Receptor
PDB id Resolution Class Description Source Keywords
3E9I 2.2 Å EC: 6.1.1.6 LYSYL-TRNA SYNTHETASE FROM BACILLUS STEAROTHERMOPHILUS COMPLEXED WITH L-LYSINE HYDROXAMATE-AMP BACILLUS STEAROTHERMOPHILUS AMINOACYL TRNA SYNTHETASE LIGASE PROTEIN BIOSYNTHESIS ATP-BINDING CYTOPLASM MAGNESIUM METAL-BINDING NUCLEOTIDE-BINDING
Ref.: TWO CRYSTAL STRUCTURES OF LYSYL-TRNA SYNTHETASE FROM BACILLUS STEAROTHERMOPHILUS IN COMPLEX WITH LYSYLADENYLATE-LIKE COMPOUNDS: INSIGHTS INTO THE IRREVERSIBLE FORMATION OF THE ENZYME-BOUND ADENYLATE OF L-LYSINE HYDROXAMATE J.BIOCHEM.
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
1PE A:494;
B:494;
C:1202;
C:494;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
submit data
238.278 C10 H22 O6 C(COC...
MG A:1000;
B:1100;
C:1200;
D:1300;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
submit data
24.305 Mg [Mg+2...
XAH A:1001;
B:1101;
C:1201;
D:1301;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
490.408 C16 H27 N8 O8 P c1nc(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3E9I 2.2 Å EC: 6.1.1.6 LYSYL-TRNA SYNTHETASE FROM BACILLUS STEAROTHERMOPHILUS COMPLEXED WITH L-LYSINE HYDROXAMATE-AMP BACILLUS STEAROTHERMOPHILUS AMINOACYL TRNA SYNTHETASE LIGASE PROTEIN BIOSYNTHESIS ATP-BINDING CYTOPLASM MAGNESIUM METAL-BINDING NUCLEOTIDE-BINDING
Ref.: TWO CRYSTAL STRUCTURES OF LYSYL-TRNA SYNTHETASE FROM BACILLUS STEAROTHERMOPHILUS IN COMPLEX WITH LYSYLADENYLATE-LIKE COMPOUNDS: INSIGHTS INTO THE IRREVERSIBLE FORMATION OF THE ENZYME-BOUND ADENYLATE OF L-LYSINE HYDROXAMATE J.BIOCHEM.
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 8 families.
1 3E9H - KAA C16 H26 N8 O7 S c1nc(c2c(n....
2 3E9I - XAH C16 H27 N8 O8 P 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: XAH; Similar ligands found: 301
No: Ligand ECFP6 Tc MDL keys Tc
1 XAH 1 1
2 AHX 0.815217 0.9375
3 LAD 0.742268 0.95
4 KAA 0.673267 0.853933
5 CA0 0.655914 0.841463
6 A2D 0.637363 0.839506
7 SRP 0.636364 0.9
8 5AL 0.632653 0.851852
9 KG4 0.631579 0.841463
10 AN2 0.62766 0.851852
11 AMO 0.627451 0.876543
12 BA3 0.623656 0.839506
13 ADP 0.617021 0.839506
14 B4P 0.617021 0.839506
15 AP5 0.617021 0.839506
16 AT4 0.610526 0.809524
17 YLP 0.607143 0.904762
18 AMP 0.604396 0.8375
19 A 0.604396 0.8375
20 M33 0.604167 0.829268
21 ADX 0.604167 0.764045
22 8LH 0.60396 0.853659
23 NB8 0.603774 0.91358
24 ME8 0.603774 0.837209
25 8QN 0.601942 0.851852
26 8LE 0.6 0.821429
27 ATP 0.597938 0.839506
28 ACP 0.597938 0.841463
29 50T 0.597938 0.807229
30 HEJ 0.597938 0.839506
31 7MD 0.594595 0.926829
32 WAQ 0.59434 0.901235
33 8LQ 0.592233 0.853659
34 AQP 0.591837 0.839506
35 AR6 0.591837 0.839506
36 PRX 0.591837 0.819277
