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 B:520;
B:521;
B:522;
B:523;
B:524;
B:525;
B:526;
 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 B:510;
 Valid;
 none;
 submit data
475.394 C16 H26 N7 O8 P c1nc(...
MG B:515;
B:516;
 Part of Protein;
Part of Protein;
 none;
none;
 submit data
24.305 Mg [Mg+2...
POP B:512;
 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 (12)
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 6HCV ic50 = 0.005 uM FYE C17 H18 F N O4 c1cc2c(cc1....
7 3BJU - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
8 6ILH - KAA C16 H26 N8 O7 S c1nc(c2c(n....
9 1E1T - LAD C16 H26 N7 O8 P c1nc(c2c(n....
10 1E24 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
11 1E1O - LYS C6 H15 N2 O2 C(CC[NH3+]....
12 1E22 - ACP C11 H18 N5 O12 P3 c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: LAD; Similar ligands found: 321
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 YLB 0.762376 0.950617
7 YLC 0.762376 0.974684
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 YAP 0.714286 0.911392
18 KG4 0.704545 0.886076
19 PAJ 0.694737 0.855422
20 4AD 0.694737 0.911392
21 YLY 0.6875 0.939024
22 N0B 0.684211 0.950617
23 A2D 0.674419 0.860759
24 8LQ 0.673684 0.898734
25 TYM 0.669811 0.923077
26 8LE 0.666667 0.864198
27 PTJ 0.666667 0.843373
28 AN2 0.662921 0.85
29 BA3 0.659091 0.860759
30 ADP 0.651685 0.860759
31 AP5 0.651685 0.860759
32 B4P 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 A 0.639535 0.858974
38 AMP 0.639535 0.858974
39 ADX 0.637363 0.781609
40 M33 0.637363 0.85
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 ACP 0.630435 0.8625
46 ATP 0.630435 0.860759
47 50T 0.630435 0.82716
48 HEJ 0.630435 0.860759
49 KAA 0.623762 0.852273
50 B5V 0.623762 0.875
51 AR6 0.623656 0.884615
52 APR 0.623656 0.884615
53 AQP 0.623656 0.860759
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 SAP 0.617021 0.819277
62 AD9 0.617021 0.839506
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 B5Y 0.6 0.864198
71 5SV 0.6 0.843373
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 3OD 0.586538 0.886076
78 FYA 0.586538 0.873418
79 6YZ 0.585859 0.8625
80 B5M 0.584906 0.864198
81 9ZA 0.584158 0.853659
82 OZV 0.584158 0.860759
83 9ZD 0.584158 0.853659
84 OAD 0.582524 0.886076
85 7MD 0.577982 0.95
86 F2R 0.577586 0.926829
87 SON 0.574468 0.923077
88 ADP MG 0.574468 0.858974
89 A22 0.574257 0.85
90 4UV 0.574074 0.864198
91 APC 0.572917 0.875
92 BIS 0.571429 0.853659
93 TAT 0.571429 0.829268
94 T99 0.571429 0.829268
95 25A 0.568627 0.860759
96 LAQ 0.567568 0.879518
97 9X8 0.567308 0.841463
98 ADV 0.56701 0.898734
99 RBY 0.56701 0.898734
100 IOT 0.565217 0.939024
101 4UU 0.563636 0.864198
102 ADQ 0.563107 0.886076
103 A3R 0.563107 0.924051
104 ATP MG 0.55102 0.858974
105 APC MG 0.55102 0.860759
106 ADP PO3 0.55102 0.858974
107 ARG AMP 0.54955 0.914634
