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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: 241
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 5CA 0.673913 0.942529
11 53H 0.673913 0.877778
12 TSB 0.673913 0.897727
13 5AS 0.670588 0.898876
14 NSS 0.659574 0.920455
15 LSS 0.659574 0.9
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 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 A 0.563218 0.75
30 AMP 0.563218 0.75
31 AOC 0.550562 0.674157
32 CA0 0.548387 0.755556
33 A2D 0.544444 0.752809
34 ABM 0.544444 0.733333
35 3DH 0.54023 0.655556
36 SRA 0.539326 0.775281
37 AT4 0.537634 0.766667
38 5N5 0.536585 0.689655
39 AP2 0.532609 0.747253
40 A12 0.532609 0.747253
41 BA3 0.532609 0.752809
42 ADX 0.531915 0.863636
43 AU1 0.531915 0.755556
44 ADN 0.530864 0.689655
45 RAB 0.530864 0.689655
46 XYA 0.530864 0.689655
47 5AL 0.530612 0.764045
48 5CD 0.53012 0.659091
49 SLU 0.529412 0.868132
50 ADP 0.526882 0.752809
51 AP5 0.526882 0.752809
52 B4P 0.526882 0.752809
53 AN2 0.521277 0.764045
54 GAP 0.520408 0.775281
55 M33 0.515789 0.744444
56 A4D 0.511905 0.689655
57 ACP 0.510417 0.755556
58 HEJ 0.510417 0.752809
59 50T 0.510417 0.725275
60 5X8 0.510417 0.704545
61 ATP 0.510417 0.752809
62 DTA 0.505747 0.685393
63 AR6 0.505155 0.752809
64 APC 0.505155 0.747253
65 5FA 0.505155 0.752809
66 APR 0.505155 0.752809
67 PRX 0.505155 0.736264
68 AQP 0.505155 0.752809
69 ANP 0.50505 0.755556
70 TAT 0.50505 0.766667
71 T99 0.50505 0.766667
72 SRP 0.504951 0.806818
73 9ZD 0.504854 0.75
74 9ZA 0.504854 0.75
75 AGS 0.5 0.777778
76 AD9 0.5 0.736264
77 SAP 0.5 0.777778
78 A3R 0.5 0.788889
79 A1R 0.5 0.788889
80 RBY 0.5 0.747253
81 ADV 0.5 0.747253
82 4AD 0.5 0.777778
83 MTA 0.5 0.655556
84 ADP PO3 0.5 0.75
85 TXA 0.495327 0.747253
86 DLL 0.495238 0.764045
87 AHX 0.495238 0.8
88 DAL AMP 0.495146 0.744444
89 A3N 0.494624 0.666667
90 EP4 0.494253 0.641304
91 3UK 0.490566 0.755556
92 8QN 0.490385 0.764045
93 OOB 0.490385 0.764045
94 ACQ 0.49 0.755556
95 GJV 0.489362 0.695652
96 6RE 0.48913 0.703297
97 M2T 0.488636 0.645161
98 PAJ 0.485714 0.734043
99 AMO 0.485714 0.786517
100 3OD 0.481481 0.755556
101 9K8 0.481481 0.737374
102 NB8 0.481481 0.78022
103 00A 0.481132 0.731183
104 MAP 0.480769 0.73913
105 A22 0.480769 0.744444
106 ATF 0.480392 0.728261
107 ALF ADP 0.480392 0.702128
108 ADP ALF 0.480392 0.702128
109 J7C 0.478723 0.711111
110 OAD 0.476636 0.755556
111 25A 0.47619 0.752809
112 ADP VO4 0.475728 0.744444
113 6YZ 0.475728 0.755556
114 VO4 ADP 0.475728 0.744444
115 9SN 0.472727 0.723404
116 B5V 0.472222 0.747253
117 WAQ 0.472222 0.769231
118 LAD 0.472222 0.811111
119 YLY 0.472 0.768421
120 ADQ 0.471698 0.755556
121 LAQ 0.469565 0.755319
122 7C5 0.469027 0.677419
123 FA5 0.468468 0.786517
124 YAP 0.468468 0.777778
125 NEC 0.468085 0.651685
126 DSH 0.468085 0.711111
127 1ZZ 0.46789 0.71875
128 BIS 0.46789 0.731183
129 PTJ 0.46789 0.723404
130 ME8 0.46789 0.774194
