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: 416
No: Ligand ECFP6 Tc MDL keys Tc
1 5FA 1 1
2 AQP 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 AGS 0.828947 0.945946
11 SAP 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 T99 0.78481 0.958904
20 ACQ 0.78481 0.972222
21 TAT 0.78481 0.958904
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 CA0 0.74359 0.945205
28 ADX 0.74359 0.873418
29 A22 0.738095 0.985915
30 50T 0.734177 0.958333
31 APC 0.725 0.958904
32 PRX 0.725 0.893333
33 ABM 0.723684 0.917808
34 ATF 0.722892 0.958904
35 ITT 0.721519 0.943662
36 7D4 0.721519 0.905405
37 A3R 0.72093 0.907895
38 ADQ 0.72093 0.945205
39 AP2 0.705128 0.958904
40 A12 0.705128 0.958904
41 A1R 0.701149 0.907895
42 SRA 0.697368 0.918919
43 G5P 0.691489 0.921053
44 5AL 0.690476 0.931507
45 HFD 0.686747 0.945946
46 OAD 0.685393 0.945205
47 9X8 0.685393 0.92
48 G3A 0.680851 0.921053
49 AU1 0.679012 0.972222
50 SRP 0.674419 0.906667
51 25A 0.670455 0.971831
52 8QN 0.670455 0.931507
53 3OD 0.67033 0.945205
54 GTA 0.666667 0.886076
55 UP5 0.663265 0.92
56 4AD 0.662921 0.92
57 00A 0.655556 0.883117
58 ADV 0.654762 0.932432
59 RBY 0.654762 0.932432
60 ADP PO3 0.654762 0.943662
61 BIS 0.652174 0.933333
62 OOB 0.651685 0.931507
63 5SV 0.651685 0.848101
64 PAJ 0.644444 0.884615
65 AMO 0.644444 0.932432
66 A4P 0.643564 0.843373
67 2A5 0.642857 0.918919
68 MAP 0.640449 0.945946
69 3AT 0.639535 0.971831
70 DLL 0.637363 0.931507
71 AHX 0.637363 0.896104
72 ATR 0.635294 0.971429
73 PAP 0.635294 0.985714
74 PTJ 0.634409 0.896104
75 T5A 0.631068 0.841463
76 3UK 0.630435 0.918919
77 7D3 0.62963 0.905405
78 SON 0.626506 0.932432
79 ALF ADP 0.625 0.87013
80 ADP ALF 0.625 0.87013
81 WAQ 0.623656 0.883117
82 PR8 0.623656 0.85
83 B5V 0.623656 0.906667
84 LAD 0.623656 0.860759
85 AFH 0.622449 0.884615
86 DTP 0.62069 0.905405
87 GAP 0.62069 0.893333
88 LMS 0.620253 0.82716
89 ADP VO4 0.617977 0.931507
90 VO4 ADP 0.617977 0.931507
91 1ZZ 0.617021 0.839506
92 NB8 0.617021 0.896104
93 TXA 0.617021 0.932432
94 FYA 0.617021 0.905405
95 ME8 0.617021 0.839506
96 DQV 0.616162 0.958333
97 RAB 0.611111 0.84507
98 XYA 0.611111 0.84507
99 ADN 0.611111 0.84507
100 DAL AMP 0.604396 0.905405
101 9SN 0.604167 0.871795
102 48N 0.60396 0.896104
103 AP0 0.601942 0.896104
104 NAI 0.598039 0.907895
105 6V0 0.598039 0.896104
106 DND 0.598039 0.932432
107 TXD 0.598039 0.907895
108 NAX 0.598039 0.873418
109 NXX 0.598039 0.932432
110 YAP 0.597938 0.894737
111 B5Y 0.597938 0.894737
112 B5M 0.597938 0.894737
113 FA5 0.597938 0.906667
114 9ZA 0.597826 0.907895
115 9ZD 0.597826 0.907895
