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: 398
No: Ligand ECFP6 Tc MDL keys Tc
1 AQP 1 1
2 5FA 1 1
3 ATP 0.985507 1
4 AP5 0.942029 0.971831
5 B4P 0.942029 0.971831
6 BA3 0.927536 0.971831
7 ADP 0.887324 1
8 A2D 0.871429 0.971831
9 AGS 0.828947 0.945946
10 SAP 0.828947 0.945946
11 25L 0.8 0.985915
12 AN2 0.8 0.985915
13 AR6 0.792208 0.971831
14 APR 0.792208 0.971831
15 M33 0.789474 0.958333
16 TAT 0.78481 0.958904
17 ACQ 0.78481 0.972222
18 AD9 0.782051 0.972222
19 ACP 0.779221 0.972222
20 A 0.777778 0.971429
21 AMP 0.777778 0.971429
22 ANP 0.7625 0.972222
23 ADX 0.74359 0.873418
24 CA0 0.74359 0.945205
25 A22 0.738095 0.985915
26 50T 0.734177 0.958333
27 PRX 0.725 0.893333
28 APC 0.725 0.958904
29 ABM 0.723684 0.917808
30 ATF 0.722892 0.958904
31 ITT 0.721519 0.943662
32 7D4 0.721519 0.905405
33 ADQ 0.72093 0.945205
34 AMP MG 0.710526 0.891892
35 A12 0.705128 0.958904
36 AP2 0.705128 0.958904
37 A1R 0.701149 0.907895
38 SRA 0.697368 0.918919
39 G5P 0.691489 0.921053
40 5AL 0.690476 0.931507
41 OAD 0.685393 0.945205
42 G3A 0.680851 0.921053
43 AU1 0.679012 0.972222
44 ADP MG 0.679012 0.905405
45 SRP 0.674419 0.906667
46 ADP BEF 0.670732 0.881579
47 BEF ADP 0.670732 0.881579
48 25A 0.670455 0.971831
49 8QN 0.670455 0.931507
50 3OD 0.67033 0.945205
51 GTA 0.666667 0.886076
52 UP5 0.663265 0.92
53 4AD 0.662921 0.92
54 00A 0.655556 0.883117
55 ADP PO3 0.654762 0.943662
56 RBY 0.654762 0.932432
57 ADV 0.654762 0.932432
58 BIS 0.652174 0.933333
59 OOB 0.651685 0.931507
60 5SV 0.651685 0.848101
61 ATP MG 0.647059 0.905405
62 PAJ 0.644444 0.884615
63 AMO 0.644444 0.932432
64 A4P 0.643564 0.843373
65 2A5 0.642857 0.918919
66 MAP 0.640449 0.945946
67 3AT 0.639535 0.971831
68 AHX 0.637363 0.896104
69 DLL 0.637363 0.931507
70 ATR 0.635294 0.971429
71 PAP 0.635294 0.985714
72 PTJ 0.634409 0.896104
73 T5A 0.631068 0.841463
74 3UK 0.630435 0.918919
75 7D3 0.62963 0.905405
76 SON 0.626506 0.932432
77 ADP ALF 0.625 0.87013
78 ALF ADP 0.625 0.87013
79 LAD 0.623656 0.860759
80 WAQ 0.623656 0.883117
81 PR8 0.623656 0.85
82 AFH 0.622449 0.884615
83 GAP 0.62069 0.893333
84 DTP 0.62069 0.905405
85 ADP VO4 0.617977 0.931507
86 VO4 ADP 0.617977 0.931507
87 ANP MG 0.617977 0.894737
88 NB8 0.617021 0.896104
89 1ZZ 0.617021 0.839506
90 ME8 0.617021 0.839506
91 TXA 0.617021 0.932432
92 FYA 0.617021 0.905405
93 ADN 0.611111 0.84507
94 RAB 0.611111 0.84507
95 XYA 0.611111 0.84507
96 9SN 0.604167 0.871795
97 48N 0.60396 0.896104
98 AP0 0.601942 0.896104
99 NXX 0.598039 0.932432
100 6V0 0.598039 0.896104
101 TXD 0.598039 0.907895
102 DND 0.598039 0.932432
103 NAX 0.598039 0.873418
104 NAI 0.598039 0.907895
105 FA5 0.597938 0.906667
