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 6 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 4 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 (7)
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 3BJU - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
4 1E1T - LAD C16 H26 N7 O8 P c1nc(c2c(n....
5 1E24 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
6 1E1O - LYS C6 H15 N2 O2 C(CC[NH3+]....
7 1E22 - ACP C11 H18 N5 O12 P3 c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: LAD; Similar ligands found: 297
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 8QN 0.72043 0.897436
15 FA5 0.714286 0.923077
16 YAP 0.714286 0.911392
17 4AD 0.694737 0.911392
18 PAJ 0.694737 0.855422
19 YLY 0.6875 0.939024
20 N0B 0.684211 0.950617
21 A2D 0.674419 0.860759
22 TYM 0.669811 0.923077
23 PTJ 0.666667 0.843373
24 AN2 0.662921 0.85
25 BA3 0.659091 0.860759
26 ADP 0.651685 0.860759
27 B4P 0.651685 0.860759
28 AP5 0.651685 0.860759
29 3UK 0.646465 0.886076
30 AT4 0.644444 0.829268
31 PRX 0.641304 0.839506
32 WAQ 0.64 0.948718
33 AMP 0.639535 0.858974
34 A 0.639535 0.858974
35 M33 0.637363 0.85
36 ADX 0.637363 0.781609
37 DLL 0.636364 0.897436
38 AHX 0.636364 0.888889
39 TXA 0.633663 0.875
40 OOB 0.632653 0.897436
41 ACP 0.630435 0.8625
42 50T 0.630435 0.82716
43 ATP 0.630435 0.860759
44 HEJ 0.630435 0.860759
45 B5V 0.623762 0.875
46 KAA 0.623762 0.852273
47 5FA 0.623656 0.860759
48 AR6 0.623656 0.884615
49 AQP 0.623656 0.860759
50 APR 0.623656 0.884615
51 ANP 0.621053 0.839506
52 00A 0.62 0.853659
53 ABM 0.617977 0.8375
54 1ZZ 0.617647 0.879518
55 AGS 0.617021 0.819277
56 AD9 0.617021 0.839506
57 SAP 0.617021 0.819277
58 ATF 0.608247 0.829268
59 PR8 0.607843 0.987179
60 9SN 0.605769 0.843373
61 AP2 0.604396 0.875
62 A12 0.604396 0.875
63 ACQ 0.604167 0.8625
64 AU1 0.602151 0.839506
65 B5Y 0.6 0.864198
66 5SV 0.6 0.843373
67 SRA 0.595506 0.817073
68 A1R 0.594059 0.924051
69 DAL AMP 0.59 0.873418
70 GAP 0.587629 0.910256
71 FYA 0.586538 0.873418
72 3OD 0.586538 0.886076
73 6YZ 0.585859 0.8625
74 B5M 0.584906 0.864198
75 9ZA 0.584158 0.853659
76 9ZD 0.584158 0.853659
77 OAD 0.582524 0.886076
78 7MD 0.577982 0.95
79 F2R 0.577586 0.926829
80 SON 0.574468 0.923077
81 A22 0.574257 0.85
82 4UV 0.574074 0.864198
83 APC 0.572917 0.875
84 T99 0.571429 0.829268
85 TAT 0.571429 0.829268
86 BIS 0.571429 0.853659
87 25A 0.568627 0.860759
88 LAQ 0.567568 0.879518
89 9X8 0.567308 0.841463
90 RBY 0.56701 0.898734
91 ADV 0.56701 0.898734
92 IOT 0.565217 0.939024
93 4UU 0.563636 0.864198
94 A3R 0.563107 0.924051
95 ADQ 0.563107 0.886076
96 ADP PO3 0.55102 0.858974
