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Receptor
PDB id Resolution Class Description Source Keywords
4HWS 1.7 Å EC: 6.1.1.3 CRYSTAL STRUCTURE OF E. COLI THREONYL-TRNA SYNTHETASE BOUND INHIBITOR ESCHERICHIA COLI AMINOACYL-TRNA SYNTHETASE PROTEIN-INHIBITOR COMPLEX ANTIBALIGASE-LIGASE INHIBITOR COMPLEX
Ref.: IDENTIFICATION OF BACTERIA-SELECTIVE THREONYL-TRNA SYNTHETASE SUBSTRATE INHIBITORS BY STRUCTURE-BASED J.MED.CHEM. V. 56 1748 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
1B3 A:702;
B:702;
Valid;
Valid;
none;
none;
Ki = 0.8 nM
435.885 C18 H18 Cl N5 O4 S C[C@H...
ZN A:701;
B:701;
Part of Protein;
Part of Protein;
none;
none;
submit data
65.409 Zn [Zn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4HWS 1.7 Å EC: 6.1.1.3 CRYSTAL STRUCTURE OF E. COLI THREONYL-TRNA SYNTHETASE BOUND INHIBITOR ESCHERICHIA COLI AMINOACYL-TRNA SYNTHETASE PROTEIN-INHIBITOR COMPLEX ANTIBALIGASE-LIGASE INHIBITOR COMPLEX
Ref.: IDENTIFICATION OF BACTERIA-SELECTIVE THREONYL-TRNA SYNTHETASE SUBSTRATE INHIBITORS BY STRUCTURE-BASED J.MED.CHEM. V. 56 1748 2013
Members (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 7 families.
1 4HWS Ki = 0.8 nM 1B3 C18 H18 Cl N5 O4 S C[C@H]([C@....
2 4P3P Ki = 4 nM 2CR C28 H43 N O6 C[C@H]1C[C....
3 4HWP Ki = 17.2 nM X16 C19 H21 N5 O4 S Cc1nc2cc(c....
4 4HWO Ki = 2.9 nM 409 C18 H19 N5 O4 S C[C@H]([C@....
5 4HWR Ki = 182 nM 1B2 C17 H18 N4 O4 S C[C@H]([C@....
6 1EVL - TSB C14 H21 N7 O8 S C[C@H]([C@....
7 1FYF - SSA C13 H19 N7 O8 S c1nc(c2c(n....
8 1EVK - THR C4 H9 N O3 C[C@H]([C@....
70% Homology Family (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 4HWS Ki = 0.8 nM 1B3 C18 H18 Cl N5 O4 S C[C@H]([C@....
2 4P3P Ki = 4 nM 2CR C28 H43 N O6 C[C@H]1C[C....
3 4HWP Ki = 17.2 nM X16 C19 H21 N5 O4 S Cc1nc2cc(c....
4 4HWO Ki = 2.9 nM 409 C18 H19 N5 O4 S C[C@H]([C@....
5 4HWR Ki = 182 nM 1B2 C17 H18 N4 O4 S C[C@H]([C@....
6 1EVL - TSB C14 H21 N7 O8 S C[C@H]([C@....
7 1FYF - SSA C13 H19 N7 O8 S c1nc(c2c(n....
8 1EVK - THR C4 H9 N O3 C[C@H]([C@....
50% Homology Family (10)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 4HWS Ki = 0.8 nM 1B3 C18 H18 Cl N5 O4 S C[C@H]([C@....
2 4P3P Ki = 4 nM 2CR C28 H43 N O6 C[C@H]1C[C....
3 4HWP Ki = 17.2 nM X16 C19 H21 N5 O4 S Cc1nc2cc(c....
4 4HWO Ki = 2.9 nM 409 C18 H19 N5 O4 S C[C@H]([C@....
5 4HWR Ki = 182 nM 1B2 C17 H18 N4 O4 S C[C@H]([C@....
6 1EVL - TSB C14 H21 N7 O8 S C[C@H]([C@....
