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 (2D)
Ligand no: 1; Ligand: 4AD; Similar ligands found: 354
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 PAJ 0.736264 0.8875
7 AMO 0.736264 0.986486
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 QA7 0.695652 0.897436
16 LAD 0.694737 0.911392
17 AP5 0.694118 0.92
18 B4P 0.694118 0.92
19 8LE 0.688889 0.897436
20 ME8 0.6875 0.888889
21 PRX 0.681818 0.848101
22 ADP 0.674419 0.92
23 50T 0.670455 0.883117
24 ACP 0.670455 0.921053
25 HEJ 0.670455 0.92
26 ATP 0.670455 0.92
27 AT4 0.666667 0.884615
28 AN2 0.666667 0.907895
29 FA5 0.666667 0.96
30 AR6 0.662921 0.945946
31 5FA 0.662921 0.92
32 APR 0.662921 0.945946
33 AQP 0.662921 0.92
34 AMP 0.662651 0.893333
35 A 0.662651 0.893333
36 ADX 0.659091 0.831325
37 M33 0.659091 0.907895
38 DLL 0.65625 0.933333
39 AGS 0.655556 0.873418
40 AD9 0.655556 0.896104
41 YLP 0.653846 0.86747
42 OOB 0.652632 0.933333
43 YLB 0.650943 0.86747
44 AP2 0.643678 0.909091
45 A12 0.643678 0.909091
46 WAQ 0.642857 0.910256
47 PR8 0.642857 0.9
48 DAL AMP 0.642105 0.933333
49 ACQ 0.641304 0.921053
50 ABM 0.639535 0.87013
51 45A 0.639535 0.87013
52 00A 0.639175 0.886076
53 1ZZ 0.636364 0.843373
54 TXA 0.636364 0.934211
55 AMP MG 0.635294 0.905405
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 JNT 0.622449 0.921053
62 6YZ 0.621053 0.921053
63 YLC 0.62037 0.888889
64 5SV 0.618557 0.807229
65 SRA 0.616279 0.848101
66 OAD 0.616162 0.946667
67 HQG 0.614583 0.933333
68 AYB 0.612613 0.857143
69 A1R 0.612245 0.910256
70 TYM 0.611111 0.96
71 ATF 0.610526 0.884615
72 ARG AMP 0.609524 0.878049
73 APC 0.608696 0.909091
74 A22 0.608247 0.907895
75 9SN 0.607843 0.875
76 AU1 0.604396 0.896104
77 3OD 0.60396 0.946667
78 YLA 0.603604 0.86747
79 RBY 0.602151 0.934211
80 ADV 0.602151 0.934211
81 9ZA 0.602041 0.886076
82 9ZD 0.602041 0.886076
83 B5Y 0.601942 0.897436
84 B5M 0.601942 0.897436
85 9X8 0.6 0.897436
86 V2G 0.6 0.898734
87 A3R 0.59596 0.910256
88 ADQ 0.59596 0.921053
89 NSS 0.59596 0.847059
90 4UU 0.59434 0.897436
91 SON 0.593407 0.934211
92 ADP BEF 0.593407 0.918919
93 ADP MG 0.593407 0.918919
94 4UV 0.590476 0.897436
95 TAT 0.589474 0.884615
96 T99 0.589474 0.884615
97 NAI 0.587156 0.886076
98 25A 0.585859 0.894737
99 OZV 0.585859 0.92
100 APC MG 0.585106 0.894737
101 XAH 0.580952 0.865854
102 N0B 0.575 0.86747
103 FYA 0.572816 0.907895
104 4UW 0.572727 0.864198
105 G3A 0.570093 0.875
106 LAQ 0.568807 0.843373
107 ADP PO3 0.568421 0.918919
108 ATP MG 0.568421 0.918919
109 TXE 0.567568 0.886076
110 25L 0.567308 0.907895
111 G5P 0.564815 0.875
112 48N 0.563636 0.923077
113 YLY 0.563025 0.857143
114 AP0 0.5625 0.851852
115 BEF ADP 0.5625 0.894737
116 ANP MG 0.561224 0.907895
117 DQV 0.559633 0.933333
118 NAX 0.558559 0.9
119 TXD 0.558559 0.886076
120 BIS 0.557692 0.8625
121 KMQ 0.556604 0.909091
122 OMR 0.553571 0.855422
123 IOT 0.552632 0.857143
124 MYR AMP 0.552381 0.843373
125 LMS 0.550562 0.788235
126 GA7 0.550459 0.884615
127 AFH 0.550459 0.8875
128 L3W 0.548673 0.909091
129 VO4 ADP 0.545455 0.896104
