Receptor
PDB id Resolution Class Description Source Keywords
6ILD 1.88 Å EC: 2.7.7.- CRYSTAL STRUCTURE OF HUMAN LYSRS: P38/AIMP2 COMPLEX II HOMO SAPIENS LYSYL-TRNA SYNTHETASE LYSRS P38 AIMP2 MULTI TRNA SYNTHETCOMPLEX SUB-COMPLEX LIGASE
Ref.: RETRACTILE LYSYL-TRNA SYNTHETASE-AIMP2 ASSEMBLY IN MULTI-AMINOACYL-TRNA SYNTHETASE COMPLEX. J. BIOL. CHEM. V. 294 4775 2019
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MG B:602;
A:604;
Part of Protein;
Part of Protein;
none;
none;
submit data
24.305 Mg [Mg+2...
45A B:605;
Valid;
none;
submit data
345.248 C11 H16 N5 O6 P CP(=O...
GOL A:602;
B:604;
A:605;
B:603;
A:603;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
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
6ILD 1.88 Å EC: 2.7.7.- CRYSTAL STRUCTURE OF HUMAN LYSRS: P38/AIMP2 COMPLEX II HOMO SAPIENS LYSYL-TRNA SYNTHETASE LYSRS P38 AIMP2 MULTI TRNA SYNTHETCOMPLEX SUB-COMPLEX LIGASE
Ref.: RETRACTILE LYSYL-TRNA SYNTHETASE-AIMP2 ASSEMBLY IN MULTI-AMINOACYL-TRNA SYNTHETASE COMPLEX. J. BIOL. CHEM. V. 294 4775 2019
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 23 families.
1 6ILD - 45A C11 H16 N5 O6 P CP(=O)(O)O....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 21 families.
1 6ILD - 45A C11 H16 N5 O6 P CP(=O)(O)O....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 20 families.
1 6ILD - 45A C11 H16 N5 O6 P CP(=O)(O)O....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: 45A; Similar ligands found: 420
No: Ligand ECFP6 Tc MDL keys Tc
1 ABM 1 1
2 45A 1 1
3 AMP 0.833333 0.943662
4 A 0.833333 0.943662
5 M33 0.816901 0.958333
6 A2D 0.797101 0.917808
7 AMP MG 0.794118 0.929577
8 AP2 0.774648 0.881579
9 BA3 0.774648 0.917808
10 A12 0.774648 0.881579
11 SRA 0.768116 0.893333
12 ADP 0.763889 0.917808
13 AP5 0.763889 0.917808
14 B4P 0.763889 0.917808
15 AN2 0.753425 0.905405
16 AT4 0.753425 0.881579
17 PRX 0.746667 0.918919
18 AU1 0.743243 0.893333
19 CA0 0.743243 0.893333
20 ADX 0.743243 0.82716
21 50T 0.733333 0.905405
22 ATP 0.733333 0.917808
23 ACP 0.733333 0.893333
24 HEJ 0.733333 0.917808
25 KG4 0.733333 0.893333
26 ADP MG 0.72973 0.916667
27 ADP BEF 0.72973 0.916667
28 AR6 0.723684 0.917808
29 APR 0.723684 0.917808
30 AQP 0.723684 0.917808
31 APC 0.723684 0.881579
32 5FA 0.723684 0.917808
33 ADV 0.714286 0.881579
34 RBY 0.714286 0.881579
35 ADP PO3 0.714286 0.916667
36 AGS 0.714286 0.87013
37 ATP MG 0.714286 0.916667
38 AD9 0.714286 0.893333
39 8LE 0.708861 0.894737
40 5AL 0.708861 0.931507
41 ACQ 0.696203 0.893333
42 T99 0.696203 0.881579
43 ANP 0.696203 0.893333
44 TAT 0.696203 0.881579
45 APC MG 0.692308 0.891892
46 8LH 0.691358 0.906667
