Receptor
PDB id Resolution Class Description Source Keywords
2OV4 2.5 Å EC: 6.1.1.2 CRYSTAL STRUCTURE OF B. STEAROTHERMOPHILUS TRYPTOPHANYL TRNA SYNTHETASE IN COMPLEX WITH ADENOSINE TETRAPHOSPHATE GEOBACILLUS STEAROTHERMOPHILUS AMINOACYL-TRNA SYNTHETASE NUCLEOTIDE BINDING SITE ROSSMANNTRANSITION STATE ANALOG INHIBITOR LIGASE
Ref.: CRYSTAL STRUCTURE OF TRYPTOPHANYL-TRNA SYNTHETASE C WITH ADENOSINE-5' TETRAPHOSPHATE: EVIDENCE FOR DIST USE OF CATALYTIC BINDING ENERGY IN AMINO ACID ACTIV CLASS I AMINOACYL-TRNA SYNTHETASES. J.MOL.BIOL. V. 369 108 2007
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ANL A:950;
Invalid;
none;
submit data
93.126 C6 H7 N c1ccc...
AQP A:400;
Valid;
none;
Ki = 2 mM
587.161 C10 H17 N5 O16 P4 c1nc(...
CS A:900;
Invalid;
none;
submit data
132.905 Cs [Cs+]
GOL A:930;
A:940;
Invalid;
Invalid;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5DK4 1.9 Å EC: 6.1.1.2 CRYSTAL STRUCTURE ANALYSIS OF TRYPTOPHANYL-TRNA SYNTHETASE F BACILLUS STEAROTHERMOPHILUS IN COMPLEX WITH INDOLMYCIN AND GEOBACILLUS STEAROTHERMOPHILUS AARS INHIBITOR LIGASE-LIGASE INHIBITOR COMPLEX
Ref.: SELECTIVE INHIBITION OF BACTERIAL TRYPTOPHANYL-TRNA SYNTHETASES BY INDOLMYCIN IS MECHANISM-BASED. J.BIOL.CHEM. V. 291 255 2016
Members (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 1I6K - TYM C21 H24 N7 O8 P c1ccc2c(c1....
2 1MAU - CIT C6 H8 O7 C(C(=O)O)C....
3 1M83 Kd = 0.4 mM ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
4 1I6M - TYM C21 H24 N7 O8 P c1ccc2c(c1....
5 5DK4 Ki = 2 nM 5BX C14 H15 N3 O2 C[C@H](c1c....
6 1I6L - TYM C21 H24 N7 O8 P c1ccc2c(c1....
7 2OV4 Ki = 2 mM AQP C10 H17 N5 O16 P4 c1nc(c2c(n....
70% Homology Family (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 1I6K - TYM C21 H24 N7 O8 P c1ccc2c(c1....
2 1MAU - CIT C6 H8 O7 C(C(=O)O)C....
3 1M83 Kd = 0.4 mM ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
4 1I6M - TYM C21 H24 N7 O8 P c1ccc2c(c1....
5 5DK4 Ki = 2 nM 5BX C14 H15 N3 O2 C[C@H](c1c....
6 1I6L - TYM C21 H24 N7 O8 P c1ccc2c(c1....
7 2OV4 Ki = 2 mM AQP C10 H17 N5 O16 P4 c1nc(c2c(n....
50% Homology Family (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 1I6K - TYM C21 H24 N7 O8 P c1ccc2c(c1....
2 1MAU - CIT C6 H8 O7 C(C(=O)O)C....
3 1M83 Kd = 0.4 mM ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
4 1I6M - TYM C21 H24 N7 O8 P c1ccc2c(c1....
5 5DK4 Ki = 2 nM 5BX C14 H15 N3 O2 C[C@H](c1c....
6 1I6L - TYM C21 H24 N7 O8 P c1ccc2c(c1....
