Receptor
PDB id Resolution Class Description Source Keywords
3G1L 1.7 Å NON-ENZYME: TRANSCRIPT_TRANSLATE ETHR FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH COMPOUN MYCOBACTERIUM TUBERCULOSIS TETR FAMILY DNA-BINDING TRANSCRIPTION TRANSCRIPTION REGUL
Ref.: SYNTHETIC ETHR INHIBITORS BOOST ANTITUBERCULOUS ACT ETHIONAMIDE. NAT.MED. (N.Y.) V. 15 537 2009
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
RF2 A:237;
Valid;
none;
submit data
239.248 C14 H10 F N3 c1ccc...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3SFI 2.31 Å NON-ENZYME: TRANSCRIPT_TRANSLATE ETHIONAMIDE BOOSTERS PART 2: COMBINING BIOISOSTERIC REPLACEM STRUCTURE-BASED DRUG DESIGN TO SOLVE PHARMACOKINETIC ISSUESS ERIES OF POTENT 1,2,4-OXADIAZOLE ETHR INHIBITORS. MYCOBACTERIUM TUBERCULOSIS TETR-FAMILY TRANSCRITPTIONAL REGULATORY REPRESSOR INHIBITODNA BINDING PROTEIN TRANSCRIPTION REPRESSOR-INHIBITOR COMP
Ref.: ETHIONAMIDE BOOSTERS. 2. COMBINING BIOISOSTERIC REP AND STRUCTURE-BASED DRUG DESIGN TO SOLVE PHARMACOKI ISSUES IN A SERIES OF POTENT 1,2,4-OXADIAZOLE ETHR INHIBITORS. J.MED.CHEM. V. 55 68 2012
Members (34)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 257 families.
1 5J1U - P93 C10 H14 N2 O2 c1cocc1CNC....
2 3SFI ic50 = 0.4 uM 3SF C15 H17 F3 N4 O2 S c1csc(n1)c....
3 3Q0W - LL5 C16 H22 N4 O2 S CC(C)[C@@H....
4 4M3E ic50 = 0.56 uM 2B3 C17 H20 F3 N3 O3 S2 CCCS(=O)(=....
5 1U9N - CNS C24 H48 O2 CCCCCCCCCC....
6 5F08 Kd = 3 uM 5TG C25 H39 N3 O3 CC(C)(C)OC....
7 3O8G ic50 = 7.4 uM O8G C13 H14 N6 O2 S c1cc(sc1)c....
8 5F0C - 5TE C19 H28 N2 O c1cc(cc(c1....
9 5IOY Kd = 6 uM 6C5 C11 H20 N2 O C1CCC(C1)C....
10 5F1J Kd = 12 uM 5TO C12 H21 N O C1CCC(C1)C....
11 5F27 - 5TT C13 H20 N2 CNCc1ccc(c....
12 5J3L Kd = 16 uM 6FR C11 H21 N O2 S C1CCC(C1)C....
13 4M3G ic50 = 0.55 uM 2G1 C13 H13 F3 N2 O2 S2 Cc1nc(cs1)....
14 3O8H ic50 = 580 nM O8H C22 H22 I N7 O4 S2 c1cc(sc1)c....
15 5MXK ic50 = 0.15 mM ZHA C12 H13 N O2 CC(=O)Nc1c....
16 5IOZ Kd = 11 uM 6C4 C12 H21 N O C1CCC(C1)C....
17 5EZH Kd = 24 uM 841 C16 H24 N4 O c1ccnc(c1)....
18 5MWO ic50 = 0.19 mM J6W C10 H10 O S Cc1ccc2c(c....
19 5EYR Kd = 5 uM 5T0 C20 H31 N3 O CNCc1ccc(c....
20 3G1O ic50 = 38 uM RF1 C16 H21 N3 O3 S CC(C)(C)OC....
21 5F0H ic50 = 33 uM 5TC C27 H34 N4 O c1cc(ccc1C....
