Receptor
PDB id Resolution Class Description Source Keywords
1E1T 2.4 Å EC: 6.1.1.6 LYSYL-TRNA SYNTHETASE (LYSU) HEXAGONAL FORM COMPLEXED WITH T LYSYL_ADENYLATE INTERMEDIATE ESCHERICHIA COLI LIGASE AMINOACYL-TRNA SYNTHETASE PROTEIN BIOSYNTHESIS
Ref.: ACTIVE SITE OF LYSYL-TRNA SYNTHETASE: STRUCTURAL ST THE ADENYLATION REACTION BIOCHEMISTRY V. 39 8418 2000
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GOL A:609;
A:605;
A:607;
A:611;
A:610;
A:606;
A:608;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
none;
none;
 submit data
92.094 C3 H8 O3 C(C(C...
LAD A:601;
 Valid;
 none;
 submit data
475.394 C16 H26 N7 O8 P c1nc(...
MG A:604;
A:603;
 Part of Protein;
Part of Protein;
 none;
none;
 submit data
24.305 Mg [Mg+2...
POP A:602;
 Invalid;
 none;
 submit data
175.959 H2 O7 P2 O[P@@...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1E1O 2.12 Å EC: 6.1.1.6 LYSYL-TRNA SYNTHETASE (LYSU) HEXAGONAL FORM, COMPLEXED WITH ESCHERICHIA COLI LIGASE AMINOACYL-TRNA SYNTHETASE PROTEIN BIOSYNTHESIS
Ref.: ACTIVE SITE OF LYSYL-TRNA SYNTHETASE: STRUCTURAL ST THE ADENYLATION REACTION BIOCHEMISTRY V. 39 8418 2000
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 8 families.
1 1E1T - LAD C16 H26 N7 O8 P c1nc(c2c(n....
2 1E24 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
3 1E1O - LYS C6 H15 N2 O2 C(CC[NH3+]....
4 1E22 - ACP C11 H18 N5 O12 P3 c1nc(c2c(n....
70% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 3E9H - KAA C16 H26 N8 O7 S c1nc(c2c(n....
2 3E9I - XAH C16 H27 N8 O8 P c1nc(c2c(n....
3 1E1T - LAD C16 H26 N7 O8 P c1nc(c2c(n....
4 1E24 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
5 1E1O - LYS C6 H15 N2 O2 C(CC[NH3+]....
6 1E22 - ACP C11 H18 N5 O12 P3 c1nc(c2c(n....
50% Homology Family (16)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 3E9H - KAA C16 H26 N8 O7 S c1nc(c2c(n....
2 3E9I - XAH C16 H27 N8 O8 P c1nc(c2c(n....
3 6HCW ic50 = 0.13 uM FYB C17 H16 F3 N O4 c1cc2c(cc1....
4 6HCU ic50 = 0.015 uM FYB C17 H16 F3 N O4 c1cc2c(cc1....
5 6AGT ic50 = 0.004 uM 9X0 C17 H19 N O3 c1ccc2c(c1....
6 6KCN ic50 = 276 nM D5F C17 H20 O4 C[C@H]1CCC....
7 6HCV ic50 = 0.005 uM FYE C17 H18 F N O4 c1cc2c(cc1....
8 6KA6 ic50 = 221 nM D4O C17 H22 O4 C[C@H]1CCC....
9 7BT5 Kd = 239 nM F6O C29 H40 N8 O3 S CC(C)S(=O)....
10 6KBF ic50 = 308 nM D4X C17 H23 N O3 C[C@H]1CCC....
11 3BJU - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
12 6ILH - KAA C16 H26 N8 O7 S c1nc(c2c(n....
13 1E1T - LAD C16 H26 N7 O8 P c1nc(c2c(n....
14 1E24 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
15 1E1O - LYS C6 H15 N2 O2 C(CC[NH3+]....
