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 9 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 9 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 (2D)
Ligand no: 1; Ligand: SRP; Similar ligands found: 407
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 FA5 0.769231 0.972973
11 KG4 0.765432 0.933333
12 4AD 0.75 0.96
13 PAJ 0.75 0.898734
14 A2D 0.734177 0.906667
15 8LQ 0.727273 0.946667
16 AHX 0.722222 0.935065
17 8LE 0.72093 0.909091
18 AN2 0.719512 0.894737
19 PTJ 0.717391 0.886076
20 BA3 0.716049 0.906667
21 YLP 0.714286 0.901235
22 QA7 0.707865 0.909091
23 AP5 0.707317 0.906667
24 B4P 0.707317 0.906667
25 ADP 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 HEJ 0.682353 0.906667
37 ACP 0.682353 0.907895
38 ATP 0.682353 0.906667
39 OOB 0.681319 0.945946
40 AQP 0.674419 0.906667
41 PRX 0.674419 0.858974
42 AR6 0.674419 0.932432
43 APR 0.674419 0.932432
44 5FA 0.674419 0.906667
45 YLA 0.673077 0.901235
46 45A 0.670732 0.881579
47 ABM 0.670732 0.881579
48 ANP 0.670455 0.883117
49 WAQ 0.670213 0.922078
50 AD9 0.666667 0.883117
51 AYB 0.666667 0.890244
52 AMP MG 0.666667 0.891892
53 00A 0.666667 0.897436
54 AGS 0.666667 0.860759
55 TXA 0.663158 0.921053
56 3UK 0.659574 0.933333
57 A12 0.654762 0.896104
58 AP2 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 JNT 0.631579 0.933333
72 6YZ 0.630435 0.907895
73 3OD 0.628866 0.933333
74 9ZD 0.62766 0.897436
75 9ZA 0.62766 0.897436
76 V2G 0.626374 0.935065
77 B5M 0.626263 0.909091
78 B5Y 0.626263 0.909091
79 OAD 0.625 0.933333
80 YLY 0.625 0.890244
81 HQG 0.623656 0.92
82 ADP MG 0.62069 0.905405
83 SON 0.62069 0.946667
84 ADP BEF 0.62069 0.905405
85 APC 0.617977 0.896104
86 A22 0.617021 0.894737
87 TAT 0.615385 0.871795
88 T99 0.615385 0.871795
89 4UV 0.613861 0.909091
90 FYA 0.612245 0.92
91 RBY 0.611111 0.921053
92 ADV 0.611111 0.921053
93 5SV 0.610526 0.817073
94 OZV 0.610526 0.906667
95 25A 0.610526 0.906667
96 N0B 0.608696 0.901235
97 9X8 0.608247 0.884615
98 A3R 0.604167 0.922078
99 ADQ 0.604167 0.933333
100 4UU 0.601942 0.909091
101 SSA 0.595745 0.835294
102 APC MG 0.593407 0.881579
103 ATP MG 0.593407 0.905405
104 ADP PO3 0.593407 0.905405
105 LAQ 0.590476 0.853659
106 BEF ADP 0.586957 0.881579
107 GA7 0.586538 0.896104
108 ANP MG 0.585106 0.894737
109 MAP 0.583333 0.860759
110 DQV 0.580952 0.92
111 BIS 0.58 0.85
112 NAI 0.579439 0.873418
113 4UW 0.579439 0.875
114 LMS 0.576471 0.797619
115 25L 0.574257 0.894737
116 IOT 0.572727 0.890244
117 ARG AMP 0.571429 0.888889
118 AFH 0.571429 0.898734
119 48N 0.570093 0.910256
