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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;
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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: 348
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 ME8 0.795455 0.9
6 NB8 0.795455 0.935065
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 AP5 0.707317 0.906667
20 ADP 0.707317 0.906667
21 B4P 0.707317 0.906667
22 DLL 0.703297 0.945946
23 50T 0.702381 0.87013
24 TYM 0.7 0.972973
25 AT4 0.698795 0.871795
26 A 0.696203 0.905405
27 AMP 0.696203 0.905405
28 YLC 0.693069 0.924051
29 YLB 0.693069 0.901235
30 ADX 0.690476 0.819277
31 M33 0.690476 0.894737
32 HEJ 0.682353 0.906667
33 ATP 0.682353 0.906667
34 ACP 0.682353 0.907895
35 OOB 0.681319 0.945946
36 AR6 0.674419 0.932432
37 PRX 0.674419 0.858974
38 AQP 0.674419 0.906667
39 APR 0.674419 0.932432
40 5FA 0.674419 0.906667
41 YLA 0.673077 0.901235
42 ABM 0.670732 0.881579
43 ANP 0.670455 0.883117
44 WAQ 0.670213 0.922078
45 SAP 0.666667 0.860759
46 AD9 0.666667 0.883117
47 00A 0.666667 0.897436
48 AGS 0.666667 0.860759
49 AYB 0.666667 0.890244
50 TXA 0.663158 0.921053
51 3UK 0.659574 0.933333
52 AP2 0.654762 0.896104
53 A12 0.654762 0.896104
54 PR8 0.652632 0.935897
55 B5V 0.652632 0.921053
56 ACQ 0.651685 0.907895
57 AU1 0.651163 0.883117
58 SRA 0.646341 0.858974
59 1ZZ 0.645833 0.853659
60 A1R 0.638298 0.922078
61 ATF 0.637363 0.871795
62 XAH 0.636364 0.9
63 DAL AMP 0.634409 0.92
64 GAP 0.633333 0.933333
65 9SN 0.632653 0.886076
66 6YZ 0.630435 0.907895
67 3OD 0.628866 0.933333
68 9ZD 0.62766 0.897436
69 9ZA 0.62766 0.897436
70 B5M 0.626263 0.909091
71 B5Y 0.626263 0.909091
72 YLY 0.625 0.890244
73 OAD 0.625 0.933333
74 SON 0.62069 0.946667
75 APC 0.617977 0.896104
76 A22 0.617021 0.894737
77 T99 0.615385 0.871795
78 TAT 0.615385 0.871795
79 4UV 0.613861 0.909091
80 FYA 0.612245 0.92
81 ADV 0.611111 0.921053
82 RBY 0.611111 0.921053
83 5SV 0.610526 0.817073
84 25A 0.610526 0.906667
85 N0B 0.608696 0.901235
86 9X8 0.608247 0.884615
87 ADQ 0.604167 0.933333
88 A3R 0.604167 0.922078
89 4UU 0.601942 0.909091
90 SSA 0.595745 0.835294
91 ADP PO3 0.593407 0.905405
92 LAQ 0.590476 0.853659
93 GA7 0.586538 0.896104
94 MAP 0.583333 0.860759
95 DQV 0.580952 0.92
96 BIS 0.58 0.85
97 4UW 0.579439 0.875
98 NAI 0.579439 0.873418
99 ADP VO4 0.578947 0.894737
100 VO4 ADP 0.578947 0.894737
101 LMS 0.576471 0.797619
102 25L 0.574257 0.894737
103 IOT 0.572727 0.890244
104 AFH 0.571429 0.898734
105 ARG AMP 0.571429 0.888889
106 48N 0.570093 0.910256
107 ADP ALF 0.568421 0.8375
108 ALF ADP 0.568421 0.8375
109 TYR AMP 0.567308 0.934211
110 5CA 0.56701 0.835294
