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 (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: XAH; Similar ligands found: 324
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 AP5 0.617021 0.839506
15 B4P 0.617021 0.839506
16 AT4 0.610526 0.809524
17 QA7 0.607843 0.821429
18 YLP 0.607143 0.904762
19 AMP 0.604396 0.8375
20 A 0.604396 0.8375
21 ADX 0.604167 0.764045
22 M33 0.604167 0.829268
23 8LH 0.60396 0.853659
24 ME8 0.603774 0.837209
25 NB8 0.603774 0.91358
26 8QN 0.601942 0.851852
27 8LE 0.6 0.821429
28 ATP 0.597938 0.839506
29 ACP 0.597938 0.841463
30 HEJ 0.597938 0.839506
31 50T 0.597938 0.807229
32 7MD 0.594595 0.926829
33 WAQ 0.59434 0.901235
34 8LQ 0.592233 0.853659
35 PRX 0.591837 0.819277
36 5FA 0.591837 0.839506
37 AR6 0.591837 0.839506
38 APR 0.591837 0.839506
39 AQP 0.591837 0.839506
40 YLB 0.591304 0.904762
41 YLC 0.591304 0.926829
42 ANP 0.59 0.841463
43 TXA 0.588785 0.831325
44 AD9 0.585859 0.819277
45 AGS 0.585859 0.8
46 ABM 0.585106 0.817073
47 45A 0.585106 0.817073
48 AYB 0.584746 0.894118
49 V2G 0.584158 0.890244
50 4AD 0.580952 0.865854
51 PAJ 0.580952 0.813953
52 AMP MG 0.580645 0.825
53 ATF 0.578431 0.809524
54 YLA 0.576271 0.904762
55 DLL 0.575472 0.851852
56 ACQ 0.574257 0.841463
57 AP2 0.572917 0.853659
58 A12 0.572917 0.853659
59 FA5 0.572727 0.876543
60 OOB 0.571429 0.851852
61 AU1 0.571429 0.841463
62 3UK 0.570093 0.841463
63 HQG 0.567308 0.829268
64 PR8 0.564815 0.938272
65 B5V 0.564815 0.831325
66 SRA 0.56383 0.797619
67 JNT 0.560748 0.864198
68 00A 0.560748 0.811765
69 PTJ 0.559633 0.802326
70 FYA 0.559633 0.851852
71 1ZZ 0.559633 0.837209
72 6YZ 0.557692 0.841463
73 9ZD 0.556604 0.833333
74 5SV 0.556604 0.823529
75 OZV 0.556604 0.839506
76 9ZA 0.556604 0.833333
77 OAD 0.555556 0.841463
78 TYM 0.555556 0.876543
79 F2R 0.553719 0.882353
80 A1R 0.551402 0.901235
81 N0B 0.551181 0.904762
82 GSU 0.550459 0.8
83 9SN 0.54955 0.802326
84 A22 0.54717 0.829268
85 BIS 0.545455 0.833333
86 SON 0.545455 0.876543
87 ADP MG 0.545455 0.8375
88 ADP BEF 0.545455 0.8375
89 3OD 0.545455 0.841463
90 B5M 0.544643 0.821429
91 APC 0.544554 0.853659
92 GAP 0.543689 0.864198
93 TAT 0.543689 0.809524
94 T99 0.543689 0.809524
95 SSA 0.542857 0.8
96 25A 0.542056 0.839506
97 IOT 0.541667 0.894118
98 9X8 0.541284 0.8
99 YLY 0.539683 0.894118
100 RBY 0.539216 0.853659
101 ADV 0.539216 0.853659
102 7MC 0.537815 0.904762
103 A3R 0.537037 0.901235
104 ADQ 0.537037 0.841463
105 DSZ 0.537037 0.78022
106 A5A 0.533333 0.766667
107 5CA 0.53271 0.8
108 TSB 0.53271 0.758242
109 DAL AMP 0.53271 0.829268
110 B5Y 0.530973 0.821429
111 TXE 0.529412 0.833333
112 4UU 0.525862 0.821429
113 48N 0.525424 0.823529
114 APC MG 0.524272 0.839506
115 ADP PO3 0.524272 0.8375
116 ATP MG 0.524272 0.8375
117 54H 0.523364 0.75
118 52H 0.523364 0.741935
119 VMS 0.523364 0.75