120 VO4 ADP 0.568421 0.883117
121 ALF ADP 0.568421 0.8375
122 5CA 0.56701 0.835294
123 TXD 0.564815 0.873418
124 NAX 0.564815 0.8875
125 KMQ 0.563107 0.896104
126 G3A 0.561905 0.8625
127 TXE 0.559633 0.873418
128 MYR AMP 0.558824 0.831325
129 F2R 0.557522 0.901235
130 7MD 0.556604 0.924051
131 G5P 0.556604 0.8625
132 80F 0.556522 0.878049
133 A5A 0.552083 0.8
134 53H 0.55102 0.772727
135 TSB 0.55102 0.790698
136 DND 0.550459 0.921053
137 6V0 0.550459 0.8625
138 AOC 0.545455 0.789474
139 OMR 0.545455 0.843373
140 ADN 0.544304 0.810811
141 RAB 0.544304 0.810811
142 XYA 0.544304 0.810811
143 5CD 0.54321 0.773333
144 VMS 0.540816 0.781609
145 54H 0.540816 0.781609
146 AP0 0.540541 0.839506
147 L3W 0.540541 0.896104
148 LSS 0.54 0.795455
149 DSZ 0.54 0.835294
150 COD 0.53913 0.847059
151 5AS 0.538462 0.772727
152 5X8 0.537634 0.826667
153 GTA 0.537037 0.831325
154 G5A 0.536842 0.835294
155 DTA 0.535714 0.75641
156 BT5 0.534483 0.86747
157 JB6 0.533981 0.873418
158 2A5 0.531915 0.883117
159 5N5 0.530864 0.786667
160 ADP BMA 0.529412 0.907895
161 M24 0.529412 0.864198
162 PAP 0.526316 0.893333
163 52H 0.525253 0.772727
164 D4F 0.525 0.876543
165 A4D 0.52439 0.786667
166 GSU 0.524272 0.835294
167 KAA 0.524272 0.806818
168 AMP DBH 0.523364 0.858974
169 7D5 0.523256 0.844156
170 TAD 0.522936 0.875
171 UP5 0.522523 0.884615
172 CNA 0.521739 0.921053
173 SFG 0.521277 0.813333
174 H1Q 0.521277 0.868421
175 ALF ADP 3PG 0.517857 0.875
176 AF3 ADP 3PG 0.517857 0.875
177 7D3 0.516484 0.846154
178 A3S 0.516129 0.851351
179 SMM 0.515152 0.741176
180 LEU LMS 0.514563 0.784091
181 YSA 0.514019 0.813953
182 LPA AMP 0.513514 0.831325
183 UPA 0.513274 0.897436
184 4TC 0.513274 0.886076
185 T5A 0.513043 0.855422
186 ADJ 0.513043 0.843373
187 NAD 0.512821 0.92
188 A3P 0.51087 0.905405
189 7D4 0.510638 0.846154
190 SA8 0.510417 0.765432
191 ATR 0.510417 0.88
192 PPS 0.510204 0.797619
193 EEM 0.510204 0.746988
194 NSS 0.509804 0.813953
195 A4P 0.508772 0.835294
196 EP4 0.505882 0.725
197 SAI 0.505155 0.794872
198 SAH 0.505155 0.805195
199 8X1 0.504951 0.806818
200 NVA LMS 0.504854 0.786517
201 ATP A 0.504673 0.893333
202 ATP A A A 0.504673 0.893333
203 AHZ 0.504505 0.831325
204 A3D 0.504202 0.907895
205 3DH 0.5 0.74359
206 6RE 0.5 0.775
207 SAM 0.5 0.746988
208 M2T 0.5 0.707317
209 7MC 0.5 0.901235
210 139 0.5 0.8875
211 NAQ 0.495935 0.8625
212 DZD 0.495798 0.875
213 J4G 0.495238 0.96
214 P5A 0.495238 0.797753
215 A2R 0.49505 0.92
216 ITT 0.494737 0.855263
217 A2P 0.494624 0.891892
218 3AM 0.494382 0.891892
219 MTA 0.494253 0.74359