7 1FYF - SSA C13 H19 N7 O8 S c1nc(c2c(n....
8 1EVK - THR C4 H9 N O3 C[C@H]([C@....
9 3UH0 - TSB C14 H21 N7 O8 S C[C@H]([C@....
10 4HWT Ki > 50000 nM 1B2 C17 H18 N4 O4 S C[C@H]([C@....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 1B3; Similar ligands found: 4
No: Ligand ECFP6 Tc MDL keys Tc
1 1B3 1 1
2 X16 0.769231 0.917808
3 409 0.674699 0.930556
4 1B2 0.533333 0.826667
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4HWS; Ligand: 1B3; Similar sites found with APoc: 209
This union binding pocket(no: 1) in the query (biounit: 4hws.bio1) has 36 residues
No: Leader PDB Ligand Sequence Similarity
1 5HSS 64Z 1.07817
2 1GQG DCD 1.14286
3 4I9B 1KA 1.21654
4 1VRP ADP 1.31234
5 1X54 4AD 1.45985
6 1SDW IYT 1.59236
7 4AZI OAN 1.70316
8 4YBN FAD 1.78571
9 3VV1 GAL FUC 1.875
10 3QSB 743 1.91257
11 3TEG DAH 1.94647
12 2HOX P1T 1.94647
13 1NJJ GET 1.94647
14 6F3G CJN 2.0339
15 3REU ATP 2.04082
16 5M0T AKG 2.04082
17 1M5W DXP 2.05761
18 3A16 PXO 2.14477
19 3E9I XAH 2.18978
20 4WOE ADP 2.18978
21 6G7N DAL 2.20126
22 5Y4K AKR 2.2113
23 4LED XXR 2.23881
24 5LDQ NAP 2.25989
25 4RGA 3PV 2.29008
26 6BU0 IHP 2.29008
27 3A5Y KAA 2.31884
28 5T96 79J 2.33918
29 5V59 8X1 2.43309
30 5H9Y BGC BGC BGC BGC 2.43309
31 5H9Y BGC BGC BGC BGC BGC 2.43309
32 2ZTG A5A 2.43309
33 3TAY MN0 2.45399
34 5W75 SUC 2.55102
35 1O5Q PYR 2.62295
36 5JJU AMP 2.64706
37 5TFZ 7BC 2.66667
38 4KBA 1QM 2.71903
39 1KJ1 MAN 2.75229
40 1H8S AIC 2.77778
41 4DXD 9PC 2.77778
42 3WG3 A2G GAL NAG FUC 2.80899
43 5LUN OGA 2.84091
44 4D1J DGJ 2.91971
45 1XE7 GUN 2.95567
46 5JSP DQY 2.98507
47 4DDY DN6 3.04183
48 3A5Z KAA 3.14136
49 5LY1 PPI 3.14961
50 2XGT NSS 3.16302
51 4RF7 ARG 3.16302
52 1OFL NGK GCD 3.16302
53 3I4X DST 3.16302
54 5TZO 7V7 3.19149
55 5EJL C2E 3.22581
56 5A67 3PO 3.30189
57 3B00 16A 3.30882
58 5TVA COA 3.33333
59 3G1Z AMP 3.40633
60 3NEM AMO 3.40633
61 3NEM ATP 3.40633
62 5KJW 53C 3.40633
63 1G51 AMO 3.40633
64 3VSV XYP 3.40633
65 6FA4 D1W 3.46821
66 5OCQ 9RN G4S 9RN G4S 3.50877
67 5GLT BGC GAL NAG GAL 3.52113
68 1N5S ADL 3.57143
69 1YFS ALA 3.64964
70 3N2O AG2 3.64964
71 3WUD GLC GAL 3.67647
72 1R87 XYP XYP XYP 3.69393
73 1F9V ADP 3.7464
74 4RQL SNE 3.78151
75 5FUI APY 3.78788
