Receptor
PDB id Resolution Class Description Source Keywords
6ILD 1.88 Å EC: 2.7.7.-_6.1.1.6 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.-_6.1.1.6 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 1 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 1 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 1 families.
1 6ILD - 45A C11 H16 N5 O6 P CP(=O)(O)O....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 45A; Similar ligands found: 389
No: Ligand ECFP6 Tc MDL keys Tc
1 45A 1 1
2 ABM 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 BA3 0.774648 0.917808
8 A12 0.774648 0.881579
9 AP2 0.774648 0.881579
10 SRA 0.768116 0.893333
11 ADP 0.763889 0.917808
12 B4P 0.763889 0.917808
13 AP5 0.763889 0.917808
14 AN2 0.753425 0.905405
15 AT4 0.753425 0.881579
16 PRX 0.746667 0.918919
17 CA0 0.743243 0.893333
18 AU1 0.743243 0.893333
19 ADX 0.743243 0.82716
20 ATP 0.733333 0.917808
21 KG4 0.733333 0.893333
22 50T 0.733333 0.905405
23 ACP 0.733333 0.893333
24 HEJ 0.733333 0.917808
25 ADP MG 0.72973 0.916667
26 5FA 0.723684 0.917808
27 AR6 0.723684 0.917808
28 APR 0.723684 0.917808
29 AQP 0.723684 0.917808
30 APC 0.723684 0.881579
31 SAP 0.714286 0.87013
32 AD9 0.714286 0.893333
33 AGS 0.714286 0.87013
34 RBY 0.714286 0.881579
35 ADP PO3 0.714286 0.916667
36 ATP MG 0.714286 0.916667
37 ADV 0.714286 0.881579
38 8LE 0.708861 0.894737
39 5AL 0.708861 0.931507
40 ACQ 0.696203 0.893333
41 T99 0.696203 0.881579
42 TAT 0.696203 0.881579
43 ANP 0.696203 0.893333
44 APC MG 0.692308 0.891892
45 8LH 0.691358 0.906667
46 SON 0.684211 0.881579
47 LMS 0.680556 0.804878
48 ATF 0.679012 0.881579
49 GAP 0.675 0.868421
50 8LQ 0.674699 0.906667
51 5AS 0.671053 0.77907
52 6YZ 0.670732 0.893333
53 SRP 0.670732 0.881579
54 9ZA 0.666667 0.907895
55 5SV 0.666667 0.896104
56 8QN 0.666667 0.931507
57 9ZD 0.666667 0.907895
58 HQG 0.662651 0.905405
59 PAJ 0.658824 0.860759
60 ALF ADP 0.658537 0.846154
61 ADP ALF 0.658537 0.846154
62 MAP 0.654762 0.87013
63 A22 0.654762 0.905405
64 DAL AMP 0.654762 0.905405
65 RAB 0.651515 0.819444
66 ADN 0.651515 0.819444
67 XYA 0.651515 0.819444
68 ADP VO4 0.650602 0.905405
69 VO4 ADP 0.650602 0.905405
70 OOB 0.647059 0.905405
71 25A 0.647059 0.917808
72 OZV 0.647059 0.917808
73 OAD 0.643678 0.918919
74 9X8 0.643678 0.894737
75 AOC 0.64 0.821918
76 A1R 0.639535 0.858974
77 ADQ 0.639535 0.893333
78 A3R 0.639535 0.858974
79 AMO 0.639535 0.881579
80 4AD 0.639535 0.87013
81 5N5 0.632353 0.794521
82 00A 0.632184 0.858974
83 AHX 0.632184 0.848101
84 DLL 0.632184 0.905405
85 3OD 0.629214 0.918919
86 1ZZ 0.629214 0.8625
87 PTJ 0.629214 0.871795
88 TXA 0.629214 0.906667