22 4M3D ic50 = 3.9 uM 2H2 C19 H17 F3 N2 O3 S c1ccc(cc1)....
23 5J1R Kd = 22 uM 6FG C11 H15 N O2 c1cocc1CCC....
24 3SDG ic50 = 2.8 uM 3SE C14 H15 F3 N4 O2 S c1csc(n1)c....
25 4DW6 - 0MN C22 H18 N2 O3 S COc1cccc(c....
26 3G1L - RF2 C14 H10 F N3 c1ccc(cc1)....
27 5IP6 - 6C9 C10 H18 N2 O2 C1CCN(C1)C....
28 5IPA Kd = 20 uM 6C8 C11 H13 N O2 c1cocc1/C=....
29 5F0F Kd = 1 uM 5TD C19 H25 N3 O c1cc(ccc1C....
30 4M3F ic50 = 4.9 uM 2D1 C15 H20 N2 O2 S2 Cc1nc(cs1)....
31 5EZG Kd = 12 uM 5T4 C15 H23 N5 O c1cnc(nc1)....
32 4M3B ic50 = 0.4 uM 2B2 C14 H13 F3 N2 O S Cc1nc(cs1)....
33 3G1M ic50 = 0.522 uM RF3 C17 H17 N3 O2 S2 c1cc(sc1)C....
34 3TP0 - FO5 C14 H14 N4 O2 S c1cc(sc1)c....
70% Homology Family (34)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 222 families.
1 5J1U - P93 C10 H14 N2 O2 c1cocc1CNC....
2 3SFI ic50 = 0.4 uM 3SF C15 H17 F3 N4 O2 S c1csc(n1)c....
3 3Q0W - LL5 C16 H22 N4 O2 S CC(C)[C@@H....
4 4M3E ic50 = 0.56 uM 2B3 C17 H20 F3 N3 O3 S2 CCCS(=O)(=....
5 1U9N - CNS C24 H48 O2 CCCCCCCCCC....
6 5F08 Kd = 3 uM 5TG C25 H39 N3 O3 CC(C)(C)OC....
7 3O8G ic50 = 7.4 uM O8G C13 H14 N6 O2 S c1cc(sc1)c....
8 5F0C - 5TE C19 H28 N2 O c1cc(cc(c1....
9 5IOY Kd = 6 uM 6C5 C11 H20 N2 O C1CCC(C1)C....
10 5F1J Kd = 12 uM 5TO C12 H21 N O C1CCC(C1)C....
11 5F27 - 5TT C13 H20 N2 CNCc1ccc(c....
12 5J3L Kd = 16 uM 6FR C11 H21 N O2 S C1CCC(C1)C....
13 4M3G ic50 = 0.55 uM 2G1 C13 H13 F3 N2 O2 S2 Cc1nc(cs1)....
14 3O8H ic50 = 580 nM O8H C22 H22 I N7 O4 S2 c1cc(sc1)c....
15 5MXK ic50 = 0.15 mM ZHA C12 H13 N O2 CC(=O)Nc1c....
16 5IOZ Kd = 11 uM 6C4 C12 H21 N O C1CCC(C1)C....
17 5EZH Kd = 24 uM 841 C16 H24 N4 O c1ccnc(c1)....
18 5MWO ic50 = 0.19 mM J6W C10 H10 O S Cc1ccc2c(c....
19 5EYR Kd = 5 uM 5T0 C20 H31 N3 O CNCc1ccc(c....
20 3G1O ic50 = 38 uM RF1 C16 H21 N3 O3 S CC(C)(C)OC....
21 5F0H ic50 = 33 uM 5TC C27 H34 N4 O c1cc(ccc1C....
22 4M3D ic50 = 3.9 uM 2H2 C19 H17 F3 N2 O3 S c1ccc(cc1)....
23 5J1R Kd = 22 uM 6FG C11 H15 N O2 c1cocc1CCC....
