 5F27 - 5TT C13 H20 N2 CNCc1ccc(c....
19 5MYR ic50 = 22 uM UDY C15 H9 F N4 S2 c1ccnc(c1)....
20 6HO5 - GH8 C30 H32 N2 O3 CC(C)N1CCC....
21 5MYM ic50 = 3.9 uM HYV C24 H29 N5 O S c1ccc(cc1)....
22 5NJ0 - 8YW C16 H14 N2 O6 c1cc(ccc1[....
23 5NIZ - 8YT C17 H24 N2 O3 C[C@@H]1C[....
24 5J3L Kd = 16 uM 6FR C11 H21 N O2 S C1CCC(C1)C....
25 6HO2 - GHN C16 H17 F3 N2 O4 S2 CCOC(=O)Cc....
26 4M3G ic50 = 0.55 uM 2G1 C13 H13 F3 N2 O2 S2 Cc1nc(cs1)....
27 6R1P - JPH C17 H17 N5 O3 CC1=CC(=O)....
28 6HOC - GJE C10 H9 F3 N4 O c1cc(ccc1C....
29 3O8H ic50 = 580 nM O8H C22 H22 I N7 O4 S2 c1cc(sc1)c....
30 5MXK ic50 = 150 uM ZHA C12 H13 N O2 CC(=O)Nc1c....
31 5IOZ Kd = 11 uM 6C4 C12 H21 N O C1CCC(C1)C....
32 6HOB - GJ5 C17 H19 F3 N2 O S CC(C)Cc1nc....
33 6HNX - GFZ C29 H30 N2 O3 CC(C)N1CCC....
34 6HO7 - GHQ C10 H10 F3 N O c1ccc(cc1)....
35 5EZH Kd = 24 uM 841 C16 H24 N4 O c1ccnc(c1)....
36 5MWO ic50 = 0.19 mM J6W C10 H10 O S Cc1ccc2c(c....
37 5EYR Kd = 5 uM 5T0 C20 H31 N3 O CNCc1ccc(c....
38 6HO4 - GFQ C19 H23 F3 N2 O S CC(C)CCCc1....
39 3G1O ic50 = 38 uM RF1 C16 H21 N3 O3 S CC(C)(C)OC....
40 5NIO - 8YH C11 H22 N2 O CCCCNC(=O)....
41 6HO1 - GFW C18 H24 N2 O4 S2 CCOC(=O)Cc....
42 5F0H ic50 = 33 uM 5TC C27 H34 N4 O c1cc(ccc1C....
43 4M3D ic50 = 3.9 uM 2H2 C19 H17 F3 N2 O3 S c1ccc(cc1)....
44 5J1R Kd = 22 uM 6FG C11 H15 N O2 c1cocc1CCC....
45 6HOE - GH2 C17 H17 F3 N2 O3 S CCOC(=O)Cc....
46 3SDG ic50 = 2.8 uM 3SE C14 H15 F3 N4 O2 S c1csc(n1)c....
47 6HOD - GHK C15 H14 N2 O4 S2 c1ccc(cc1)....
48 6HNZ - GH5 C17 H18 F3 N3 O2 c1ccc(cc1)....
49 6HO9 - GHB C16 H19 F3 N4 O CC(C)Cc1cn....
50 4DW6 - 0MN C22 H18 N2 O3 S COc1cccc(c....
51 3G1L - RF2 C14 H10 F N3 c1ccc(cc1)....
52 5IP6 - 6C9 C10 H18 N2 O2 C1CCN(C1)C....
53 5MXV ic50 = 12 uM K3T C12 H8 Cl F N2 O S2 c1cc2c(cc1....
54 5IPA Kd = 20 uM 6C8 C11 H13 N O2 c1cocc1/C=....
55 5NIM - 8YE C14 H16 N4 O3 CCCc1cc(no....
56 6HO6 - GGK C13 H15 F3 N2 O4 S2 CS(=O)(=O)....
57 5F0F Kd = 1 uM 5TD C19 H25 N3 O c1cc(ccc1C....