220 8PZ 0.490741 0.813953
221 9K8 0.490566 0.728261
222 J7C 0.48913 0.78481
223 NWW 0.488095 0.72973
224 NAE 0.487805 0.884615
225 BTX 0.487395 0.855422
226 NAD TDB 0.486957 0.906667
227 NAD IBO 0.486957 0.906667
228 AR6 AR6 0.486486 0.906667
229 S7M 0.485149 0.746988
230 EAD 0.484127 0.864198
231 NDE 0.48062 0.896104
232 ZID 0.48 0.907895
233 6AD 0.48 0.829268
234 WSA 0.478261 0.823529
235 ARU 0.47619 0.785714
236 NAJ PZO 0.47541 0.839506
237 0WD 0.475 0.8625
238 AMP NAD 0.475 0.92
239 JSQ 0.474747 0.860759
240 HFD 0.474747 0.860759
241 A3N 0.473118 0.75641
242 IMO 0.473118 0.866667
243 ZAS 0.472527 0.759494
244 NAJ PYZ 0.472 0.8
245 GEK 0.471154 0.797468
246 V3L 0.47 0.932432
247 P1H 0.469231 0.843373
248 A7D 0.46875 0.792208
249 6MZ 0.468085 0.868421
250 S4M 0.468085 0.701149
251 GJV 0.468085 0.765432
252 0UM 0.466667 0.777778
253 2AM 0.466667 0.88
254 A5D 0.464646 0.75641
255 MAO 0.463158 0.77381
256 A3G 0.462366 0.84
257 DSH 0.462366 0.7625
258 62X 0.462264 0.72093
259 FB0 0.462121 0.818182
260 2SA 0.460784 0.946667
261 O02 0.46 0.8625
262 B1U 0.459459 0.731183
263 CUU 0.459184 0.906667
264 A3T 0.459184 0.813333
265 NA7 0.457944 0.896104
266 K15 0.457944 0.738095
267 QXP 0.457143 0.758621
268 3AT 0.455446 0.906667
269 NO7 0.451923 0.871795
270 OVE 0.451613 0.846154
271 7C5 0.451327 0.810127
272 NDC 0.451128 0.8625
273 NDP 0.45 0.8625
274 8Q2 0.449153 0.786517
275 KOY 0.448276 0.818182
276 NEC 0.446809 0.74026
277 AV2 0.446602 0.833333
278 NZQ 0.446281 0.875
279 5AD 0.445783 0.716216
280 KB1 0.445455 0.756098
281 38V 0.445312 0.853659
282 DAT 0.444444 0.87013
283 QXG 0.444444 0.75
284 4YB 0.443478 0.816092
285 AVV 0.443396 0.8625
286 NJP 0.442623 0.884615
287 V47 0.442308 0.8
288 Y3J 0.44186 0.697368
289 6IA 0.441176 0.851852
290 DTP 0.441176 0.87013
291 649 0.440678 0.777778
292 7D7 0.440476 0.736842
293 R2V 0.440367 0.758621
294 C2R 0.43956 0.868421
295 AMZ 0.43956 0.855263
296 4TA 0.439024 0.843373
297 NPW 0.438017 0.876543
298 K3K 0.4375 0.772152
299 AAT 0.436893 0.743902
300 ETB 0.436508 0.847059
301 DCA 0.436508 0.837209
302 OZP 0.435897 0.7875
303 SFD 0.434783 0.729167
304 NWQ 0.434783 0.710526
305 TXP 0.434426 0.8625
306 MHZ 0.434343 0.732558
307 PGS 0.434343 0.804878
308 GGZ 0.433962 0.77381
309 D3Y 0.433962 0.828947
310 FDA 0.433824 0.804598
311 KYE 0.433628 0.771084
312 LQJ 0.433628 0.906667
313 71V 0.43299 0.82716
314 FNK 0.432624 0.797753
315 N5O 0.431579 0.802632
316 6C6 0.431373 0.871795
317 VRT 0.431373 0.807692
318 A6D 0.431193 0.697674
319 KXW 0.431034 0.7875
320 ODP 0.430894 0.851852