24 3SDG ic50 = 2.8 uM 3SE C14 H15 F3 N4 O2 S c1csc(n1)c....
25 4DW6 - 0MN C22 H18 N2 O3 S COc1cccc(c....
26 3G1L - RF2 C14 H10 F N3 c1ccc(cc1)....
27 5IP6 - 6C9 C10 H18 N2 O2 C1CCN(C1)C....
28 5IPA Kd = 20 uM 6C8 C11 H13 N O2 c1cocc1/C=....
29 5F0F Kd = 1 uM 5TD C19 H25 N3 O c1cc(ccc1C....
30 4M3F ic50 = 4.9 uM 2D1 C15 H20 N2 O2 S2 Cc1nc(cs1)....
31 5EZG Kd = 12 uM 5T4 C15 H23 N5 O c1cnc(nc1)....
32 4M3B ic50 = 0.4 uM 2B2 C14 H13 F3 N2 O S Cc1nc(cs1)....
33 3G1M ic50 = 0.522 uM RF3 C17 H17 N3 O2 S2 c1cc(sc1)C....
34 3TP0 - FO5 C14 H14 N4 O2 S c1cc(sc1)c....
50% Homology Family (34)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 185 families.
1 5J1U - P93 C10 H14 N2 O2 c1cocc1CNC....
2 3SFI ic50 = 0.4 uM 3SF C15 H17 F3 N4 O2 S c1csc(n1)c....
3 3Q0W - LL5 C16 H22 N4 O2 S CC(C)[C@@H....
4 4M3E ic50 = 0.56 uM 2B3 C17 H20 F3 N3 O3 S2 CCCS(=O)(=....
5 1U9N - CNS C24 H48 O2 CCCCCCCCCC....
6 5F08 Kd = 3 uM 5TG C25 H39 N3 O3 CC(C)(C)OC....
7 3O8G ic50 = 7.4 uM O8G C13 H14 N6 O2 S c1cc(sc1)c....
8 5F0C - 5TE C19 H28 N2 O c1cc(cc(c1....
9 5IOY Kd = 6 uM 6C5 C11 H20 N2 O C1CCC(C1)C....
10 5F1J Kd = 12 uM 5TO C12 H21 N O C1CCC(C1)C....
11 5F27 - 5TT C13 H20 N2 CNCc1ccc(c....
12 5J3L Kd = 16 uM 6FR C11 H21 N O2 S C1CCC(C1)C....
13 4M3G ic50 = 0.55 uM 2G1 C13 H13 F3 N2 O2 S2 Cc1nc(cs1)....
14 3O8H ic50 = 580 nM O8H C22 H22 I N7 O4 S2 c1cc(sc1)c....
15 5MXK ic50 = 0.15 mM ZHA C12 H13 N O2 CC(=O)Nc1c....
16 5IOZ Kd = 11 uM 6C4 C12 H21 N O C1CCC(C1)C....
17 5EZH Kd = 24 uM 841 C16 H24 N4 O c1ccnc(c1)....
18 5MWO ic50 = 0.19 mM J6W C10 H10 O S Cc1ccc2c(c....
19 5EYR Kd = 5 uM 5T0 C20 H31 N3 O CNCc1ccc(c....
20 3G1O ic50 = 38 uM RF1 C16 H21 N3 O3 S CC(C)(C)OC....
21 5F0H ic50 = 33 uM 5TC C27 H34 N4 O c1cc(ccc1C....
22 4M3D ic50 = 3.9 uM 2H2 C19 H17 F3 N2 O3 S c1ccc(cc1)....
23 5J1R Kd = 22 uM 6FG C11 H15 N O2 c1cocc1CCC....
24 3SDG ic50 = 2.8 uM 3SE C14 H15 F3 N4 O2 S c1csc(n1)c....
25 4DW6 - 0MN C22 H18 N2 O3 S COc1cccc(c....
26 3G1L - RF2 C14 H10 F N3 c1ccc(cc1)....