116 ADP BMA 0.595745 0.918919
117 A2R 0.593407 0.985915
118 OMR 0.592233 0.851852
119 TXE 0.592233 0.907895
120 XAH 0.591837 0.839506
121 7DT 0.586207 0.985714
122 4UV 0.585859 0.894737
123 AOC 0.585366 0.821918
124 139 0.584906 0.873418
125 DDS 0.58427 0.878378
126 CNA 0.579439 0.932432
127 6AD 0.577778 0.909091
128 5AS 0.576471 0.77907
129 GA7 0.574257 0.906667
130 4UU 0.574257 0.894737
131 5N5 0.573333 0.819444
132 4TC 0.571429 0.896104
133 ADJ 0.570093 0.851852
134 A4D 0.565789 0.819444
135 5CD 0.565789 0.805556
136 RGT 0.565657 0.958904
137 A3P 0.564706 0.971429
138 LAQ 0.563107 0.839506
139 7D5 0.5625 0.878378
140 F2R 0.559633 0.864198
141 80F 0.558559 0.841463
142 YLP 0.557692 0.819277
143 A A 0.556701 0.944444
144 UPA 0.556604 0.907895
145 COD 0.554545 0.811765
146 AV2 0.554348 0.917808
147 4UW 0.552381 0.860759
148 JB6 0.55102 0.883117
149 ATP A A A 0.55 0.930556
150 3AM 0.548781 0.929577
151 TYM 0.54717 0.906667
152 A2P 0.546512 0.957143
153 NA7 0.546392 0.958904
154 MYR AMP 0.545455 0.817073
155 EP4 0.544304 0.753247
156 PPS 0.543478 0.873418
157 YLC 0.542056 0.839506
158 YLB 0.542056 0.819277
159 NAD 0.540541 0.931507
160 DAT 0.539326 0.905405
161 TYR AMP 0.539216 0.87013
162 G5A 0.538462 0.77907
163 128 0.537736 0.776471
164 M2T 0.5375 0.734177
165 DTA 0.5375 0.786667
166 TSB 0.536842 0.819277
167 3DH 0.536585 0.773333
168 AHZ 0.533333 0.817073
169 IOT 0.53211 0.831325
170 SSA 0.531915 0.8
171 GTP 0.531915 0.92
172 A3D 0.530973 0.918919
173 MTA 0.530864 0.773333
174 AR6 AR6 0.528846 0.917808
175 ARG AMP 0.528846 0.829268
176 7MD 0.528846 0.8625
177 YLA 0.527273 0.819277
178 VMS 0.526316 0.788235
179 54H 0.526316 0.788235
180 AMP DBH 0.524272 0.893333
181 TAD 0.52381 0.884615
182 IMO 0.523256 0.929577
183 AYB 0.522523 0.809524
184 HDV 0.521277 0.893333
185 A5A 0.521277 0.807229
186 EAD 0.521008 0.873418
187 2AM 0.518072 0.943662
188 6RE 0.517647 0.759494
189 7DD 0.516854 0.985714
190 V3L 0.516129 0.971831
191 AVV 0.515464 0.896104
192 BTX 0.513274 0.841463
193 NAE 0.512821 0.894737
194 52H 0.510417 0.77907
195 NSS 0.510204 0.8
196 BT5 0.508772 0.831325
197 NAQ 0.508475 0.871795
198 ZAS 0.505882 0.766234
199 J7C 0.505747 0.769231
200 A3N 0.505747 0.786667
201 5X8 0.505495 0.763158
202 8X1 0.505155 0.752809
203 5CA 0.505155 0.8
204 53H 0.505155 0.77907
205 ARU 0.50505 0.860759
206 NVA LMS 0.50505 0.752809
207 9K8 0.504951 0.714286
208 AF3 ADP 3PG 0.504587 0.8375
209 ZID 0.504202 0.918919
210 P1H 0.504065 0.851852
211 LPA AMP 0.5 0.817073
212 6G0 0.5 0.884615
213 7MC 0.5 0.841463
214 LEU LMS 0.5 0.752809
215 S4M 0.5 0.666667
216 OVE 0.5 0.905405