120 LSS 0.522936 0.763441
121 4UV 0.521739 0.821429
122 BEF ADP 0.519231 0.817073
123 VO4 ADP 0.518868 0.819277
124 ANP MG 0.518868 0.851852
125 53H 0.518519 0.741935
126 MAP 0.518519 0.821429
127 LAQ 0.516949 0.837209
128 25L 0.513274 0.829268
129 GA7 0.512821 0.831325
130 ARG AMP 0.512821 0.870588
131 J4G 0.508929 0.888889
132 DQV 0.508475 0.851852
133 4UW 0.508333 0.793103
134 TXD 0.508333 0.833333
135 6V0 0.508333 0.823529
136 LMS 0.505155 0.764045
137 G5A 0.504762 0.820225
138 ALF ADP 0.504673 0.77907
139 NVA LMS 0.504505 0.774194
140 KMQ 0.504348 0.809524
141 OMR 0.504132 0.827586
142 MYR AMP 0.5 0.816092
143 YSA 0.5 0.78022
144 COD 0.5 0.873563
145 AFH 0.5 0.813953
146 DND 0.495868 0.831325
147 NAX 0.495868 0.847059
148 UP5 0.495868 0.821429
149 NAI 0.495868 0.811765
150 GTA 0.495798 0.775281
151 TAD 0.495798 0.835294
152 AMP DBH 0.495726 0.776471
153 NSS 0.495495 0.78022
154 SA8 0.495238 0.752941
155 DSH 0.494949 0.792683
156 80F 0.492188 0.797753
157 G3A 0.491525 0.802326
158 JB6 0.491228 0.833333
159 5X8 0.490385 0.743902
160 5AS 0.490196 0.76087
161 T5A 0.488 0.818182
162 L3W 0.487805 0.831325
163 4TC 0.487805 0.823529
164 G5P 0.487395 0.802326
165 BT5 0.484375 0.850575
166 CNA 0.484127 0.853659
167 AOC 0.48 0.731707
168 WSA 0.479675 0.788889
169 8PZ 0.478632 0.78022
170 5N5 0.478261 0.75
171 SAH 0.476636 0.768293
172 SFG 0.47619 0.775
173 AP0 0.475806 0.781609
174 J7C 0.475248 0.771084
175 FB0 0.47482 0.844444
176 ADP BMA 0.473684 0.819277
177 5CD 0.473118 0.716049
178 RAB 0.472527 0.75
179 ADN 0.472527 0.75
180 XYA 0.472527 0.75
181 A4P 0.472 0.8
182 2A5 0.471698 0.841463
183 S4M 0.470588 0.730337
184 6RE 0.47 0.761905
185 3DH 0.469388 0.690476
186 DTA 0.46875 0.722892
187 ALF ADP 3PG 0.467742 0.793103
188 D4F 0.466165 0.795455
189 BTX 0.465116 0.860465
190 NAD 0.465116 0.851852
191 139 0.464567 0.847059
192 ADJ 0.464567 0.827586
193 8X1 0.464286 0.813187
194 UPA 0.464 0.833333
195 LPA AMP 0.463415 0.816092
196 SAI 0.462963 0.759036
197 NAQ 0.462687 0.802326
198 DZD 0.461538 0.857143
199 LEU LMS 0.46087 0.734043
200 S7M 0.459459 0.715909
201 SMM 0.459459 0.711111
202 7D5 0.459184 0.804878
203 6IA 0.458716 0.835294
204 SAM 0.458716 0.715909
205 EP4 0.458333 0.694118
206 A3D 0.458015 0.841463
207 A4D 0.457447 0.728395
208 A3S 0.457143 0.7875
209 P5A 0.456897 0.844444
210 GJV 0.456311 0.77381
211 7D3 0.456311 0.807229
212 AF3 ADP 3PG 0.456 0.793103
213 AHZ 0.455285 0.775281
214 AAT 0.454545 0.77381
215 EEM 0.454545 0.715909
216 ATP A 0.453782 0.82716
217 ATP A A A 0.453782 0.82716
218 ATR 0.453704 0.814815
219 PAP 0.453704 0.82716
220 7D4 0.45283 0.807229
221 62X 0.452174 0.730337
222 A3P 0.451923 0.8375
223 KY2 0.451327 0.776471
224 AR6 AR6 0.45082 0.817073
225 2SA 0.45045 0.853659
226 KYE 0.45 0.77907
227 MTA 0.44898 0.690476
228 H1Q 0.448598 0.804878