89 ME8 0.629214 0.886076
90 3UK 0.625 0.893333
91 A4D 0.623188 0.794521
92 5CD 0.623188 0.805556
93 EP4 0.619718 0.8
94 WAQ 0.617977 0.858974
95 B5V 0.617977 0.881579
96 LAD 0.617977 0.8375
97 PR8 0.617977 0.82716
98 M2T 0.611111 0.779221
99 NB8 0.611111 0.848101
100 FYA 0.611111 0.905405
101 BIS 0.611111 0.858974
102 B5Y 0.608696 0.894737
103 B5M 0.608696 0.894737
104 3DH 0.608108 0.821918
105 ADP BMA 0.606742 0.868421
106 H1Q 0.604938 0.90411
107 MYR AMP 0.604396 0.839506
108 25L 0.604396 0.905405
109 MTA 0.60274 0.821918
110 A A 0.6 0.917808
111 9SN 0.597826 0.848101
112 A3P 0.594937 0.916667
113 7D5 0.594595 0.853333
114 JB6 0.593407 0.858974
115 FA5 0.591398 0.881579
116 ATP A A A 0.591398 0.90411
117 YAP 0.591398 0.87013
118 ATP A 0.591398 0.90411
119 DTA 0.589041 0.786667
120 XAH 0.585106 0.817073
121 GA7 0.583333 0.906667
122 G5A 0.583333 0.758621
123 6MZ 0.582278 0.957747
124 YLP 0.581633 0.819277
125 48N 0.581633 0.871795
126 A5A 0.581395 0.807229
127 TSB 0.579545 0.797619
128 4UV 0.578947 0.87013
129 3AM 0.578947 0.902778
130 GTA 0.57732 0.8625
131 DQV 0.57732 0.905405
132 A2P 0.575 0.902778
133 G3A 0.572917 0.848101
134 54H 0.568182 0.788235
135 52H 0.568182 0.77907
136 VMS 0.568182 0.788235
137 4UU 0.56701 0.87013
138 AFH 0.56701 0.8375
139 G5P 0.56701 0.848101
140 LSS 0.566667 0.761364
141 YLB 0.564356 0.819277
142 YLC 0.564356 0.839506
143 6RE 0.564103 0.7375
144 TYR AMP 0.5625 0.846154
145 S4M 0.5625 0.72619
146 AMP DBH 0.5625 0.868421
147 53H 0.561798 0.77907
148 TAD 0.561224 0.8375
149 DND 0.56 0.881579
150 NXX 0.56 0.881579
151 4UW 0.56 0.884615
152 9K8 0.55914 0.714286
153 SSA 0.556818 0.758621
154 LAQ 0.555556 0.817073
155 MAO 0.555556 0.825
156 AHZ 0.555556 0.839506
157 OMR 0.554455 0.851852
158 LEU LMS 0.554348 0.752809
159 PAP 0.552941 0.90411
160 ZAS 0.551282 0.766234
161 ARG AMP 0.55102 0.785714
162 7MD 0.55102 0.817073
163 AR6 AR6 0.55102 0.891892
164 5AD 0.550725 0.771429
165 J7C 0.55 0.746835
166 A3N 0.55 0.763158
167 IMO 0.55 0.876712
168 AP0 0.54902 0.896104
169 2AM 0.545455 0.890411
170 TXD 0.544554 0.858974
171 NAX 0.544554 0.82716
172 6V0 0.544554 0.848101
173 UP5 0.544554 0.87013
174 NAI 0.544554 0.858974
175 5CA 0.544444 0.758621
176 8X1 0.544444 0.733333
177 NVA LMS 0.543478 0.752809
178 7D3 0.54321 0.831169
179 CNA 0.542857 0.881579
180 AYB 0.542857 0.809524
181 2A5 0.541176 0.844156
182 V3L 0.54023 0.917808
183 TXE 0.539216 0.858974
184 TYM 0.539216 0.881579
185 DSH 0.5375 0.725
186 7D4 0.535714 0.831169
187 ATR 0.534884 0.890411
188 LPA AMP 0.534653 0.795181
189 PPS 0.534091 0.804878
190 UPA 0.533981 0.858974
191 7MC 0.533981 0.819277