106 YAP 0.597938 0.894737
107 ADP BMA 0.595745 0.918919
108 A2R 0.593407 0.985915
109 OMR 0.592233 0.851852
110 TXE 0.592233 0.907895
111 XAH 0.591837 0.839506
112 DAL AMP 0.586957 0.905405
113 7DT 0.586207 0.985714
114 4UV 0.585859 0.894737
115 AOC 0.585366 0.821918
116 139 0.584906 0.873418
117 DDS 0.58427 0.878378
118 CNA 0.579439 0.932432
119 6AD 0.577778 0.909091
120 5AS 0.576471 0.77907
121 4UU 0.574257 0.894737
122 5N5 0.573333 0.819444
123 4TC 0.571429 0.896104
124 ADJ 0.570093 0.851852
125 A4D 0.565789 0.819444
126 5CD 0.565789 0.805556
127 RGT 0.565657 0.958904
128 A3P 0.564706 0.971429
129 LAQ 0.563107 0.839506
130 7D5 0.5625 0.878378
131 YLP 0.557692 0.819277
132 A A 0.556701 0.944444
133 UPA 0.556604 0.907895
134 COD 0.554545 0.811765
135 AV2 0.554348 0.917808
136 4UW 0.552381 0.860759
137 JB6 0.55102 0.883117
138 ATP A A A 0.55 0.930556
139 3AM 0.548781 0.929577
140 TYM 0.54717 0.906667
141 A2P 0.546512 0.957143
142 NA7 0.546392 0.958904
143 MYR AMP 0.545455 0.817073
144 EP4 0.544304 0.753247
145 PPS 0.543478 0.873418
146 YLB 0.542056 0.819277
147 YLC 0.542056 0.839506
148 NAD 0.540541 0.931507
149 DAT 0.539326 0.905405
150 G5A 0.538462 0.77907
151 128 0.537736 0.776471
152 DTA 0.5375 0.786667
153 M2T 0.5375 0.734177
154 TSB 0.536842 0.819277
155 3DH 0.536585 0.773333
156 AHZ 0.533333 0.817073
157 IOT 0.53211 0.831325
158 GTP 0.531915 0.92
159 SSA 0.531915 0.8
160 A3D 0.530973 0.918919
161 MTA 0.530864 0.773333
162 TYR AMP 0.529412 0.881579
163 7MD 0.528846 0.8625
164 AR6 AR6 0.528846 0.917808
165 YLA 0.527273 0.819277
166 54H 0.526316 0.788235
167 VMS 0.526316 0.788235
168 AMP DBH 0.524272 0.893333
169 TAD 0.52381 0.884615
170 IMO 0.523256 0.929577
171 AYB 0.522523 0.809524
172 A5A 0.521277 0.807229
173 EAD 0.521008 0.873418
174 2AM 0.518072 0.943662
175 6RE 0.517647 0.759494
176 7DD 0.516854 0.985714
177 V3L 0.516129 0.971831
178 AVV 0.515464 0.896104
179 BTX 0.513274 0.841463
180 NAE 0.512821 0.894737
181 52H 0.510417 0.77907
182 NSS 0.510204 0.8
183 BT5 0.508772 0.831325
184 NAQ 0.508475 0.871795
185 ZAS 0.505882 0.766234
186 J7C 0.505747 0.769231
187 A3N 0.505747 0.786667
188 5X8 0.505495 0.763158
189 53H 0.505155 0.77907
190 5CA 0.505155 0.8
191 ARU 0.50505 0.860759
192 ARG AMP 0.504673 0.829268
193 LA8 ALF 3PG 0.504587 0.8375
194 ALF ADP 3PG 0.504587 0.8375
195 AF3 ADP 3PG 0.504587 0.8375
196 ZID 0.504202 0.918919
197 P1H 0.504065 0.851852
198 S4M 0.5 0.666667
199 OVE 0.5 0.905405
200 6G0 0.5 0.884615
201 7MC 0.5 0.841463
202 LPA AMP 0.5 0.817073
203 FB0 0.496 0.804598
204 DZD 0.495652 0.884615
205 P5A 0.49505 0.744444
206 LSS 0.494949 0.761364
207 DSZ 0.494949 0.8