111 TXD 0.564815 0.873418
112 NAX 0.564815 0.8875
113 G3A 0.561905 0.8625
114 TXE 0.559633 0.873418
115 MYR AMP 0.558824 0.831325
116 F2R 0.557522 0.901235
117 7MD 0.556604 0.924051
118 G5P 0.556604 0.8625
119 80F 0.556522 0.878049
120 A5A 0.552083 0.8
121 53H 0.55102 0.772727
122 TSB 0.55102 0.790698
123 6V0 0.550459 0.8625
124 NXX 0.550459 0.921053
125 DND 0.550459 0.921053
126 AOC 0.545455 0.789474
127 OMR 0.545455 0.843373
128 RAB 0.544304 0.810811
129 XYA 0.544304 0.810811
130 ADN 0.544304 0.810811
131 5CD 0.54321 0.773333
132 54H 0.540816 0.781609
133 VMS 0.540816 0.781609
134 AP0 0.540541 0.839506
135 DSZ 0.54 0.835294
136 LSS 0.54 0.795455
137 COD 0.53913 0.847059
138 5AS 0.538462 0.772727
139 5X8 0.537634 0.826667
140 GTA 0.537037 0.831325
141 G5A 0.536842 0.835294
142 DTA 0.535714 0.75641
143 BT5 0.534483 0.86747
144 JB6 0.533981 0.873418
145 2A5 0.531915 0.883117
146 5N5 0.530864 0.786667
147 ADP BMA 0.529412 0.907895
148 M24 0.529412 0.864198
149 PAP 0.526316 0.893333
150 52H 0.525253 0.772727
151 A4D 0.52439 0.786667
152 KAA 0.524272 0.806818
153 GSU 0.524272 0.835294
154 A A 0.524272 0.881579
155 AMP DBH 0.523364 0.858974
156 7D5 0.523256 0.844156
157 TAD 0.522936 0.875
158 UP5 0.522523 0.884615
159 CNA 0.521739 0.921053
160 SFG 0.521277 0.813333
161 AF3 ADP 3PG 0.517857 0.875
162 7D3 0.516484 0.846154
163 A3S 0.516129 0.851351
164 SMM 0.515152 0.741176
165 YSA 0.514019 0.813953
166 LPA AMP 0.513514 0.831325
167 UPA 0.513274 0.897436
168 4TC 0.513274 0.886076
169 T5A 0.513043 0.855422
170 ADJ 0.513043 0.843373
171 NAD 0.512821 0.92
172 A3P 0.51087 0.905405
173 7D4 0.510638 0.846154
174 SA8 0.510417 0.765432
175 ATR 0.510417 0.88
176 PPS 0.510204 0.797619
177 EEM 0.510204 0.746988
178 NSS 0.509804 0.813953
179 A4P 0.508772 0.835294
180 EP4 0.505882 0.725
181 SAI 0.505155 0.794872
182 SAH 0.505155 0.805195
183 8X1 0.504951 0.806818
184 NVA LMS 0.504854 0.786517
185 ATP A A A 0.504673 0.893333
186 AHZ 0.504505 0.831325
187 A3D 0.504202 0.907895
188 3DH 0.5 0.74359
189 SAM 0.5 0.746988
190 6RE 0.5 0.775
191 139 0.5 0.8875
192 7MC 0.5 0.901235
193 LEU LMS 0.5 0.786517
194 M2T 0.5 0.707317
195 NAQ 0.495935 0.8625
196 DZD 0.495798 0.875
197 P5A 0.495238 0.797753
198 A2R 0.49505 0.92
199 ITT 0.494737 0.855263
200 A2P 0.494624 0.891892
201 3AM 0.494382 0.891892
202 MTA 0.494253 0.74359
203 8PZ 0.490741 0.813953
204 9K8 0.490566 0.728261
205 J7C 0.48913 0.78481
206 NAE 0.487805 0.884615
207 BTX 0.487395 0.855422
208 AR6 AR6 0.486486 0.906667
209 S7M 0.485149 0.746988
210 EAD 0.484127 0.864198
211 NDE 0.48062 0.896104
212 6AD 0.48 0.829268
213 ZID 0.48 0.907895
214 WSA 0.478261 0.823529
215 ARU 0.47619 0.785714