16 1E22 - ACP C11 H18 N5 O12 P3 c1nc(c2c(n....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: LAD; Similar ligands found: 344
No: Ligand ECFP6 Tc MDL keys Tc
1 LAD 1 1
2 SRP 0.804598 0.948052
3 YLP 0.785714 0.950617
4 ME8 0.774194 0.879518
5 AMO 0.769231 0.923077
6 YLC 0.762376 0.974684
7 YLB 0.762376 0.950617
8 5AL 0.761364 0.897436
9 AYB 0.75 0.939024
10 XAH 0.742268 0.95
11 YLA 0.740385 0.950617
12 NB8 0.736842 0.888889
13 CA0 0.732558 0.886076
14 8LH 0.725275 0.898734
15 8QN 0.72043 0.897436
16 FA5 0.714286 0.923077
17 KG4 0.704545 0.886076
18 4AD 0.694737 0.911392
19 PAJ 0.694737 0.855422
20 YLY 0.6875 0.939024
21 N0B 0.684211 0.950617
22 A2D 0.674419 0.860759
23 8LQ 0.673684 0.898734
24 TYM 0.669811 0.923077
25 8LE 0.666667 0.864198
26 PTJ 0.666667 0.843373
27 AN2 0.662921 0.85
28 BA3 0.659091 0.860759
29 QA7 0.65625 0.864198
30 AP5 0.651685 0.860759
31 B4P 0.651685 0.860759
32 ADP 0.651685 0.860759
33 3UK 0.646465 0.886076
34 AT4 0.644444 0.829268
35 PRX 0.641304 0.839506
36 WAQ 0.64 0.948718
37 AMP 0.639535 0.858974
38 A 0.639535 0.858974
39 M33 0.637363 0.85
40 ADX 0.637363 0.781609
41 AHX 0.636364 0.888889
42 DLL 0.636364 0.897436
43 TXA 0.633663 0.875
44 OOB 0.632653 0.897436
45 HEJ 0.630435 0.860759
46 ACP 0.630435 0.8625
47 ATP 0.630435 0.860759
48 50T 0.630435 0.82716
49 KAA 0.623762 0.852273
50 B5V 0.623762 0.875
51 AQP 0.623656 0.860759
52 APR 0.623656 0.884615
53 AR6 0.623656 0.884615
54 5FA 0.623656 0.860759
55 ANP 0.621053 0.839506
56 00A 0.62 0.853659
57 ABM 0.617977 0.8375
58 45A 0.617977 0.8375
59 1ZZ 0.617647 0.879518
60 AGS 0.617021 0.819277
61 AD9 0.617021 0.839506
62 AMP MG 0.613636 0.846154
63 ATF 0.608247 0.829268
64 PR8 0.607843 0.987179
65 9SN 0.605769 0.843373
66 A12 0.604396 0.875
67 AP2 0.604396 0.875
68 ACQ 0.604167 0.8625
69 AU1 0.602151 0.839506
70 5SV 0.6 0.843373
71 B5Y 0.6 0.864198
72 HQG 0.59596 0.873418
73 SRA 0.595506 0.817073
74 A1R 0.594059 0.924051
75 DAL AMP 0.59 0.873418
76 GAP 0.587629 0.910256
77 FYA 0.586538 0.873418
78 3OD 0.586538 0.886076
79 6YZ 0.585859 0.8625
80 B5M 0.584906 0.864198
81 OZV 0.584158 0.860759
82 9ZA 0.584158 0.853659
83 9ZD 0.584158 0.853659
84 OAD 0.582524 0.886076
85 V2G 0.581633 0.9125
86 7MD 0.577982 0.95
87 F2R 0.577586 0.926829
88 SON 0.574468 0.923077
89 ADP BEF 0.574468 0.858974
90 ADP MG 0.574468 0.858974
91 A22 0.574257 0.85
92 4UV 0.574074 0.864198
93 APC 0.572917 0.875
94 JNT 0.572816 0.886076
95 TAT 0.571429 0.829268
96 T99 0.571429 0.829268
97 BIS 0.571429 0.853659
98 25A 0.568627 0.860759
99 LAQ 0.567568 0.879518
100 9X8 0.567308 0.841463
101 RBY 0.56701 0.898734
102 ADV 0.56701 0.898734
103 IOT 0.565217 0.939024
104 4UU 0.563636 0.864198
105 A3R 0.563107 0.924051
106 ADQ 0.563107 0.886076
107 ADP PO3 0.55102 0.858974
108 ATP MG 0.55102 0.858974
109 APC MG 0.55102 0.860759
110 ARG AMP 0.54955 0.914634
111 BEF ADP 0.545455 0.8375
112 ANP MG 0.544554 0.85
113 4UW 0.54386 0.833333
114 NAI 0.54386 0.831325
115 MAP 0.543689 0.819277
116 G3A 0.540541 0.821429
117 TXE 0.53913 0.853659
118 MYR AMP 0.537037 0.857143
119 25L 0.537037 0.85
120 GA7 0.535714 0.851852