208 MAO 0.494382 0.759036
209 DSH 0.494253 0.725
210 NDE 0.491935 0.932432
211 N0B 0.491667 0.819277
212 YLY 0.491525 0.809524
213 M24 0.491525 0.85
214 NJP 0.491228 0.945946
215 NVA LMS 0.49 0.761364
216 MGP 0.489583 0.884615
217 GP3 0.489362 0.921053
218 6C6 0.489362 0.881579
219 NAJ PZO 0.487179 0.848101
220 0WD 0.486957 0.921053
221 LEU LMS 0.485149 0.761364
222 6FA 0.484375 0.841463
223 GJV 0.483146 0.75
224 5AD 0.480519 0.746479
225 GSU 0.480392 0.77907
226 KAA 0.480392 0.752809
227 NAD IBO 0.478261 0.87013
228 ODP 0.478261 0.909091
229 71V 0.477778 0.907895
230 A3G 0.477273 0.8
231 NEC 0.477273 0.746667
232 FAS 0.476923 0.851852
233 FAD 0.476923 0.851852
234 FDA 0.476562 0.833333
235 N6P 0.475248 0.915493
236 7D7 0.474359 0.743243
237 2SA 0.474227 0.932432
238 G A A A 0.474138 0.871795
239 4TA 0.474138 0.807229
240 NDP 0.473684 0.921053
241 NPW 0.473684 0.886076
242 SFG 0.473118 0.75
243 NDC 0.472441 0.871795
244 YSA 0.471698 0.77907
245 TXP 0.469565 0.921053
246 NZQ 0.469565 0.909091
247 MGO 0.469388 0.860759
248 6IA 0.46875 0.8375
249 GDP 0.46875 0.92
250 A7D 0.467391 0.776316
251 SFD 0.465649 0.734043
252 12D 0.463636 0.785714
253 A5D 0.463158 0.786667
254 SA8 0.463158 0.707317
255 ZDA 0.463158 0.864865
256 62F 0.462687 0.8625
257 PGS 0.462366 0.883117
258 MHZ 0.462366 0.697674
259 DA 0.460674 0.878378
260 D5M 0.460674 0.878378
261 GGZ 0.46 0.825
262 FAY 0.459259 0.8625
263 NAJ PYZ 0.459016 0.85
264 SAI 0.458333 0.734177
265 SAH 0.458333 0.74359
266 A3T 0.457447 0.821918
267 Y3J 0.45679 0.726027
268 PO4 PO4 A A A A PO4 0.456311 0.902778
269 RFL 0.455882 0.821429
270 AAM 0.455556 0.971429
271 SMM 0.454545 0.686047
272 SAM 0.453608 0.690476
273 AMZ 0.453488 0.916667
274 C2R 0.453488 0.90411
275 FNK 0.451852 0.804598
276 A3S 0.451613 0.810811
277 7C5 0.449541 0.818182
278 XNP 0.449153 0.873418
279 AAT 0.44898 0.707317
280 EEM 0.44898 0.690476
281 62X 0.446602 0.666667
282 DCA 0.446281 0.823529
283 ETB 0.446281 0.833333
284 AIR 0.445783 0.901408
285 GSP 0.445545 0.873418
286 U A G G 0.445378 0.883117
287 AMP NAD 0.443548 0.881579
288 NIA 0.443182 0.822785
289 PUA 0.442623 0.884615
290 K15 0.442308 0.682353
291 A A A 0.442308 0.905405
292 4YB 0.441441 0.761364
293 GEK 0.441176 0.7375
294 6K6 0.441176 0.930556
295 S7M 0.44 0.690476
296 Z5A 0.44 0.77907
297 DG1 0.44 0.921053
298 1DG 0.44 0.921053
299 0T1 0.439024 0.823529
300 COA 0.439024 0.823529
301 WSA 0.438596 0.788235
302 8BR 0.434783 0.906667
303 101 0.433333 0.878378
304 IDP 0.43299 0.918919
305 NAP 0.432 0.945205
306 APU 0.431034 0.894737
307 A U 0.431034 0.87013
308 CAO 0.428571 0.795455
309 A6D 0.428571 0.722892
310 COS 0.428571 0.804598
