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Receptor
PDB id Resolution Class Description Source Keywords
3UH0 2 Å EC: 6.1.1.3 CRYSTAL STRUCTURE OF THE YEAST MITOCHONDRIAL THREONYL-TRNA S (MST1) IN COMPLEX WITH THREONYL SULFAMOYL ADENYLATE SACCHAROMYCES CEREVISIAE THREONYL-TRNA SYNTHETASE TRNA THREONINE TRNA THREONYL ADETHREONYL SULFAMOYL ADENYLATE AMINOACYL-TRNA SYNTHETASE CLALIGASE
Ref.: YEAST MITOCHONDRIAL THREONYL-TRNA SYNTHETASE RECOGN ISOACCEPTORS BY DISTINCT MECHANISMS AND PROMOTES CU REASSIGNMENT. PROC.NATL.ACAD.SCI.USA V. 109 3281 2012
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SO4 A:463;
Invalid;
none;
submit data
96.063 O4 S [O-]S...
TSB A:1002;
Valid;
none;
submit data
447.424 C14 H21 N7 O8 S C[C@H...
ZN A:1;
Part of Protein;
none;
submit data
65.409 Zn [Zn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3UH0 2 Å EC: 6.1.1.3 CRYSTAL STRUCTURE OF THE YEAST MITOCHONDRIAL THREONYL-TRNA S (MST1) IN COMPLEX WITH THREONYL SULFAMOYL ADENYLATE SACCHAROMYCES CEREVISIAE THREONYL-TRNA SYNTHETASE TRNA THREONINE TRNA THREONYL ADETHREONYL SULFAMOYL ADENYLATE AMINOACYL-TRNA SYNTHETASE CLALIGASE
Ref.: YEAST MITOCHONDRIAL THREONYL-TRNA SYNTHETASE RECOGN ISOACCEPTORS BY DISTINCT MECHANISMS AND PROMOTES CU REASSIGNMENT. PROC.NATL.ACAD.SCI.USA V. 109 3281 2012
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 7 families.
1 3UH0 - TSB C14 H21 N7 O8 S C[C@H]([C@....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 3UH0 - TSB C14 H21 N7 O8 S 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: TSB; Similar ligands found: 258
No: Ligand ECFP6 Tc MDL keys Tc
1 TSB 1 1
2 VMS 0.865854 0.963855
3 54H 0.865854 0.963855
4 A5A 0.841463 0.987654
5 52H 0.8 0.952381
6 LSS 0.793103 0.930233
7 53H 0.790698 0.952381
8 SSA 0.788235 0.952381
9 5CA 0.770115 0.952381
10 LEU LMS 0.755556 0.91954
11 DSZ 0.752809 0.952381
12 NVA LMS 0.744444 0.91954
13 NSS 0.733333 0.952381
14 KAA 0.728261 0.897727
15 GSU 0.728261 0.929412
16 G5A 0.72093 0.929412
17 YSA 0.690722 0.929412
18 5AS 0.690476 0.929412
19 8X1 0.673913 0.897727
20 8PZ 0.646465 0.952381
21 P5A 0.639175 0.88764
22 LMS 0.638554 0.962963
23 WSA 0.638095 0.940476
24 8QN 0.631579 0.831325
25 5AL 0.612903 0.831325
26 SON 0.588889 0.790698
27 8Q2 0.587156 0.91954
28 4YB 0.584906 0.908046
29 TXA 0.584158 0.833333
30 AMP 0.581395 0.795181
31 A 0.581395 0.795181
32 ABM 0.579545 0.797619
33 A3T 0.576087 0.756098
34 AHX 0.57 0.804598
35 BA3 0.566667 0.819277
36 9ZA 0.565657 0.813953
37 9ZD 0.565657 0.813953
38 CA0 0.565217 0.821429
39 649 0.563636 0.88764
40 A2D 0.561798 0.819277
41 B4P 0.56044 0.819277
42 AP5 0.56044 0.819277
43 SRA 0.556818 0.821429
44 DAL AMP 0.555556 0.809524
45 AN2 0.554348 0.831325
46 SRP 0.55102 0.790698
47 A12 0.549451 0.790698
48 AP2 0.549451 0.790698
49 M33 0.548387 0.831325
50 AU1 0.548387 0.821429