37 5FA 0.591837 0.839506
38 APR 0.591837 0.839506
39 YLC 0.591304 0.926829
40 YLB 0.591304 0.904762
41 ANP 0.59 0.841463
42 TXA 0.588785 0.831325
43 AGS 0.585859 0.8
44 SAP 0.585859 0.8
45 AD9 0.585859 0.819277
46 ABM 0.585106 0.817073
47 45A 0.585106 0.817073
48 AYB 0.584746 0.894118
49 PAJ 0.580952 0.813953
50 4AD 0.580952 0.865854
51 ATF 0.578431 0.809524
52 YLA 0.576271 0.904762
53 DLL 0.575472 0.851852
54 ACQ 0.574257 0.841463
55 AP2 0.572917 0.853659
56 A12 0.572917 0.853659
57 YAP 0.572727 0.865854
58 FA5 0.572727 0.876543
59 AU1 0.571429 0.841463
60 OOB 0.571429 0.851852
61 3UK 0.570093 0.841463
62 HQG 0.567308 0.829268
63 PR8 0.564815 0.938272
64 B5V 0.564815 0.831325
65 SRA 0.56383 0.797619
66 00A 0.560748 0.811765
67 1ZZ 0.559633 0.837209
68 FYA 0.559633 0.851852
69 PTJ 0.559633 0.802326
70 6YZ 0.557692 0.841463
71 OZV 0.556604 0.839506
72 9ZA 0.556604 0.833333
73 9ZD 0.556604 0.833333
74 5SV 0.556604 0.823529
75 OAD 0.555556 0.841463
76 TYM 0.555556 0.876543
77 F2R 0.553719 0.882353
78 A1R 0.551402 0.901235
79 N0B 0.551181 0.904762
80 GSU 0.550459 0.8
81 9SN 0.54955 0.802326
82 A22 0.54717 0.829268
83 SON 0.545455 0.876543
84 ADP MG 0.545455 0.8375
85 BIS 0.545455 0.833333
86 3OD 0.545455 0.841463
87 B5M 0.544643 0.821429
88 APC 0.544554 0.853659
89 T99 0.543689 0.809524
90 TAT 0.543689 0.809524
91 GAP 0.543689 0.864198
92 SSA 0.542857 0.8
93 25A 0.542056 0.839506
94 IOT 0.541667 0.894118
95 9X8 0.541284 0.8
96 YLY 0.539683 0.894118
97 RBY 0.539216 0.853659
98 ADV 0.539216 0.853659
99 7MC 0.537815 0.904762
100 A3R 0.537037 0.901235
101 DSZ 0.537037 0.78022
102 ADQ 0.537037 0.841463
103 A5A 0.533333 0.766667
104 TSB 0.53271 0.758242
105 5CA 0.53271 0.8
106 DAL AMP 0.53271 0.829268
107 B5Y 0.530973 0.821429
108 TXE 0.529412 0.833333
109 4UU 0.525862 0.821429
110 48N 0.525424 0.823529
111 ADP PO3 0.524272 0.8375
112 ATP MG 0.524272 0.8375
113 APC MG 0.524272 0.839506
114 54H 0.523364 0.75
115 VMS 0.523364 0.75
116 52H 0.523364 0.741935
117 LSS 0.522936 0.763441
118 4UV 0.521739 0.821429
119 MAP 0.518519 0.821429
120 53H 0.518519 0.741935
121 LAQ 0.516949 0.837209
122 25L 0.513274 0.829268
123 GA7 0.512821 0.831325
124 ARG AMP 0.512821 0.870588
125 J4G 0.508929 0.888889
126 DQV 0.508475 0.851852
127 TXD 0.508333 0.833333
128 6V0 0.508333 0.823529
129 4UW 0.508333 0.793103
130 LMS 0.505155 0.764045
131 G5A 0.504762 0.820225
132 ALF ADP 0.504673 0.77907
133 ADP ALF 0.504673 0.77907
134 NVA LMS 0.504505 0.774194
135 OMR 0.504132 0.827586
136 VO4 ADP 0.5 0.829268
137 MYR AMP 0.5 0.816092
138 COD 0.5 0.873563
139 AFH 0.5 0.813953
140 ADP VO4 0.5 0.829268
141 YSA 0.5 0.78022