27 5IP6 - 6C9 C10 H18 N2 O2 C1CCN(C1)C....
28 5IPA Kd = 20 uM 6C8 C11 H13 N O2 c1cocc1/C=....
29 5F0F Kd = 1 uM 5TD C19 H25 N3 O c1cc(ccc1C....
30 4M3F ic50 = 4.9 uM 2D1 C15 H20 N2 O2 S2 Cc1nc(cs1)....
31 5EZG Kd = 12 uM 5T4 C15 H23 N5 O c1cnc(nc1)....
32 4M3B ic50 = 0.4 uM 2B2 C14 H13 F3 N2 O S Cc1nc(cs1)....
33 3G1M ic50 = 0.522 uM RF3 C17 H17 N3 O2 S2 c1cc(sc1)C....
34 3TP0 - FO5 C14 H14 N4 O2 S c1cc(sc1)c....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: RF2; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 RF2 1 1
2 39R 0.5 0.75
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3SFI; Ligand: 3SF; Similar sites found: 163
This union binding pocket(no: 1) in the query (biounit: 3sfi.bio1) has 41 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1BTN I3P 0.0006424 0.54494 None
2 2QLX RM4 0.0003628 0.51564 None
3 2FR6 CTN 0.0003335 0.45523 None
4 1N9L FMN 0.0009879 0.43761 None
5 2E1A MSE 0.006138 0.43208 None
6 3F81 STT 0.03486 0.42786 None
7 1Y75 NAG 0.009129 0.42449 None
8 2FR6 URI 0.00291 0.42007 None
9 4NAT ADP 0.0004726 0.41605 None
10 3KPE TM3 0.04918 0.4041 None
11 1RYI GOA 0.0001251 0.40477 0.847458
12 2Y7G AAE 0.008691 0.40917 1.27119
13 2WMO GTP 0.0002423 0.47566 1.69492
14 2R5T ANP 0.002537 0.4151 1.69492
15 3RF4 FUN 0.01962 0.41409 1.72414
16 4KCT FDP 0.004913 0.42712 2.11864
17 4OB6 S2T 0.003785 0.42339 2.11864
18 1QDS PGA 0.009029 0.42028 2.11864
19 4KCT PYR 0.01419 0.41604 2.11864
20 3DGB MUC 0.0109 0.41273 2.11864
21 3P7I P7I 0.02779 0.40718 2.11864
22 2YGO PCF 0.0009693 0.40679 2.11864
23 1MXI SAH 0.002473 0.42271 2.5
24 3A2Y TS5 0.005957 0.41194 2.53807
25 3S9K CIT 0.00705 0.49568 2.54237
26 1P1M MET 0.0001289 0.45673 2.54237
27 3I51 45C 0.001065 0.45467 2.54237
28 4E28 9MZ 0.006027 0.44848 2.54237
29 3QV9 QV7 0.006293 0.44184 2.54237
30 2V6O FAD 0.0002644 0.41913 2.54237
31 4L1F COS 0.001449 0.41676 2.54237
32 4E28 0MZ 0.0217 0.41662 2.54237
33 2F2U M77 0.01315 0.41329 2.54237
34 1F3L SAH 0.002807 0.41019 2.54237
35 3UEC ALA ARG TPO LYS 0.003602 0.46591 2.73973
36 1C1L GAL BGC 0.01693 0.43225 2.91971
37 1XE7 GUN 0.02109 0.43976 2.95567
38 1EYE PMM 0.001115 0.45384 2.9661
39 3SHR CMP 0.002024 0.44802 2.9661
40 2NCD ADP 0.01012 0.43218 2.9661
41 4PNI KQQ 0.0004527 0.43027 2.9661
42 3CF6 SP1 0.003653 0.424 2.9661