192 4TC 0.533981 0.848101
193 YLA 0.533333 0.797619
194 ADJ 0.533333 0.807229
195 T5A 0.533333 0.819277
196 NAD 0.53271 0.905405
197 NSS 0.532609 0.758621
198 DSZ 0.532609 0.758621
199 P5A 0.531915 0.725275
200 5X8 0.529412 0.763158
201 A4P 0.528846 0.77907
202 OVE 0.525 0.855263
203 GJV 0.52439 0.728395
204 AF3 ADP 3PG 0.524272 0.814815
205 IOT 0.52381 0.788235
206 A7D 0.52381 0.776316
207 F2R 0.523364 0.797619
208 A3D 0.522936 0.918919
209 139 0.518868 0.82716
210 COD 0.518519 0.790698
211 4TA 0.518519 0.807229
212 ITT 0.517647 0.864865
213 MHZ 0.517647 0.759036
214 SA8 0.517241 0.772152
215 A2R 0.516484 0.905405
216 KAA 0.515789 0.733333
217 GSU 0.515789 0.758621
218 DZD 0.513761 0.8375
219 SFG 0.511628 0.75
220 SAI 0.511364 0.734177
221 YLY 0.508929 0.831325
222 6IA 0.505618 0.860759
223 SAM 0.505618 0.753086
224 SMM 0.505495 0.746988
225 PO4 PO4 A A A A PO4 0.505263 0.876712
226 YSA 0.50505 0.758621
227 AMP NAD 0.504587 0.88
228 BTX 0.504587 0.797619
229 NAE 0.504425 0.894737
230 BT5 0.5 0.788235
231 A3G 0.5 0.776316
232 DA 0.5 0.853333
233 6AD 0.5 0.884615
234 EEM 0.5 0.753086
235 71V 0.5 0.858974
236 A5D 0.5 0.786667
237 NEC 0.5 0.746667
238 7D7 0.5 0.743243
239 Y3J 0.5 0.726027
240 NAQ 0.5 0.896104
241 D5M 0.5 0.853333
242 80F 0.495495 0.797619
243 8PZ 0.494949 0.758621
244 ARU 0.494737 0.8375
245 HFD 0.494382 0.87013
246 6C6 0.494382 0.857143
247 JSQ 0.494382 0.87013
248 SAH 0.494382 0.74359
249 G A A A 0.490909 0.825
250 B1U 0.49 0.717391
251 A A A 0.489583 0.88
252 NA7 0.489583 0.881579
253 S7M 0.48913 0.731707
254 EAD 0.487179 0.85
255 J4G 0.484536 0.87013
256 PGS 0.482759 0.8125
257 N0B 0.482759 0.797619
258 ZID 0.482759 0.893333
259 M24 0.482456 0.82716
260 7C5 0.480392 0.772152
261 Z5A 0.478632 0.77907
262 AV2 0.478261 0.842105
263 2SA 0.478261 0.857143
264 NAJ PZO 0.477876 0.825
265 U A 0.477876 0.858974
266 A G 0.477477 0.835443
267 A3T 0.477273 0.821918
268 DAT 0.477273 0.831169
269 KOY 0.47619 0.779221
270 AAM 0.47619 0.943662
271 C2R 0.475 0.828947
272 AMZ 0.475 0.84
273 AVV 0.473684 0.848101
274 U A G G 0.473214 0.835443
275 DTP 0.472527 0.831169
276 3AT 0.472527 0.891892
277 A3S 0.471264 0.786667
278 4YB 0.471154 0.741573
279 101 0.46988 0.853333
280 0UM 0.46875 0.719512
281 NO7 0.468085 0.857143
282 AIR 0.467532 0.875
283 AAT 0.467391 0.707317
284 649 0.46729 0.725275
285 WSA 0.46729 0.767442
286 N5O 0.464286 0.74026
287 62X 0.463918 0.72619
288 NIA 0.463415 0.777778
289 GGZ 0.463158 0.780488
290 NAJ PYZ 0.461538 0.785714
291 LQJ 0.460784 0.891892
292 A6D 0.459184 0.722892
293 K15 0.459184 0.722892
294 NDE 0.459016 0.881579
295 P1H 0.459016 0.829268