131 LPA AMP 0.465517 0.736842
132 SAH 0.465347 0.707865
133 7MD 0.464912 0.813187
134 SFG 0.464646 0.693182
135 XAH 0.464286 0.813187
136 MYR AMP 0.463636 0.701031
137 ADP BMA 0.462963 0.736264
138 9X8 0.462963 0.758242
139 ZAS 0.462366 0.688889
140 5SV 0.462264 0.705263
141 NAX 0.461538 0.763441
142 NXX 0.461538 0.747253
143 DND 0.461538 0.747253
144 TAD 0.46087 0.752688
145 AMP DBH 0.460177 0.698925
146 S4M 0.458333 0.677083
147 TXE 0.457627 0.75
148 SA8 0.455446 0.677419
149 B5M 0.455357 0.73913
150 B5Y 0.455357 0.73913
151 MAO 0.453608 0.723404
152 A3G 0.452632 0.735632
153 4UU 0.452174 0.73913
154 ARG AMP 0.452174 0.765957
155 SAI 0.45098 0.681319
156 25L 0.45045 0.744444
157 6V0 0.449153 0.741935
158 4UW 0.449153 0.715789
159 S7M 0.447619 0.680851
160 SMM 0.447619 0.677083
161 4UV 0.447368 0.73913
162 TYR AMP 0.447368 0.758242
163 SAM 0.446602 0.680851
164 A A 0.445455 0.733333
165 OMR 0.445378 0.71134
166 AHZ 0.444444 0.71875
167 A7D 0.444444 0.715909
168 G3A 0.443478 0.723404
169 EO7 0.443299 0.866667
170 139 0.442623 0.744681
171 EEM 0.442308 0.645833
172 7MC 0.441667 0.795699
173 JB6 0.441441 0.788889
174 FYA 0.441441 0.764045
175 YLP 0.440678 0.776596
176 48N 0.440678 0.741935
177 MHZ 0.44 0.6875
178 G5P 0.439655 0.723404
179 CNA 0.439024 0.766667
180 UP5 0.436975 0.73913
181 NAI 0.436975 0.731183
182 TXD 0.436975 0.75
183 3AM 0.43617 0.738636
184 GTA 0.435897 0.701031
185 DQV 0.435897 0.764045
186 5AD 0.435294 0.609195
187 IOT 0.434426 0.768421
188 TYM 0.433333 0.786517
189 AF3 ADP 3PG 0.433333 0.715789
190 NAD 0.432 0.764045
191 0UM 0.431193 0.688172
192 YLA 0.430894 0.776596
193 A3S 0.43 0.724138
194 ATP A A A 0.429825 0.741573
195 YLB 0.429752 0.776596
196 UPA 0.429752 0.75
197 YLC 0.429752 0.793478
198 4TC 0.429752 0.741935
199 594 0.429688 0.826531
200 BT5 0.428571 0.75
201 SXZ 0.428571 0.680851
202 AR6 AR6 0.42735 0.733333
203 A5D 0.427184 0.685393
204 A4P 0.42623 0.72449
205 A2P 0.424242 0.738636
206 A3P 0.424242 0.75
207 F2R 0.424 0.776596
208 K15 0.423423 0.65625
209 GEK 0.422018 0.722222
210 A3T 0.421569 0.693182
211 AMP NAD 0.420635 0.744444
212 T5A 0.419355 0.721649
213 BS5 0.416 0.831579
214 AYB 0.416 0.768421
215 GA7 0.415254 0.747253
216 AFH 0.415254 0.734043
217 AAT 0.415094 0.695652
218 7D5 0.414894 0.741573
219 62X 0.414414 0.642857
220 A3D 0.414062 0.755556
221 7D7 0.413793 0.666667
222 3AD 0.411111 0.697674
223 NAJ PZO 0.410853 0.723404
224 A6D 0.410714 0.65625
225 2AM 0.410526 0.730337
226 BTX 0.409449 0.757895
227 4TA 0.409449 0.71134
228 COD 0.409449 0.770833
229 2VA 0.407767 0.677778
230 AP0 0.406504 0.705263
231 SFB 0.406504 0.829787
232 DZD 0.40625 0.752688
233 V3L 0.40566 0.752809
234 67D 0.404762 0.9
235 590 0.404412 0.836735
236 PPS 0.401869 0.842697
237 NVA 2AD 0.4 0.703297
238 PAP 0.4 0.741573
239 KB1 0.4 0.670213
240 ATR 0.4 0.730337
241 U A 0.4 0.731183
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: 132
