Receptor
PDB id Resolution Class Description Source Keywords
1WLE 1.65 Å EC: 6.1.1.11 CRYSTAL STRUCTURE OF MAMMALIAN MITOCHONDRIAL SERYL-TRNA SYNTHETASE COMPLEXED WITH SERYL-ADENYLATE BOS TAURUS LIGASE
Ref.: DUAL-MODE RECOGNITION OF NONCANONICAL TRNAS(SER) BY SERYL-TRNA SYNTHETASE IN MAMMALIAN MITOCHONDRIA EMBO J. V. 24 3369 2005
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SRP A:900;
B:901;
 Valid;
Valid;
 none;
none;
 submit data
434.299 C13 H19 N6 O9 P c1nc(...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1WLE 1.65 Å EC: 6.1.1.11 CRYSTAL STRUCTURE OF MAMMALIAN MITOCHONDRIAL SERYL-TRNA SYNTHETASE COMPLEXED WITH SERYL-ADENYLATE BOS TAURUS LIGASE
Ref.: DUAL-MODE RECOGNITION OF NONCANONICAL TRNAS(SER) BY SERYL-TRNA SYNTHETASE IN MAMMALIAN MITOCHONDRIA EMBO J. V. 24 3369 2005
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 1WLE - SRP C13 H19 N6 O9 P c1nc(c2c(n....
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 1WLE - SRP C13 H19 N6 O9 P c1nc(c2c(n....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 1WLE - SRP C13 H19 N6 O9 P c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: SRP; Similar ligands found: 379
No: Ligand ECFP6 Tc MDL keys Tc
1 SRP 1 1
2 AMO 0.833333 0.972973
3 5AL 0.82716 0.945946
4 8LH 0.807229 0.946667
5 LAD 0.804598 0.948052
6 ME8 0.795455 0.9
7 NB8 0.795455 0.935065
8 8QN 0.77907 0.945946
9 CA0 0.775 0.933333
10 YAP 0.769231 0.96
11 FA5 0.769231 0.972973
12 KG4 0.765432 0.933333
13 4AD 0.75 0.96
14 PAJ 0.75 0.898734
15 A2D 0.734177 0.906667
16 8LQ 0.727273 0.946667
17 AHX 0.722222 0.935065
18 8LE 0.72093 0.909091
19 AN2 0.719512 0.894737
20 PTJ 0.717391 0.886076
21 BA3 0.716049 0.906667
22 YLP 0.714286 0.901235
23 B4P 0.707317 0.906667
24 ADP 0.707317 0.906667
25 AP5 0.707317 0.906667
26 DLL 0.703297 0.945946
27 50T 0.702381 0.87013
28 TYM 0.7 0.972973
29 AT4 0.698795 0.871795
30 A 0.696203 0.905405
31 AMP 0.696203 0.905405
32 YLB 0.693069 0.901235
33 YLC 0.693069 0.924051
34 ADX 0.690476 0.819277
35 M33 0.690476 0.894737
36 ACP 0.682353 0.907895
37 ATP 0.682353 0.906667
38 HEJ 0.682353 0.906667
39 OOB 0.681319 0.945946
40 5FA 0.674419 0.906667
41 APR 0.674419 0.932432
42 AR6 0.674419 0.932432
43 AQP 0.674419 0.906667
44 PRX 0.674419 0.858974
45 YLA 0.673077 0.901235
46 ABM 0.670732 0.881579
47 45A 0.670732 0.881579
48 ANP 0.670455 0.883117
49 WAQ 0.670213 0.922078
50 AD9 0.666667 0.883117
51 SAP 0.666667 0.860759
52 AGS 0.666667 0.860759
53 00A 0.666667 0.897436
54 AYB 0.666667 0.890244
55 TXA 0.663158 0.921053
56 3UK 0.659574 0.933333
57 AP2 0.654762 0.896104
58 A12 0.654762 0.896104
59 B5V 0.652632 0.921053
60 PR8 0.652632 0.935897
61 ACQ 0.651685 0.907895
62 AU1 0.651163 0.883117
63 SRA 0.646341 0.858974
64 1ZZ 0.645833 0.853659
65 A1R 0.638298 0.922078
66 ATF 0.637363 0.871795
67 XAH 0.636364 0.9
68 DAL AMP 0.634409 0.92