216 NAJ PZO 0.47541 0.839506
217 AMP NAD 0.475 0.92
218 0WD 0.475 0.8625
219 HFD 0.474747 0.860759
220 A3N 0.473118 0.75641
221 IMO 0.473118 0.866667
222 ZAS 0.472527 0.759494
223 NAJ PYZ 0.472 0.8
224 GEK 0.471154 0.797468
225 V3L 0.47 0.932432
226 P1H 0.469231 0.843373
227 A7D 0.46875 0.792208
228 GJV 0.468085 0.765432
229 S4M 0.468085 0.701149
230 0UM 0.466667 0.777778
231 2AM 0.466667 0.88
232 A5D 0.464646 0.75641
233 MAO 0.463158 0.77381
234 A3G 0.462366 0.84
235 DSH 0.462366 0.7625
236 62X 0.462264 0.72093
237 FB0 0.462121 0.818182
238 2SA 0.460784 0.946667
239 A3T 0.459184 0.813333
240 NA7 0.457944 0.896104
241 K15 0.457944 0.738095
242 3AT 0.455446 0.906667
243 OVE 0.451613 0.846154
244 7C5 0.451327 0.810127
245 NDC 0.451128 0.8625
246 G A A A 0.45082 0.8625
247 NDP 0.45 0.8625
248 8Q2 0.449153 0.786517
249 NEC 0.446809 0.74026
250 AV2 0.446602 0.833333
251 NZQ 0.446281 0.875
252 5AD 0.445783 0.716216
253 KB1 0.445455 0.756098
254 DAT 0.444444 0.87013
255 4YB 0.443478 0.816092
256 AVV 0.443396 0.8625
257 NJP 0.442623 0.884615
258 Y3J 0.44186 0.697368
259 DTP 0.441176 0.87013
260 6IA 0.441176 0.851852
261 649 0.440678 0.777778
262 7D7 0.440476 0.736842
263 AMZ 0.43956 0.855263
264 C2R 0.43956 0.868421
265 4TA 0.439024 0.843373
266 A G 0.439024 0.85
267 NPW 0.438017 0.876543
268 AAT 0.436893 0.743902
269 DCA 0.436508 0.837209
270 ETB 0.436508 0.847059
271 U A G G 0.435484 0.85
272 SFD 0.434783 0.729167
273 TXP 0.434426 0.8625
274 PGS 0.434343 0.804878
275 MHZ 0.434343 0.732558
276 D3Y 0.433962 0.828947
277 GGZ 0.433962 0.77381
278 FDA 0.433824 0.804598
279 71V 0.43299 0.82716
280 FNK 0.432624 0.797753
281 6C6 0.431373 0.871795
282 VRT 0.431373 0.807692
283 A6D 0.431193 0.697674
284 ODP 0.430894 0.851852
285 30N 0.430769 0.765957
286 6FA 0.430657 0.833333
287 NIA 0.430108 0.771084
288 2VA 0.43 0.792208
289 0T1 0.429688 0.837209
290 COA 0.429688 0.837209
291 U A 0.428571 0.873418
292 3NZ 0.427273 0.820513
293 FAS 0.42446 0.843373
294 FAD 0.42446 0.843373
295 SXZ 0.423423 0.768293
296 NVA 2AD 0.421569 0.797468
297 CAO 0.419847 0.808989
298 COS 0.419847 0.818182
299 AMX 0.419847 0.847059
300 KH3 0.418803 0.75
301 PO4 PO4 A A A A PO4 0.418182 0.866667
302 A A A 0.418182 0.894737
303 SO8 0.417476 0.782051
304 D5M 0.416667 0.868421
305 CMX 0.416667 0.858824
306 S8M 0.416667 0.775
307 SCO 0.416667 0.858824
308 DA 0.416667 0.868421
309 6K6 0.416667 0.893333
310 XNP 0.416 0.841463
311 FCX 0.413534 0.829545
312 FAM 0.413534 0.818182
313 ACO 0.413534 0.808989
314 F0P 0.413223 0.7875
315 62F 0.412587 0.853659
316 AAM 0.412371 0.905405
317 FAI 0.412371 0.855263
318 NMX 0.411765 0.774194
319 HAX 0.410448 0.818182
320 7DD 0.41 0.893333