142 NAX 0.495868 0.847059
143 NXX 0.495868 0.831325
144 UP5 0.495868 0.821429
145 DND 0.495868 0.831325
146 NAI 0.495868 0.811765
147 GTA 0.495798 0.775281
148 TAD 0.495798 0.835294
149 AMP DBH 0.495726 0.776471
150 NSS 0.495495 0.78022
151 SA8 0.495238 0.752941
152 DSH 0.494949 0.792683
153 80F 0.492188 0.797753
154 G3A 0.491525 0.802326
155 JB6 0.491228 0.833333
156 5X8 0.490385 0.743902
157 5AS 0.490196 0.76087
158 T5A 0.488 0.818182
159 4TC 0.487805 0.823529
160 G5P 0.487395 0.802326
161 LEU LMS 0.486726 0.755319
162 BT5 0.484375 0.850575
163 CNA 0.484127 0.853659
164 TYR AMP 0.483051 0.843373
165 AOC 0.48 0.731707
166 WSA 0.479675 0.788889
167 8PZ 0.478632 0.78022
168 5N5 0.478261 0.75
169 SAH 0.476636 0.768293
170 SFG 0.47619 0.775
171 AP0 0.475806 0.781609
172 J7C 0.475248 0.771084
173 FB0 0.47482 0.844444
174 ADP BMA 0.473684 0.819277
175 5CD 0.473118 0.716049
176 RAB 0.472527 0.75
177 ADN 0.472527 0.75
178 XYA 0.472527 0.75
179 A4P 0.472 0.8
180 2A5 0.471698 0.841463
181 S4M 0.470588 0.730337
182 6RE 0.47 0.761905
183 A A 0.469565 0.817073
184 3DH 0.469388 0.690476
185 DTA 0.46875 0.722892
186 NAD 0.465116 0.851852
187 BTX 0.465116 0.860465
188 ADJ 0.464567 0.827586
189 139 0.464567 0.847059
190 8X1 0.464286 0.813187
191 UPA 0.464 0.833333
192 LPA AMP 0.463415 0.816092
193 SAI 0.462963 0.759036
194 NAQ 0.462687 0.802326
195 DZD 0.461538 0.857143
196 SMM 0.459459 0.711111
197 S7M 0.459459 0.715909
198 7D5 0.459184 0.804878
199 6IA 0.458716 0.835294
200 SAM 0.458716 0.715909
201 EP4 0.458333 0.694118
202 A3D 0.458015 0.841463
203 A4D 0.457447 0.728395
204 A3S 0.457143 0.7875
205 P5A 0.456897 0.844444
206 7D3 0.456311 0.807229
207 GJV 0.456311 0.77381
208 AF3 ADP 3PG 0.456 0.793103
209 AHZ 0.455285 0.775281
210 AAT 0.454545 0.77381
211 EEM 0.454545 0.715909
212 ATP A 0.453782 0.82716
213 ATP A A A 0.453782 0.82716
214 ATR 0.453704 0.814815
215 PAP 0.453704 0.82716
216 7D4 0.45283 0.807229
217 62X 0.452174 0.730337
218 A3P 0.451923 0.8375
219 AR6 AR6 0.45082 0.817073
220 2SA 0.45045 0.853659
221 MTA 0.44898 0.690476
222 H1Q 0.448598 0.804878
223 K15 0.448276 0.747126
224 M24 0.447761 0.825581
225 NAE 0.444444 0.821429
226 0UM 0.443478 0.785714
227 A7D 0.443396 0.777778
228 NO7 0.442478 0.831325
229 A2R 0.442478 0.829268
230 6MZ 0.442308 0.804878
231 6AD 0.441441 0.772727
232 PPS 0.441441 0.744444
233 8Q2 0.440945 0.755319
234 9K8 0.440678 0.666667
235 ARU 0.439655 0.752809
236 ITT 0.439252 0.792683
237 M2T 0.438776 0.659091
238 A2P 0.438095 0.825
239 B1U 0.438017 0.739583
240 ZID 0.437956 0.841463
241 KB1 0.436975 0.744186
242 A3G 0.436893 0.8
243 HFD 0.436364 0.8
244 JSQ 0.436364 0.8
245 VRT 0.436364 0.771084