121 G5P 0.535714 0.821429
122 48N 0.535088 0.865854
123 LMS 0.532609 0.761364
124 DQV 0.530973 0.873418
125 NAX 0.530435 0.86747
126 TXD 0.530435 0.853659
127 6V0 0.530435 0.843373
128 ALF ADP 0.529412 0.797619
129 VO4 ADP 0.529412 0.839506
130 KMQ 0.527273 0.851852
131 OMR 0.525862 0.869048
132 80F 0.52459 0.837209
133 SSA 0.524272 0.797753
134 AFH 0.522124 0.855422
135 7MC 0.521368 0.926829
136 GTA 0.517544 0.793103
137 DND 0.517241 0.875
138 BT5 0.516393 0.892857
139 G5A 0.514852 0.818182
140 A5A 0.514563 0.764045
141 5CA 0.514286 0.797753
142 TSB 0.514286 0.755556
143 JB6 0.513761 0.853659
144 M24 0.512 0.823529
145 SMM 0.509615 0.747126
146 AP0 0.508475 0.8
147 L3W 0.508475 0.851852
148 5N5 0.505747 0.769231
149 AOC 0.505263 0.75
150 DSH 0.505263 0.8125
151 SA8 0.504951 0.792683
152 VMS 0.504762 0.747253
153 54H 0.504762 0.747253
154 DSZ 0.504673 0.797753
155 LSS 0.504673 0.76087
156 GSU 0.504587 0.818182
157 TAD 0.504348 0.855422
158 UP5 0.504274 0.841463
159 RAB 0.5 0.769231
160 ALF ADP 3PG 0.5 0.833333
161 5AS 0.5 0.758242
162 SFG 0.5 0.818182
163 5CD 0.5 0.734177
164 5X8 0.5 0.78481
165 ADN 0.5 0.769231
166 XYA 0.5 0.769231
167 53H 0.5 0.73913
168 D4F 0.496063 0.835294
169 COD 0.495935 0.894118
170 T5A 0.495868 0.837209
171 4TC 0.495798 0.843373
172 LPA AMP 0.495726 0.857143
173 ADP BMA 0.495413 0.8625
174 LEU LMS 0.495413 0.75
175 2A5 0.49505 0.8625
176 S4M 0.494845 0.747126
177 NAQ 0.492188 0.821429
178 CNA 0.491803 0.875
179 AMP DBH 0.491228 0.817073
180 52H 0.490566 0.73913
181 EEM 0.490385 0.752941
182 PAP 0.490196 0.848101
183 AF3 ADP 3PG 0.487395 0.833333
184 62X 0.486239 0.767442
185 NVA LMS 0.486239 0.771739
186 SAH 0.485437 0.810127
187 SAI 0.485437 0.8
188 BTX 0.483871 0.880952
189 7D5 0.483871 0.825
190 NAD 0.483871 0.873418
191 ADJ 0.483607 0.869048
192 EP4 0.483516 0.710843
193 UPA 0.483333 0.853659
194 A4D 0.483146 0.746835
195 YSA 0.482456 0.777778
196 K15 0.481818 0.785714
197 SAM 0.480769 0.752941
198 7D3 0.479592 0.82716
199 A4P 0.479339 0.818182
200 6RE 0.479167 0.780488
201 DTA 0.478261 0.740741
202 J4G 0.477477 0.935897
203 NSS 0.477064 0.777778
204 A3D 0.47619 0.8625
205 PPS 0.47619 0.761364
206 ATR 0.475728 0.835443
207 7D4 0.475248 0.82716
208 A3P 0.474747 0.858974
209 AHZ 0.474576 0.813953
210 ATP A 0.473684 0.848101
211 ATP A A A 0.473684 0.848101
212 NAE 0.472868 0.841463
213 ARU 0.472727 0.770115
214 8X1 0.472222 0.811111
215 139 0.471545 0.86747
216 H1Q 0.470588 0.825
217 FB0 0.470588 0.863636
218 AR6 AR6 0.470085 0.860759
219 J7C 0.469388 0.790123
220 DZD 0.468254 0.878049
221 S7M 0.46729 0.752941
222 ZID 0.465649 0.8625
223 GJV 0.464646 0.792683
224 P5A 0.464286 0.842697
225 3DH 0.463158 0.707317
226 A2R 0.462963 0.873418
227 WSA 0.46281 0.786517
228 M2T 0.462366 0.674419
229 AAT 0.462264 0.792683
230 6AD 0.462264 0.790698
231 8PZ 0.46087 0.777778
232 ITT 0.460784 0.8125
233 9K8 0.460177 0.697917
234 A2P 0.46 0.846154
235 NAD IBO 0.459016 0.860759
236 NAD TDB 0.459016 0.860759
237 KY2 0.458716 0.795181
238 EAD 0.458647 0.823529
239 OZP 0.458333 0.8375
240 3AM 0.458333 0.846154
241 MTA 0.457447 0.707317