51 ADX 0.548387 0.939024
52 PAJ 0.544554 0.795455
53 ADP 0.543478 0.819277
54 5X8 0.542553 0.705882
55 3DH 0.54023 0.714286
56 9K8 0.538462 0.795699
57 AT4 0.537634 0.833333
58 AQP 0.536842 0.819277
59 PRX 0.536842 0.77907
60 5FA 0.536842 0.819277
61 GAP 0.536082 0.77907
62 AOC 0.533333 0.714286
63 XAH 0.53271 0.758242
64 48N 0.531532 0.804598
65 ADN 0.530864 0.731707
66 XYA 0.530864 0.731707
67 RAB 0.530864 0.731707
68 5CD 0.53012 0.698795
69 SLU 0.529412 0.918605
70 AMO 0.529412 0.811765
71 ATP 0.526316 0.819277
72 50T 0.526316 0.788235
73 HEJ 0.526316 0.819277
74 ACP 0.526316 0.8
75 PTJ 0.52381 0.784091
76 NB8 0.52381 0.804598
77 ME8 0.52381 0.777778
78 APC 0.520833 0.790698
79 APR 0.520833 0.819277
80 AR6 0.520833 0.819277
81 ANP 0.520408 0.821429
82 5N5 0.518072 0.710843
83 SA8 0.515464 0.659341
84 ADV 0.515464 0.790698
85 SAP 0.515464 0.845238
86 RBY 0.515464 0.790698
87 AGS 0.515464 0.845238
88 AD9 0.515464 0.8
89 ADP PO3 0.515464 0.795181
90 4AD 0.514563 0.802326
91 LAD 0.514286 0.755556
92 A4D 0.511905 0.731707
93 EP4 0.511628 0.678161
94 DLL 0.509615 0.809524
95 M2T 0.505747 0.701149
96 DTA 0.505747 0.72619
97 T99 0.50505 0.833333
98 ACQ 0.50505 0.8
99 TAT 0.50505 0.833333
100 OOB 0.504854 0.809524
101 3UK 0.504762 0.8
102 OAD 0.504762 0.843373
103 7MD 0.504505 0.777778
104 MTA 0.5 0.714286
105 YAP 0.495413 0.781609
106 FA5 0.495413 0.790698
107 1ZZ 0.495327 0.758242
108 3OD 0.495327 0.843373
109 FYA 0.495327 0.767442
110 00A 0.495238 0.772727
111 MAP 0.495146 0.802326
112 A22 0.495146 0.809524
113 ALF ADP 0.49505 0.741573
114 ADP ALF 0.49505 0.741573
115 ATF 0.49505 0.790698
116 SAH 0.494949 0.689655
117 SFG 0.494845 0.674419
118 YLP 0.491228 0.741935
119 MYR AMP 0.490741 0.73913
120 9X8 0.490566 0.845238
121 25A 0.490385 0.797619
122 5SV 0.490385 0.744444
123 SMM 0.490196 0.677419
124 ADP VO4 0.490196 0.788235
125 VO4 ADP 0.490196 0.788235
126 S7M 0.490196 0.681319
127 6YZ 0.490196 0.8
128 SAM 0.49 0.681319
129 S4M 0.489362 0.642105
130 6RE 0.48913 0.648352
131 AMP DBH 0.486486 0.758621
132 9SN 0.486239 0.764045
133 WAQ 0.485981 0.772727
134 PR8 0.485981 0.747253
135 B5V 0.485981 0.790698
136 ADQ 0.485714 0.8
137 A3R 0.485714 0.772727
138 A1R 0.485714 0.772727
139 EEM 0.485149 0.645161
140 NEC 0.483871 0.690476
141 B5Y 0.481818 0.802326
142 B5M 0.481818 0.802326
143 JB6 0.481481 0.793103
144 SAI 0.48 0.662921
145 2VA 0.479592 0.738095
146 J7C 0.478723 0.655556
147 A3N 0.478723 0.686047
148 7MC 0.478632 0.78022
149 YLC 0.478632 0.758242
150 YLB 0.478632 0.741935
151 GA7 0.477876 0.790698
152 ARG AMP 0.477876 0.712766
153 ADP BMA 0.476636 0.77907
154 A3S 0.474227 0.72619
155 A7D 0.474227 0.697674
156 TAD 0.473684 0.795455
157 GJV 0.473684 0.641304
158 TYR AMP 0.473214 0.761364
159 0UM 0.471698 0.652174
160 F2R 0.471074 0.741935
161 TYM 0.470085 0.790698
162 AF3 ADP 3PG 0.470085 0.736264