246 3AM 0.435644 0.825
247 KH3 0.435484 0.758621
248 A3T 0.435185 0.753086
249 NAJ PZO 0.432836 0.802326
250 IMO 0.432692 0.802469
251 A3N 0.432692 0.722892
252 V3L 0.432432 0.839506
253 HZ2 0.432 0.797619
254 4TA 0.431818 0.806818
255 EAD 0.431655 0.804598
256 NDE 0.429577 0.831325
257 OZP 0.428571 0.795181
258 N5A 0.428571 0.7625
259 FNK 0.426667 0.765957
260 MHZ 0.425926 0.781609
261 HY8 0.425197 0.797619
262 MAO 0.424528 0.845238
263 NA7 0.423729 0.853659
264 NDC 0.423611 0.86747
265 AVV 0.422414 0.823529
266 AMP NAD 0.421053 0.829268
267 P1H 0.41958 0.806818
268 SFD 0.418919 0.72
269 F0P 0.418605 0.795181
270 ZAS 0.417476 0.746988
271 SXZ 0.416667 0.735632
272 A5D 0.414414 0.722892
273 NVA 2AD 0.414414 0.761905
274 D3Y 0.413793 0.768293
275 4YB 0.412698 0.782609
276 AV2 0.412281 0.77381
277 2AM 0.411765 0.814815
278 U A 0.411765 0.811765
279 649 0.410853 0.804348
280 6C6 0.410714 0.876543
281 GEK 0.410256 0.761905
282 NAJ PYZ 0.410072 0.766667
283 NEC 0.409524 0.707317
284 2VA 0.409091 0.73494
285 3NZ 0.408333 0.761905
286 FDA 0.408163 0.771739
287 7C5 0.408 0.732558
288 BVT 0.40678 0.808511
289 KOY 0.40625 0.759036
290 6FA 0.405405 0.797753
291 P5F 0.405063 0.763441
292 Z5A 0.404255 0.78022
293 BV8 0.403409 0.817204
294 NJP 0.402985 0.821429
295 SCO 0.401408 0.863636
296 CMX 0.401408 0.863636
297 G A A A 0.4 0.802326
298 0WD 0.4 0.802326
299 FAS 0.4 0.806818
300 FAD 0.4 0.806818
301 OVE 0.4 0.785714
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3E9I; Ligand: XAH; Similar sites found with APoc: 2
This union binding pocket(no: 1) in the query (biounit: 3e9i.bio1) has 30 residues
No: Leader PDB Ligand Sequence Similarity
1 6AAD 9TU 22.2628
2 6AAD ATP 22.2628
Pocket No.: 2; Query (leader) PDB : 3E9I; Ligand: XAH; Similar sites found with APoc: 2
This union binding pocket(no: 2) in the query (biounit: 3e9i.bio1) has 30 residues
No: Leader PDB Ligand Sequence Similarity
1 6AAD ATP 22.2628
2 6AAD 9TU 22.2628
Pocket No.: 3; Query (leader) PDB : 3E9I; Ligand: XAH; Similar sites found with APoc: 6
This union binding pocket(no: 3) in the query (biounit: 3e9i.bio2) has 30 residues
No: Leader PDB Ligand Sequence Similarity
1 2I4O ATP 3.93013
2 2I4O ATP 3.93013
3 2I4O ATP 3.93013
4 3REU ATP 20.068
5 3REU ATP 20.068
6 2XGT NSS 32.6437
Pocket No.: 4; Query (leader) PDB : 3E9I; Ligand: XAH; Similar sites found with APoc: 5
This union binding pocket(no: 4) in the query (biounit: 3e9i.bio2) has 30 residues
No: Leader PDB Ligand Sequence Similarity
1 2I4O ATP 3.93013
2 2I4O ATP 3.93013
3 2I4O ATP 3.93013
4 3REU ATP 20.068
5 3REU ATP 20.068
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