Receptor
PDB id Resolution Class Description Source Keywords
1X54 1.45 Å EC: 6.1.1.22 CRYSTAL STRUCTURE OF ASPARAGINYL-TRNA SYNTHETASE FROM PYROCO HORIKOSHII COMPLEXED WITH ASPARAGINYL-ADENYLATE PYROCOCCUS HORIKOSHII AMINOACYL-TRNA SYNTHETASE RIKEN STRUCTURAL GENOMICS/PROTEOMINITIATIVE RSGI STRUCTURAL GENOMICS LIGASE
Ref.: STRUCTURAL BASIS OF THE WATER-ASSISTED ASPARAGINE RECOGNITION BY ASPARAGINYL-TRNA SYNTHETASE. J.MOL.BIOL. V. 360 329 2006
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
4AD A:2001;
 Valid;
 none;
 submit data
462.332 C14 H21 N7 O9 P c1nc(...
MG A:2000;
 Part of Protein;
 none;
 submit data
24.305 Mg [Mg+2...
MPD A:2002;
 Invalid;
 none;
 submit data
118.174 C6 H14 O2 C[C@@...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1X54 1.45 Å EC: 6.1.1.22 CRYSTAL STRUCTURE OF ASPARAGINYL-TRNA SYNTHETASE FROM PYROCO HORIKOSHII COMPLEXED WITH ASPARAGINYL-ADENYLATE PYROCOCCUS HORIKOSHII AMINOACYL-TRNA SYNTHETASE RIKEN STRUCTURAL GENOMICS/PROTEOMINITIATIVE RSGI STRUCTURAL GENOMICS LIGASE
Ref.: STRUCTURAL BASIS OF THE WATER-ASSISTED ASPARAGINE RECOGNITION BY ASPARAGINYL-TRNA SYNTHETASE. J.MOL.BIOL. V. 360 329 2006
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 1X54 - 4AD C14 H21 N7 O9 P c1nc(c2c(n....
2 1X55 - NSS C14 H21 N8 O8 S c1nc(c2c(n....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 1X54 - 4AD C14 H21 N7 O9 P c1nc(c2c(n....
2 1X55 - NSS C14 H21 N8 O8 S c1nc(c2c(n....
50% Homology Family (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 2XTI - NB8 C14 H20 N7 O10 P c1nc(c2c(n....
2 2XGT - NSS C14 H21 N8 O8 S c1nc(c2c(n....
3 1B8A - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
4 3NEL - ASP C4 H7 N O4 C([C@@H](C....
5 3NEM - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
6 1X54 - 4AD C14 H21 N7 O9 P c1nc(c2c(n....
7 1X55 - NSS C14 H21 N8 O8 S c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 4AD; Similar ligands found: 338
No: Ligand ECFP6 Tc MDL keys Tc
1 4AD 1 1
2 5AL 0.767442 0.933333
3 SRP 0.75 0.96
4 8LH 0.75 0.909091
5 CA0 0.738095 0.946667
6 AMO 0.736264 0.986486
7 PAJ 0.736264 0.8875
8 KG4 0.729412 0.946667
9 8QN 0.725275 0.933333
10 A2D 0.719512 0.92
11 8LQ 0.714286 0.934211
12 PTJ 0.705263 0.875
13 NB8 0.705263 0.948052
14 BA3 0.702381 0.92
15 LAD 0.694737 0.911392
16 B4P 0.694118 0.92
17 AP5 0.694118 0.92
18 8LE 0.688889 0.897436
19 ME8 0.6875 0.888889
20 PRX 0.681818 0.848101
21 ADP 0.674419 0.92
22 HEJ 0.670455 0.92
23 ACP 0.670455 0.921053
24 50T 0.670455 0.883117
25 ATP 0.670455 0.92
26 AN2 0.666667 0.907895
27 FA5 0.666667 0.96
28 AT4 0.666667 0.884615
29 YAP 0.666667 0.947368
30 APR 0.662921 0.945946
31 AQP 0.662921 0.92
32 5FA 0.662921 0.92
33 AR6 0.662921 0.945946
34 A 0.662651 0.893333
35 AMP 0.662651 0.893333
