Receptor
PDB id Resolution Class Description Source Keywords
5V59 2.03 Å EC: 6.1.1.7 CRYSTAL STRUCTURE OF CATALYTIC FRAGMENT OF HUMAN ALARS IN CO AZE-SA HOMO SAPIENS LIGASE AMINOACYL-TRNA SYNTHETASE NON-PROTEINOGENIC AMINO A
Ref.: DOUBLE MIMICRY EVADES TRNA SYNTHETASE EDITING BY TO VEGETABLE-SOURCED NON-PROTEINOGENIC AMINO ACID. NAT COMMUN V. 8 2281 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
8X1 A:501;
Valid;
none;
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429.408 C14 H19 N7 O7 S c1nc(...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5V59 2.03 Å EC: 6.1.1.7 CRYSTAL STRUCTURE OF CATALYTIC FRAGMENT OF HUMAN ALARS IN CO AZE-SA HOMO SAPIENS LIGASE AMINOACYL-TRNA SYNTHETASE NON-PROTEINOGENIC AMINO A
Ref.: DOUBLE MIMICRY EVADES TRNA SYNTHETASE EDITING BY TO VEGETABLE-SOURCED NON-PROTEINOGENIC AMINO ACID. NAT COMMUN V. 8 2281 2017
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 5V59 - 8X1 C14 H19 N7 O7 S c1nc(c2c(n....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 5V59 - 8X1 C14 H19 N7 O7 S c1nc(c2c(n....
50% Homology Family (11)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 3HXX - ACP C11 H18 N5 O12 P3 c1nc(c2c(n....
2 3HXU - A5A C13 H19 N7 O7 S C[C@@H](C(....
3 3HXW - SSA C13 H19 N7 O8 S c1nc(c2c(n....
4 3HXZ - A5A C13 H19 N7 O7 S C[C@@H](C(....
5 3HXV - G5A C12 H17 N7 O7 S c1nc(c2c(n....
6 3HXY - ACP C11 H18 N5 O12 P3 c1nc(c2c(n....
7 3HY0 - G5A C12 H17 N7 O7 S c1nc(c2c(n....
8 5V59 - 8X1 C14 H19 N7 O7 S c1nc(c2c(n....
9 1YFS - ALA C3 H7 N O2 C[C@@H](C(....
10 1YGB - SER C3 H7 N O3 C([C@@H](C....
11 1YFT - GLY C2 H5 N O2 C(C(=O)O)N
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: 8X1; Similar ligands found: 279
No: Ligand ECFP6 Tc MDL keys Tc
1 8X1 1 1
2 P5A 0.892857 0.94382
3 G5A 0.72093 0.965116
4 54H 0.7 0.88764
5 VMS 0.7 0.88764
6 A5A 0.696629 0.908046
7 SSA 0.688889 0.942529
8 52H 0.681319 0.877778
9 DSZ 0.677419 0.920455
10 TSB 0.673913 0.897727
11 5CA 0.673913 0.942529
12 53H 0.673913 0.877778
13 5AS 0.670588 0.898876
14 LSS 0.659574 0.9
15 NSS 0.659574 0.920455
16 NVA LMS 0.652632 0.911111
17 GSU 0.639175 0.942529
18 KAA 0.639175 0.954545
19 LMS 0.638554 0.906977
20 B1U 0.623762 0.831579
21 8PZ 0.613861 0.920455
22 YSA 0.607843 0.920455
23 SON 0.588889 0.766667
24 4YB 0.584906 0.921348
25 WSA 0.577982 0.931035
26 PR8 0.574257 0.802198
27 8Q2 0.572727 0.89011
28 649 0.563636 0.901099
29 AMP 0.563218 0.75
30 A 0.563218 0.75
31 AMP MG 0.556818 0.738636
32 AOC 0.550562 0.674157
33 CA0 0.548387 0.755556
34 A2D 0.544444 0.752809
35 45A 0.544444 0.733333
36 ABM 0.544444 0.733333
37 KG4 0.542553 0.755556
38 3DH 0.54023 0.655556
39 SRA 0.539326 0.775281
40 AT4 0.537634 0.766667
41 5N5 0.536585 0.689655
42 LEU LMS 0.533981 0.827957
43 A12 0.532609 0.747253
44 BA3 0.532609 0.752809
45 AP2 0.532609 0.747253
46 ADX 0.531915 0.863636
47 AU1 0.531915 0.755556
48 ADN 0.530864 0.689655
49 XYA 0.530864 0.689655
50 RAB 0.530864 0.689655
51 5AL 0.530612 0.764045
52 8LE 0.530612 0.73913
53 V2G 0.530612 0.8
54 5CD 0.53012 0.659091
55 SLU 0.529412 0.868132
56 B4P 0.526882 0.752809
57 AP5 0.526882 0.752809
