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 5 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 5 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: 333
No: Ligand ECFP6 Tc MDL keys Tc
1 SRP 1 1
2 AMO 0.833333 0.972973
3 5AL 0.82716 0.945946
4 LAD 0.804598 0.948052
5 NB8 0.795455 0.935065
6 ME8 0.795455 0.9
7 8QN 0.77907 0.945946
8 CA0 0.775 0.933333
9 YAP 0.769231 0.96
10 FA5 0.769231 0.972973
11 4AD 0.75 0.96
12 PAJ 0.75 0.898734
13 A2D 0.734177 0.906667
14 AHX 0.722222 0.935065
15 AN2 0.719512 0.894737
16 PTJ 0.717391 0.886076
17 BA3 0.716049 0.906667
18 YLP 0.714286 0.901235
19 ADP 0.707317 0.906667
20 B4P 0.707317 0.906667
21 AP5 0.707317 0.906667
22 DLL 0.703297 0.945946
23 50T 0.702381 0.87013
24 TYM 0.7 0.972973
25 A 0.696203 0.905405
26 AMP 0.696203 0.905405
27 YLC 0.693069 0.924051
28 YLB 0.693069 0.901235
29 ADX 0.690476 0.819277
30 M33 0.690476 0.894737
31 ACP 0.682353 0.907895
32 ATP 0.682353 0.906667
33 OOB 0.681319 0.945946
34 PRX 0.674419 0.858974
35 AR6 0.674419 0.932432
36 APR 0.674419 0.932432
37 5FA 0.674419 0.906667
38 AQP 0.674419 0.906667
39 YLA 0.673077 0.901235
40 ABM 0.670732 0.881579
41 ANP 0.670455 0.883117
42 WAQ 0.670213 0.922078
43 AYB 0.666667 0.890244
44 00A 0.666667 0.897436
45 SAP 0.666667 0.860759
46 AGS 0.666667 0.860759
47 AD9 0.666667 0.883117
48 TXA 0.663158 0.921053
49 3UK 0.659574 0.933333
50 AMP MG 0.658537 0.857143
51 AP2 0.654762 0.896104
52 A12 0.654762 0.896104
53 PR8 0.652632 0.935897
54 ACQ 0.651685 0.907895
55 AU1 0.651163 0.883117
56 SRA 0.646341 0.858974
57 1ZZ 0.645833 0.853659
58 A1R 0.638298 0.922078
59 ATF 0.637363 0.871795
60 XAH 0.636364 0.9
61 DAL AMP 0.634409 0.92
62 GAP 0.633333 0.933333
63 9SN 0.632653 0.886076
64 3OD 0.628866 0.933333
65 OAD 0.625 0.933333
66 YLY 0.625 0.890244
67 SON 0.62069 0.946667
68 APC 0.617977 0.896104
69 A22 0.617021 0.894737
70 TAT 0.615385 0.871795
71 4UV 0.613861 0.909091
72 ADP MG 0.613636 0.87013
73 FYA 0.612245 0.92
74 RBY 0.611111 0.921053
75 ADV 0.611111 0.921053
76 5SV 0.610526 0.817073
77 25A 0.610526 0.906667
78 N0B 0.608696 0.901235
79 BEF ADP 0.606742 0.848101
80 ADP BEF 0.606742 0.848101
81 ADQ 0.604167 0.933333
82 4UU 0.601942 0.909091
83 SSA 0.595745 0.835294
84 ADP PO3 0.593407 0.905405
85 LAQ 0.590476 0.853659
86 ATP MG 0.586957 0.87013
87 MAP 0.583333 0.860759
88 BIS 0.58 0.85
89 NAI 0.579439 0.873418
90 4UW 0.579439 0.875
91 VO4 ADP 0.578947 0.894737
92 ADP VO4 0.578947 0.894737
93 ANP MG 0.578947 0.860759
94 25L 0.574257 0.894737
95 TYR AMP 0.572816 0.921053
96 IOT 0.572727 0.890244
97 AFH 0.571429 0.898734
98 48N 0.570093 0.910256
99 ALF ADP 0.568421 0.8375
100 ADP ALF 0.568421 0.8375
101 5CA 0.56701 0.835294
102 NAX 0.564815 0.8875
103 TXD 0.564815 0.873418