7 2OV4 Ki = 2 mM AQP C10 H17 N5 O16 P4 c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: AQP; Similar ligands found: 447
No: Ligand ECFP6 Tc MDL keys Tc
1 AQP 1 1
2 5FA 1 1
3 ATP 0.985507 1
4 HEJ 0.985507 1
5 B4P 0.942029 0.971831
6 AP5 0.942029 0.971831
7 BA3 0.927536 0.971831
8 ADP 0.887324 1
9 A2D 0.871429 0.971831
10 SAP 0.828947 0.945946
11 AGS 0.828947 0.945946
12 6YZ 0.822785 0.972222
13 25L 0.8 0.985915
14 AT4 0.8 0.958904
15 AN2 0.8 0.985915
16 APR 0.792208 0.971831
17 AR6 0.792208 0.971831
18 M33 0.789474 0.958333
19 TAT 0.78481 0.958904
20 T99 0.78481 0.958904
21 ACQ 0.78481 0.972222
22 AD9 0.782051 0.972222
23 ACP 0.779221 0.972222
24 A 0.777778 0.971429
25 AMP 0.777778 0.971429
26 ANP 0.7625 0.972222
27 HQG 0.746988 0.985915
28 ADX 0.74359 0.873418
29 CA0 0.74359 0.945205
30 A22 0.738095 0.985915
31 KG4 0.734177 0.945205
32 50T 0.734177 0.958333
33 APC 0.725 0.958904
34 PRX 0.725 0.893333
35 45A 0.723684 0.917808
36 ABM 0.723684 0.917808
37 ATF 0.722892 0.958904
38 7D4 0.721519 0.905405
39 ITT 0.721519 0.943662
40 ADQ 0.72093 0.945205
41 A3R 0.72093 0.907895
42 A12 0.705128 0.958904
43 AP2 0.705128 0.958904
44 A1R 0.701149 0.907895
45 SRA 0.697368 0.918919
46 G5P 0.691489 0.921053
47 5AL 0.690476 0.931507
48 8LE 0.690476 0.894737
49 ADP MG 0.6875 0.943662
50 HFD 0.686747 0.945946
51 JSQ 0.686747 0.945946
52 9X8 0.685393 0.92
53 OAD 0.685393 0.945205
54 G3A 0.680851 0.921053
55 AU1 0.679012 0.972222
56 APC MG 0.674699 0.917808
57 8LH 0.674419 0.906667
58 SRP 0.674419 0.906667
59 8QN 0.670455 0.931507
60 25A 0.670455 0.971831
61 OZV 0.670455 0.971831
62 3OD 0.67033 0.945205
63 GTA 0.666667 0.886076
64 UP5 0.663265 0.92
65 4AD 0.662921 0.92
66 8LQ 0.659091 0.906667
67 00A 0.655556 0.883117
68 ADV 0.654762 0.932432
69 RBY 0.654762 0.932432
70 ADP PO3 0.654762 0.943662
71 ATP MG 0.654762 0.943662
72 BIS 0.652174 0.933333
73 OOB 0.651685 0.931507
74 5SV 0.651685 0.848101
75 PAJ 0.644444 0.884615
76 AMO 0.644444 0.932432
77 A4P 0.643564 0.843373
78 2A5 0.642857 0.918919
79 MAP 0.640449 0.945946
80 3AT 0.639535 0.971831
81 DLL 0.637363 0.931507
82 AHX 0.637363 0.896104
83 ATR 0.635294 0.971429
84 PAP 0.635294 0.985714
85 PTJ 0.634409 0.896104
86 T5A 0.631068 0.841463
87 3UK 0.630435 0.918919
88 7D3 0.62963 0.905405
89 SON 0.626506 0.932432
90 ADP ALF 0.625 0.87013
91 ALF ADP 0.625 0.87013
92 B5V 0.623656 0.906667
93 PR8 0.623656 0.85
94 WAQ 0.623656 0.883117
95 LAD 0.623656 0.860759
96 AFH 0.622449 0.884615
97 DTP 0.62069 0.905405
98 GAP 0.62069 0.893333
99 LMS 0.620253 0.82716
100 ADP VO4 0.617977 0.931507
101 VO4 ADP 0.617977 0.931507
102 ME8 0.617021 0.839506
103 TXA 0.617021 0.932432
104 1ZZ 0.617021 0.839506
105 NB8 0.617021 0.896104
106 FYA 0.617021 0.905405
107 DQV 0.616162 0.958333
108 XYA 0.611111 0.84507
109 RAB 0.611111 0.84507
110 ADN 0.611111 0.84507
111 DAL AMP 0.604396 0.905405
112 9SN 0.604167 0.871795
113 48N 0.60396 0.896104
114 AP0 0.601942 0.896104
115 NAX 0.598039 0.873418
116 DND 0.598039 0.932432
117 TXD 0.598039 0.907895
118 NAI 0.598039 0.907895