130 ALF ADP 0.545455 0.85
131 DND 0.544643 0.96
132 UP5 0.544643 0.897436
133 6V0 0.544643 0.875
134 MAP 0.544554 0.873418
135 JB6 0.542857 0.8625
136 LEU LMS 0.538462 0.795455
137 80F 0.537815 0.890244
138 M24 0.53719 0.853659
139 7MD 0.536364 0.9125
140 5AS 0.531915 0.744444
141 GTA 0.531532 0.865854
142 TAD 0.531532 0.8875
143 G5A 0.530612 0.804598
144 NVA LMS 0.528846 0.797753
145 F2R 0.525424 0.890244
146 4TC 0.521739 0.898734
147 AOC 0.521739 0.779221
148 COD 0.521008 0.837209
149 D4F 0.520325 0.865854
150 RAB 0.518072 0.8
151 ADN 0.518072 0.8
152 XYA 0.518072 0.8
153 5CD 0.517647 0.763158
154 CNA 0.516949 0.96
155 BT5 0.516667 0.857143
156 A5A 0.514852 0.790698
157 TSB 0.514563 0.802326
158 SSA 0.509804 0.825581
159 GEK 0.509615 0.810127
160 ADP BMA 0.509434 0.921053
161 UPA 0.508621 0.886076
162 T5A 0.508475 0.86747
163 ADJ 0.508475 0.855422
164 139 0.508475 0.876543
165 5N5 0.505882 0.776316
166 54H 0.504854 0.772727
167 VMS 0.504854 0.772727
168 52H 0.504854 0.764045
169 DSZ 0.504762 0.847059
170 AMP DBH 0.504505 0.896104
171 A4P 0.504274 0.825581
172 EAD 0.503937 0.876543
173 8X1 0.5 0.777778
174 53H 0.5 0.764045
175 ATP A 0.5 0.906667
176 ALF ADP 3PG 0.5 0.8875
177 A4D 0.5 0.776316
178 ATP A A A 0.5 0.906667
179 AF3 ADP 3PG 0.5 0.8875
180 5CA 0.5 0.825581
181 NAD 0.495868 0.933333
182 7MC 0.495726 0.890244
183 LPA AMP 0.495652 0.843373
184 2A5 0.494949 0.871795
185 6RE 0.494624 0.765432
186 3DH 0.494505 0.734177
187 DTA 0.494382 0.746835
188 M2T 0.494382 0.719512
189 NAQ 0.492063 0.875
190 P5A 0.490741 0.769231
191 LSS 0.490566 0.786517
192 A2R 0.490385 0.933333
193 ATR 0.49 0.893333
194 PAP 0.49 0.906667
195 ITT 0.489796 0.868421
196 7D4 0.489796 0.835443
197 A3P 0.489583 0.893333
198 P1H 0.48855 0.855422
199 A3D 0.487805 0.921053
200 AHZ 0.486957 0.843373
201 9K8 0.486239 0.72043
202 5X8 0.484848 0.815789
203 H1Q 0.484848 0.881579
204 J7C 0.484211 0.753086
205 NAJ PZO 0.483871 0.851852
206 BTX 0.483607 0.845238
207 7D5 0.483516 0.810127
208 EP4 0.483146 0.716049
209 AR6 AR6 0.482456 0.92
210 S7M 0.480769 0.759036
211 SMM 0.480769 0.752941
212 DZD 0.479675 0.8875
213 6MZ 0.479167 0.857143
214 7D3 0.479167 0.835443
215 KAA 0.477064 0.777778
216 GSU 0.477064 0.825581
217 ZID 0.476562 0.921053
218 PPS 0.475728 0.809524
219 A2P 0.474227 0.88
220 NEC 0.473684 0.730769
221 8PZ 0.473214 0.825581
222 3AM 0.473118 0.855263
223 MTA 0.472527 0.734177
224 NAE 0.472441 0.897436
225 ARU 0.472222 0.797619
226 0WD 0.471545 0.875
227 AMP NAD 0.471545 0.933333
228 2SA 0.471154 0.96
229 HFD 0.470588 0.873418
230 NAD IBO 0.470588 0.92
231 NAD TDB 0.470588 0.92
232 JSQ 0.470588 0.873418
233 SFG 0.47 0.802632
234 YSA 0.469027 0.804598
235 A3N 0.46875 0.746835
236 NAJ PYZ 0.46875 0.811765
237 SAM 0.466019 0.759036
238 V3L 0.466019 0.92
239 NWW 0.465909 0.743243
240 GJV 0.463918 0.756098
241 S4M 0.463918 0.693182
242 NO7 0.462264 0.860759
243 6AD 0.461538 0.841463
244 EEM 0.461538 0.759036
245 SA8 0.460784 0.756098
246 FB0 0.459259 0.808989
247 NDP 0.459016 0.875