104 G3A 0.561905 0.8625
105 TXE 0.559633 0.873418
106 MYR AMP 0.558824 0.831325
107 G5P 0.556604 0.8625
108 7MD 0.556604 0.924051
109 A5A 0.552083 0.8
110 TSB 0.55102 0.790698
111 53H 0.55102 0.772727
112 NXX 0.550459 0.921053
113 DND 0.550459 0.921053
114 6V0 0.550459 0.8625
115 ARG AMP 0.546296 0.888889
116 AOC 0.545455 0.789474
117 OMR 0.545455 0.843373
118 ADN 0.544304 0.810811
119 RAB 0.544304 0.810811
120 XYA 0.544304 0.810811
121 5CD 0.54321 0.773333
122 VMS 0.540816 0.781609
123 54H 0.540816 0.781609
124 AP0 0.540541 0.839506
125 DSZ 0.54 0.835294
126 LSS 0.54 0.795455
127 COD 0.53913 0.847059
128 5AS 0.538462 0.772727
129 5X8 0.537634 0.826667
130 GTA 0.537037 0.831325
131 G5A 0.536842 0.835294
132 DTA 0.535714 0.75641
133 BT5 0.534483 0.86747
134 JB6 0.533981 0.873418
135 2A5 0.531915 0.883117
136 5N5 0.530864 0.786667
137 M24 0.529412 0.864198
138 ADP BMA 0.529412 0.907895
139 PAP 0.526316 0.893333
140 52H 0.525253 0.772727
141 A4D 0.52439 0.786667
142 KAA 0.524272 0.806818
143 A A 0.524272 0.881579
144 GSU 0.524272 0.835294
145 AMP DBH 0.523364 0.858974
146 7D5 0.523256 0.844156
147 TAD 0.522936 0.875
148 UP5 0.522523 0.884615
149 CNA 0.521739 0.921053
150 SFG 0.521277 0.813333
151 ALF ADP 3PG 0.517857 0.875
152 LA8 ALF 3PG 0.517857 0.875
153 AF3 ADP 3PG 0.517857 0.875
154 7D3 0.516484 0.846154
155 A3S 0.516129 0.851351
156 SMM 0.515152 0.741176
157 YSA 0.514019 0.813953
158 LPA AMP 0.513514 0.831325
159 4TC 0.513274 0.886076
160 UPA 0.513274 0.897436
161 T5A 0.513043 0.855422
162 ADJ 0.513043 0.843373
163 NAD 0.512821 0.92
164 A3P 0.51087 0.905405
165 7D4 0.510638 0.846154
166 ATR 0.510417 0.88
167 SA8 0.510417 0.765432
168 PPS 0.510204 0.797619
169 EEM 0.510204 0.746988
170 NSS 0.509804 0.813953
171 A4P 0.508772 0.835294
172 EP4 0.505882 0.725
173 SAH 0.505155 0.805195
174 SAI 0.505155 0.794872
175 NVA LMS 0.504854 0.775281
176 ATP A A A 0.504673 0.893333
177 AHZ 0.504505 0.831325
178 A3D 0.504202 0.907895
179 7MC 0.5 0.901235
180 3DH 0.5 0.74359
181 6RE 0.5 0.775
182 M2T 0.5 0.707317
183 SAM 0.5 0.746988
184 LEU LMS 0.5 0.775281
185 139 0.5 0.8875
186 NAQ 0.495935 0.8625
187 DZD 0.495798 0.875
188 P5A 0.495238 0.797753
189 A2R 0.49505 0.92
190 ITT 0.494737 0.855263
191 A2P 0.494624 0.891892
192 3AM 0.494382 0.891892
193 MTA 0.494253 0.74359
194 J7C 0.48913 0.78481
195 NAE 0.487805 0.884615
196 BTX 0.487395 0.855422
197 AR6 AR6 0.486486 0.906667
198 S7M 0.485149 0.746988
199 EAD 0.484127 0.864198
200 NDE 0.48062 0.896104
201 6AD 0.48 0.829268
202 ZID 0.48 0.907895
203 NAD IBO 0.478992 0.860759
204 WSA 0.478261 0.823529
205 ARU 0.47619 0.785714
206 NAJ PZO 0.47541 0.839506
207 0WD 0.475 0.8625
208 IMO 0.473118 0.866667
209 A3N 0.473118 0.75641