43 2PR5 FMN 0.0002718 0.45855 3.0303
44 1QD0 RR6 0.01145 0.41183 3.125
45 4RPM HXC 0.04431 0.43597 3.38983
46 1SQ5 PAU 0.007687 0.4326 3.38983
47 5LX9 OLB 0.04879 0.41985 3.38983
48 3D2Y AH0 ALA FGA LYS 0.003741 0.41599 3.38983
49 1SQ5 ADP 0.01327 0.40916 3.38983
50 4P53 NAI 0.001185 0.40703 3.38983
51 1QZZ SAM 0.01229 0.40679 3.38983
52 1K6M AGS 0.00415 0.40428 3.38983
53 4KOA NDP 0.01071 0.40214 3.38983
54 1EB9 HBA 0.0009779 0.4562 3.43511
55 2V5E SCR 0.00003081 0.60606 3.5
56 3GX0 GDS 0.003224 0.41481 3.72093
57 2EB5 OXL 0.001504 0.47756 3.81356
58 3I0O SMI 0.003312 0.45487 3.81356
59 2Q28 ADP 0.00057 0.44227 3.81356
60 3I0O ADP 0.003661 0.43704 3.81356
61 1Q0H NDP 0.00005284 0.41861 3.81356
62 4CS4 AXZ 0.00007905 0.40972 3.81356
63 4IMG NGF 0.004945 0.40803 3.81356
64 4IXW IXW 0.02415 0.40582 3.81356
65 4F4S EFO 0.0001283 0.513 3.94737
66 1S8F GDP 0.00101 0.41224 3.9548
67 2OFE NAG 0.002746 0.46496 4.22535
68 3ZPG 5GP 0.0008992 0.51363 4.23729
69 4COQ SAN 0.001755 0.47434 4.23729
70 2YVF NAD 0.0001056 0.42229 4.23729
71 2Z9V PXM 0.02292 0.41101 4.23729
72 3O2K QRP 0.01726 0.40821 4.23729
73 1WDA BAG 0.02183 0.40777 4.23729
74 1CKM GTP 0.00766 0.40108 4.24242
75 1YOA FAD 0.003615 0.40637 4.40252
76 1XX4 BAM 0.0000791 0.57036 4.66102
77 3M31 FAD 0.0002109 0.44521 4.66102
78 2C5S AMP 0.03077 0.40114 4.66102
79 1MZV AMP 0.02138 0.40421 4.68085
80 1ZS6 ADP 0.03164 0.4006 4.73373
81 1VE3 SAM 0.000698 0.44325 4.84582
82 4K30 NLG 0.03778 0.40105 5
83 2Q8H TF4 0.0009172 0.51316 5.08475
84 1RZM E4P 0.0006356 0.5035 5.08475
85 1RZM PEP 0.002193 0.45728 5.08475
86 2QCX PF1 0.002969 0.45709 5.08475
87 1V6A TRE 0.007408 0.43853 5.08475
88 4B9E FAH 0.01853 0.43028 5.08475
89 3HB5 E2B 0.0007603 0.42278 5.08475
90 3I8P 840 0.009637 0.40739 5.08475
91 1FW1 GSH 0.002464 0.43502 5.09259
92 2O66 FLC 0.0002336 0.50859 5.18518
93 1SS4 GSH 0.00116 0.53195 5.22876
94 1SS4 CIT 0.01613 0.43695 5.22876
95 3BHO B4P 0.04283 0.42947 5.28846
96 1Z44 FMN 0.009615 0.41111 5.32544
97 1Z41 FMN 0.01111 0.40495 5.32544
98 3LTW HLZ 0.00288 0.46396 5.35714
99 1O9U ADZ 0.009421 0.4587 5.50847
100 1I0Z OXM 0.02477 0.43595 5.50847
101 4DYO SD4 0.007672 0.42782 5.50847
102 4JWX 1N4 0.0235 0.41052 5.50847
103 3P3N AKG 0.003651 0.45899 5.73066
104 3MAG 3MA 0.01288 0.45908 5.9322
105 4LHM AZZ 0.007717 0.4377 5.9322
