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;
submit data
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
Ligand no: 1; Ligand: 8X1; Similar ligands found: 258
No: Ligand ECFP6 Tc MDL keys Tc
1 8X1 1 1
2 P5A 0.892857 0.94382
3 G5A 0.72093 0.965116
4 VMS 0.7 0.88764
5 54H 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 LEU LMS 0.645833 0.89011
18 KAA 0.639175 0.954545
19 GSU 0.639175 0.942529
20 LMS 0.638554 0.906977
21 B1U 0.623762 0.831579
22 8PZ 0.613861 0.920455
23 YSA 0.607843 0.920455
24 SON 0.588889 0.766667
25 4YB 0.584906 0.921348
26 WSA 0.577982 0.931035
27 PR8 0.574257 0.802198
28 8Q2 0.572727 0.89011
29 649 0.563636 0.901099
30 A 0.563218 0.75
31 AMP 0.563218 0.75
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 BA3 0.532609 0.752809
43 A12 0.532609 0.747253
44 AP2 0.532609 0.747253
45 ADX 0.531915 0.863636
46 AU1 0.531915 0.755556
47 RAB 0.530864 0.689655
48 ADN 0.530864 0.689655
49 XYA 0.530864 0.689655
50 8LE 0.530612 0.73913
51 5AL 0.530612 0.764045
52 5CD 0.53012 0.659091
53 SLU 0.529412 0.868132
54 ADP 0.526882 0.752809
55 AP5 0.526882 0.752809
56 B4P 0.526882 0.752809
57 AN2 0.521277 0.764045
58 ADP MG 0.521277 0.75
59 GAP 0.520408 0.775281
60 M33 0.515789 0.744444
61 APC MG 0.515464 0.733333
62 A4D 0.511905 0.689655
63 5X8 0.510417 0.704545
64 ATP 0.510417 0.752809
65 50T 0.510417 0.725275
66 ACP 0.510417 0.755556
67 HEJ 0.510417 0.752809
68 DTA 0.505747 0.685393
69 AR6 0.505155 0.752809
70 5FA 0.505155 0.752809
71 AQP 0.505155 0.752809
72 APC 0.505155 0.747253
73 APR 0.505155 0.752809
74 PRX 0.505155 0.736264
75 TAT 0.50505 0.766667
76 ANP 0.50505 0.755556
77 T99 0.50505 0.766667
78 SRP 0.504951 0.806818
79 8LH 0.504951 0.766667
80 9ZD 0.504854 0.75
81 9ZA 0.504854 0.75
82 RBY 0.5 0.747253
83 MTA 0.5 0.655556
84 AD9 0.5 0.736264
85 ADP PO3 0.5 0.75
86 A1R 0.5 0.788889
87 A3R 0.5 0.788889
88 ADV 0.5 0.747253
89 SAP 0.5 0.777778
90 AGS 0.5 0.777778
91 4AD 0.5 0.777778
92 ATP MG 0.5 0.75
93 TXA 0.495327 0.747253
94 AHX 0.495238 0.8
95 DLL 0.495238 0.764045
96 DAL AMP 0.495146 0.744444
97 8LQ 0.495146 0.766667
98 H1Q 0.494845 0.741573
99 A3N 0.494624 0.666667
100 EP4 0.494253 0.641304
101 3UK 0.490566 0.755556
102 8QN 0.490385 0.764045
103 OOB 0.490385 0.764045
104 ACQ 0.49 0.755556
105 GJV 0.489362 0.695652
106 6RE 0.48913 0.703297
107 M2T 0.488636 0.645161
108 PAJ 0.485714 0.734043
109 AMO 0.485714 0.786517
110 3OD 0.481481 0.755556
111 9K8 0.481481 0.737374
112 NB8 0.481481 0.78022
113 00A 0.481132 0.731183
114 MAP 0.480769 0.73913
115 A22 0.480769 0.744444
116 ALF ADP 0.480392 0.702128
117 ATF 0.480392 0.728261
118 ADP ALF 0.480392 0.702128
119 J7C 0.478723 0.711111
120 OAD 0.476636 0.755556
121 25A 0.47619 0.752809
122 VO4 ADP 0.475728 0.744444
123 ADP VO4 0.475728 0.744444
124 6YZ 0.475728 0.755556
125 9SN 0.472727 0.723404
126 B5V 0.472222 0.747253
127 LAD 0.472222 0.811111
128 WAQ 0.472222 0.769231
129 YLY 0.472 0.768421
130 ADQ 0.471698 0.755556
131 HQG 0.471154 0.744444
132 LAQ 0.469565 0.755319
133 7C5 0.469027 0.677419
134 YAP 0.468468 0.777778
135 FA5 0.468468 0.786517
136 DSH 0.468085 0.711111
137 NEC 0.468085 0.651685
138 ME8 0.46789 0.774194