69 GAP 0.633333 0.933333
70 9SN 0.632653 0.886076
71 6YZ 0.630435 0.907895
72 3OD 0.628866 0.933333
73 9ZD 0.62766 0.897436
74 9ZA 0.62766 0.897436
75 B5M 0.626263 0.909091
76 B5Y 0.626263 0.909091
77 OAD 0.625 0.933333
78 YLY 0.625 0.890244
79 HQG 0.623656 0.92
80 SON 0.62069 0.946667
81 ADP MG 0.62069 0.905405
82 APC 0.617977 0.896104
83 A22 0.617021 0.894737
84 T99 0.615385 0.871795
85 TAT 0.615385 0.871795
86 4UV 0.613861 0.909091
87 FYA 0.612245 0.92
88 ADV 0.611111 0.921053
89 RBY 0.611111 0.921053
90 25A 0.610526 0.906667
91 OZV 0.610526 0.906667
92 5SV 0.610526 0.817073
93 N0B 0.608696 0.901235
94 9X8 0.608247 0.884615
95 A3R 0.604167 0.922078
96 ADQ 0.604167 0.933333
97 4UU 0.601942 0.909091
98 SSA 0.595745 0.835294
99 APC MG 0.593407 0.881579
100 ATP MG 0.593407 0.905405
101 ADP PO3 0.593407 0.905405
102 LAQ 0.590476 0.853659
103 GA7 0.586538 0.896104
104 MAP 0.583333 0.860759
105 DQV 0.580952 0.92
106 BIS 0.58 0.85
107 NAI 0.579439 0.873418
108 4UW 0.579439 0.875
109 ADP VO4 0.578947 0.894737
110 VO4 ADP 0.578947 0.894737
111 LMS 0.576471 0.797619
112 25L 0.574257 0.894737
113 IOT 0.572727 0.890244
114 ARG AMP 0.571429 0.888889
115 AFH 0.571429 0.898734
116 48N 0.570093 0.910256
117 ADP ALF 0.568421 0.8375
118 ALF ADP 0.568421 0.8375
119 TYR AMP 0.567308 0.934211
120 5CA 0.56701 0.835294
121 TXD 0.564815 0.873418
122 NAX 0.564815 0.8875
123 G3A 0.561905 0.8625
124 TXE 0.559633 0.873418
125 MYR AMP 0.558824 0.831325
126 F2R 0.557522 0.901235
127 G5P 0.556604 0.8625
128 7MD 0.556604 0.924051
129 80F 0.556522 0.878049
130 A5A 0.552083 0.8
131 TSB 0.55102 0.790698
132 53H 0.55102 0.772727
133 NXX 0.550459 0.921053
134 6V0 0.550459 0.8625
135 DND 0.550459 0.921053
136 OMR 0.545455 0.843373
137 AOC 0.545455 0.789474
138 XYA 0.544304 0.810811
139 ADN 0.544304 0.810811
140 RAB 0.544304 0.810811
141 5CD 0.54321 0.773333
142 54H 0.540816 0.781609
143 VMS 0.540816 0.781609
144 AP0 0.540541 0.839506
145 DSZ 0.54 0.835294
146 LSS 0.54 0.795455
147 COD 0.53913 0.847059
148 5AS 0.538462 0.772727
149 5X8 0.537634 0.826667
150 GTA 0.537037 0.831325
151 G5A 0.536842 0.835294
152 DTA 0.535714 0.75641
153 BT5 0.534483 0.86747
154 JB6 0.533981 0.873418
155 2A5 0.531915 0.883117
156 5N5 0.530864 0.786667
157 M24 0.529412 0.864198
158 ADP BMA 0.529412 0.907895
159 PAP 0.526316 0.893333
160 52H 0.525253 0.772727
161 A4D 0.52439 0.786667
162 GSU 0.524272 0.835294
163 A A 0.524272 0.881579
164 KAA 0.524272 0.806818
165 AMP DBH 0.523364 0.858974
166 7D5 0.523256 0.844156
167 TAD 0.522936 0.875
168 UP5 0.522523 0.884615
169 CNA 0.521739 0.921053
170 H1Q 0.521277 0.868421
171 SFG 0.521277 0.813333
172 AF3 ADP 3PG 0.517857 0.875
173 7D3 0.516484 0.846154
174 A3S 0.516129 0.851351
175 SMM 0.515152 0.741176
176 YSA 0.514019 0.813953
177 LPA AMP 0.513514 0.831325
178 4TC 0.513274 0.886076