58 5MYW - WCU C13 H12 N2 O2 c1ccc(c(c1....
59 5MYN ic50 = 30 uM ZUF C13 H9 Cl N4 S c1ccnc(c1)....
60 6HO3 - GJ2 C18 H17 F3 N2 O4 S2 c1ccc(cc1)....
61 4M3F ic50 = 4.9 uM 2D1 C15 H20 N2 O2 S2 Cc1nc(cs1)....
62 5EZG Kd = 12 uM 5T4 C15 H23 N5 O c1cnc(nc1)....
63 4M3B ic50 = 0.4 uM 2B2 C14 H13 F3 N2 O S Cc1nc(cs1)....
64 3G1M ic50 = 0.522 uM RF3 C17 H17 N3 O2 S2 c1cc(sc1)C....
65 3TP0 - FO5 C14 H14 N4 O2 S c1cc(sc1)c....
66 6R1S - JPK C21 H24 N4 O3 Cc1cccc(c1....
70% Homology Family (66)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 266 families.
1 5J1U - P93 C10 H14 N2 O2 c1cocc1CNC....
2 5MYT - ZQC C16 H13 N3 O S2 CSc1ccc(cc....
3 3SFI ic50 = 0.4 uM 3SF C15 H17 F3 N4 O2 S c1csc(n1)c....
4 3Q0W - LL5 C16 H22 N4 O2 S CC(C)[C@@H....
5 6HO0 - GFK C19 H19 F3 N4 O3 S COc1ccc2c(....
6 4M3E ic50 = 0.56 uM 2B3 C17 H20 F3 N3 O3 S2 CCCS(=O)(=....
7 1U9N - CNS C24 H48 O2 CCCCCCCCCC....
8 5MYS ic50 = 50 uM YP6 C16 H12 F N3 O2 S c1ccnc(c1)....
9 6HOF - GJ8 C20 H18 F3 N3 O3 S2 c1ccc(cc1)....
10 5F08 Kd = 3 uM 5TG C25 H39 N3 O3 CC(C)(C)OC....
11 5MYL ic50 = 9.9 uM Q2N C16 H12 F N3 O S c1ccnc(c1)....
12 6HOA - GGN C21 H20 F3 N3 O S CCCc1cc(cc....
13 3O8G ic50 = 7.4 uM O8G C13 H14 N6 O2 S c1cc(sc1)c....
14 5F0C - 5TE C19 H28 N2 O c1cc(cc(c1....
15 6HO8 - GG8 C9 H10 F3 N O2 S c1ccc(cc1)....
16 5IOY Kd = 6 uM 6C5 C11 H20 N2 O C1CCC(C1)C....
17 5F1J Kd = 12 uM 5TO C12 H21 N O C1CCC(C1)C....
18 5F27 - 5TT C13 H20 N2 CNCc1ccc(c....
19 5MYR ic50 = 22 uM UDY C15 H9 F N4 S2 c1ccnc(c1)....
20 6HO5 - GH8 C30 H32 N2 O3 CC(C)N1CCC....
21 5MYM ic50 = 3.9 uM HYV C24 H29 N5 O S c1ccc(cc1)....
22 5NJ0 - 8YW C16 H14 N2 O6 c1cc(ccc1[....
23 5NIZ - 8YT C17 H24 N2 O3 C[C@@H]1C[....
24 5J3L Kd = 16 uM 6FR C11 H21 N O2 S C1CCC(C1)C....
25 6HO2 - GHN C16 H17 F3 N2 O4 S2 CCOC(=O)Cc....
26 4M3G ic50 = 0.55 uM 2G1 C13 H13 F3 N2 O2 S2 Cc1nc(cs1)....
27 6R1P - JPH C17 H17 N5 O3 CC1=CC(=O)....
28 6HOC - GJE C10 H9 F3 N4 O c1cc(ccc1C....
29 3O8H ic50 = 580 nM O8H C22 H22 I N7 O4 S2 c1cc(sc1)c....
30 5MXK ic50 = 150 uM ZHA C12 H13 N O2 CC(=O)Nc1c....
