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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: 188
This union binding pocket(no: 1) in the query (biounit: 1e1o.bio1) has 29 residues
No: Leader PDB Ligand Sequence Similarity
1 4HNN LYS 1.15607
2 2VDF OCT 1.18577
3 1HXD BTN 1.24611
4 2WPU KYT 1.25786
5 4BLW AMP 1.38408
6 2CJA ATP 1.38889
7 2CJ9 SSA 1.5873
8 4WOE ADP 1.5873
9 3A16 PXO 1.60858
10 4RF7 ARG 1.78571
11 5G48 1FL 1.87166
12 1SES AMP 1.90024
13 1SES AHX 1.90024
14 3TEG DAH 1.92771
15 2I4O ATP 1.96507
16 2J3M ATP 1.98413
17 2J3M PRI 1.98413
18 5W75 SUC 2.04082
19 5LY1 PPI 2.09974
20 4DQ2 BTX 2.13415
21 2JLD AG1 2.14286
22 3IAL PR8 2.18254
23 5XIO ANP 2.20884
24 5XIO HFG 2.20884
25 2E5A LAQ 2.30548
26 1RYD GLC 2.32558
27 3P7N FMN 2.32558
28 5T96 79J 2.33918
29 1RJW ETF 2.35988
30 3OV6 MK0 2.38095
31 3UH0 TSB 2.3913
32 1F5F DHT 2.43902
33 3L5R 47X 2.45902
34 3QO8 SSA 2.47423
35 3HXU A5A 2.49433
36 5EO8 TFU 2.57235
37 5KJW 53C 2.57611
38 2VGK REZ 2.65849
39 2G30 ALA ALA PHE 2.71318
40 5T8U LPA 2.77778
41 4XOE KGM 2.86738
42 4AVV CD 2.94118
43 3T4L ZEA 2.96296
44 1ZDQ MSM 2.97619
45 1YFS ALA 3.01075
46 4MOB ADP 3.01205
47 4YDQ HFG 3.01811
48 4YDQ ANP 3.01811
49 5FUI APY 3.0303
50 2Z3U CRR 3.05882
51 5HWV MBN 3.07692
52 1LSH PLD 3.1348
53 1Y7P RIP 3.13901
54 1VRP ADP 3.14961
55 3ERR AMP 3.1746
56 5XIJ 873 3.2
57 5XIJ ANP 3.2
58 1OFZ FUL 3.20513
59 3JU6 ANP 3.24324
60 5MST FUM 3.37302
61 3ACL 3F1 3.37838
62 5HV7 RBL 3.44037
63 3ZW2 NAG GAL FUC 3.44828
64 1OFL NGK GCD 3.5343
65 3QSB 743 3.55191
66 1P7T PYR 3.57143
67 3V8S 0HD 3.65854
68 5L2R MLA 3.76984
69 4B1M FRU FRU 3.78378
70 3GD9 GLC BGC BGC BGC 3.81471
71 3UDZ ADP 3.85396
72 4WUJ FMN 4.08163
73 4A59 AMP 4.16667
74 3BJE URA 4.29799
75 4HWT 1B2 4.35835
76 5VAD PRO 4.36508
77 5VAD 91Y 4.36508
78 4L9Z OXL 4.42478
79 3A7R LAQ 4.45104
80 1SDW IYT 4.4586
81 1UYY BGC BGC 4.58015
82 4P8K 38C 4.58333
83 4P8K FAD 4.58333
84 1WLE SRP 4.59082
85 2Z6D FMN 4.61538
86 3MF2 AMP 4.62428
87 2QHS OCA 4.64135
88 5C79 PBU 4.66667
89 4ZTD ALA GLY ALA GLY ALA 4.74308
90 2RDE C2E 4.78088
91 5URY PAM 4.79452
92 5V59 8X1 4.84211
93 5H9Y BGC BGC BGC BGC 4.95496
94 4PQG NAG 4.96032
95 4L9I 8PR 4.96032
96 4FE2 AIR 5.09804
97 4HIA FMN 5.11364
98 1B7Y FYA 5.15873
99 4XTX 590 5.18518
100 3B8I OXL 5.22648
101 2QHV OC9 5.2381
102 2VRQ XYP XYP AHR 5.24194
103 3KYG 5GP 5GP 5.28634
104 5JJU AMP 5.29412
105 1KNM LAT 5.38462
106 4L80 OXL 5.45977
107 2OJW ADP 5.46875
108 3HCH RSM 5.47945
109 2GQS C2R 5.48523
110 2JK0 ASP 5.53846
111 2GND MAN 5.55556
112 5A0U CHT 5.55556
113 2PHU MAN MAN 5.55556
114 3V1S 0LH 5.59006
115 3KIF GDL 5.66038
116 5AB1 BCD TA5 HP6 MAN 5.66667
117 2HZQ STR 5.74713
118 5DBX ANP 5.79268
119 5OCG 9R5 5.82011
120 4Z3E GAL NGA GLA BGC GAL 6.06061
121 3SAO DBH 6.25
122 6FA4 D1W 6.35838
123 5DYO FLU 6.42202
124 5LHT TIH 6.46258
125 5VM6 9EG 6.56934
126 5NM7 GLY 6.76692
127 2B1Q TRE 6.96721
128 5IDB BMA 7.04225
129 1U6R ADP 7.10526
130 2ART LPA AMP 7.25191
131 5X2N ALA 7.55556
132 6GNO XDI 8.14815
133 1N9L FMN 8.25688
134 3QRC SCR 8.28025
135 2FMD MAN MAN 8.33333
136 2DXU BT5 8.51064
137 1WPY BTN 8.51064
138 2BS5 BGC GAL FUC 8.88889
139 2QL9 CIT 9.24856
140 2RHQ GAX 9.52381
141 4EES FMN 9.56522
142 1ZNY GDP 9.66184
143 2PR5 FMN 9.84848
144 4QPW XYP XYP XYP 9.85915
145 1QKQ MAN 9.85915
146 5YJS SAL 10
147 2D24 XYS XYS 10.0917
148 1HBK MYR 10.1124
149 4HWS 1B3 10.219
150 6DZN AE3 10.3286
151 4IEN GDP 10.4294
152 4K55 H6P 10.4839
153 3ZJX BOG 10.7266
154 1QAW TRP 10.8108
155 2YKL NLD 10.8491
156 5ODY 9SK 10.8696
157 2ZTG A5A 10.9127
158 3CBC DBS 11.6162
159 2Z6C FMN 11.6279
160 4IAW LIZ 11.7021
161 4H2V AMP 11.8182
162 5W7B MYR 12.0567
163 3ZZS TRP 12.3077
164 4H2X G5A 12.6214
165 4H2W AMP 12.6214
166 4H2W 5GP 12.6214
167 3ZO7 K6H 12.766
168 3EFS BTN 12.8755
169 12AS AMP 13.3333
170 1WAP TRP 13.3333
171 6AR9 3L4 13.6029
172 5SVV FMN 14.5985
173 4D52 GXL 15.5556
174 4D52 GIV 15.5556
175 4D4U FUC GAL NDG FUC 15.5556
176 3H0L ADP 15.9574
177 4NS0 PIO 16.5414
178 3RF4 FUN 17.2414
179 2PEL LBT 18.6441
180 4CS4 ANP 24.4526
181 4CS4 AXZ 24.4526
182 3IWD M2T 27.4194
183 1G51 AMO 30.1587
184 2XGT NSS 31.0345
185 3REU ATP 43.1973
186 1X54 4AD 44.0092
187 3NEM AMO 45.8904
188 3NEM ATP 45.8904
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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