217 FB0 0.496 0.804598
218 DZD 0.495652 0.884615
219 P5A 0.49505 0.744444
220 LSS 0.494949 0.761364
221 DSZ 0.494949 0.8
222 MAO 0.494382 0.759036
223 DSH 0.494253 0.725
224 NDE 0.491935 0.932432
225 N0B 0.491667 0.819277
226 YLY 0.491525 0.809524
227 M24 0.491525 0.85
228 NJP 0.491228 0.945946
229 MGP 0.489583 0.884615
230 GP3 0.489362 0.921053
231 6C6 0.489362 0.881579
232 NAJ PZO 0.487179 0.848101
233 0WD 0.486957 0.921053
234 6FA 0.484375 0.841463
235 GJV 0.483146 0.75
236 5AD 0.480519 0.746479
237 GSU 0.480392 0.77907
238 KAA 0.480392 0.752809
239 ODP 0.478261 0.909091
240 71V 0.477778 0.907895
241 A3G 0.477273 0.8
242 NEC 0.477273 0.746667
243 FAS 0.476923 0.851852
244 FAD 0.476923 0.851852
245 FDA 0.476562 0.833333
246 N6P 0.475248 0.915493
247 7D7 0.474359 0.743243
248 2SA 0.474227 0.932432
249 G A A A 0.474138 0.871795
250 4TA 0.474138 0.807229
251 AMP NAD 0.474138 0.905405
252 NPW 0.473684 0.886076
253 NDP 0.473684 0.921053
254 SFG 0.473118 0.75
255 NDC 0.472441 0.871795
256 YSA 0.471698 0.77907
257 NAJ PYZ 0.471074 0.807229
258 NZQ 0.469565 0.909091
259 TXP 0.469565 0.921053
260 MGO 0.469388 0.860759
261 6IA 0.46875 0.8375
262 GDP 0.46875 0.92
263 A7D 0.467391 0.776316
264 SFD 0.465649 0.734043
265 12D 0.463636 0.785714
266 SA8 0.463158 0.707317
267 A5D 0.463158 0.786667
268 ZDA 0.463158 0.864865
269 62F 0.462687 0.8625
270 MHZ 0.462366 0.697674
271 PGS 0.462366 0.883117
272 8PZ 0.462264 0.8
273 D5M 0.460674 0.878378
274 DA 0.460674 0.878378
275 GGZ 0.46 0.825
276 FAY 0.459259 0.8625
277 SAI 0.458333 0.734177
278 SAH 0.458333 0.74359
279 A3T 0.457447 0.821918
280 Y3J 0.45679 0.726027
281 PO4 PO4 A A A A PO4 0.456311 0.902778
282 RFL 0.455882 0.821429
283 AAM 0.455556 0.971429
284 HF7 0.454545 0.893333
285 SMM 0.454545 0.686047
286 SAM 0.453608 0.690476
287 AMZ 0.453488 0.916667
288 C2R 0.453488 0.90411
289 FNK 0.451852 0.804598
290 A3S 0.451613 0.810811
291 U A 0.45 0.907895
292 7C5 0.449541 0.818182
293 A G 0.449153 0.883117
294 XNP 0.449153 0.873418
295 EEM 0.44898 0.690476
296 AAT 0.44898 0.707317
297 PRT 0.448598 0.931507
298 62X 0.446602 0.666667
299 ETB 0.446281 0.833333
300 DCA 0.446281 0.823529
301 AIR 0.445783 0.901408
302 GSP 0.445545 0.873418
303 U A G G 0.445378 0.883117
304 NIA 0.443182 0.822785
305 PUA 0.442623 0.884615
306 K15 0.442308 0.682353
307 A A A 0.442308 0.905405
308 4YB 0.441441 0.761364
309 6K6 0.441176 0.930556
310 GEK 0.441176 0.7375
311 Z5A 0.44 0.77907
312 1DG 0.44 0.921053
313 S7M 0.44 0.690476
314 DG1 0.44 0.921053
315 0T1 0.439024 0.823529
316 COA 0.439024 0.823529
317 WSA 0.438596 0.788235
318 8Q2 0.434783 0.772727