242 KYE 0.456897 0.819277
243 NDE 0.455882 0.851852
244 IMO 0.454545 0.822785
245 GEK 0.454545 0.802469
246 KXW 0.453782 0.8375
247 V3L 0.45283 0.884615
248 A7D 0.45098 0.797468
249 A3S 0.45098 0.807692
250 NWW 0.450549 0.692308
251 0UM 0.45045 0.82716
252 KYB 0.45045 0.795181
253 NAJ PZO 0.449612 0.8
254 AMP NAD 0.448819 0.873418
255 0WD 0.448819 0.821429
256 F0P 0.447154 0.8375
257 MAO 0.445545 0.8
258 P1H 0.445255 0.825581
259 B1U 0.444444 0.701031
260 A3G 0.444444 0.820513
261 KB1 0.443478 0.783133
262 HFD 0.443396 0.819277
263 JSQ 0.443396 0.819277
264 KH3 0.441667 0.797619
265 QXP 0.441441 0.744444
266 V47 0.440367 0.782051
267 A3N 0.44 0.740741
268 6IA 0.439252 0.855422
269 NDC 0.438849 0.888889
270 ZAS 0.438776 0.743902
271 NO7 0.436364 0.851852
272 NAJ PYZ 0.43609 0.764045
273 6MZ 0.435644 0.825
274 KOY 0.434426 0.8
275 2AM 0.43299 0.835443
276 MHZ 0.432692 0.77907
277 2SA 0.431193 0.898734
278 KY5 0.431034 0.8125
279 HY8 0.430894 0.839506
280 O02 0.429907 0.843373
281 NA7 0.429825 0.875
282 4YB 0.429752 0.8
283 A3T 0.428571 0.772152
284 CUU 0.428571 0.860759
285 Q2P 0.426357 0.755814
286 4TA 0.426357 0.825581
287 HZ2 0.42623 0.839506
288 KY8 0.426087 0.814815
289 3AT 0.425926 0.860759
290 NDP 0.425197 0.821429
291 7C5 0.425 0.771084
292 Q34 0.424 0.755814
293 8Q2 0.424 0.752688
294 38V 0.422222 0.835294
295 FNK 0.421769 0.782609
296 N5A 0.421569 0.782051
297 A5D 0.420561 0.740741
298 OVE 0.42 0.804878
299 NJP 0.418605 0.841463
300 P5F 0.418301 0.8
301 AV2 0.418182 0.792683
302 QXG 0.417391 0.736264
303 K3E 0.416667 0.746988
304 VRT 0.416667 0.790123
305 649 0.416 0.802198
306 AVV 0.415929 0.843373
307 NEC 0.415842 0.725
308 DAT 0.415094 0.85
309 NPW 0.414062 0.857143
310 R2V 0.413793 0.744444
311 SFD 0.413793 0.717172
312 ETB 0.413534 0.850575
313 DTP 0.412844 0.85
314 Q2M 0.412698 0.77381
315 FDA 0.412587 0.788889
316 K3K 0.411765 0.73494
317 5AD 0.411111 0.679487
318 NZQ 0.410853 0.833333
319 TXP 0.410853 0.843373
320 SXZ 0.410256 0.77381
321 6FA 0.409722 0.816092
322 Y3J 0.408602 0.6625
323 LQJ 0.408333 0.860759
324 C2R 0.408163 0.825
325 AMZ 0.408163 0.8125
326 ODP 0.407692 0.811765
327 NVA 2AD 0.407407 0.780488
328 GGZ 0.40708 0.738636
329 D3Y 0.40708 0.7875
330 7D7 0.406593 0.721519
331 PGS 0.40566 0.767442
332 FAD 0.40411 0.825581
333 FAS 0.40411 0.825581
334 NWQ 0.40404 0.675
335 71V 0.403846 0.788235
336 6C6 0.40367 0.898734
337 6K6 0.403509 0.871795
338 S8M 0.403509 0.780488
339 Q2V 0.403101 0.804878
340 DCA 0.402985 0.862069
341 N5O 0.401961 0.807692
342 2VA 0.401869 0.753086
343 3NZ 0.401709 0.780488
344 NIA 0.4 0.735632
Similar Ligands (3D)
Ligand no: 1; Ligand: LAD; Similar ligands found: 1
No: Ligand Similarity coefficient
1 RSN 0.8938
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1E1O; Ligand: LYS; 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: 1e1o.bio1) has 31 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 1E1O; Ligand: LYS; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 1e1o.bio1) has 31 residues
No: Leader PDB Ligand Sequence Similarity
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