296 AS 0.458824 0.810127
297 GEK 0.458333 0.716049
298 6K6 0.458333 0.90411
299 3AD 0.454545 0.805556
300 N5A 0.453488 0.714286
301 NDC 0.451613 0.848101
302 FB0 0.451613 0.784091
303 SXZ 0.45 0.710843
304 8Q2 0.449541 0.733333
305 N6P 0.44898 0.888889
306 26A 0.448718 0.786667
307 SO8 0.445652 0.789474
308 A U 0.445455 0.846154
309 FDA 0.444444 0.790698
310 2VA 0.444444 0.8
311 S8M 0.443299 0.759494
312 NJP 0.442478 0.87013
313 V1N 0.442308 0.917808
314 7RA 0.44186 0.930556
315 RMB 0.44186 0.873239
316 6FA 0.440945 0.819277
317 DDS 0.44086 0.805195
318 ACK 0.440476 0.861111
319 QQY 0.440476 0.815789
320 103 0.440476 0.863014
321 CC5 0.44 0.816901
322 N01 0.439655 0.905405
323 EO7 0.436782 0.767442
324 8BR 0.436782 0.881579
325 3L1 0.435897 0.75
326 3D1 0.435897 0.75
327 NVA 2AD 0.434783 0.759494
328 SFD 0.434109 0.715789
329 FAS 0.434109 0.829268
330 FAD 0.434109 0.829268
331 CMP 0.431818 0.901408
332 2BA 0.431818 0.888889
333 FNK 0.431818 0.764045
334 TM1 0.431373 0.732558
335 KB1 0.431373 0.698795
336 6MD 0.43038 0.833333
337 7RP 0.430233 0.901408
338 VRT 0.430108 0.769231
339 ODP 0.429825 0.8375
340 QQX 0.428571 0.805195
341 SLU 0.42735 0.75
342 0WD 0.426087 0.848101
343 3NZ 0.425743 0.805195
344 5F1 0.425 0.710526
345 RP1 0.423529 0.842105
346 SP1 0.423529 0.842105
347 9JJ 0.423358 0.817073
348 7DD 0.422222 0.90411
349 OZP 0.422018 0.707317
350 62F 0.421053 0.839506
351 NZQ 0.421053 0.8375
352 ANZ 0.420561 0.777778
353 APU 0.419643 0.846154
354 RBZ 0.418605 0.849315
355 D3Y 0.418367 0.766234
356 FAY 0.41791 0.839506
357 MTP 0.417722 0.753247
358 5GP 0.417582 0.857143
359 G 0.417582 0.857143
360 KH3 0.416667 0.714286
361 A C A C 0.415254 0.825
362 RFL 0.414815 0.821429
363 N37 0.414414 0.7125
364 NMN AMP PO4 0.413793 0.846154
365 2FA 0.4125 0.789474
366 NPW 0.412281 0.817073
367 NDP 0.412281 0.848101
368 DCA 0.411765 0.781609
369 ETB 0.411765 0.833333
370 F0P 0.410714 0.707317
371 NAP 0.409836 0.893333
372 RGT 0.409524 0.881579
373 P2P 0.409091 0.876712
374 FAI 0.409091 0.84
375 TXP 0.408696 0.848101
376 7DT 0.408602 0.90411
377 1RB 0.406977 0.859155
378 128 0.405405 0.715909
379 HY8 0.405405 0.710843
380 9BG 0.405172 0.825
381 0T1 0.404959 0.781609
382 COA 0.404959 0.781609
383 U A C C 0.403361 0.835443
384 NA0 0.403226 0.906667
385 NHD 0.401709 0.88
386 F2N 0.401408 0.772727
387 12D 0.4 0.724138
388 PMO 0.4 0.875
389 HZ2 0.4 0.710843
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: 1
This union binding pocket(no: 1) in the query (biounit: 6ild.bio1) has 14 residues
No: Leader PDB Ligand Sequence Similarity
1 1G51 AMO 25.3448
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