179 UPA 0.513274 0.897436
180 T5A 0.513043 0.855422
181 ADJ 0.513043 0.843373
182 NAD 0.512821 0.92
183 A3P 0.51087 0.905405
184 7D4 0.510638 0.846154
185 ATR 0.510417 0.88
186 SA8 0.510417 0.765432
187 PPS 0.510204 0.797619
188 EEM 0.510204 0.746988
189 NSS 0.509804 0.813953
190 A4P 0.508772 0.835294
191 EP4 0.505882 0.725
192 SAI 0.505155 0.794872
193 SAH 0.505155 0.805195
194 8X1 0.504951 0.806818
195 NVA LMS 0.504854 0.786517
196 ATP A A A 0.504673 0.893333
197 ATP A 0.504673 0.893333
198 AHZ 0.504505 0.831325
199 A3D 0.504202 0.907895
200 M2T 0.5 0.707317
201 SAM 0.5 0.746988
202 6RE 0.5 0.775
203 7MC 0.5 0.901235
204 139 0.5 0.8875
205 LEU LMS 0.5 0.786517
206 3DH 0.5 0.74359
207 NAQ 0.495935 0.8625
208 DZD 0.495798 0.875
209 J4G 0.495238 0.96
210 P5A 0.495238 0.797753
211 A2R 0.49505 0.92
212 ITT 0.494737 0.855263
213 A2P 0.494624 0.891892
214 3AM 0.494382 0.891892
215 MTA 0.494253 0.74359
216 8PZ 0.490741 0.813953
217 9K8 0.490566 0.728261
218 J7C 0.48913 0.78481
219 NAE 0.487805 0.884615
220 BTX 0.487395 0.855422
221 AR6 AR6 0.486486 0.906667
222 S7M 0.485149 0.746988
223 EAD 0.484127 0.864198
224 NDE 0.48062 0.896104
225 ZID 0.48 0.907895
226 6AD 0.48 0.829268
227 WSA 0.478261 0.823529
228 ARU 0.47619 0.785714
229 NAJ PZO 0.47541 0.839506
230 0WD 0.475 0.8625
231 AMP NAD 0.475 0.92
232 HFD 0.474747 0.860759
233 JSQ 0.474747 0.860759
234 A3N 0.473118 0.75641
235 IMO 0.473118 0.866667
236 ZAS 0.472527 0.759494
237 NAJ PYZ 0.472 0.8
238 GEK 0.471154 0.797468
239 V3L 0.47 0.932432
240 P1H 0.469231 0.843373
241 A7D 0.46875 0.792208
242 S4M 0.468085 0.701149
243 6MZ 0.468085 0.868421
244 GJV 0.468085 0.765432
245 0UM 0.466667 0.777778
246 2AM 0.466667 0.88
247 A5D 0.464646 0.75641
248 MAO 0.463158 0.77381
249 A3G 0.462366 0.84
250 DSH 0.462366 0.7625
251 62X 0.462264 0.72093
252 FB0 0.462121 0.818182
253 2SA 0.460784 0.946667
254 B1U 0.459459 0.731183
255 A3T 0.459184 0.813333
256 NA7 0.457944 0.896104
257 K15 0.457944 0.738095
258 3AT 0.455446 0.906667
259 NO7 0.451923 0.871795
260 OVE 0.451613 0.846154
261 7C5 0.451327 0.810127
262 NDC 0.451128 0.8625
263 G A A A 0.45082 0.8625
264 NDP 0.45 0.8625
265 8Q2 0.449153 0.786517
266 KOY 0.448276 0.818182
267 NEC 0.446809 0.74026
268 AV2 0.446602 0.833333
269 NZQ 0.446281 0.875
270 5AD 0.445783 0.716216
271 KB1 0.445455 0.756098
272 DAT 0.444444 0.87013
273 4YB 0.443478 0.816092
274 AVV 0.443396 0.8625
275 NJP 0.442623 0.884615
276 Y3J 0.44186 0.697368
277 6IA 0.441176 0.851852
278 DTP 0.441176 0.87013
279 649 0.440678 0.777778
280 7D7 0.440476 0.736842
281 C2R 0.43956 0.868421
282 AMZ 0.43956 0.855263
283 4TA 0.439024 0.843373
284 A G 0.439024 0.85
285 NPW 0.438017 0.876543
286 AAT 0.436893 0.743902
287 ETB 0.436508 0.847059
288 DCA 0.436508 0.837209
289 OZP 0.435897 0.7875
290 U A G G 0.435484 0.85
291 SFD 0.434783 0.729167