47 V2G 0.6875 0.848101
48 SON 0.684211 0.881579
49 BEF ADP 0.683544 0.891892
50 LMS 0.680556 0.804878
51 ATF 0.679012 0.881579
52 GAP 0.675 0.868421
53 QA7 0.674699 0.894737
54 8LQ 0.674699 0.906667
55 5AS 0.671053 0.77907
56 SRP 0.670732 0.881579
57 6YZ 0.670732 0.893333
58 5SV 0.666667 0.896104
59 8QN 0.666667 0.931507
60 9ZD 0.666667 0.907895
61 9ZA 0.666667 0.907895
62 HQG 0.662651 0.905405
63 PAJ 0.658824 0.860759
64 ANP MG 0.658537 0.905405
65 ALF ADP 0.658537 0.846154
66 VO4 ADP 0.658537 0.893333
67 MAP 0.654762 0.87013
68 A22 0.654762 0.905405
69 DAL AMP 0.654762 0.905405
70 RAB 0.651515 0.819444
71 ADN 0.651515 0.819444
72 XYA 0.651515 0.819444
73 25A 0.647059 0.917808
74 OOB 0.647059 0.905405
75 OZV 0.647059 0.917808
76 OAD 0.643678 0.918919
77 9X8 0.643678 0.894737
78 AOC 0.64 0.821918
79 A3R 0.639535 0.858974
80 AMO 0.639535 0.881579
81 4AD 0.639535 0.87013
82 A1R 0.639535 0.858974
83 ADQ 0.639535 0.893333
84 5N5 0.632353 0.794521
85 00A 0.632184 0.858974
86 JNT 0.632184 0.893333
87 DLL 0.632184 0.905405
88 AHX 0.632184 0.848101
89 ME8 0.629214 0.886076
90 TXA 0.629214 0.906667
91 3OD 0.629214 0.918919
92 1ZZ 0.629214 0.8625
93 PTJ 0.629214 0.871795
94 3UK 0.625 0.893333
95 A4D 0.623188 0.794521
96 5CD 0.623188 0.805556
97 EP4 0.619718 0.8
98 WAQ 0.617977 0.858974
99 PR8 0.617977 0.82716
100 B5V 0.617977 0.881579
101 LAD 0.617977 0.8375
102 M2T 0.611111 0.779221
103 FYA 0.611111 0.905405
104 BIS 0.611111 0.858974
105 NB8 0.611111 0.848101
106 B5M 0.608696 0.894737
107 B5Y 0.608696 0.894737
108 KMQ 0.608696 0.932432
109 3DH 0.608108 0.821918
110 ADP BMA 0.606742 0.868421
111 H1Q 0.604938 0.90411
112 MYR AMP 0.604396 0.839506
113 25L 0.604396 0.905405
114 MTA 0.60274 0.821918
115 9SN 0.597826 0.848101
116 A3P 0.594937 0.916667
117 7D5 0.594595 0.853333
118 JB6 0.593407 0.858974
119 FA5 0.591398 0.881579
120 ATP A 0.591398 0.90411
121 ATP A A A 0.591398 0.90411
122 DTA 0.589041 0.786667
123 XAH 0.585106 0.817073
124 G5A 0.583333 0.758621
125 GA7 0.583333 0.906667
126 6MZ 0.582278 0.957747
127 48N 0.581633 0.871795
128 YLP 0.581633 0.819277
129 A5A 0.581395 0.807229
130 TSB 0.579545 0.797619
131 3AM 0.578947 0.902778
132 4UV 0.578947 0.87013
133 DQV 0.57732 0.905405
134 GTA 0.57732 0.8625
135 A2P 0.575 0.902778
136 G3A 0.572917 0.848101
137 LEU LMS 0.571429 0.75
138 VMS 0.568182 0.788235
139 52H 0.568182 0.77907
140 54H 0.568182 0.788235
141 G5P 0.56701 0.848101
142 AFH 0.56701 0.8375
143 4UU 0.56701 0.87013
144 LSS 0.566667 0.761364
145 YLC 0.564356 0.839506
146 YLB 0.564356 0.819277
147 6RE 0.564103 0.7375
148 S4M 0.5625 0.72619