108 4UW 0.54386 0.833333
109 NAI 0.54386 0.831325
110 MAP 0.543689 0.819277
111 G3A 0.540541 0.821429
112 TXE 0.53913 0.853659
113 25L 0.537037 0.85
114 MYR AMP 0.537037 0.857143
115 GA7 0.535714 0.851852
116 G5P 0.535714 0.821429
117 48N 0.535088 0.865854
118 LMS 0.532609 0.761364
119 TYR AMP 0.531532 0.8875
120 DQV 0.530973 0.873418
121 6V0 0.530435 0.843373
122 TXD 0.530435 0.853659
123 NAX 0.530435 0.86747
124 ALF ADP 0.529412 0.797619
125 ADP ALF 0.529412 0.797619
126 OMR 0.525862 0.869048
127 80F 0.52459 0.837209
128 VO4 ADP 0.524272 0.85
129 ADP VO4 0.524272 0.85
130 SSA 0.524272 0.797753
131 AFH 0.522124 0.855422
132 7MC 0.521368 0.926829
133 GTA 0.517544 0.793103
134 DND 0.517241 0.875
135 NXX 0.517241 0.875
136 BT5 0.516393 0.892857
137 G5A 0.514852 0.818182
138 A5A 0.514563 0.764045
139 TSB 0.514286 0.755556
140 5CA 0.514286 0.797753
141 JB6 0.513761 0.853659
142 M24 0.512 0.823529
143 SMM 0.509615 0.747126
144 AP0 0.508475 0.8
145 5N5 0.505747 0.769231
146 AOC 0.505263 0.75
147 DSH 0.505263 0.8125
148 SA8 0.504951 0.792683
149 VMS 0.504762 0.747253
150 54H 0.504762 0.747253
151 LSS 0.504673 0.76087
152 DSZ 0.504673 0.797753
153 GSU 0.504587 0.818182
154 TAD 0.504348 0.855422
155 UP5 0.504274 0.841463
156 ADN 0.5 0.769231
157 XYA 0.5 0.769231
158 5X8 0.5 0.78481
159 RAB 0.5 0.769231
160 5CD 0.5 0.734177
161 53H 0.5 0.73913
162 SFG 0.5 0.818182
163 5AS 0.5 0.758242
164 COD 0.495935 0.894118
165 T5A 0.495868 0.837209
166 4TC 0.495798 0.843373
167 LPA AMP 0.495726 0.857143
168 ADP BMA 0.495413 0.8625
169 2A5 0.49505 0.8625
170 S4M 0.494845 0.747126
171 NAQ 0.492188 0.821429
172 CNA 0.491803 0.875
173 AMP DBH 0.491228 0.817073
174 A A 0.490909 0.8375
175 52H 0.490566 0.73913
176 EEM 0.490385 0.752941
177 PAP 0.490196 0.848101
178 AF3 ADP 3PG 0.487395 0.833333
179 62X 0.486239 0.767442
180 NVA LMS 0.486239 0.771739
181 SAH 0.485437 0.810127
182 SAI 0.485437 0.8
183 7D5 0.483871 0.825
184 BTX 0.483871 0.880952
185 NAD 0.483871 0.873418
186 ADJ 0.483607 0.869048
187 EP4 0.483516 0.710843
188 UPA 0.483333 0.853659
189 A4D 0.483146 0.746835
190 YSA 0.482456 0.777778
191 K15 0.481818 0.785714
192 SAM 0.480769 0.752941
193 7D3 0.479592 0.82716
194 A4P 0.479339 0.818182
195 6RE 0.479167 0.780488
196 DTA 0.478261 0.740741
197 J4G 0.477477 0.935897
198 NSS 0.477064 0.777778
199 PPS 0.47619 0.761364
200 A3D 0.47619 0.8625
201 ATR 0.475728 0.835443
202 7D4 0.475248 0.82716
203 A3P 0.474747 0.858974
204 AHZ 0.474576 0.813953
205 ATP A 0.473684 0.848101
206 ATP A A A 0.473684 0.848101
207 NAE 0.472868 0.841463
208 ARU 0.472727 0.770115
209 8X1 0.472222 0.811111
210 139 0.471545 0.86747
211 H1Q 0.470588 0.825
212 FB0 0.470588 0.863636
213 AR6 AR6 0.470085 0.860759
214 J7C 0.469388 0.790123
215 LEU LMS 0.468468 0.752688
216 DZD 0.468254 0.878049
217 S7M 0.46729 0.752941