36 M33 0.659091 0.907895
37 ADX 0.659091 0.831325
38 DLL 0.65625 0.933333
39 AD9 0.655556 0.896104
40 AGS 0.655556 0.873418
41 SAP 0.655556 0.873418
42 YLP 0.653846 0.86747
43 OOB 0.652632 0.933333
44 YLB 0.650943 0.86747
45 A12 0.643678 0.909091
46 AP2 0.643678 0.909091
47 PR8 0.642857 0.9
48 WAQ 0.642857 0.910256
49 DAL AMP 0.642105 0.933333
50 ACQ 0.641304 0.921053
51 45A 0.639535 0.87013
52 ABM 0.639535 0.87013
53 00A 0.639175 0.886076
54 1ZZ 0.636364 0.843373
55 TXA 0.636364 0.934211
56 3UK 0.632653 0.921053
57 B5V 0.626263 0.909091
58 GAP 0.623656 0.921053
59 ANP 0.623656 0.896104
60 AHX 0.622449 0.923077
61 6YZ 0.621053 0.921053
62 YLC 0.62037 0.888889
63 5SV 0.618557 0.807229
64 SRA 0.616279 0.848101
65 OAD 0.616162 0.946667
66 HQG 0.614583 0.933333
67 AYB 0.612613 0.857143
68 A1R 0.612245 0.910256
69 TYM 0.611111 0.96
70 ATF 0.610526 0.884615
71 ARG AMP 0.609524 0.878049
72 APC 0.608696 0.909091
73 A22 0.608247 0.907895
74 9SN 0.607843 0.875
75 TYR AMP 0.605769 0.947368
76 AU1 0.604396 0.896104
77 3OD 0.60396 0.946667
78 YLA 0.603604 0.86747
79 ADV 0.602151 0.934211
80 RBY 0.602151 0.934211
81 9ZD 0.602041 0.886076
82 9ZA 0.602041 0.886076
83 B5Y 0.601942 0.897436
84 B5M 0.601942 0.897436
85 9X8 0.6 0.897436
86 ADQ 0.59596 0.921053
87 A3R 0.59596 0.910256
88 NSS 0.59596 0.847059
89 4UU 0.59434 0.897436
90 SON 0.593407 0.934211
91 ADP MG 0.593407 0.918919
92 4UV 0.590476 0.897436
93 TAT 0.589474 0.884615
94 T99 0.589474 0.884615
95 NAI 0.587156 0.886076
96 OZV 0.585859 0.92
97 25A 0.585859 0.894737
98 APC MG 0.585106 0.894737
99 XAH 0.580952 0.865854
100 N0B 0.575 0.86747
101 FYA 0.572816 0.907895
102 4UW 0.572727 0.864198
103 G3A 0.570093 0.875
104 LAQ 0.568807 0.843373
105 ATP MG 0.568421 0.918919
106 ADP PO3 0.568421 0.918919
107 TXE 0.567568 0.886076
108 25L 0.567308 0.907895
109 G5P 0.564815 0.875
110 48N 0.563636 0.923077
111 YLY 0.563025 0.857143
112 AP0 0.5625 0.851852
113 DQV 0.559633 0.933333
114 TXD 0.558559 0.886076
115 NAX 0.558559 0.9
116 BIS 0.557692 0.8625
117 VO4 ADP 0.555556 0.907895
118 ADP VO4 0.555556 0.907895
119 OMR 0.553571 0.855422
120 IOT 0.552632 0.857143
121 MYR AMP 0.552381 0.843373
122 LMS 0.550562 0.788235
123 GA7 0.550459 0.884615
124 AFH 0.550459 0.8875
125 ALF ADP 0.545455 0.85
126 ADP ALF 0.545455 0.85
127 NXX 0.544643 0.96
128 DND 0.544643 0.96
129 6V0 0.544643 0.875
130 UP5 0.544643 0.897436
131 MAP 0.544554 0.873418
132 JB6 0.542857 0.8625
133 80F 0.537815 0.890244
134 M24 0.53719 0.853659
135 7MD 0.536364 0.9125
136 5AS 0.531915 0.744444
137 GTA 0.531532 0.865854
138 TAD 0.531532 0.8875
139 G5A 0.530612 0.804598
140 NVA LMS 0.528846 0.797753
141 F2R 0.525424 0.890244
142 LEU LMS 0.52381 0.797753
143 AOC 0.521739 0.779221
144 4TC 0.521739 0.898734