149 AMP DBH 0.5625 0.868421
150 53H 0.561798 0.77907
151 TAD 0.561224 0.8375
152 DND 0.56 0.881579
153 4UW 0.56 0.884615
154 9K8 0.55914 0.714286
155 SSA 0.556818 0.758621
156 AHZ 0.555556 0.839506
157 MAO 0.555556 0.825
158 LAQ 0.555556 0.817073
159 OMR 0.554455 0.851852
160 PAP 0.552941 0.90411
161 ZAS 0.551282 0.766234
162 ARG AMP 0.55102 0.785714
163 7MD 0.55102 0.817073
164 AR6 AR6 0.55102 0.891892
165 5AD 0.550725 0.771429
166 J7C 0.55 0.746835
167 IMO 0.55 0.876712
168 A3N 0.55 0.763158
169 NAD IBO 0.54902 0.891892
170 AP0 0.54902 0.896104
171 NAD TDB 0.54902 0.891892
172 2AM 0.545455 0.890411
173 TXD 0.544554 0.858974
174 NAX 0.544554 0.82716
175 UP5 0.544554 0.87013
176 NAI 0.544554 0.858974
177 6V0 0.544554 0.848101
178 8X1 0.544444 0.733333
179 5CA 0.544444 0.758621
180 NVA LMS 0.543478 0.752809
181 7D3 0.54321 0.831169
182 CNA 0.542857 0.881579
183 AYB 0.542857 0.809524
184 2A5 0.541176 0.844156
185 V3L 0.54023 0.917808
186 TXE 0.539216 0.858974
187 TYM 0.539216 0.881579
188 DSH 0.5375 0.725
189 7D4 0.535714 0.831169
190 ATR 0.534884 0.890411
191 LPA AMP 0.534653 0.795181
192 NWW 0.534247 0.736111
193 PPS 0.534091 0.804878
194 7MC 0.533981 0.819277
195 L3W 0.533981 0.881579
196 4TC 0.533981 0.848101
197 UPA 0.533981 0.858974
198 ADJ 0.533333 0.807229
199 T5A 0.533333 0.819277
200 YLA 0.533333 0.797619
201 NAD 0.53271 0.905405
202 NSS 0.532609 0.758621
203 DSZ 0.532609 0.758621
204 P5A 0.531915 0.725275
205 5X8 0.529412 0.763158
206 A4P 0.528846 0.77907
207 O02 0.528736 0.848101
208 OVE 0.525 0.855263
209 GJV 0.52439 0.728395
210 ALF ADP 3PG 0.524272 0.814815
211 AF3 ADP 3PG 0.524272 0.814815
212 IOT 0.52381 0.788235
213 A7D 0.52381 0.776316
214 F2R 0.523364 0.797619
215 A3D 0.522936 0.918919
216 139 0.518868 0.82716
217 COD 0.518519 0.790698
218 4TA 0.518519 0.807229
219 ITT 0.517647 0.864865
220 MHZ 0.517647 0.759036
221 SA8 0.517241 0.772152
222 A2R 0.516484 0.905405
223 GSU 0.515789 0.758621
224 KAA 0.515789 0.733333
225 DZD 0.513761 0.8375
226 SFG 0.511628 0.75
227 SAI 0.511364 0.734177
228 YLY 0.508929 0.831325
229 SAM 0.505618 0.753086
230 6IA 0.505618 0.860759
231 SMM 0.505495 0.746988
232 PO4 PO4 A A A A PO4 0.505263 0.876712
233 YSA 0.50505 0.758621
234 BTX 0.504587 0.797619
235 AMP NAD 0.504587 0.88
236 NAE 0.504425 0.894737
237 Y3J 0.5 0.726027
238 71V 0.5 0.858974
239 D5M 0.5 0.853333
240 NAQ 0.5 0.896104
241 A3G 0.5 0.776316
242 DA 0.5 0.853333
243 BT5 0.5 0.788235
244 A5D 0.5 0.786667
245 EEM 0.5 0.753086
246 NEC 0.5 0.746667
247 6AD 0.5 0.884615
248 7D7 0.5 0.743243
249 80F 0.495495 0.797619
250 8PZ 0.494949 0.758621
251 ARU 0.494737 0.8375