119 6V0 0.598039 0.896104
120 NXX 0.598039 0.932432
121 B5Y 0.597938 0.894737
122 B5M 0.597938 0.894737
123 YAP 0.597938 0.894737
124 FA5 0.597938 0.906667
125 9ZA 0.597826 0.907895
126 9ZD 0.597826 0.907895
127 ADP BMA 0.595745 0.918919
128 A2R 0.593407 0.985915
129 TXE 0.592233 0.907895
130 OMR 0.592233 0.851852
131 XAH 0.591837 0.839506
132 7DT 0.586207 0.985714
133 4UV 0.585859 0.894737
134 AOC 0.585366 0.821918
135 139 0.584906 0.873418
136 DDS 0.58427 0.878378
137 CNA 0.579439 0.932432
138 6AD 0.577778 0.909091
139 5AS 0.576471 0.77907
140 4UU 0.574257 0.894737
141 GA7 0.574257 0.906667
142 5N5 0.573333 0.819444
143 4TC 0.571429 0.896104
144 ADJ 0.570093 0.851852
145 5CD 0.565789 0.805556
146 A4D 0.565789 0.819444
147 RGT 0.565657 0.958904
148 A3P 0.564706 0.971429
149 LAQ 0.563107 0.839506
150 7D5 0.5625 0.878378
151 F2R 0.559633 0.864198
152 NO7 0.55914 0.932432
153 80F 0.558559 0.841463
154 YLP 0.557692 0.819277
155 A A 0.556701 0.944444
156 UPA 0.556604 0.907895
157 COD 0.554545 0.811765
158 AV2 0.554348 0.917808
159 4UW 0.552381 0.860759
160 JB6 0.55102 0.883117
161 ATP A A A 0.55 0.930556
162 ATP A 0.55 0.930556
163 3AM 0.548781 0.929577
164 TYM 0.54717 0.906667
165 A2P 0.546512 0.957143
166 NA7 0.546392 0.958904
167 MYR AMP 0.545455 0.817073
168 EP4 0.544304 0.753247
169 PPS 0.543478 0.873418
170 YLC 0.542056 0.839506
171 YLB 0.542056 0.819277
172 NAD 0.540541 0.931507
173 H1Q 0.539326 0.90411
174 DAT 0.539326 0.905405
175 TYR AMP 0.539216 0.87013
176 G5A 0.538462 0.77907
177 128 0.537736 0.776471
178 DTA 0.5375 0.786667
179 M2T 0.5375 0.734177
180 TSB 0.536842 0.819277
181 3DH 0.536585 0.773333
182 AHZ 0.533333 0.817073
183 IOT 0.53211 0.831325
184 GTP 0.531915 0.92
185 SSA 0.531915 0.8
186 A3D 0.530973 0.918919
187 MTA 0.530864 0.773333
188 ARG AMP 0.528846 0.829268
189 7MD 0.528846 0.8625
190 AR6 AR6 0.528846 0.917808
191 YLA 0.527273 0.819277
192 VMS 0.526316 0.788235
193 54H 0.526316 0.788235
194 AMP DBH 0.524272 0.893333
195 TAD 0.52381 0.884615
196 IMO 0.523256 0.929577
197 AYB 0.522523 0.809524
198 A5A 0.521277 0.807229
199 HDV 0.521277 0.893333
200 EAD 0.521008 0.873418
201 2AM 0.518072 0.943662
202 6RE 0.517647 0.759494
203 6MZ 0.517241 0.930556
204 7DD 0.516854 0.985714
205 V3L 0.516129 0.971831
206 AVV 0.515464 0.896104
207 BTX 0.513274 0.841463
208 NAE 0.512821 0.894737
209 52H 0.510417 0.77907
210 NSS 0.510204 0.8
211 BT5 0.508772 0.831325
212 NAQ 0.508475 0.871795
213 ZAS 0.505882 0.766234
214 J7C 0.505747 0.769231
215 A3N 0.505747 0.786667
216 5X8 0.505495 0.763158
217 5CA 0.505155 0.8
218 8X1 0.505155 0.752809
219 53H 0.505155 0.77907
220 ARU 0.50505 0.860759
221 NVA LMS 0.50505 0.752809
222 9K8 0.504951 0.714286
223 AF3 ADP 3PG 0.504587 0.8375
224 ZID 0.504202 0.918919
225 P1H 0.504065 0.851852
226 LPA AMP 0.5 0.817073
227 S4M 0.5 0.666667
228 6G0 0.5 0.884615
229 7MC 0.5 0.841463
230 LEU LMS 0.5 0.752809
231 OVE 0.5 0.905405
232 FB0 0.496 0.804598
233 DZD 0.495652 0.884615
234 P5A 0.49505 0.744444
235 LSS 0.494949 0.761364
236 DSZ 0.494949 0.8