218 ZID 0.465649 0.8625
219 GJV 0.464646 0.792683
220 P5A 0.464286 0.842697
221 3DH 0.463158 0.707317
222 A2R 0.462963 0.873418
223 WSA 0.46281 0.786517
224 M2T 0.462366 0.674419
225 6AD 0.462264 0.790698
226 AAT 0.462264 0.792683
227 8PZ 0.46087 0.777778
228 ITT 0.460784 0.8125
229 9K8 0.460177 0.697917
230 A2P 0.46 0.846154
231 EAD 0.458647 0.823529
232 OZP 0.458333 0.8375
233 3AM 0.458333 0.846154
234 MTA 0.457447 0.707317
235 NDE 0.455882 0.851852
236 GEK 0.454545 0.802469
237 IMO 0.454545 0.822785
238 V3L 0.45283 0.884615
239 A7D 0.45098 0.797468
240 A3S 0.45098 0.807692
241 0UM 0.45045 0.82716
242 NAJ PZO 0.449612 0.8
243 0WD 0.448819 0.821429
244 AMP NAD 0.448819 0.873418
245 F0P 0.447154 0.8375
246 MAO 0.445545 0.8
247 P1H 0.445255 0.825581
248 B1U 0.444444 0.701031
249 A3G 0.444444 0.820513
250 KB1 0.443478 0.783133
251 JSQ 0.443396 0.819277
252 HFD 0.443396 0.819277
253 KH3 0.441667 0.797619
254 A3N 0.44 0.740741
255 6IA 0.439252 0.855422
256 NDC 0.438849 0.888889
257 ZAS 0.438776 0.743902
258 G A A A 0.4375 0.821429
259 NO7 0.436364 0.851852
260 NAJ PYZ 0.43609 0.764045
261 6MZ 0.435644 0.825
262 KOY 0.434426 0.8
263 2AM 0.43299 0.835443
264 MHZ 0.432692 0.77907
265 2SA 0.431193 0.898734
266 HY8 0.430894 0.839506
267 NA7 0.429825 0.875
268 4YB 0.429752 0.8
269 A3T 0.428571 0.772152
270 A G 0.426357 0.809524
271 4TA 0.426357 0.825581
272 HZ2 0.42623 0.839506
273 3AT 0.425926 0.860759
274 NDP 0.425197 0.821429
275 7C5 0.425 0.771084
276 8Q2 0.424 0.752688
277 U A G G 0.423077 0.809524
278 FNK 0.421769 0.782609
279 N5A 0.421569 0.782051
280 A5D 0.420561 0.740741
281 OVE 0.42 0.804878
282 NJP 0.418605 0.841463
283 P5F 0.418301 0.8
284 AV2 0.418182 0.792683
285 VRT 0.416667 0.790123
286 U A 0.416667 0.831325
287 649 0.416 0.802198
288 AVV 0.415929 0.843373
289 NEC 0.415842 0.725
290 DAT 0.415094 0.85
291 NPW 0.414062 0.857143
292 SFD 0.413793 0.717172
293 ETB 0.413534 0.850575
294 DTP 0.412844 0.85
295 FDA 0.412587 0.788889
296 5AD 0.411111 0.679487
297 TXP 0.410853 0.843373
298 NZQ 0.410853 0.833333
299 SXZ 0.410256 0.77381
300 6FA 0.409722 0.816092
301 Y3J 0.408602 0.6625
302 LQJ 0.408333 0.860759
303 C2R 0.408163 0.825
304 AMZ 0.408163 0.8125
305 ODP 0.407692 0.811765
306 NVA 2AD 0.407407 0.780488
307 D3Y 0.40708 0.7875
308 GGZ 0.40708 0.738636
309 7D7 0.406593 0.721519
310 PGS 0.40566 0.767442
311 FAS 0.40411 0.825581
312 FAD 0.40411 0.825581
313 71V 0.403846 0.788235
314 6C6 0.40367 0.898734
315 6K6 0.403509 0.871795
316 S8M 0.403509 0.780488
317 DCA 0.402985 0.862069
318 N5O 0.401961 0.807692
319 2VA 0.401869 0.753086
320 3NZ 0.401709 0.780488
321 NIA 0.4 0.735632
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 29 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 29 residues
No: Leader PDB Ligand Sequence Similarity
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