252 HFD 0.494382 0.87013
253 6C6 0.494382 0.857143
254 JSQ 0.494382 0.87013
255 SAH 0.494382 0.74359
256 B1U 0.49 0.717391
257 NA7 0.489583 0.881579
258 S7M 0.48913 0.731707
259 NWQ 0.4875 0.763889
260 EAD 0.487179 0.85
261 J4G 0.484536 0.87013
262 ZID 0.482759 0.893333
263 PGS 0.482759 0.8125
264 N0B 0.482759 0.797619
265 M24 0.482456 0.82716
266 7C5 0.480392 0.772152
267 K3K 0.48 0.779221
268 Z5A 0.478632 0.77907
269 AV2 0.478261 0.842105
270 D4F 0.478261 0.817073
271 2SA 0.478261 0.857143
272 NAJ PZO 0.477876 0.825
273 A3T 0.477273 0.821918
274 CUU 0.477273 0.891892
275 DAT 0.477273 0.831169
276 AAM 0.47619 0.943662
277 KOY 0.47619 0.779221
278 C2R 0.475 0.828947
279 AMZ 0.475 0.84
280 AVV 0.473684 0.848101
281 QXP 0.473684 0.724138
282 V47 0.473118 0.76
283 DTP 0.472527 0.831169
284 3AT 0.472527 0.891892
285 A3S 0.471264 0.786667
286 4YB 0.471154 0.741573
287 K3E 0.470588 0.769231
288 101 0.46988 0.853333
289 0UM 0.46875 0.719512
290 NO7 0.468085 0.857143
291 AIR 0.467532 0.875
292 AAT 0.467391 0.707317
293 WSA 0.46729 0.767442
294 649 0.46729 0.725275
295 N5O 0.464286 0.74026
296 62X 0.463918 0.72619
297 K2H 0.463918 0.779221
298 NIA 0.463415 0.777778
299 GGZ 0.463158 0.780488
300 NAJ PYZ 0.461538 0.785714
301 LQJ 0.460784 0.891892
302 QXG 0.459184 0.715909
303 K15 0.459184 0.722892
304 A6D 0.459184 0.722892
305 P1H 0.459016 0.829268
306 NDE 0.459016 0.881579
307 AS 0.458824 0.810127
308 6K6 0.458333 0.90411
309 GEK 0.458333 0.716049
310 38V 0.457627 0.817073
311 R2V 0.454545 0.724138
312 3AD 0.454545 0.805556
313 K2K 0.454545 0.716049
314 N5A 0.453488 0.714286
315 FB0 0.451613 0.784091
316 NDC 0.451613 0.848101
317 SXZ 0.45 0.710843
318 O05 0.45 0.77907
319 8Q2 0.449541 0.733333
320 N6P 0.44898 0.888889
321 26A 0.448718 0.786667
322 KY2 0.447917 0.710843
323 SO8 0.445652 0.789474
324 KY5 0.445545 0.725
325 FDA 0.444444 0.790698
326 2VA 0.444444 0.8
327 KL2 0.444444 0.813333
328 S8M 0.443299 0.759494
329 NJP 0.442478 0.87013
330 V1N 0.442308 0.917808
331 7RA 0.44186 0.930556
332 RMB 0.44186 0.873239
333 6FA 0.440945 0.819277
334 DDS 0.44086 0.805195
335 103 0.440476 0.863014
336 ACK 0.440476 0.861111
337 QQY 0.440476 0.815789
338 CC5 0.44 0.816901
339 KY8 0.44 0.728395
340 N01 0.439655 0.905405
341 KYB 0.438776 0.710843
342 EO7 0.436782 0.767442
343 8BR 0.436782 0.881579
344 DZ4 0.43617 0.810127
345 3D1 0.435897 0.75
346 3L1 0.435897 0.75
347 K2R 0.435644 0.831169
348 NVA 2AD 0.434783 0.759494
349 FAS 0.434109 0.829268
350 FAD 0.434109 0.829268
351 SFD 0.434109 0.715789
352 K3H 0.432692 0.772152
353 K2W 0.432692 0.719512
354 2BA 0.431818 0.888889