210 ZAS 0.472527 0.759494
211 GEK 0.471154 0.797468
212 V3L 0.47 0.932432
213 P1H 0.469231 0.843373
214 A7D 0.46875 0.792208
215 GJV 0.468085 0.765432
216 S4M 0.468085 0.701149
217 0UM 0.466667 0.777778
218 2AM 0.466667 0.88
219 A5D 0.464646 0.75641
220 MAO 0.463158 0.77381
221 DSH 0.462366 0.7625
222 A3G 0.462366 0.84
223 62X 0.462264 0.72093
224 FB0 0.462121 0.818182
225 2SA 0.460784 0.946667
226 NAJ PYZ 0.460317 0.841463
227 A3T 0.459184 0.813333
228 K15 0.457944 0.738095
229 NA7 0.457944 0.896104
230 3AT 0.455446 0.906667
231 OVE 0.451613 0.846154
232 7C5 0.451327 0.810127
233 NDC 0.451128 0.8625
234 G A A A 0.45082 0.8625
235 NDP 0.45 0.8625
236 NEC 0.446809 0.74026
237 AV2 0.446602 0.833333
238 NZQ 0.446281 0.875
239 5AD 0.445783 0.716216
240 KB1 0.445455 0.756098
241 AMP NAD 0.445312 0.896104
242 DAT 0.444444 0.87013
243 4YB 0.443478 0.816092
244 AVV 0.443396 0.8625
245 NJP 0.442623 0.884615
246 Y3J 0.44186 0.697368
247 6IA 0.441176 0.851852
248 DTP 0.441176 0.87013
249 649 0.440678 0.777778
250 7D7 0.440476 0.736842
251 AMZ 0.43956 0.855263
252 C2R 0.43956 0.868421
253 4TA 0.439024 0.843373
254 NPW 0.438017 0.876543
255 AAT 0.436893 0.743902
256 ETB 0.436508 0.847059
257 DCA 0.436508 0.837209
258 U A G G 0.435484 0.85
259 SFD 0.434783 0.729167
260 TXP 0.434426 0.8625
261 MHZ 0.434343 0.732558
262 PGS 0.434343 0.804878
263 GGZ 0.433962 0.77381
264 D3Y 0.433962 0.828947
265 FDA 0.433824 0.804598
266 71V 0.43299 0.82716
267 FNK 0.432624 0.797753
268 6C6 0.431373 0.871795
269 VRT 0.431373 0.807692
270 A6D 0.431193 0.697674
271 ODP 0.430894 0.851852
272 30N 0.430769 0.765957
273 6FA 0.430657 0.833333
274 NIA 0.430108 0.771084
275 2VA 0.43 0.792208
276 COA 0.429688 0.837209
277 0T1 0.429688 0.837209
278 3NZ 0.427273 0.820513
279 FAD 0.42446 0.843373
280 FAS 0.42446 0.843373
281 SXZ 0.423423 0.768293
282 CAO 0.419847 0.808989
283 AMX 0.419847 0.847059
284 COS 0.419847 0.818182
285 KH3 0.418803 0.75
286 NAD BBN 0.41844 0.811765
287 PO4 PO4 A A A A PO4 0.418182 0.866667
288 A A A 0.418182 0.894737
289 SO8 0.417476 0.782051
290 D5M 0.416667 0.868421
291 S8M 0.416667 0.775
292 DA 0.416667 0.868421
293 CMX 0.416667 0.858824
294 SCO 0.416667 0.858824
295 6K6 0.416667 0.893333
296 XNP 0.416 0.841463
297 FCX 0.413534 0.829545
298 FAM 0.413534 0.818182
299 ACO 0.413534 0.808989
300 62F 0.412587 0.853659
301 FAI 0.412371 0.855263
302 AAM 0.412371 0.905405
303 NMX 0.411765 0.774194
304 HAX 0.410448 0.818182
305 7DD 0.41 0.893333
306 APU 0.409836 0.884615
307 FAY 0.409722 0.853659
308 P5F 0.409396 0.816092
309 Z5A 0.409091 0.793103
310 N6P 0.409091 0.853333
311 2MC 0.408759 0.782609
312 SCD 0.408759 0.858824
313 3KK 0.407407 0.818182
314 FYN 0.407407 0.837209
315 RFL 0.406897 0.813953