97 ARG AMP 0.54955 0.914634
98 4UW 0.54386 0.833333
99 NAI 0.54386 0.831325
100 MAP 0.543689 0.819277
101 G3A 0.540541 0.821429
102 TXE 0.53913 0.853659
103 MYR AMP 0.537037 0.857143
104 25L 0.537037 0.85
105 G5P 0.535714 0.821429
106 GA7 0.535714 0.851852
107 48N 0.535088 0.865854
108 LMS 0.532609 0.761364
109 TYR AMP 0.531532 0.8875
110 DQV 0.530973 0.873418
111 NAX 0.530435 0.86747
112 TXD 0.530435 0.853659
113 6V0 0.530435 0.843373
114 ADP ALF 0.529412 0.797619
115 ALF ADP 0.529412 0.797619
116 OMR 0.525862 0.869048
117 80F 0.52459 0.837209
118 SSA 0.524272 0.797753
119 VO4 ADP 0.524272 0.85
120 ADP VO4 0.524272 0.85
121 AFH 0.522124 0.855422
122 7MC 0.521368 0.926829
123 GTA 0.517544 0.793103
124 DND 0.517241 0.875
125 NXX 0.517241 0.875
126 BT5 0.516393 0.892857
127 G5A 0.514852 0.818182
128 A5A 0.514563 0.764045
129 5CA 0.514286 0.797753
130 TSB 0.514286 0.755556
131 JB6 0.513761 0.853659
132 M24 0.512 0.823529
133 SMM 0.509615 0.747126
134 AP0 0.508475 0.8
135 5N5 0.505747 0.769231
136 AOC 0.505263 0.75
137 DSH 0.505263 0.8125
138 SA8 0.504951 0.792683
139 VMS 0.504762 0.747253
140 54H 0.504762 0.747253
141 DSZ 0.504673 0.797753
142 LSS 0.504673 0.76087
143 GSU 0.504587 0.818182
144 TAD 0.504348 0.855422
145 UP5 0.504274 0.841463
146 ADN 0.5 0.769231
147 53H 0.5 0.73913
148 RAB 0.5 0.769231
149 XYA 0.5 0.769231
150 SFG 0.5 0.818182
151 5AS 0.5 0.758242
152 5X8 0.5 0.78481
153 5CD 0.5 0.734177
154 COD 0.495935 0.894118
155 T5A 0.495868 0.837209
156 4TC 0.495798 0.843373
157 LPA AMP 0.495726 0.857143
158 ADP BMA 0.495413 0.8625
159 2A5 0.49505 0.8625
160 S4M 0.494845 0.747126
161 NAQ 0.492188 0.821429
162 CNA 0.491803 0.875
163 AMP DBH 0.491228 0.817073
164 A A 0.490909 0.8375
165 52H 0.490566 0.73913
166 EEM 0.490385 0.752941
167 PAP 0.490196 0.848101
168 AF3 ADP 3PG 0.487395 0.833333
169 NVA LMS 0.486239 0.771739
170 62X 0.486239 0.767442
171 SAI 0.485437 0.8
172 SAH 0.485437 0.810127
173 7D5 0.483871 0.825
174 NAD 0.483871 0.873418
175 BTX 0.483871 0.880952
176 ADJ 0.483607 0.869048
177 EP4 0.483516 0.710843
178 UPA 0.483333 0.853659
179 A4D 0.483146 0.746835
180 YSA 0.482456 0.777778
181 K15 0.481818 0.785714
182 SAM 0.480769 0.752941
183 7D3 0.479592 0.82716
184 A4P 0.479339 0.818182
185 6RE 0.479167 0.780488
186 DTA 0.478261 0.740741
187 NSS 0.477064 0.777778
188 PPS 0.47619 0.761364
189 A3D 0.47619 0.8625
190 ATR 0.475728 0.835443
191 7D4 0.475248 0.82716
192 A3P 0.474747 0.858974
193 AHZ 0.474576 0.813953
194 ATP A A A 0.473684 0.848101
195 NAE 0.472868 0.841463
196 ARU 0.472727 0.770115
197 8X1 0.472222 0.811111
198 139 0.471545 0.86747