321 APU 0.409836 0.884615
322 FAY 0.409722 0.853659
323 P5F 0.409396 0.816092
324 Z5A 0.409091 0.793103
325 N6P 0.409091 0.853333
326 2MC 0.408759 0.782609
327 SCD 0.408759 0.858824
328 FYN 0.407407 0.837209
329 3KK 0.407407 0.818182
330 RFL 0.406897 0.813953
331 SLU 0.40625 0.764045
332 9JJ 0.405405 0.831325
333 V1N 0.405172 0.906667
334 NMN AMP PO4 0.404762 0.860759
335 OXK 0.404412 0.83908
336 MCD 0.404412 0.83908
337 CA6 0.404412 0.742268
338 SOP 0.404412 0.818182
339 COK 0.404412 0.818182
340 F2N 0.403974 0.806818
341 12D 0.403361 0.738636
342 NAP 0.401515 0.907895
343 CMC 0.40146 0.83908
344 CO6 0.40146 0.818182
345 1VU 0.40146 0.808989
346 DDS 0.4 0.820513
347 AIR 0.4 0.84
348 RGT 0.4 0.896104
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: 70
This union binding pocket(no: 1) in the query (biounit: 1wle.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
1 4RF7 ARG 0.998004
2 1ORR NAD 1.15274
3 3CQL NAG 1.64609
4 2I4O ATP 1.96507
5 3E9I XAH 2.23124
6 3NEM ATP 2.28311
7 3NEM AMO 2.28311
8 3UH0 TSB 2.3913
9 3HXU A5A 2.49433
10 1CT9 AMP 2.53165
11 1G51 AMO 2.59481
12 3A5Y KAA 2.6087
13 2GQT FAD 2.98507
14 4ZUL UN1 3.39321
15 3A5Z KAA 3.66492
16 1I7E IBS 3.77358
17 5DNC ASN 3.79242
18 2XGT NSS 3.90805
19 4J25 OGA 3.93013
20 12AS AMP 3.93939
21 3G1Z AMP 3.98773
22 2ZTG A5A 3.99202
23 3TEG DAH 4.09639
24 1UNB PN1 4.18006
25 1UNB AKG 4.18006
26 3RK0 AMP 4.21941
27 4ZTD ALA GLY ALA GLY ALA 4.34783
28 5OUH L0B 4.39024
29 6EMU SAM 4.56853
30 1E1O LYS 4.59082
31 5J6Y GLC 4.78723
32 5J6Y BGC 4.78723
33 3IAL PR8 4.79042
34 2Z77 HE7 5.03597
35 6GNO XDI 5.18518
36 3BJU ATP 5.18962
37 6C74 PC 5.40541
38 2P0D I3P 5.42636
39 3QX9 ATP 5.7971
40 1YFS ALA 6.02151
41 3T4L ZEA 6.2963
42 5V59 8X1 6.58683
43 2E5A LAQ 6.62824
44 1B7Y FYA 7.38523
45 3A7R LAQ 7.4184
46 1X54 4AD 7.60369
47 1M5W DXP 7.81893
48 4H2V AMP 8.3815
49 3MF2 AMP 8.3815
50 3REU ATP 9.86395
51 4H2X G5A 11.6505
52 4H2W AMP 11.6505
53 4H2W 5GP 11.6505
54 2ART LPA AMP 12.2137
55 5VAD 91Y 12.7907
56 6BU0 IHP 12.9771
57 4YLZ LAT NAG GAL 13.0719
58 2J3M ATP 13.3733
59 2J3M PRI 13.3733
60 4HWS 1B3 14.8418
61 5XIO ANP 15.261
62 5XIJ ANP 15.6
63 5XIJ 873 15.6
64 4YDQ ANP 16.9014
65 4YDQ HFG 16.9014
66 4HWT 1B2 18.1598
67 4AIA ADK 18.617
68 4CS4 ANP 21.5328
69 4CS4 AXZ 21.5328
70 3ERR AMP 38.3234
Pocket No.: 2; Query (leader) PDB : 1WLE; Ligand: SRP; Similar sites found with APoc: 6
This union binding pocket(no: 2) in the query (biounit: 1wle.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
1 4RGA 3PV 3.39321
2 2G30 ALA ALA PHE 3.48837
3 4NDN PPK 4.33437
4 5L13 6ZE 4.39122
5 4IGQ OGA 5.27778
6 3K7S R52 6.14525
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