319 8BR 0.434783 0.906667
320 101 0.433333 0.878378
321 IDP 0.43299 0.918919
322 NVA 2AD 0.43299 0.759494
323 9JJ 0.432624 0.8625
324 NAP 0.432 0.945205
325 APU 0.431034 0.894737
326 A U 0.431034 0.87013
327 COS 0.428571 0.804598
328 CAO 0.428571 0.795455
329 A6D 0.428571 0.722892
330 AMX 0.428571 0.833333
331 30N 0.428571 0.752688
332 J7V 0.428571 0.833333
333 7RP 0.428571 0.928571
334 TAP 0.428571 0.907895
335 V1N 0.427273 0.917808
336 2VA 0.427083 0.8
337 P5F 0.426573 0.823529
338 649 0.426087 0.744444
339 CMX 0.425197 0.823529
340 SCO 0.425197 0.823529
341 NA0 0.425197 0.932432
342 7RA 0.423913 0.957747
343 0UM 0.423077 0.698795
344 GAV 0.423077 0.884615
345 QQY 0.422222 0.815789
346 1RB 0.422222 0.885714
347 ACK 0.422222 0.861111
348 ACO 0.421875 0.795455
349 FAM 0.421875 0.804598
350 FCX 0.421875 0.795455
351 GCP 0.421569 0.896104
352 G1R 0.421569 0.907895
353 F2N 0.42069 0.813953
354 GNH 0.42 0.907895
355 HAX 0.418605 0.804598
356 GDC 0.418182 0.884615
357 GKE 0.418182 0.884615
358 GDD 0.418182 0.884615
359 FA9 0.417808 0.864198
360 9GM 0.417476 0.896104
361 GNP 0.417476 0.896104
362 KB1 0.416667 0.698795
363 2MC 0.416667 0.769231
364 TM1 0.416667 0.77381
365 3AD 0.416667 0.805556
366 H6Y 0.415842 0.945205
367 FYN 0.415385 0.823529
368 3KK 0.415385 0.804598
369 GTG 0.414414 0.886076
370 SO8 0.414141 0.789474
371 7L1 0.414062 0.795455
372 S8M 0.413462 0.759494
373 NHD 0.413223 0.905405
374 COK 0.412214 0.804598
375 MCD 0.412214 0.804598
376 CA6 0.412214 0.729167
377 SOP 0.412214 0.804598
378 OXK 0.412214 0.804598
379 26A 0.411765 0.763158
380 QQX 0.411111 0.805195
381 YE1 0.410448 0.813953
382 CO6 0.409091 0.804598
383 NMX 0.409091 0.76087
384 CMC 0.409091 0.804598
385 1VU 0.409091 0.795455
386 FAI 0.408602 0.916667
387 RMB 0.408602 0.873239
388 AS 0.408602 0.833333
389 SCA 0.407407 0.804598
390 SXZ 0.407407 0.710843
391 ANZ 0.40708 0.8
392 SCD 0.406015 0.823529
393 CAJ 0.406015 0.804598
394 EO7 0.404255 0.788235
395 D3Y 0.403846 0.789474
396 KH3 0.403509 0.674419
397 SLU 0.403226 0.770115
398 A C A C 0.403226 0.848101
399 3HC 0.402985 0.813953
400 MLC 0.402985 0.804598
401 IVC 0.402985 0.813953
402 1HE 0.402985 0.786517
403 A1S 0.402985 0.804598
404 BCO 0.402985 0.804598
405 CC5 0.402439 0.816901
406 5GP 0.402062 0.906667
407 G 0.402062 0.906667
408 NMN AMP PO4 0.401639 0.87013
409 MCA 0.4 0.795455
410 2BA 0.4 0.915493
411 COO 0.4 0.804598
412 3L1 0.4 0.773333
413 VRT 0.4 0.769231
414 CMP 0.4 0.901408
415 3D1 0.4 0.773333
416 CAA 0.4 0.813953
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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