163 LAQ 0.469565 0.777778
164 7C5 0.469027 0.715909
165 MAO 0.46875 0.706522
166 DSH 0.468085 0.655556
167 BIS 0.46789 0.772727
168 SXZ 0.46789 0.681319
169 COD 0.467213 0.755319
170 LPA AMP 0.465517 0.758242
171 SO8 0.465347 0.729412
172 25L 0.463636 0.809524
173 K15 0.462963 0.638298
174 AYB 0.46281 0.734043
175 ZAS 0.462366 0.689655
176 GTA 0.46087 0.777778
177 DQV 0.46087 0.831325
178 4UV 0.460177 0.781609
179 A A 0.458716 0.776471
180 OMR 0.457627 0.769231
181 TXE 0.457627 0.793103
182 AHZ 0.456897 0.758242
183 YLA 0.454545 0.723404
184 MHZ 0.454545 0.652632
185 AP0 0.453782 0.784091
186 62X 0.453704 0.625
187 A3G 0.452632 0.717647
188 5AD 0.452381 0.666667
189 AFH 0.452174 0.755556
190 4UU 0.452174 0.781609
191 3AM 0.451613 0.761905
192 NAX 0.449153 0.766667
193 6V0 0.449153 0.784091
194 NXX 0.449153 0.811765
195 TXD 0.449153 0.793103
196 4UW 0.449153 0.775281
197 DND 0.449153 0.811765
198 IOT 0.446281 0.715789
199 7D5 0.445652 0.724138
200 G3A 0.443478 0.784091
201 EO7 0.443299 0.917647
202 ATP A A A 0.442478 0.785714
203 G5P 0.439655 0.784091
204 AR6 AR6 0.439655 0.776471
205 CNA 0.439024 0.811765
206 A3P 0.438776 0.795181
207 A2P 0.438776 0.783133
208 YLY 0.4375 0.734043
209 NAI 0.436975 0.793103
210 UP5 0.436975 0.802326
211 VRT 0.436893 0.712644
212 A3D 0.436508 0.821429
213 GEK 0.435185 0.704545
214 3NZ 0.432432 0.724138
215 Y3J 0.431818 0.630952
216 T5A 0.430894 0.76087
217 NAQ 0.430769 0.784091
218 7D7 0.430233 0.647059
219 BT5 0.428571 0.734043
220 A5D 0.427184 0.72619
221 NVA 2AD 0.427184 0.704545
222 A4P 0.42623 0.726316
223 D3Y 0.425926 0.709302
224 2AM 0.425532 0.77381
225 80F 0.425197 0.76087
226 KB1 0.424779 0.634409
227 KH3 0.423729 0.631579
228 FB0 0.423358 0.714286
229 S8M 0.422018 0.704545
230 AMP NAD 0.420635 0.788235
231 NAD 0.420635 0.809524
232 ADJ 0.419355 0.731183
233 6IA 0.419048 0.717391
234 V3L 0.419048 0.797619
235 594 0.418605 0.8125
236 4TC 0.418033 0.784091
237 UPA 0.418033 0.793103
238 2A5 0.417476 0.758621
239 N0B 0.416667 0.723404
240 AAT 0.415094 0.641304
241 PPS 0.415094 0.915663
242 7D3 0.414141 0.747126
243 PAP 0.413462 0.807229
244 ATR 0.413462 0.795181
245 OVE 0.412371 0.788235
246 NAE 0.412214 0.802326
247 7D4 0.411765 0.747126
248 2SA 0.411215 0.790698
249 NAJ PZO 0.410853 0.764045
250 BTX 0.409449 0.741935
251 4TA 0.409449 0.731183
252 139 0.408 0.766667
253 IXN 0.407407 0.84375
254 J1D 0.40625 0.708738
255 DZD 0.40625 0.775281
256 BS5 0.404762 0.797872
257 590 0.404412 0.822917
258 A2R 0.40367 0.809524
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3UH0; Ligand: TSB; Similar sites found with APoc: 129
This union binding pocket(no: 1) in the query (biounit: 3uh0.bio1) has 25 residues
No: Leader PDB Ligand Sequence Similarity
1 2QPU QPU 1.7284
2 2QPU QPS 1.7284
3 1YFS ALA 1.73913
4 12AS AMP 1.81818
5 3BJU ATP 1.95652