229 K15 0.448276 0.747126
230 M24 0.447761 0.825581
231 NAE 0.444444 0.821429
232 0UM 0.443478 0.785714
233 KYB 0.443478 0.776471
234 A7D 0.443396 0.777778
235 NO7 0.442478 0.831325
236 A2R 0.442478 0.829268
237 6MZ 0.442308 0.804878
238 PPS 0.441441 0.744444
239 6AD 0.441441 0.772727
240 NAD IBO 0.440945 0.839506
241 NAD TDB 0.440945 0.839506
242 8Q2 0.440945 0.755319
243 9K8 0.440678 0.666667
244 ARU 0.439655 0.752809
245 ITT 0.439252 0.792683
246 M2T 0.438776 0.659091
247 A2P 0.438095 0.825
248 B1U 0.438017 0.739583
249 ZID 0.437956 0.841463
250 KB1 0.436975 0.744186
251 A3G 0.436893 0.8
252 VRT 0.436364 0.771084
253 HFD 0.436364 0.8
254 JSQ 0.436364 0.8
255 3AM 0.435644 0.825
256 KXW 0.435484 0.795181
257 KH3 0.435484 0.758621
258 A3T 0.435185 0.753086
259 NAJ PZO 0.432836 0.802326
260 A3N 0.432692 0.722892
261 IMO 0.432692 0.802469
262 V3L 0.432432 0.839506
263 HZ2 0.432 0.797619
264 4TA 0.431818 0.806818
265 EAD 0.431655 0.804598
266 NDE 0.429577 0.831325
267 N5A 0.428571 0.7625
268 OZP 0.428571 0.795181
269 NWW 0.427083 0.675
270 FNK 0.426667 0.765957
271 MHZ 0.425926 0.781609
272 HY8 0.425197 0.797619
273 MAO 0.424528 0.845238
274 NA7 0.423729 0.853659
275 NDC 0.423611 0.86747
276 O02 0.423423 0.845238
277 QXP 0.422414 0.747253
278 AVV 0.422414 0.823529
279 V47 0.421053 0.740741
280 AMP NAD 0.421053 0.829268
281 Q2P 0.421053 0.719101
282 R2V 0.420168 0.747253
283 KY8 0.420168 0.795181
284 P1H 0.41958 0.806818
285 SFD 0.418919 0.72
286 Q34 0.418605 0.719101
287 F0P 0.418605 0.795181
288 ZAS 0.417476 0.746988
289 SXZ 0.416667 0.735632
290 NVA 2AD 0.414414 0.761905
291 A5D 0.414414 0.722892
292 D3Y 0.413793 0.768293
293 KY5 0.413223 0.792683
294 4YB 0.412698 0.782609
295 AV2 0.412281 0.77381
296 QXG 0.411765 0.73913
297 2AM 0.411765 0.814815
298 649 0.410853 0.804348
299 6C6 0.410714 0.876543
300 GEK 0.410256 0.761905
301 NAJ PYZ 0.410072 0.766667
302 NEC 0.409524 0.707317
303 2VA 0.409091 0.73494
304 Q2V 0.409091 0.764706
305 3NZ 0.408333 0.761905
306 FDA 0.408163 0.771739
307 7C5 0.408 0.732558
308 Q2M 0.407692 0.735632
309 38V 0.407143 0.816092
310 BVT 0.40678 0.808511
311 KOY 0.40625 0.759036
312 6FA 0.405405 0.797753
313 P5F 0.405063 0.763441
314 Z5A 0.404255 0.78022
315 BV8 0.403409 0.817204
316 EU9 0.403101 0.766667
317 NJP 0.402985 0.821429
318 SCO 0.401408 0.863636
319 CMX 0.401408 0.863636
320 FAS 0.4 0.806818
321 OVE 0.4 0.785714
322 K3E 0.4 0.729412
323 FAD 0.4 0.806818
324 0WD 0.4 0.802326
Similar Ligands (3D)
Ligand no: 1; Ligand: XAH; Similar ligands found: 1
No: Ligand Similarity coefficient
1 RSN 0.8575
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 ATP 22.2628
2 6AAD 9TU 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 9TU 22.2628
2 6AAD ATP 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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