This union binding pocket(no: 1) in the query (biounit: 5v59.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
1 4YDQ HFG 1.26316
2 4YDQ ANP 1.26316
3 5XIJ ANP 1.26316
4 5XIJ 873 1.26316
5 3IAL PR8 1.47368
6 4MRP GSH 1.47368
7 4GID 0GH 1.54639
8 3ERR AMP 1.68421
9 2WZF BGC 1.68421
10 4B0T ADP 1.68421
11 3TW1 AHN 1.68776
12 3NEM AMO 1.82648
13 3NEM ATP 1.82648
14 1QHO MAL 1.89474
15 5VAD 91Y 1.93798
16 5VAD PRO 1.93798
17 1MJT ITU 2.01729
18 1X54 4AD 2.07373
19 12AS AMP 2.12121
20 3TEG DAH 2.16867
21 5LRT ADP 2.31579
22 4J75 TYM 2.31579
23 4OYA 1VE 2.34043
24 4HWS 1B3 2.43309
25 3QO8 SSA 2.47423
26 2J3M ATP 2.52632
27 2J3M PRI 2.52632
28 6E1Q CFA 2.52632
29 2ART LPA AMP 2.67176
30 2XGT NSS 2.75862
31 1L7P SEP 2.8436
32 1VRP ADP 2.88714
33 5EOO CIT 3.01887
34 3E9I XAH 3.15789
35 4K55 H6P 3.22581
36 5XDT MB3 3.24675
37 3R6K FUC GAL GLA 3.27869
38 4MOB ADP 3.31325
39 5VKM GAL SIA 3.39506
40 5KJW 53C 3.51288
41 3G1Z AMP 3.68098
42 3T4L ZEA 3.7037
43 5G48 1FL 3.74332
44 2Z3U CRR 3.76471
45 1ZEI CRS 3.77358
46 1G51 AMO 3.78947
47 3G2Y GF4 3.80228
48 2CJA ATP 4
49 5WXU FLC 4
50 4BTV RB3 4.06977
51 3HCH RSM 4.10959
52 5XIO ANP 4.21053
53 5XIO HFG 4.21053
54 3JQQ A2P 4.21053
55 2AG4 OLA 4.26829
56 2AG4 LP3 4.26829
57 2JLD AG1 4.28571
58 2JLD ALA GLY GLY ALA ALA ALA ALA ALA 4.28571
59 4ZTD ALA GLY ALA GLY ALA 4.34783
60 2CJ9 SSA 4.42105
61 3DU4 KAP 4.46429
62 2P1E LAC 4.50161
63 4R57 ACO 4.54545
64 3UH0 TSB 4.78261
65 1E1O LYS 4.84211
66 1VA6 ADP 4.84211
67 1VA6 P2S 4.84211
68 5DK4 5BX 4.86322
69 5DK4 ATP 4.86322
70 5YJS SAL 4.87179
71 5H4S RAM 4.92958
72 1SES AHX 4.98812
73 1SES AMP 4.98812
74 1LSH PLD 5.01567
75 3BJU ATP 5.05263
76 5F7U GLC GLC 5.05263
77 3JU6 ANP 5.13514
78 3LL5 ADP 5.22088
79 3LL5 IPE 5.22088
80 3LL5 IP8 5.22088
81 4LEB THR THR THR THR THR THR THR 5.33333
82 3E7S AT2 5.33643
83 5LXT GTP 5.39326
84 3A5Z KAA 5.4878
85 3MEH THP 5.59441
86 1USF NAP 5.61798
87 2QHV OC9 5.71429
88 4CS4 ANP 5.83942
89 4CS4 AXZ 5.83942
90 2Y91 98J 6.03774
91 4RF7 ARG 6.31579
92 1QKQ MAN 6.33803
93 3MF2 AMP 6.35838
94 2G36 TRP 6.47059
95 1WLE SRP 6.58683
96 5ML3 DL3 6.71141
97 3BIB PSF 6.89655
98 3IWD M2T 7.35294
99 5CIC 51R 7.48299
100 3SAO DBH 7.5
101 2I4O ATP 7.78947
102 2G30 ALA ALA PHE 8.13953
103 4V1F BQ1 8.13953
104 4HWT 1B2 8.23245
105 4WOE ADP 8.42105
106 2RBK VN4 8.81226
107 5WL1 D3D 9.09091
108 5WL1 CUY 9.09091
109 2QHS OCA 9.2827
110 5DYO FLU 9.63303
111 3CM2 X23 10
112 3A5Y KAA 10.1449
113 1F9V ADP 10.3746
114 4Z2S NDG 10.5634
115 4Z2S NAG 10.5634
116 3KP6 SAL 10.596
117 3JQ3 ADP 10.929
118 4YRI 4JH 10.9649
119 6GNO XDI 11.1111
120 1B7Y FYA 11.4286
121 3H0L ADP 11.7021
122 4QB6 GCU XYP 12.1951
123 4OIT MAN 13.2743
124 3REU ATP 16.3265
125 4TW7 37K 18.75
126 2BVE PH5 20.1681
127 3UEC ALA ARG TPO LYS 21.2329
128 4H2V AMP 26.3636
129 3QX9 ATP 26.8116
130 4H2X G5A 28.1553
131 4H2W AMP 28.1553
132 4H2W 5GP 28.1553
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