139 BIS 0.46789 0.731183
140 1ZZ 0.46789 0.71875
141 PTJ 0.46789 0.723404
142 LPA AMP 0.465517 0.736842
143 SAH 0.465347 0.707865
144 7MD 0.464912 0.813187
145 SFG 0.464646 0.693182
146 XAH 0.464286 0.813187
147 MYR AMP 0.463636 0.701031
148 ADP BMA 0.462963 0.736264
149 9X8 0.462963 0.758242
150 ZAS 0.462366 0.688889
151 5SV 0.462264 0.705263
152 OZV 0.462264 0.752809
153 NAX 0.461538 0.763441
154 NXX 0.461538 0.747253
155 DND 0.461538 0.747253
156 TAD 0.46087 0.752688
157 AMP DBH 0.460177 0.698925
158 S4M 0.458333 0.677083
159 TXE 0.457627 0.75
160 SA8 0.455446 0.677419
161 B5Y 0.455357 0.73913
162 B5M 0.455357 0.73913
163 MAO 0.453608 0.723404
164 A3G 0.452632 0.735632
165 N5O 0.452632 0.724138
166 ARG AMP 0.452174 0.765957
167 4UU 0.452174 0.73913
168 SAI 0.45098 0.681319
169 25L 0.45045 0.744444
170 6V0 0.449153 0.741935
171 4UW 0.449153 0.715789
172 S7M 0.447619 0.680851
173 SMM 0.447619 0.677083
174 TYR AMP 0.447368 0.758242
175 4UV 0.447368 0.73913
176 SAM 0.446602 0.680851
177 A A 0.445455 0.733333
178 OMR 0.445378 0.71134
179 AHZ 0.444444 0.71875
180 A7D 0.444444 0.715909
181 G3A 0.443478 0.723404
182 EO7 0.443299 0.866667
183 N5A 0.443299 0.701149
184 139 0.442623 0.744681
185 EEM 0.442308 0.645833
186 7MC 0.441667 0.795699
187 JB6 0.441441 0.788889
188 FYA 0.441441 0.764045
189 KOY 0.440678 0.7
190 YLP 0.440678 0.776596
191 48N 0.440678 0.741935
192 MHZ 0.44 0.6875
193 G5P 0.439655 0.723404
194 CNA 0.439024 0.766667
195 TXD 0.436975 0.75
196 NAI 0.436975 0.731183
197 UP5 0.436975 0.73913
198 3AM 0.43617 0.738636
199 DQV 0.435897 0.764045
200 GTA 0.435897 0.701031
201 5AD 0.435294 0.609195
202 IOT 0.434426 0.768421
203 TYM 0.433333 0.786517
204 AF3 ADP 3PG 0.433333 0.715789
205 NAD 0.432 0.764045
206 0UM 0.431193 0.688172
207 YLA 0.430894 0.776596
208 A3S 0.43 0.724138
209 ATP A 0.429825 0.741573
210 ATP A A A 0.429825 0.741573
211 YLB 0.429752 0.776596
212 4TC 0.429752 0.741935
213 YLC 0.429752 0.793478
214 UPA 0.429752 0.75
215 594 0.429688 0.826531
216 SXZ 0.428571 0.680851
217 BT5 0.428571 0.75
218 AR6 AR6 0.42735 0.733333
219 A5D 0.427184 0.685393
220 A4P 0.42623 0.72449
221 A2P 0.424242 0.738636
222 A3P 0.424242 0.75
223 F2R 0.424 0.776596
224 K15 0.423423 0.65625
225 GEK 0.422018 0.722222
226 A3T 0.421569 0.693182
227 AMP NAD 0.420635 0.744444
228 T5A 0.419355 0.721649
229 AYB 0.416 0.768421
230 BS5 0.416 0.831579
231 AFH 0.415254 0.734043
232 GA7 0.415254 0.747253
233 AAT 0.415094 0.695652
234 7D5 0.414894 0.741573
235 62X 0.414414 0.642857
236 A3D 0.414062 0.755556
237 7D7 0.413793 0.666667
238 3AD 0.411111 0.697674
239 NAJ PZO 0.410853 0.723404
240 A6D 0.410714 0.65625
241 2AM 0.410526 0.730337
242 4TA 0.409449 0.71134
243 BTX 0.409449 0.757895
244 COD 0.409449 0.770833
245 2VA 0.407767 0.677778
246 J4G 0.40708 0.797753
247 AP0 0.406504 0.705263
248 SFB 0.406504 0.829787
249 DZD 0.40625 0.752688
250 V3L 0.40566 0.752809
251 67D 0.404762 0.9
252 590 0.404412 0.836735
253 PPS 0.401869 0.842697
254 U A 0.4 0.731183
255 ATR 0.4 0.730337
256 KB1 0.4 0.670213
257 NVA 2AD 0.4 0.703297
258 PAP 0.4 0.741573
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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