199 FB0 0.470588 0.863636
200 AR6 AR6 0.470085 0.860759
201 J7C 0.469388 0.790123
202 LEU LMS 0.468468 0.752688
203 DZD 0.468254 0.878049
204 S7M 0.46729 0.752941
205 ZID 0.465649 0.8625
206 GJV 0.464646 0.792683
207 P5A 0.464286 0.842697
208 3DH 0.463158 0.707317
209 A2R 0.462963 0.873418
210 WSA 0.46281 0.786517
211 M2T 0.462366 0.674419
212 AAT 0.462264 0.792683
213 6AD 0.462264 0.790698
214 8PZ 0.46087 0.777778
215 ITT 0.460784 0.8125
216 9K8 0.460177 0.697917
217 A2P 0.46 0.846154
218 EAD 0.458647 0.823529
219 3AM 0.458333 0.846154
220 MTA 0.457447 0.707317
221 NDE 0.455882 0.851852
222 GEK 0.454545 0.802469
223 IMO 0.454545 0.822785
224 V3L 0.45283 0.884615
225 A3S 0.45098 0.807692
226 A7D 0.45098 0.797468
227 0UM 0.45045 0.82716
228 NAJ PZO 0.449612 0.8
229 AMP NAD 0.448819 0.873418
230 0WD 0.448819 0.821429
231 F0P 0.447154 0.8375
232 MAO 0.445545 0.8
233 P1H 0.445255 0.825581
234 A3G 0.444444 0.820513
235 KB1 0.443478 0.783133
236 HFD 0.443396 0.819277
237 KH3 0.441667 0.797619
238 A3N 0.44 0.740741
239 6IA 0.439252 0.855422
240 NDC 0.438849 0.888889
241 ZAS 0.438776 0.743902
242 G A A A 0.4375 0.821429
243 NAJ PYZ 0.43609 0.764045
244 2AM 0.43299 0.835443
245 MHZ 0.432692 0.77907
246 2SA 0.431193 0.898734
247 NA7 0.429825 0.875
248 4YB 0.429752 0.8
249 A3T 0.428571 0.772152
250 4TA 0.426357 0.825581
251 A G 0.426357 0.809524
252 3AT 0.425926 0.860759
253 NDP 0.425197 0.821429
254 7C5 0.425 0.771084
255 8Q2 0.424 0.752688
256 U A G G 0.423077 0.809524
257 FNK 0.421769 0.782609
258 A5D 0.420561 0.740741
259 OVE 0.42 0.804878
260 NJP 0.418605 0.841463
261 P5F 0.418301 0.8
262 AV2 0.418182 0.792683
263 VRT 0.416667 0.790123
264 U A 0.416667 0.831325
265 649 0.416 0.802198
266 AVV 0.415929 0.843373
267 NEC 0.415842 0.725
268 DAT 0.415094 0.85
269 NPW 0.414062 0.857143
270 SFD 0.413793 0.717172
271 ETB 0.413534 0.850575
272 DTP 0.412844 0.85
273 FDA 0.412587 0.788889
274 5AD 0.411111 0.679487
275 TXP 0.410853 0.843373
276 NZQ 0.410853 0.833333
277 SXZ 0.410256 0.77381
278 6FA 0.409722 0.816092
279 Y3J 0.408602 0.6625
280 AMZ 0.408163 0.8125
281 C2R 0.408163 0.825
282 ODP 0.407692 0.811765
283 NVA 2AD 0.407407 0.780488
284 GGZ 0.40708 0.738636
285 D3Y 0.40708 0.7875
286 7D7 0.406593 0.721519
287 PGS 0.40566 0.767442
288 FAD 0.40411 0.825581
289 FAS 0.40411 0.825581
290 71V 0.403846 0.788235
291 6C6 0.40367 0.898734
292 6K6 0.403509 0.871795
293 S8M 0.403509 0.780488
294 DCA 0.402985 0.862069
295 2VA 0.401869 0.753086
296 3NZ 0.401709 0.780488
297 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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