31 5IOZ Kd = 11 uM 6C4 C12 H21 N O C1CCC(C1)C....
32 6HOB - GJ5 C17 H19 F3 N2 O S CC(C)Cc1nc....
33 6HNX - GFZ C29 H30 N2 O3 CC(C)N1CCC....
34 6HO7 - GHQ C10 H10 F3 N O c1ccc(cc1)....
35 5EZH Kd = 24 uM 841 C16 H24 N4 O c1ccnc(c1)....
36 5MWO ic50 = 0.19 mM J6W C10 H10 O S Cc1ccc2c(c....
37 5EYR Kd = 5 uM 5T0 C20 H31 N3 O CNCc1ccc(c....
38 6HO4 - GFQ C19 H23 F3 N2 O S CC(C)CCCc1....
39 3G1O ic50 = 38 uM RF1 C16 H21 N3 O3 S CC(C)(C)OC....
40 5NIO - 8YH C11 H22 N2 O CCCCNC(=O)....
41 6HO1 - GFW C18 H24 N2 O4 S2 CCOC(=O)Cc....
42 5F0H ic50 = 33 uM 5TC C27 H34 N4 O c1cc(ccc1C....
43 4M3D ic50 = 3.9 uM 2H2 C19 H17 F3 N2 O3 S c1ccc(cc1)....
44 5J1R Kd = 22 uM 6FG C11 H15 N O2 c1cocc1CCC....
45 6HOE - GH2 C17 H17 F3 N2 O3 S CCOC(=O)Cc....
46 3SDG ic50 = 2.8 uM 3SE C14 H15 F3 N4 O2 S c1csc(n1)c....
47 6HOD - GHK C15 H14 N2 O4 S2 c1ccc(cc1)....
48 6HNZ - GH5 C17 H18 F3 N3 O2 c1ccc(cc1)....
49 6HO9 - GHB C16 H19 F3 N4 O CC(C)Cc1cn....
50 4DW6 - 0MN C22 H18 N2 O3 S COc1cccc(c....
51 3G1L - RF2 C14 H10 F N3 c1ccc(cc1)....
52 5IP6 - 6C9 C10 H18 N2 O2 C1CCN(C1)C....
53 5MXV ic50 = 12 uM K3T C12 H8 Cl F N2 O S2 c1cc2c(cc1....
54 5IPA Kd = 20 uM 6C8 C11 H13 N O2 c1cocc1/C=....
55 5NIM - 8YE C14 H16 N4 O3 CCCc1cc(no....
56 6HO6 - GGK C13 H15 F3 N2 O4 S2 CS(=O)(=O)....
57 5F0F Kd = 1 uM 5TD C19 H25 N3 O c1cc(ccc1C....
58 5MYW - WCU C13 H12 N2 O2 c1ccc(c(c1....
59 5MYN ic50 = 30 uM ZUF C13 H9 Cl N4 S c1ccnc(c1)....
60 6HO3 - GJ2 C18 H17 F3 N2 O4 S2 c1ccc(cc1)....
61 4M3F ic50 = 4.9 uM 2D1 C15 H20 N2 O2 S2 Cc1nc(cs1)....
62 5EZG Kd = 12 uM 5T4 C15 H23 N5 O c1cnc(nc1)....
63 4M3B ic50 = 0.4 uM 2B2 C14 H13 F3 N2 O S Cc1nc(cs1)....
64 3G1M ic50 = 0.522 uM RF3 C17 H17 N3 O2 S2 c1cc(sc1)C....
65 3TP0 - FO5 C14 H14 N4 O2 S c1cc(sc1)c....
66 6R1S - JPK C21 H24 N4 O3 Cc1cccc(c1....
50% Homology Family (66)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 220 families.
1 5J1U - P93 C10 H14 N2 O2 c1cocc1CNC....
2 5MYT - ZQC C16 H13 N3 O S2 CSc1ccc(cc....
3 3SFI ic50 = 0.4 uM 3SF C15 H17 F3 N4 O2 S c1csc(n1)c....
4 3Q0W - LL5 C16 H22 N4 O2 S CC(C)[C@@H....