145 COD 0.521008 0.837209
146 A A 0.518868 0.894737
147 ADN 0.518072 0.8
148 XYA 0.518072 0.8
149 RAB 0.518072 0.8
150 5CD 0.517647 0.763158
151 CNA 0.516949 0.96
152 BT5 0.516667 0.857143
153 A5A 0.514852 0.790698
154 TSB 0.514563 0.802326
155 SSA 0.509804 0.825581
156 GEK 0.509615 0.810127
157 ADP BMA 0.509434 0.921053
158 UPA 0.508621 0.886076
159 T5A 0.508475 0.86747
160 ADJ 0.508475 0.855422
161 139 0.508475 0.876543
162 5N5 0.505882 0.776316
163 54H 0.504854 0.772727
164 VMS 0.504854 0.772727
165 52H 0.504854 0.764045
166 DSZ 0.504762 0.847059
167 AMP DBH 0.504505 0.896104
168 A4P 0.504274 0.825581
169 EAD 0.503937 0.876543
170 AF3 ADP 3PG 0.5 0.8875
171 ATP A 0.5 0.906667
172 A4D 0.5 0.776316
173 5CA 0.5 0.825581
174 53H 0.5 0.764045
175 8X1 0.5 0.777778
176 ATP A A A 0.5 0.906667
177 NAD 0.495868 0.933333
178 7MC 0.495726 0.890244
179 LPA AMP 0.495652 0.843373
180 2A5 0.494949 0.871795
181 6RE 0.494624 0.765432
182 3DH 0.494505 0.734177
183 DTA 0.494382 0.746835
184 M2T 0.494382 0.719512
185 NAQ 0.492063 0.875
186 P5A 0.490741 0.769231
187 LSS 0.490566 0.786517
188 A2R 0.490385 0.933333
189 PAP 0.49 0.906667
190 ATR 0.49 0.893333
191 7D4 0.489796 0.835443
192 ITT 0.489796 0.868421
193 A3P 0.489583 0.893333
194 P1H 0.48855 0.855422
195 A3D 0.487805 0.921053
196 AHZ 0.486957 0.843373
197 9K8 0.486239 0.72043
198 H1Q 0.484848 0.881579
199 5X8 0.484848 0.815789
200 J7C 0.484211 0.753086
201 NAJ PZO 0.483871 0.851852
202 BTX 0.483607 0.845238
203 7D5 0.483516 0.810127
204 EP4 0.483146 0.716049
205 AR6 AR6 0.482456 0.92
206 S7M 0.480769 0.759036
207 SMM 0.480769 0.752941
208 DZD 0.479675 0.8875
209 7D3 0.479167 0.835443
210 6MZ 0.479167 0.857143
211 KAA 0.477064 0.777778
212 GSU 0.477064 0.825581
213 ZID 0.476562 0.921053
214 PPS 0.475728 0.809524
215 A2P 0.474227 0.88
216 NEC 0.473684 0.730769
217 8PZ 0.473214 0.825581
218 3AM 0.473118 0.855263
219 MTA 0.472527 0.734177
220 NAE 0.472441 0.897436
221 ARU 0.472222 0.797619
222 AMP NAD 0.471545 0.933333
223 0WD 0.471545 0.875
224 2SA 0.471154 0.96
225 JSQ 0.470588 0.873418
226 HFD 0.470588 0.873418
227 SFG 0.47 0.802632
228 YSA 0.469027 0.804598
229 A3N 0.46875 0.746835
230 NAJ PYZ 0.46875 0.811765
231 V3L 0.466019 0.92
232 SAM 0.466019 0.759036
233 S4M 0.463918 0.693182
234 GJV 0.463918 0.756098
235 NO7 0.462264 0.860759
236 6AD 0.461538 0.841463
237 EEM 0.461538 0.759036
238 SA8 0.460784 0.756098
239 G A A A 0.459677 0.851852
240 FB0 0.459259 0.808989
241 NDP 0.459016 0.875
242 DSH 0.458333 0.731707
243 SAH 0.456311 0.794872
244 SAI 0.456311 0.78481
245 NDE 0.455224 0.909091
246 NA7 0.454545 0.909091
247 IMO 0.453608 0.855263
248 ZAS 0.452632 0.772152
249 DTP 0.451923 0.883117
250 6IA 0.451923 0.819277
251 3AT 0.451923 0.92
252 J4G 0.45045 0.947368