237 MAO 0.494382 0.759036
238 DSH 0.494253 0.725
239 NDE 0.491935 0.932432
240 N0B 0.491667 0.819277
241 M24 0.491525 0.85
242 YLY 0.491525 0.809524
243 NJP 0.491228 0.945946
244 MGP 0.489583 0.884615
245 6C6 0.489362 0.881579
246 GP3 0.489362 0.921053
247 NAJ PZO 0.487179 0.848101
248 0WD 0.486957 0.921053
249 6FA 0.484375 0.841463
250 GJV 0.483146 0.75
251 5AD 0.480519 0.746479
252 KAA 0.480392 0.752809
253 GSU 0.480392 0.77907
254 ODP 0.478261 0.909091
255 71V 0.477778 0.907895
256 NEC 0.477273 0.746667
257 A3G 0.477273 0.8
258 FAD 0.476923 0.851852
259 FAS 0.476923 0.851852
260 FDA 0.476562 0.833333
261 N6P 0.475248 0.915493
262 7D7 0.474359 0.743243
263 2SA 0.474227 0.932432
264 G A A A 0.474138 0.871795
265 AMP NAD 0.474138 0.905405
266 4TA 0.474138 0.807229
267 NDP 0.473684 0.921053
268 NPW 0.473684 0.886076
269 SFG 0.473118 0.75
270 NDC 0.472441 0.871795
271 YSA 0.471698 0.77907
272 LQJ 0.471698 0.917808
273 NAJ PYZ 0.471074 0.807229
274 TXP 0.469565 0.921053
275 NZQ 0.469565 0.909091
276 MGO 0.469388 0.860759
277 GDP 0.46875 0.92
278 6IA 0.46875 0.8375
279 A7D 0.467391 0.776316
280 J4G 0.466019 0.92
281 SFD 0.465649 0.734043
282 12D 0.463636 0.785714
283 A5D 0.463158 0.786667
284 SA8 0.463158 0.707317
285 ZDA 0.463158 0.864865
286 62F 0.462687 0.8625
287 MHZ 0.462366 0.697674
288 PGS 0.462366 0.883117
289 8PZ 0.462264 0.8
290 DA 0.460674 0.878378
291 D5M 0.460674 0.878378
292 GGZ 0.46 0.825
293 FAY 0.459259 0.8625
294 SAH 0.458333 0.74359
295 SAI 0.458333 0.734177
296 B1U 0.457944 0.736264
297 A3T 0.457447 0.821918
298 Y3J 0.45679 0.726027
299 PO4 PO4 A A A A PO4 0.456311 0.902778
300 RFL 0.455882 0.821429
301 AAM 0.455556 0.971429
302 SMM 0.454545 0.686047
303 HF7 0.454545 0.893333
304 SAM 0.453608 0.690476
305 C2R 0.453488 0.90411
306 AMZ 0.453488 0.916667
307 FNK 0.451852 0.804598
308 A3S 0.451613 0.810811
309 U A 0.45 0.907895
310 7C5 0.449541 0.818182
311 A G 0.449153 0.883117
312 XNP 0.449153 0.873418
313 AAT 0.44898 0.707317
314 EEM 0.44898 0.690476
315 PRT 0.448598 0.931507
316 62X 0.446602 0.666667
317 KOY 0.446429 0.802632
318 DCA 0.446281 0.823529
319 ETB 0.446281 0.833333
320 AIR 0.445783 0.901408
321 GSP 0.445545 0.873418
322 U A G G 0.445378 0.883117
323 N5O 0.444444 0.763158
324 NIA 0.443182 0.822785
325 PUA 0.442623 0.884615
326 K15 0.442308 0.682353
327 A A A 0.442308 0.905405
328 4YB 0.441441 0.761364
329 GEK 0.441176 0.7375
330 6K6 0.441176 0.930556
331 1DG 0.44 0.921053
332 DG1 0.44 0.921053
333 Z5A 0.44 0.77907
334 S7M 0.44 0.690476
335 COA 0.439024 0.823529
336 0T1 0.439024 0.823529
337 WSA 0.438596 0.788235
338 8BR 0.434783 0.906667
339 8Q2 0.434783 0.772727
340 N5A 0.434783 0.736842
341 101 0.433333 0.878378
342 IDP 0.43299 0.918919
343 NVA 2AD 0.43299 0.759494
344 9JJ 0.432624 0.8625
345 NAP 0.432 0.945205
346 APU 0.431034 0.894737
347 A U 0.431034 0.87013
348 CAO 0.428571 0.795455
349 30N 0.428571 0.752688
350 7RP 0.428571 0.928571
351 AMX 0.428571 0.833333
352 A6D 0.428571 0.722892
353 J7V 0.428571 0.833333
354 COS 0.428571 0.804598