248 DSH 0.458333 0.731707
249 O02 0.456311 0.875
250 SAI 0.456311 0.78481
251 SAH 0.456311 0.794872
252 NDE 0.455224 0.909091
253 NA7 0.454545 0.909091
254 38V 0.453846 0.865854
255 IMO 0.453608 0.855263
256 ZAS 0.452632 0.772152
257 6IA 0.451923 0.819277
258 DTP 0.451923 0.883117
259 3AT 0.451923 0.92
260 J4G 0.45045 0.947368
261 6FA 0.449275 0.845238
262 2AM 0.446809 0.868421
263 NVA 2AD 0.446602 0.810127
264 MAO 0.444444 0.764706
265 NZQ 0.443548 0.8875
266 B1U 0.443478 0.741935
267 A3G 0.443299 0.828947
268 DAT 0.441176 0.883117
269 CUU 0.441176 0.92
270 FNK 0.440559 0.808989
271 AVV 0.440367 0.875
272 NJP 0.44 0.922078
273 ODP 0.44 0.8875
274 V47 0.439252 0.789474
275 WSA 0.438017 0.813953
276 NDC 0.437956 0.875
277 7DT 0.436893 0.906667
278 0UM 0.436364 0.746988
279 7C5 0.435897 0.8
280 A3S 0.435644 0.84
281 7DD 0.435644 0.906667
282 A7D 0.435644 0.759494
283 NPW 0.435484 0.888889
284 8Q2 0.434426 0.797753
285 KOY 0.433333 0.807692
286 OVE 0.43299 0.835443
287 A5D 0.432692 0.746835
288 FAS 0.432624 0.855422
289 FAD 0.432624 0.855422
290 TXP 0.432 0.875
291 FDA 0.431655 0.816092
292 GGZ 0.431193 0.785714
293 LQJ 0.431034 0.87013
294 AV2 0.429907 0.846154
295 6C6 0.428571 0.860759
296 QXG 0.428571 0.741573
297 4YB 0.428571 0.806818
298 K15 0.428571 0.729412
299 QXP 0.427273 0.75
300 A3T 0.427184 0.802632
301 5AD 0.425287 0.706667
302 4TA 0.425197 0.855422
303 DCA 0.423077 0.827586
304 SFD 0.422535 0.739583
305 K3K 0.422414 0.7625
306 Y3J 0.422222 0.688312
307 SXZ 0.421053 0.759036
308 C2R 0.421053 0.881579
309 AMZ 0.421053 0.868421
310 AAT 0.420561 0.714286
311 62X 0.419643 0.712644
312 1DG 0.41791 0.875
313 DG1 0.41791 0.875
314 FAY 0.417808 0.865854
315 PGS 0.417476 0.839506
316 MHZ 0.417476 0.704545
317 0T1 0.416667 0.827586
318 NWQ 0.416667 0.723684
319 PO4 PO4 A A A A PO4 0.415929 0.88
320 71V 0.415842 0.839506
321 K3E 0.415254 0.753086
322 RFL 0.414966 0.825581
323 649 0.414634 0.769231
324 6K6 0.414414 0.857143
325 DA 0.414141 0.857143
326 N5O 0.414141 0.792208
327 D5M 0.414141 0.857143
328 NMN AMP PO4 0.414062 0.873418
329 R2V 0.412281 0.75
330 ETB 0.412214 0.837209
331 62F 0.410959 0.843373
332 O05 0.408696 0.847059
333 P5F 0.407895 0.848837
334 Z5A 0.407407 0.804598
335 AMX 0.407407 0.837209
336 COA 0.406015 0.827586
337 N5A 0.405941 0.766234
338 KY2 0.405405 0.717647
339 KB1 0.405172 0.746988
340 KXW 0.404959 0.756098
341 7D7 0.404494 0.705128
342 9JJ 0.403974 0.865854
343 FAJ 0.403846 0.857143
344 A6D 0.403509 0.709302
345 V1N 0.403361 0.894737
346 XNP 0.403101 0.853659
347 F2N 0.402597 0.818182
348 VRT 0.401869 0.797468
349 GP3 0.401869 0.875
350 SO8 0.401869 0.772152
351 K2K 0.4 0.743902
352 3NZ 0.4 0.810127
353 2VA 0.4 0.782051
354 FA9 0.4 0.86747
Similar Ligands (3D)
Ligand no: 1; Ligand: 4AD; Similar ligands found: 2
No: Ligand Similarity coefficient
1 RSN 0.8955
2 GNP 0.8639
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 9TU 7.29927
2 6AAD ATP 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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