76 2VFT SOR 3.89294
77 1B7Y FYA 3.89294
78 12AS AMP 3.93939
79 3GD9 GLC BGC BGC BGC 4.08719
80 5HZ7 BGC 4.13625
81 2Z5Y HRM 4.13625
82 2YKL NLD 4.16667
83 2PFC PLM 4.37158
84 1WW5 SGA BGC 4.375
85 2Z3U CRR 4.37956
86 1GT4 UNA 4.40252
87 4YVN EBS 4.62287
88 5XQW 8EU 4.73934
89 4D4U FUC NDG GAL FUC 4.7619
90 3AIH BMA MAN MAN 4.83871
91 1Y7P RIP 4.93274
92 3SAO DBH 5
93 3SAO NKN 5
94 6DW2 HD4 5.06329
95 4OWK NGA 5.07246
96 4RYV ZEA 5.16129
97 4V15 PLP 5.27704
98 5JIB OIA 5.34125
99 2R2N KYN 5.3528
100 5Y4R C2E 5.51724
101 4PTX BGC 5.59611
102 5DYO FLU 5.66038
103 4MOB ADP 5.72289
104 3JQM GTP 5.73248
105 3WV6 GAL BGC 5.74324
106 3WV6 GAL GLC 5.74324
107 4WCX MET 5.83942
108 1C1L GAL BGC 5.83942
109 2QPU QPU 5.92593
110 2QPU QPS 5.92593
111 5M6N 7H9 5.9322
112 1LSH PLD 5.95611
113 1A78 TDG 5.97015
114 6EV2 BGC 5.99078
115 3CBC DBS 6.06061
116 4MTI 2DX 6.08696
117 3ENG CBI 6.10329
118 4IEN GDP 6.13497
119 5FPE 3TR 6.20155
120 3WD6 GSH 6.25
121 5N2D 8J8 6.25
122 5W7B MYR 6.38298
123 3H0L ADP 6.38298
124 5AIG VPR 6.4
125 5NLD LBT 6.47482
126 4UP4 NDG 6.48379
127 4UP4 NAG 6.48379
128 3BJU ATP 6.56934
129 5J75 6GQ 6.56934
130 5DG2 GAL GLC 6.66667
131 2F62 12M 6.8323
132 2D6M LBT 6.91824
133 3QRC SCR 7.00637
134 5NIU 8YZ 7.03125
135 5T7I LAT NAG GAL 7.09677
136 4C1K PEP 7.25191
137 5YRV 5AD 7.29927
138 1U0A BGC BGC BGC BGC 7.47664
139 6EWZ APC 7.59494
140 6FOF LAT 7.65306
141 3CM2 X23 7.69231
142 2YMZ LAT 7.69231
143 5OQW A4E 7.87402
144 2HO2 PRO PRO PRO PRO PRO PRO PRO PRO PRO LEU 7.89474
145 2YIP YIO 7.97101
146 5L2R MLA 8.0292
147 3M3E GAL A2G NPO 8.07453
148 1SLT NDG GAL 8.20895
149 5F6U 5VK 8.28025
150 5NFB 8VT 8.52273
151 2VDF OCT 8.69565
152 2WLT ASP 8.73494
153 5H9P TD2 9.49367
154 5H9Q TD2 9.67742
155 3IWD M2T 9.67742
156 3HXU A5A 9.73236
157 3UW4 MAA CHG PRO 0DQ 9.78261
158 4RT1 C2E 9.82143
159 1SES AMP 9.97567
160 1SES AHX 9.97567
161 3ERR AMP 9.97567
162 5OCG 9R5 10.0529
163 1E1O LYS 10.219
164 2BOS GLA GAL GLC NBU 10.2941
165 2BOS GLA GAL GLC 10.2941
166 4YLZ LAT NAG GAL 10.4575
167 1QKQ MAN 10.5634
168 5ODY 9SK 10.8696
169 1SBR VIB 11
170 4Y24 TD2 11.039
171 4WVW SLT 11.1111
172 1IS3 LAT 11.1111
173 5UC4 83S 11.3636
174 5N2F 8HW 12.0968