58 ADP 0.526882 0.752809
59 QA7 0.524752 0.73913
60 ADP MG 0.521277 0.75
61 AN2 0.521277 0.764045
62 ADP BEF 0.521277 0.75
63 GAP 0.520408 0.775281
64 M33 0.515789 0.744444
65 APC MG 0.515464 0.733333
66 A4D 0.511905 0.689655
67 HEJ 0.510417 0.752809
68 ATP 0.510417 0.752809
69 50T 0.510417 0.725275
70 ACP 0.510417 0.755556
71 5X8 0.510417 0.704545
72 DTA 0.505747 0.685393
73 APC 0.505155 0.747253
74 APR 0.505155 0.752809
75 AR6 0.505155 0.752809
76 5FA 0.505155 0.752809
77 PRX 0.505155 0.736264
78 AQP 0.505155 0.752809
79 TAT 0.50505 0.766667
80 T99 0.50505 0.766667
81 ANP 0.50505 0.755556
82 SRP 0.504951 0.806818
83 8LH 0.504951 0.766667
84 9ZA 0.504854 0.75
85 9ZD 0.504854 0.75
86 AD9 0.5 0.736264
87 ADV 0.5 0.747253
88 MTA 0.5 0.655556
89 ATP MG 0.5 0.75
90 4AD 0.5 0.777778
91 A3R 0.5 0.788889
92 ADP PO3 0.5 0.75
93 AGS 0.5 0.777778
94 A1R 0.5 0.788889
95 RBY 0.5 0.747253
96 TXA 0.495327 0.747253
97 AHX 0.495238 0.8
98 DLL 0.495238 0.764045
99 DAL AMP 0.495146 0.744444
100 8LQ 0.495146 0.766667
101 ANP MG 0.49505 0.764045
102 BEF ADP 0.494949 0.733333
103 H1Q 0.494845 0.741573
104 A3N 0.494624 0.666667
105 EP4 0.494253 0.641304
106 3UK 0.490566 0.755556
107 8QN 0.490385 0.764045
108 OOB 0.490385 0.764045
109 QXP 0.490385 0.844444
110 ACQ 0.49 0.755556
111 GJV 0.489362 0.695652
112 6RE 0.48913 0.703297
113 M2T 0.488636 0.645161
114 PAJ 0.485714 0.734043
115 AMO 0.485714 0.786517
116 9K8 0.481481 0.737374
117 NB8 0.481481 0.78022
118 3OD 0.481481 0.755556
119 00A 0.481132 0.731183
120 MAP 0.480769 0.73913
121 A22 0.480769 0.744444
122 VO4 ADP 0.480392 0.736264
123 ALF ADP 0.480392 0.702128
124 ATF 0.480392 0.728261
125 J7C 0.478723 0.711111
126 NWW 0.476744 0.62069
127 OAD 0.476636 0.755556
128 25A 0.47619 0.752809
129 6YZ 0.475728 0.755556
130 NX8 0.475248 0.684783
131 9SN 0.472727 0.723404
132 B5V 0.472222 0.747253
133 LAD 0.472222 0.811111
134 WAQ 0.472222 0.769231
135 YLY 0.472 0.768421
136 ADQ 0.471698 0.755556
137 HQG 0.471154 0.744444
138 LAQ 0.469565 0.755319
139 7C5 0.469027 0.677419
140 FA5 0.468468 0.786517
141 DSH 0.468085 0.711111
142 NEC 0.468085 0.651685
143 ME8 0.46789 0.774194
144 PTJ 0.46789 0.723404
145 1ZZ 0.46789 0.71875
146 BIS 0.46789 0.731183
147 JNT 0.46729 0.775281
148 LPA AMP 0.465517 0.736842
149 SAH 0.465347 0.707865
150 7MD 0.464912 0.813187
151 SFG 0.464646 0.693182
152 XAH 0.464286 0.813187
153 MYR AMP 0.463636 0.701031
154 QXG 0.462963 0.835165
155 9X8 0.462963 0.758242
156 ADP BMA 0.462963 0.736264
157 ZAS 0.462366 0.688889
158 OZV 0.462264 0.752809
159 5SV 0.462264 0.705263
160 NAX 0.461538 0.763441
161 DND 0.461538 0.747253
162 TAD 0.46087 0.752688
163 AMP DBH 0.460177 0.698925
164 NWZ 0.46 0.673913
165 R2V 0.458716 0.844444
166 S4M 0.458333 0.677083
167 TXE 0.457627 0.75
168 NWQ 0.456522 0.606742
169 SA8 0.455446 0.677419
170 B5Y 0.455357 0.73913
171 B5M 0.455357 0.73913
172 NAD IBO 0.453782 0.752809
173 NAD TDB 0.453782 0.752809
174 MAO 0.453608 0.723404
175 N5O 0.452632 0.724138
176 A3G 0.452632 0.735632
177 ARG AMP 0.452174 0.765957
178 4UU 0.452174 0.73913
179 SAI 0.45098 0.681319
180 25L 0.45045 0.744444