321 30N 0.430769 0.765957
322 6FA 0.430657 0.833333
323 NIA 0.430108 0.771084
324 2VA 0.43 0.792208
325 K3E 0.429825 0.7625
326 0T1 0.429688 0.837209
327 COA 0.429688 0.837209
328 Q2P 0.427419 0.729412
329 3NZ 0.427273 0.820513
330 Q34 0.425 0.729412
331 FAS 0.42446 0.843373
332 FAD 0.42446 0.843373
333 SXZ 0.423423 0.768293
334 N5A 0.42268 0.776316
335 NVA 2AD 0.421569 0.797468
336 CAO 0.419847 0.808989
337 AMX 0.419847 0.847059
338 COS 0.419847 0.818182
339 KH3 0.418803 0.75
340 NAD BBN 0.41844 0.811765
341 PO4 PO4 A A A A PO4 0.418182 0.866667
342 SO8 0.417476 0.782051
343 SCO 0.416667 0.858824
344 6K6 0.416667 0.893333
345 D5M 0.416667 0.868421
346 DA 0.416667 0.868421
347 S8M 0.416667 0.775
348 CMX 0.416667 0.858824
349 XNP 0.416 0.841463
350 HZ2 0.415254 0.790123
351 ACO 0.413534 0.808989
352 FCX 0.413534 0.829545
353 FAM 0.413534 0.818182
354 Q2M 0.413223 0.746988
355 F0P 0.413223 0.7875
356 62F 0.412587 0.853659
357 FAI 0.412371 0.855263
358 AAM 0.412371 0.905405
359 U4Y 0.411765 0.797468
360 NMX 0.411765 0.774194
361 K2R 0.410714 0.894737
362 HAX 0.410448 0.818182
363 7DD 0.41 0.893333
364 APU 0.409836 0.884615
365 FAY 0.409722 0.853659
366 P5F 0.409396 0.816092
367 Z5A 0.409091 0.793103
368 K2H 0.409091 0.707317
369 N6P 0.409091 0.853333
370 2MC 0.408759 0.782609
371 SCD 0.408759 0.858824
372 EU9 0.408333 0.738636
373 HY8 0.408333 0.790123
374 3KK 0.407407 0.818182
375 KY2 0.407407 0.746988
376 FYN 0.407407 0.837209
377 KGA 0.407143 0.776596
378 RFL 0.406897 0.813953
379 SLU 0.40625 0.764045
380 KGJ 0.405797 0.765957
381 9JJ 0.405405 0.831325
382 V1N 0.405172 0.906667
383 N37 0.404959 0.794872
384 NMN AMP PO4 0.404762 0.860759
385 KGP 0.404412 0.742268
386 SOP 0.404412 0.818182
387 CA6 0.404412 0.742268
388 MCD 0.404412 0.83908
389 COK 0.404412 0.818182
390 YZS 0.404412 0.742268
391 OXK 0.404412 0.83908
392 F2N 0.403974 0.806818
393 12D 0.403361 0.738636
394 Q2V 0.403226 0.756098
395 LCV 0.402878 0.752577
396 SO5 0.402878 0.752577
397 NAD CJ3 0.402778 0.784091
398 K2K 0.401786 0.753086
399 NAP 0.401515 0.907895
400 1VU 0.40146 0.808989
401 CMC 0.40146 0.83908
402 CO6 0.40146 0.818182
403 NX8 0.4 0.753086
404 KYB 0.4 0.746988
405 AIR 0.4 0.84
406 RGT 0.4 0.896104
407 DDS 0.4 0.820513
Similar Ligands (3D)
Ligand no: 1; Ligand: SRP; Similar ligands found: 8
No: Ligand Similarity coefficient
1 FZQ 0.9259
2 FZT 0.9218
3 GDP 0.9155
4 FZK 0.9143
5 RUZ 0.8827
6 GDP MG 0.8781
7 GNP 0.8665
8 IDP 0.8567
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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