6 2XGT NSS 2.06897
7 4MOB ADP 2.10843
8 2WLT ASP 2.10843
9 4V15 PLP 2.11082
10 5OCG 9R5 2.1164
11 5FPE 3TR 2.32558
12 5KJW 53C 2.34192
13 1WLE SRP 2.3913
14 1E1O LYS 2.3913
15 4YVN EBS 2.3913
16 4FFG 0U8 2.6087
17 4KBA 1QM 2.71903
18 1F9V ADP 2.88184
19 1RJW ETF 2.94985
20 3NEM ATP 2.96804
21 3NEM AMO 2.96804
22 4RGA 3PV 3.05344
23 1X54 4AD 3.22581
24 3JU6 ANP 3.24324
25 2D24 XYS XYS 3.66972
26 4A91 GLU 3.69128
27 5GLT BGC GAL NAG GAL 3.87324
28 1JQY A32 3.91304
29 1B7Y FYA 4
30 6GR0 F8W 4.02299
31 3CQL NAG 4.11523
32 2YFT DQR 4.13043
33 4G9N NGA 4.1958
34 2ZTG A5A 4.34783
35 2PFC PLM 4.37158
36 1DZK PRZ 4.4586
37 3CBC DBS 4.54545
38 1G51 AMO 4.56522
39 5IXB LGA 4.62963
40 3WD6 GSH 4.6875
41 4JZ8 CIT 4.73186
42 5V59 8X1 4.78261
43 3E9I XAH 4.78261
44 3HQP OXL 4.78261
45 4LED XXR 4.85075
46 3M3E GAL A2G NPO 4.96894
47 5LY1 PPI 4.98688
48 5F6U 5VK 5.09554
49 5DG2 GAL GLC 5.18518
50 3HXU A5A 5.21542
51 5TZO 7V7 5.31915
52 5H9Y BGC BGC BGC BGC 5.40541
53 3KFF ZBT 5.55556
54 3KFF XBT 5.55556
55 3A5Z KAA 5.75916
56 3ZXE PGZ 6.01504
57 5FUI APY 6.06061
58 5L2R MLA 6.08696
59 2YMZ LAT 6.15385
60 1QKQ MAN 6.33803
61 5T7I LAT NAG GAL 6.45161
62 5V8E CIT 6.47249
63 5LDQ NAP 6.77966
64 6F3G CJN 6.77966
65 1KNM LAT 6.92308
66 2Z77 HE7 7.19424
67 3WUD GLC GAL 7.35294
68 3A16 PXO 7.5067
69 1LSH PLD 7.52351
70 4WVW SLT 7.63889
71 4L6T GAL NGA GAL BGC SIA 8.03571
72 6GNO XDI 8.14815
73 1KJ1 MAN 8.25688
74 5J75 6GQ 8.33333
75 3A5Y KAA 8.4058
76 5DYO FLU 8.49057
77 4YLZ LAT NAG GAL 8.49673
78 5NLD LBT 8.63309
79 1ULE GLA GAL NAG 8.66667
80 1OFL NGK GCD 8.69565
81 3G1Z AMP 8.89571
82 3OYW TDG 8.95522
83 1W6P NDG GAL 8.95522
84 6EV2 BGC 9.00901
85 4RYV ZEA 9.03226
86 3WV6 GAL GLC 9.12162
87 5N2F 8HW 9.67742
88 3WUC GLC GAL 10.219
89 3UW4 MAA CHG PRO 0DQ 10.8696
90 3ERR AMP 11.087
91 3L9R L9Q 11.2245
92 3L9R L9R 11.2245
93 2D6M LBT 11.9497
94 6FA4 D1W 12.1387
95 1SES AMP 12.3515
96 1SES AHX 12.3515
97 3QO8 SSA 12.3913
98 2CJA ATP 12.6437
99 5H9P TD2 12.6582
100 2CJ9 SSA 12.8261
101 4Y24 TD2 13.6364
102 3GUZ PAF 13.6364
103 4LO2 GAL BGC 13.8514
104 3MF2 AMP 13.8728
105 2J3M PRI 13.913
106 2J3M ATP 13.913
107 3REU ATP 13.9456
108 3WG3 A2G GAL NAG FUC 14.0449
109 5VAD 91Y 15
110 5VAD PRO 15
111 2ZQO NGA 15.3846
112 5H9Q TD2 15.4839
113 5M6N 7H9 18.6441
114 4YGF AZM 18.8034
115 4CS4 ANP 19.3431
116 4CS4 AXZ 19.3431
117 4H2V AMP 20
118 2I4O ATP 20.0873
119 4K55 H6P 21.7742
120 4H2X G5A 27.1845
121 4H2W AMP 27.1845
122 4H2W 5GP 27.1845
123 3IAL PR8 27.6087
124 5XIJ ANP 28.4783
125 5XIJ 873 28.4783
126 5XIO ANP 31.3253
127 5XIO HFG 31.3253
128 4YDQ ANP 33.913
129 4YDQ HFG 33.913
Pocket No.: 2; Query (leader) PDB : 3UH0; Ligand: TSB; 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: 3uh0.bio1) has 25 residues
No: Leader PDB Ligand Sequence Similarity
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