355 TAP 0.428571 0.907895
356 V1N 0.427273 0.917808
357 2VA 0.427083 0.8
358 P5F 0.426573 0.823529
359 649 0.426087 0.744444
360 NA0 0.425197 0.932432
361 CMX 0.425197 0.823529
362 SCO 0.425197 0.823529
363 7RA 0.423913 0.957747
364 GAV 0.423077 0.884615
365 0UM 0.423077 0.698795
366 1RB 0.422222 0.885714
367 ACK 0.422222 0.861111
368 QQY 0.422222 0.815789
369 FCX 0.421875 0.795455
370 ACO 0.421875 0.795455
371 FAM 0.421875 0.804598
372 GCP 0.421569 0.896104
373 G1R 0.421569 0.907895
374 OZP 0.421053 0.728395
375 F2N 0.42069 0.813953
376 GNH 0.42 0.907895
377 HAX 0.418605 0.804598
378 GDD 0.418182 0.884615
379 GDC 0.418182 0.884615
380 GKE 0.418182 0.884615
381 FA9 0.417808 0.864198
382 9GM 0.417476 0.896104
383 GNP 0.417476 0.896104
384 9BG 0.416667 0.896104
385 KB1 0.416667 0.698795
386 3AD 0.416667 0.805556
387 2MC 0.416667 0.769231
388 TM1 0.416667 0.77381
389 H6Y 0.415842 0.945205
390 FYN 0.415385 0.823529
391 3KK 0.415385 0.804598
392 GTG 0.414414 0.886076
393 SO8 0.414141 0.789474
394 7L1 0.414062 0.795455
395 S8M 0.413462 0.759494
396 NHD 0.413223 0.905405
397 HZ2 0.412281 0.731707
398 SOP 0.412214 0.804598
399 OXK 0.412214 0.804598
400 COK 0.412214 0.804598
401 YZS 0.412214 0.729167
402 CA6 0.412214 0.729167
403 MCD 0.412214 0.804598
404 KGP 0.412214 0.729167
405 26A 0.411765 0.763158
406 QQX 0.411111 0.805195
407 YE1 0.410448 0.813953
408 NMX 0.409091 0.76087
409 1VU 0.409091 0.795455
410 CO6 0.409091 0.804598
411 CMC 0.409091 0.804598
412 RMB 0.408602 0.873239
413 AS 0.408602 0.833333
414 FAI 0.408602 0.916667
415 SXZ 0.407407 0.710843
416 SCA 0.407407 0.804598
417 ANZ 0.40708 0.8
418 CAJ 0.406015 0.804598
419 SCD 0.406015 0.823529
420 HY8 0.405172 0.731707
421 KGA 0.404412 0.744681
422 EO7 0.404255 0.788235
423 D3Y 0.403846 0.789474
424 KH3 0.403509 0.674419
425 A C A C 0.403226 0.848101
426 SLU 0.403226 0.770115
427 KGJ 0.402985 0.752688
428 A1S 0.402985 0.804598
429 1HE 0.402985 0.786517
430 BCO 0.402985 0.804598
431 3HC 0.402985 0.813953
432 MLC 0.402985 0.804598
433 IVC 0.402985 0.813953
434 CC5 0.402439 0.816901
435 G 0.402062 0.906667
436 5GP 0.402062 0.906667
437 NMN AMP PO4 0.401639 0.87013
438 CAA 0.4 0.813953
439 3L1 0.4 0.773333
440 3D1 0.4 0.773333
441 MCA 0.4 0.795455
442 LCV 0.4 0.721649
443 VRT 0.4 0.769231
444 SO5 0.4 0.721649
445 CMP 0.4 0.901408
446 COO 0.4 0.804598
447 2BA 0.4 0.915493
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5DK4; Ligand: 5BX; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 5dk4.bio1) has 43 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5DK4; Ligand: 5BX; 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: 5dk4.bio1) has 43 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 5DK4; Ligand: ATP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 5dk4.bio1) has 42 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 5DK4; Ligand: ATP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 5dk4.bio1) has 42 residues
No: Leader PDB Ligand Sequence Similarity
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