5 6HO0 - GFK C19 H19 F3 N4 O3 S COc1ccc2c(....
6 4M3E ic50 = 0.56 uM 2B3 C17 H20 F3 N3 O3 S2 CCCS(=O)(=....
7 1U9N - CNS C24 H48 O2 CCCCCCCCCC....
8 5MYS ic50 = 50 uM YP6 C16 H12 F N3 O2 S c1ccnc(c1)....
9 6HOF - GJ8 C20 H18 F3 N3 O3 S2 c1ccc(cc1)....
10 5F08 Kd = 3 uM 5TG C25 H39 N3 O3 CC(C)(C)OC....
11 5MYL ic50 = 9.9 uM Q2N C16 H12 F N3 O S c1ccnc(c1)....
12 6HOA - GGN C21 H20 F3 N3 O S CCCc1cc(cc....
13 3O8G ic50 = 7.4 uM O8G C13 H14 N6 O2 S c1cc(sc1)c....
14 5F0C - 5TE C19 H28 N2 O c1cc(cc(c1....
15 6HO8 - GG8 C9 H10 F3 N O2 S c1ccc(cc1)....
16 5IOY Kd = 6 uM 6C5 C11 H20 N2 O C1CCC(C1)C....
17 5F1J Kd = 12 uM 5TO C12 H21 N O C1CCC(C1)C....
18 5F27 - 5TT C13 H20 N2 CNCc1ccc(c....
19 5MYR ic50 = 22 uM UDY C15 H9 F N4 S2 c1ccnc(c1)....
20 6HO5 - GH8 C30 H32 N2 O3 CC(C)N1CCC....
21 5MYM ic50 = 3.9 uM HYV C24 H29 N5 O S c1ccc(cc1)....
22 5NJ0 - 8YW C16 H14 N2 O6 c1cc(ccc1[....
23 5NIZ - 8YT C17 H24 N2 O3 C[C@@H]1C[....
24 5J3L Kd = 16 uM 6FR C11 H21 N O2 S C1CCC(C1)C....
25 6HO2 - GHN C16 H17 F3 N2 O4 S2 CCOC(=O)Cc....
26 4M3G ic50 = 0.55 uM 2G1 C13 H13 F3 N2 O2 S2 Cc1nc(cs1)....
27 6R1P - JPH C17 H17 N5 O3 CC1=CC(=O)....
28 6HOC - GJE C10 H9 F3 N4 O c1cc(ccc1C....
29 3O8H ic50 = 580 nM O8H C22 H22 I N7 O4 S2 c1cc(sc1)c....
30 5MXK ic50 = 150 uM ZHA C12 H13 N O2 CC(=O)Nc1c....
31 5IOZ Kd = 11 uM 6C4 C12 H21 N O C1CCC(C1)C....
32 6HOB - GJ5 C17 H19 F3 N2 O S CC(C)Cc1nc....
33 6HNX - GFZ C29 H30 N2 O3 CC(C)N1CCC....
34 6HO7 - GHQ C10 H10 F3 N O c1ccc(cc1)....
35 5EZH Kd = 24 uM 841 C16 H24 N4 O c1ccnc(c1)....
36 5MWO ic50 = 0.19 mM J6W C10 H10 O S Cc1ccc2c(c....
37 5EYR Kd = 5 uM 5T0 C20 H31 N3 O CNCc1ccc(c....
38 6HO4 - GFQ C19 H23 F3 N2 O S CC(C)CCCc1....
39 3G1O ic50 = 38 uM RF1 C16 H21 N3 O3 S CC(C)(C)OC....
40 5NIO - 8YH C11 H22 N2 O CCCCNC(=O)....
41 6HO1 - GFW C18 H24 N2 O4 S2 CCOC(=O)Cc....
42 5F0H ic50 = 33 uM 5TC C27 H34 N4 O c1cc(ccc1C....
43 4M3D ic50 = 3.9 uM 2H2 C19 H17 F3 N2 O3 S c1ccc(cc1)....