253 6FA 0.449275 0.845238
254 A G 0.448 0.8625
255 2AM 0.446809 0.868421
256 NVA 2AD 0.446602 0.810127
257 U A G G 0.444444 0.8625
258 MAO 0.444444 0.764706
259 NZQ 0.443548 0.8875
260 B1U 0.443478 0.741935
261 A3G 0.443299 0.828947
262 DAT 0.441176 0.883117
263 FNK 0.440559 0.808989
264 AVV 0.440367 0.875
265 NJP 0.44 0.922078
266 ODP 0.44 0.8875
267 WSA 0.438017 0.813953
268 NDC 0.437956 0.875
269 U A 0.4375 0.886076
270 7DT 0.436893 0.906667
271 0UM 0.436364 0.746988
272 7C5 0.435897 0.8
273 A3S 0.435644 0.84
274 7DD 0.435644 0.906667
275 A7D 0.435644 0.759494
276 NPW 0.435484 0.888889
277 8Q2 0.434426 0.797753
278 KOY 0.433333 0.807692
279 OVE 0.43299 0.835443
280 A5D 0.432692 0.746835
281 FAD 0.432624 0.855422
282 FAS 0.432624 0.855422
283 TXP 0.432 0.875
284 FDA 0.431655 0.816092
285 GGZ 0.431193 0.785714
286 LQJ 0.431034 0.87013
287 AV2 0.429907 0.846154
288 4YB 0.428571 0.806818
289 K15 0.428571 0.729412
290 6C6 0.428571 0.860759
291 A3T 0.427184 0.802632
292 5AD 0.425287 0.706667
293 4TA 0.425197 0.855422
294 DCA 0.423077 0.827586
295 SFD 0.422535 0.739583
296 Y3J 0.422222 0.688312
297 SXZ 0.421053 0.759036
298 C2R 0.421053 0.881579
299 AMZ 0.421053 0.868421
300 AAT 0.420561 0.714286
301 62X 0.419643 0.712644
302 A U 0.419355 0.873418
303 DG1 0.41791 0.875
304 1DG 0.41791 0.875
305 FAY 0.417808 0.865854
306 PGS 0.417476 0.839506
307 MHZ 0.417476 0.704545
308 0T1 0.416667 0.827586
309 A A A 0.415929 0.907895
310 PO4 PO4 A A A A PO4 0.415929 0.88
311 71V 0.415842 0.839506
312 RFL 0.414966 0.825581
313 649 0.414634 0.769231
314 6K6 0.414414 0.857143
315 N5O 0.414141 0.792208
316 D5M 0.414141 0.857143
317 DA 0.414141 0.857143
318 NMN AMP PO4 0.414062 0.873418
319 ETB 0.412214 0.837209
320 62F 0.410959 0.843373
321 P5F 0.407895 0.848837
322 AMX 0.407407 0.837209
323 Z5A 0.407407 0.804598
324 COA 0.406015 0.827586
325 N5A 0.405941 0.766234
326 KB1 0.405172 0.746988
327 7D7 0.404494 0.705128
328 9JJ 0.403974 0.865854
329 A6D 0.403509 0.709302
330 V1N 0.403361 0.894737
331 XNP 0.403101 0.853659
332 F2N 0.402597 0.818182
333 SO8 0.401869 0.772152
334 GP3 0.401869 0.875
335 VRT 0.401869 0.797468
336 2VA 0.4 0.782051
337 3NZ 0.4 0.810127
338 FA9 0.4 0.86747
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1X54; Ligand: 4AD; Similar sites found with APoc: 4
This union binding pocket(no: 1) in the query (biounit: 1x54.bio1) has 26 residues
No: Leader PDB Ligand Sequence Similarity
1 6AAD ATP 7.29927
2 6AAD 9TU 7.29927
3 3G1Z AMP 36.8098
4 3G1Z AMP 36.8098
Pocket No.: 2; Query (leader) PDB : 1X54; Ligand: 4AD; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 1x54.bio1) has 26 residues
No: Leader PDB Ligand Sequence Similarity
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