355 CMP 0.431818 0.901408
356 FNK 0.431818 0.764045
357 KB1 0.431373 0.698795
358 TM1 0.431373 0.732558
359 6MD 0.43038 0.833333
360 7RP 0.430233 0.901408
361 VRT 0.430108 0.769231
362 KXW 0.429907 0.707317
363 ODP 0.429825 0.8375
364 QQX 0.428571 0.805195
365 NAD BBN 0.427481 0.797619
366 PLP AAD 0.42735 0.793103
367 SLU 0.42735 0.75
368 K38 0.427184 0.75641
369 0WD 0.426087 0.848101
370 3NZ 0.425743 0.805195
371 NX8 0.425532 0.695122
372 5F1 0.425 0.710526
373 SP1 0.423529 0.842105
374 RP1 0.423529 0.842105
375 9JJ 0.423358 0.817073
376 7DD 0.422222 0.90411
377 OZP 0.422018 0.707317
378 NAD CJ3 0.421053 0.770115
379 62F 0.421053 0.839506
380 NZQ 0.421053 0.8375
381 ANZ 0.420561 0.777778
382 APU 0.419643 0.846154
383 KYE 0.419048 0.694118
384 RBZ 0.418605 0.849315
385 D3Y 0.418367 0.766234
386 FAY 0.41791 0.839506
387 MTP 0.417722 0.753247
388 G 0.417582 0.857143
389 5GP 0.417582 0.857143
390 KH3 0.416667 0.714286
391 RFL 0.414815 0.821429
392 N37 0.414414 0.7125
393 NAD NDT 0.414286 0.708333
394 NMN AMP PO4 0.413793 0.846154
395 2FA 0.4125 0.789474
396 NPW 0.412281 0.817073
397 NDP 0.412281 0.848101
398 ETB 0.411765 0.833333
399 DCA 0.411765 0.781609
400 F0P 0.410714 0.707317
401 NAP 0.409836 0.893333
402 RGT 0.409524 0.881579
403 P2P 0.409091 0.876712
404 FAI 0.409091 0.84
405 TXP 0.408696 0.848101
406 7DT 0.408602 0.90411
407 NWZ 0.408602 0.682927
408 G 6MZ C 0.408602 0.902778
409 1RB 0.406977 0.859155
410 128 0.405405 0.715909
411 HY8 0.405405 0.710843
412 9BG 0.405172 0.825
413 COA 0.404959 0.781609
414 0T1 0.404959 0.781609
415 NA0 0.403226 0.906667
416 NHD 0.401709 0.88
417 F2N 0.401408 0.772727
418 12D 0.4 0.724138
419 PMO 0.4 0.875
420 HZ2 0.4 0.710843
Similar Ligands (3D)
Ligand no: 1; Ligand: 45A; Similar ligands found: 40
No: Ligand Similarity coefficient
1 IMP 0.9770
2 FMP 0.9652
3 IRP 0.9642
4 IMU 0.9475
5 6OG 0.9462
6 6MA 0.9455
7 DGP 0.9444
8 6CG 0.9387
9 UP6 0.9386
10 8OG 0.9358
11 TMP 0.9357
12 PFU 0.9352
13 FNU 0.9315
14 DI 0.9302
15 XMP 0.9253
16 8GM 0.9249
17 8OP 0.9239
18 G7M 0.9171
19 JLN 0.9160
20 DG 0.9160
21 NYM 0.9095
22 UFP 0.9090
23 9L3 0.9081
24 PSU 0.9006
25 93A 0.9004
26 MZP 0.8927
27 EU2 0.8898
28 INR 0.8836
29 RVP 0.8826
30 MCF 0.8824
31 K8W 0.8817
32 NOS 0.8815
33 8QB 0.8812
34 FDM 0.8812
35 2GE 0.8720
36 MTE 0.8710
37 9ZS 0.8678
38 1BJ 0.8669
39 FGN 0.8624
40 RVA 0.8530
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6ILD; Ligand: 45A; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 6ild.bio1) has 14 residues
No: Leader PDB Ligand Sequence Similarity
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