44 5J1R Kd = 22 uM 6FG C11 H15 N O2 c1cocc1CCC....
45 6HOE - GH2 C17 H17 F3 N2 O3 S CCOC(=O)Cc....
46 3SDG ic50 = 2.8 uM 3SE C14 H15 F3 N4 O2 S c1csc(n1)c....
47 6HOD - GHK C15 H14 N2 O4 S2 c1ccc(cc1)....
48 6HNZ - GH5 C17 H18 F3 N3 O2 c1ccc(cc1)....
49 6HO9 - GHB C16 H19 F3 N4 O CC(C)Cc1cn....
50 4DW6 - 0MN C22 H18 N2 O3 S COc1cccc(c....
51 3G1L - RF2 C14 H10 F N3 c1ccc(cc1)....
52 5IP6 - 6C9 C10 H18 N2 O2 C1CCN(C1)C....
53 5MXV ic50 = 12 uM K3T C12 H8 Cl F N2 O S2 c1cc2c(cc1....
54 5IPA Kd = 20 uM 6C8 C11 H13 N O2 c1cocc1/C=....
55 5NIM - 8YE C14 H16 N4 O3 CCCc1cc(no....
56 6HO6 - GGK C13 H15 F3 N2 O4 S2 CS(=O)(=O)....
57 5F0F Kd = 1 uM 5TD C19 H25 N3 O c1cc(ccc1C....
58 5MYW - WCU C13 H12 N2 O2 c1ccc(c(c1....
59 5MYN ic50 = 30 uM ZUF C13 H9 Cl N4 S c1ccnc(c1)....
60 6HO3 - GJ2 C18 H17 F3 N2 O4 S2 c1ccc(cc1)....
61 4M3F ic50 = 4.9 uM 2D1 C15 H20 N2 O2 S2 Cc1nc(cs1)....
62 5EZG Kd = 12 uM 5T4 C15 H23 N5 O c1cnc(nc1)....
63 4M3B ic50 = 0.4 uM 2B2 C14 H13 F3 N2 O S Cc1nc(cs1)....
64 3G1M ic50 = 0.522 uM RF3 C17 H17 N3 O2 S2 c1cc(sc1)C....
65 3TP0 - FO5 C14 H14 N4 O2 S c1cc(sc1)c....
66 6R1S - JPK C21 H24 N4 O3 Cc1cccc(c1....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: 2B2; Similar ligands found: 10
No: Ligand ECFP6 Tc MDL keys Tc
1 2B2 1 1
2 GJ5 0.671875 0.933333
3 GH2 0.632353 0.777778
4 GFQ 0.632353 0.875
5 2B3 0.597222 0.608696
6 GGN 0.564103 0.893617
7 GJ8 0.551282 0.630769
8 2G1 0.507692 0.65
9 GHQ 0.473684 0.642857
10 GHB 0.402597 0.655172
Similar Ligands (3D)
Ligand no: 1; Ligand: 2B2; Similar ligands found: 23
No: Ligand Similarity coefficient
1 2D1 0.9209
2 077 0.9176
3 GJE 0.9140
4 576 0.8998
5 F6F 0.8922
6 BZH 0.8884
7 88S 0.8788
8 NZO 0.8775
9 1YW 0.8769
10 TE4 0.8749
11 2YO 0.8731
12 Y0R 0.8727
13 C65 0.8695
14 675 0.8692
15 YP6 0.8651
16 SQO 0.8645
17 4BS 0.8637
18 RF1 0.8629
19 FDZ 0.8616
20 4BG 0.8608
21 3RM 0.8593
22 OYQ 0.8582
23 MS7 0.8548
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4M3B; Ligand: 2B2; Similar sites found with APoc: 1
This union binding pocket(no: 1) in the query (biounit: 4m3b.bio1) has 43 residues
No: Leader PDB Ligand Sequence Similarity
1 5LX9 OLB 5.40541
Pocket No.: 2; Query (leader) PDB : 4M3B; Ligand: 2B2; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 4m3b.bio1) has 43 residues
No: Leader PDB Ligand Sequence Similarity
APoc FAQ
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