311 J7V 0.428571 0.833333
312 7RP 0.428571 0.928571
313 30N 0.428571 0.752688
314 AMX 0.428571 0.833333
315 TAP 0.428571 0.907895
316 V1N 0.427273 0.917808
317 2VA 0.427083 0.8
318 P5F 0.426573 0.823529
319 649 0.426087 0.744444
320 CMX 0.425197 0.823529
321 SCO 0.425197 0.823529
322 NA0 0.425197 0.932432
323 7RA 0.423913 0.957747
324 GAV 0.423077 0.884615
325 0UM 0.423077 0.698795
326 QQY 0.422222 0.815789
327 ACK 0.422222 0.861111
328 1RB 0.422222 0.885714
329 FAM 0.421875 0.804598
330 ACO 0.421875 0.795455
331 FCX 0.421875 0.795455
332 G1R 0.421569 0.907895
333 GCP 0.421569 0.896104
334 F2N 0.42069 0.813953
335 GNH 0.42 0.907895
336 HAX 0.418605 0.804598
337 GDD 0.418182 0.884615
338 GKE 0.418182 0.884615
339 GDC 0.418182 0.884615
340 FA9 0.417808 0.864198
341 GNP 0.417476 0.896104
342 3AD 0.416667 0.805556
343 TM1 0.416667 0.77381
344 KB1 0.416667 0.698795
345 2MC 0.416667 0.769231
346 H6Y 0.415842 0.945205
347 3KK 0.415385 0.804598
348 FYN 0.415385 0.823529
349 GTG 0.414414 0.886076
350 SO8 0.414141 0.789474
351 S8M 0.413462 0.759494
352 NHD 0.413223 0.905405
353 CA6 0.412214 0.729167
354 OXK 0.412214 0.804598
355 MCD 0.412214 0.804598
356 COK 0.412214 0.804598
357 SOP 0.412214 0.804598
358 26A 0.411765 0.763158
359 QQX 0.411111 0.805195
360 YE1 0.410448 0.813953
361 NMX 0.409091 0.76087
362 CMC 0.409091 0.804598
363 1VU 0.409091 0.795455
364 CO6 0.409091 0.804598
365 FAI 0.408602 0.916667
366 RMB 0.408602 0.873239
367 AS 0.408602 0.833333
368 SXZ 0.407407 0.710843
369 SCA 0.407407 0.804598
370 ANZ 0.40708 0.8
371 PLP AAD 0.406504 0.741573
372 CAJ 0.406015 0.804598
373 SCD 0.406015 0.823529
374 NAD BBN 0.405797 0.841463
375 U G A 0.404412 0.839506
376 NVA 2AD 0.40404 0.74359
377 D3Y 0.403846 0.789474
378 KH3 0.403509 0.674419
379 SLU 0.403226 0.770115
380 MLC 0.402985 0.804598
381 A1S 0.402985 0.804598
382 1HE 0.402985 0.786517
383 IVC 0.402985 0.813953
384 3HC 0.402985 0.813953
385 BCO 0.402985 0.804598
386 CC5 0.402439 0.816901
387 5GP 0.402062 0.906667
388 G 0.402062 0.906667
389 NMN AMP PO4 0.401639 0.87013
390 CMP 0.4 0.901408
391 COO 0.4 0.804598
392 CAA 0.4 0.813953
393 NAD CJ3 0.4 0.811765
394 3D1 0.4 0.773333
395 VRT 0.4 0.769231
396 3L1 0.4 0.773333
397 2BA 0.4 0.915493
398 MCA 0.4 0.795455
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5DK4; Ligand: 5BX; Similar sites found: 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 P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5DK4; Ligand: ATP; Similar sites found: 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 42 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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