106 1Q11 TYE 0.01014 0.42715 5.9322
107 1UF5 CDT 0.008061 0.42239 5.9322
108 2JBH 5GP 0.01356 0.41691 6.22222
109 3QDY CBS 0.004142 0.46288 6.29371
110 3QDT A2G GAL 0.006787 0.45892 6.29371
111 3QDY A2G GAL 0.01557 0.44017 6.29371
112 3DER ALA LYS 0.002304 0.41658 6.35593
113 1B7Y FYA 0.002585 0.40213 6.35593
114 1XIU REA 0.0002524 0.46456 6.52174
115 2FH5 GTP 0.001535 0.42658 6.54206
116 2Q37 3AL 0.009407 0.43367 6.62983
117 4RJK PYR 0.01184 0.44637 6.77966
118 1TFZ 869 0.0009514 0.43415 6.77966
119 2IZ1 ATR 0.01822 0.42521 6.77966
120 2Q09 DI6 0.01406 0.41622 6.77966
121 4RJK TDL 0.001031 0.40313 6.77966
122 2Y7P SAL 0.00114 0.47013 6.88073
123 1U5R ATP 0.00402 0.42236 7.20339
124 4L7I SAM 0.007589 0.4079 7.20339
125 2C2A ADP 0.01154 0.40089 7.20339
126 3KJQ B94 0.004133 0.43024 7.36842
127 1T0S BML 0.00002647 0.58353 7.62712
128 2C7G FAD 0.0001013 0.41836 7.62712
129 2C7G ODP 0.0001114 0.41635 7.62712
130 1TV5 N8E 0.005748 0.40901 7.62712
131 4L6C 0BT 0.004955 0.4016 7.92079
132 4CCO OGA 0.005731 0.43838 8.05085
133 1A8S PPI 0.0142 0.40987 8.05085
134 3BY8 MLT 0.02937 0.42019 8.4507
135 1Y42 TYR 0.001819 0.46095 8.47458
136 1KTC NGA 0.03801 0.40093 8.47458
137 1ULE GLA GAL NAG 0.04519 0.41591 8.66667
138 2XDQ MGX 0.002292 0.49177 8.8983
139 4M5P MLA 0.005683 0.47907 8.8983
140 4M5P 23W 0.008171 0.45473 8.8983
141 4M5P FMN 0.006033 0.40168 8.8983
142 2Y6P CTP 0.004032 0.43525 8.97436
143 1F1V DHY 0.0007294 0.4727 9.32203
144 4WVH ASP HIS ASP ALA HIS ALA 0.001412 0.46012 9.32203
145 3A1I UNU 0.01677 0.40875 9.32203
146 4M4Q 21A 0.001541 0.41259 9.74576
147 1M2Z DEX 0.04887 0.40894 9.74576
148 2FYU FDN 0.0005437 0.4473 10
149 3KMT SAH 0.01136 0.40817 10.084
150 1ZJ6 G3D 0.01296 0.40959 10.1604
151 3TFC PEP 0.0196 0.41412 10.1695
152 4DEC UDP 0.0003919 0.42531 11.0169
153 4DEC 3PG 0.0003919 0.42531 11.0169
154 3IPQ 965 0.0001754 0.42607 11.8644
155 1ECM TSA 0.007401 0.42851 11.9266
156 2RHQ GAX 0.00002328 0.48257 13.1356
157 2PP3 LGT 0.013 0.4058 13.9831
158 2JFV FLC 0.0005246 0.49961 14.4068
159 3DG6 MUC 0.001249 0.44694 14.4068
160 4Q0A 4OA 0.002563 0.42213 14.9007
161 4Q0A GLY HIS LYS ILE LEU HIS ARG LEU LEU GLN 0.005788 0.40889 14.9007
162 1ZZ7 S0H 0.01196 0.42389 15.1515
163 1RHC F42 ACN 0.0005832 0.41051 16.9492
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