181 4UW 0.449153 0.715789
182 6V0 0.449153 0.741935
183 SMM 0.447619 0.677083
184 S7M 0.447619 0.680851
185 V47 0.447619 0.681818
186 4UV 0.447368 0.73913
187 SAM 0.446602 0.680851
188 OMR 0.445378 0.71134
189 AHZ 0.444444 0.71875
190 A7D 0.444444 0.715909
191 G3A 0.443478 0.723404
192 EO7 0.443299 0.866667
193 N5A 0.443299 0.701149
194 139 0.442623 0.744681
195 KMQ 0.442478 0.728261
196 EEM 0.442308 0.645833
197 7MC 0.441667 0.795699
198 FYA 0.441441 0.764045
199 JB6 0.441441 0.788889
200 48N 0.440678 0.741935
201 KOY 0.440678 0.7
202 YLP 0.440678 0.776596
203 MHZ 0.44 0.6875
204 G5P 0.439655 0.723404
205 CNA 0.439024 0.766667
206 NAI 0.436975 0.731183
207 TXD 0.436975 0.75
208 UP5 0.436975 0.73913
209 3AM 0.43617 0.738636
210 GTA 0.435897 0.701031
211 DQV 0.435897 0.764045
212 5AD 0.435294 0.609195
213 IOT 0.434426 0.768421
214 TYM 0.433333 0.786517
215 AF3 ADP 3PG 0.433333 0.715789
216 ALF ADP 3PG 0.433333 0.715789
217 NAD 0.432 0.764045
218 0UM 0.431193 0.688172
219 YLA 0.430894 0.776596
220 A3S 0.43 0.724138
221 ATP A 0.429825 0.741573
222 ATP A A A 0.429825 0.741573
223 4TC 0.429752 0.741935
224 UPA 0.429752 0.75
225 YLC 0.429752 0.793478
226 YLB 0.429752 0.776596
227 L3W 0.429752 0.747253
228 594 0.429688 0.826531
229 SXZ 0.428571 0.680851
230 BT5 0.428571 0.75
231 AR6 AR6 0.42735 0.733333
232 A5D 0.427184 0.685393
233 A4P 0.42623 0.72449
234 KY2 0.425926 0.680851
235 A2P 0.424242 0.738636
236 A3P 0.424242 0.75
237 F2R 0.424 0.776596
238 K15 0.423423 0.65625
239 GEK 0.422018 0.722222
240 A3T 0.421569 0.693182
241 AMP NAD 0.420635 0.744444
242 K2K 0.419643 0.684783
243 T5A 0.419355 0.721649
244 K3K 0.417391 0.663043
245 BS5 0.416 0.831579
246 AYB 0.416 0.768421
247 AFH 0.415254 0.734043
248 GA7 0.415254 0.747253
249 AAT 0.415094 0.695652
250 7D5 0.414894 0.741573
251 62X 0.414414 0.642857
252 A3D 0.414062 0.755556
253 7D7 0.413793 0.666667
254 D4F 0.412214 0.736842
255 3AD 0.411111 0.697674
256 NAJ PZO 0.410853 0.723404
257 A6D 0.410714 0.65625
258 2AM 0.410526 0.730337
259 K3E 0.410256 0.673913
260 4TA 0.409449 0.71134
261 COD 0.409449 0.770833
262 BTX 0.409449 0.757895
263 2VA 0.407767 0.677778
264 J4G 0.40708 0.797753
265 SFB 0.406504 0.829787
266 AP0 0.406504 0.705263
267 DZD 0.40625 0.752688
268 V3L 0.40566 0.752809
269 KYB 0.405405 0.680851
270 67D 0.404762 0.9
271 590 0.404412 0.836735
272 PPS 0.401869 0.842697
273 K2W 0.401709 0.688172
274 KYE 0.401709 0.684211
275 EU9 0.401639 0.693878
276 ATR 0.4 0.730337
277 PAP 0.4 0.741573
278 NVA 2AD 0.4 0.703297
279 KB1 0.4 0.670213
Similar Ligands (3D)
Ligand no: 1; Ligand: 8X1; Similar ligands found: 7
No: Ligand Similarity coefficient
1 FZQ 0.9014
2 FZT 0.8956
3 FZK 0.8871
4 GDP 0.8861
5 GNP 0.8806
6 GTP 0.8616
7 3AT 0.8582
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5V59; Ligand: 8X1; Similar sites found with APoc: 5
This union binding pocket(no: 1) in the query (biounit: 5v59.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
1 2XGT NSS 2.75862
2 3G1Z AMP 3.68098
3 3G1Z AMP 3.68098
4 3A5Z KAA 5.4878
5 3A5Y KAA 10.1449
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