316 SLU 0.40625 0.764045
317 V1N 0.405172 0.906667
318 NMN AMP PO4 0.404762 0.860759
319 COK 0.404412 0.818182
320 SOP 0.404412 0.818182
321 MCD 0.404412 0.83908
322 CA6 0.404412 0.742268
323 OXK 0.404412 0.83908
324 F2N 0.403974 0.806818
325 12D 0.403361 0.738636
326 NAD CJ3 0.402778 0.784091
327 NAP 0.401515 0.907895
328 CO6 0.40146 0.818182
329 1VU 0.40146 0.808989
330 CMC 0.40146 0.83908
331 DDS 0.4 0.820513
332 RGT 0.4 0.896104
333 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: 48
This union binding pocket(no: 1) in the query (biounit: 1wle.bio1) has 21 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3CQL NAG 0.02569 0.4009 1.64609
2 2I4O ATP 0.000001781 0.59259 1.96507
3 3E9I XAH 0.0000009933 0.48866 2.23124
4 3NEM ATP 0.0000005493 0.6172 2.28311
5 3NEM AMO 0.00000002958 0.56044 2.28311
6 3UH0 TSB 0.0000008245 0.53236 2.3913
7 3HXU A5A 0.0000001477 0.5657 2.49433
8 1G51 AMO 0.000002354 0.48901 2.59481
9 3A5Y KAA 0.0000003096 0.53581 2.6087
10 3A5Z KAA 0.000000351 0.52494 3.66492
11 1I7E IBS 0.02049 0.40629 3.77358
12 2XGT NSS 0.00000008174 0.53593 3.90805
13 4J25 OGA 0.01635 0.41191 3.93013
14 12AS AMP 0.0000007377 0.50474 3.93939
15 3G1Z AMP 0.000005649 0.56845 3.98773
16 2ZTG A5A 0.00000004422 0.6317 3.99202
17 3TEG DAH 0.0004586 0.4391 4.09639
18 3RK0 AMP 0.01085 0.40609 4.21941
19 4ZTD ALA GLY ALA GLY ALA 0.006096 0.42999 4.34783
20 1E1O LYS 0.00001339 0.47209 4.59082
21 5J6Y GLC 0.03 0.40006 4.78723
22 5J6Y BGC 0.03 0.40006 4.78723
23 3IAL PR8 0.000001799 0.52663 4.79042
24 3BJU ATP 0.00004628 0.51115 5.18962
25 2P0D I3P 0.002536 0.45955 5.42636
26 3QX9 ATP 0.02704 0.40079 5.7971
27 1YFS ALA 0.0008102 0.47777 6.02151
28 3T4L ZEA 0.006416 0.40526 6.2963
29 1B7Y FYA 0.00006317 0.44957 7.38523
30 1X54 4AD 0.000000145 0.61554 7.60369
31 1M5W DXP 0.02225 0.40314 7.81893
32 4H2V AMP 0.0000007837 0.54793 8.3815
33 3MF2 AMP 0.0000007054 0.53996 8.3815
34 1MG1 MAL 0.01281 0.40665 9.55556
35 3REU ATP 0.000001194 0.56892 9.86395
36 4H2X G5A 0.0000004511 0.58006 11.6505
37 4H2W AMP 0.00000521 0.54759 11.6505
38 4H2W 5GP 0.000005137 0.54113 11.6505
39 5VAD 91Y 0.00001172 0.44674 12.7907
40 4YLZ LAT NAG GAL 0.01453 0.41507 13.0719
41 2J3M ATP 0.000001149 0.53442 13.3733
42 2J3M PRI 0.0000013 0.52389 13.3733
43 4HWS 1B3 0.000001384 0.447 14.8418
44 4HWT 1B2 0.0008027 0.44057 18.1598
45 4AIA ADK 0.01331 0.4217 18.617
46 4CS4 ANP 0.0000002087 0.45665 21.5328
47 4CS4 AXZ 0.0000003585 0.42409 21.5328
48 3ERR AMP 0.0000000000337 0.69769 38.3234
Pocket No.: 2; Query (leader) PDB : 1WLE; Ligand: SRP; 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: 1wle.bio1) has 21 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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