175 3NV3 GAL NAG MAN 12.3188
176 1GZW GAL BGC 12.6866
177 1W6O LAT 12.6866
178 3OYW TDG 12.6866
179 1DZK PRZ 12.7389
180 3ZXE PGZ 13.5338
181 4CS4 ANP 13.8686
182 4CS4 AXZ 13.8686
183 4H2X G5A 13.8728
184 4H2V AMP 13.8728
185 3MF2 AMP 13.8728
186 4H2W AMP 13.8728
187 4H2W 5GP 13.8728
188 6GNO XDI 14.0741
189 1WLE SRP 14.8418
190 2ZHL NAG GAL GAL NAG 15.5405
191 2CJA ATP 15.8151
192 3I8T LBT 15.8537
193 2CJ9 SSA 16.0584
194 3QO8 SSA 16.3017
195 2J3M ATP 17.0316
196 2J3M PRI 17.0316
197 5VIT MLI 18.1818
198 1ULE GLA GAL NAG 18.6667
199 4K55 H6P 19.3548
200 5XIJ ANP 27.2506
201 5XIJ 873 27.2506
202 3IAL PR8 29.4404
203 4YDQ HFG 29.927
204 4YDQ ANP 29.927
205 5VAD 91Y 37.9562
206 5VAD PRO 37.9562
207 5XIO HFG 38.1995
208 5XIO ANP 38.1995
209 2I4O ATP 41.3625
Pocket No.: 2; Query (leader) PDB : 4HWS; Ligand: 1B3; Similar sites found with APoc: 54
This union binding pocket(no: 2) in the query (biounit: 4hws.bio1) has 37 residues
No: Leader PDB Ligand Sequence Similarity
1 1OJK GLC BGC 1.24378
2 3ZRM ZRM 1.61725
3 3GXA MET 2.18182
4 3MKN DNB 2.53165
5 4XJ6 GH3 2.7027
6 2RDE C2E 2.78884
7 1B09 PC 2.91262
8 4PXE GLV 2.91971
9 3KYF 5GP 5GP 3.0303
10 5DBX ANP 3.04878
11 1GPM CIT 3.16302
12 5KJU 6TO 3.40633
13 4HIA FMN 3.40909
14 1GWC GTX 3.47826
15 3PCJ INO 3.5
16 4BT5 23B 3.50195
17 5V8E CIT 3.55987
18 6D61 4AA 3.58974
19 2EAE FUL 3.64964
20 1R87 XYP XYP 3.69393
21 3AQZ BGC BGC BGC BGC BGC BGC 3.77358
22 5X7Q GLC GLC GLC GLC GLC 3.89294
23 5X7Q GLC GLC GLC GLC 3.89294
24 4RD0 GDP 3.89294
25 5HCA BGC 3.89294
26 1CEN BGC BGC 4.37318
27 1R4W GSH 4.42478
28 6CZI 38E 4.46429
29 4A91 GLU 4.69799
30 1M1B SPV 4.74576
31 3WUC GLC GAL 5.10949
32 2VPY PCI 5.12821
33 1SS4 GSH 5.22876
34 6HLY G9Z 5.27859
35 2ZMF CMP 5.29101
36 5XH2 NPO 5.34351
37 3ACL 3F1 6.08108
38 4ZTD ALA GLY ALA GLY ALA 6.32411
39 2RHQ GAX 6.32603
40 4R38 RBF 6.42857
41 3TTZ 07N 6.56566
42 3KFF XBT 6.79012
43 3KFF ZBT 6.79012
44 1MDC PLM 6.81818
45 2F67 12B 6.8323
46 4IAW LIZ 6.91489
47 5OM2 DXT 7.04607
48 1NSZ GLC 7.20461
49 3VPD ANP 7.82918
50 1ZM1 BGC BGC BGC 8.29876
51 4ZXA H8N 8.55457
52 2G30 ALA ALA PHE 8.91473
53 1W6P NDG GAL 12.6866
54 6BSX E7S 14.0449
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