292 TXP 0.434426 0.8625
293 MHZ 0.434343 0.732558
294 PGS 0.434343 0.804878
295 D3Y 0.433962 0.828947
296 GGZ 0.433962 0.77381
297 FDA 0.433824 0.804598
298 LQJ 0.433628 0.906667
299 71V 0.43299 0.82716
300 FNK 0.432624 0.797753
301 N5O 0.431579 0.802632
302 6C6 0.431373 0.871795
303 VRT 0.431373 0.807692
304 A6D 0.431193 0.697674
305 ODP 0.430894 0.851852
306 30N 0.430769 0.765957
307 6FA 0.430657 0.833333
308 NIA 0.430108 0.771084
309 2VA 0.43 0.792208
310 0T1 0.429688 0.837209
311 COA 0.429688 0.837209
312 U A 0.428571 0.873418
313 3NZ 0.427273 0.820513
314 FAS 0.42446 0.843373
315 FAD 0.42446 0.843373
316 SXZ 0.423423 0.768293
317 N5A 0.42268 0.776316
318 NVA 2AD 0.421569 0.797468
319 CAO 0.419847 0.808989
320 AMX 0.419847 0.847059
321 COS 0.419847 0.818182
322 KH3 0.418803 0.75
323 A A A 0.418182 0.894737
324 PO4 PO4 A A A A PO4 0.418182 0.866667
325 SO8 0.417476 0.782051
326 6K6 0.416667 0.893333
327 D5M 0.416667 0.868421
328 DA 0.416667 0.868421
329 S8M 0.416667 0.775
330 SCO 0.416667 0.858824
331 CMX 0.416667 0.858824
332 XNP 0.416 0.841463
333 HZ2 0.415254 0.790123
334 FCX 0.413534 0.829545
335 ACO 0.413534 0.808989
336 FAM 0.413534 0.818182
337 F0P 0.413223 0.7875
338 62F 0.412587 0.853659
339 FAI 0.412371 0.855263
340 AAM 0.412371 0.905405
341 NMX 0.411765 0.774194
342 HAX 0.410448 0.818182
343 7DD 0.41 0.893333
344 APU 0.409836 0.884615
345 FAY 0.409722 0.853659
346 P5F 0.409396 0.816092
347 Z5A 0.409091 0.793103
348 N6P 0.409091 0.853333
349 SCD 0.408759 0.858824
350 2MC 0.408759 0.782609
351 HY8 0.408333 0.790123
352 3KK 0.407407 0.818182
353 FYN 0.407407 0.837209
354 KGA 0.407143 0.776596
355 RFL 0.406897 0.813953
356 SLU 0.40625 0.764045
357 KGJ 0.405797 0.765957
358 9JJ 0.405405 0.831325
359 V1N 0.405172 0.906667
360 N37 0.404959 0.794872
361 NMN AMP PO4 0.404762 0.860759
362 MCD 0.404412 0.83908
363 CA6 0.404412 0.742268
364 OXK 0.404412 0.83908
365 COK 0.404412 0.818182
366 SOP 0.404412 0.818182
367 YZS 0.404412 0.742268
368 KGP 0.404412 0.742268
369 F2N 0.403974 0.806818
370 12D 0.403361 0.738636
371 LCV 0.402878 0.752577
372 SO5 0.402878 0.752577
373 NAP 0.401515 0.907895
374 CO6 0.40146 0.818182
375 1VU 0.40146 0.808989
376 CMC 0.40146 0.83908
377 RGT 0.4 0.896104
378 DDS 0.4 0.820513
379 AIR 0.4 0.84
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1WLE; Ligand: SRP; Similar sites found with APoc: 2
This union binding pocket(no: 1) in the query (biounit: 1wle.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
1 3ERR AMP 38.3234
2 3ERR AMP 38.3234
Pocket No.: 2; Query (leader) PDB : 1WLE; Ligand: SRP; Similar sites found with APoc: 2
This union binding pocket(no: 2) in the query (biounit: 1wle.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
1 3ERR AMP 38.3234
2 3ERR AMP 38.3234
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