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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: 317
No: Ligand ECFP6 Tc MDL keys Tc
1 4AD 1 1
2 5AL 0.767442 0.933333
3 SRP 0.75 0.96
4 CA0 0.738095 0.946667
5 AMO 0.736264 0.986486
6 PAJ 0.736264 0.8875
7 8QN 0.725275 0.933333
8 A2D 0.719512 0.92
9 PTJ 0.705263 0.875
10 NB8 0.705263 0.948052
11 BA3 0.702381 0.92
12 LAD 0.694737 0.911392
13 AP5 0.694118 0.92
14 B4P 0.694118 0.92
15 ME8 0.6875 0.888889
16 PRX 0.681818 0.848101
17 ADP 0.674419 0.92
18 ATP 0.670455 0.92
19 HEJ 0.670455 0.92
20 50T 0.670455 0.883117
21 ACP 0.670455 0.921053
22 AN2 0.666667 0.907895
23 FA5 0.666667 0.96
24 YAP 0.666667 0.947368
25 AT4 0.666667 0.884615
26 APR 0.662921 0.945946
27 AR6 0.662921 0.945946
28 AQP 0.662921 0.92
29 5FA 0.662921 0.92
30 A 0.662651 0.893333
31 AMP 0.662651 0.893333
32 M33 0.659091 0.907895
33 ADX 0.659091 0.831325
34 DLL 0.65625 0.933333
35 AD9 0.655556 0.896104
36 SAP 0.655556 0.873418
37 AGS 0.655556 0.873418
38 YLP 0.653846 0.86747
39 OOB 0.652632 0.933333
40 YLB 0.650943 0.86747
41 AP2 0.643678 0.909091
42 A12 0.643678 0.909091
43 WAQ 0.642857 0.910256
44 PR8 0.642857 0.9
45 DAL AMP 0.642105 0.933333
46 ACQ 0.641304 0.921053
47 ABM 0.639535 0.87013
48 00A 0.639175 0.886076
49 TXA 0.636364 0.934211
50 1ZZ 0.636364 0.843373
51 3UK 0.632653 0.921053
52 B5V 0.626263 0.909091
53 GAP 0.623656 0.921053
54 ANP 0.623656 0.896104
55 AHX 0.622449 0.923077
56 6YZ 0.621053 0.921053
57 YLC 0.62037 0.888889
58 5SV 0.618557 0.807229
59 SRA 0.616279 0.848101
60 OAD 0.616162 0.946667
61 AYB 0.612613 0.857143
62 A1R 0.612245 0.910256
63 TYM 0.611111 0.96
64 ATF 0.610526 0.884615
65 ARG AMP 0.609524 0.878049
66 APC 0.608696 0.909091
67 A22 0.608247 0.907895
68 9SN 0.607843 0.875
69 TYR AMP 0.605769 0.947368
70 AU1 0.604396 0.896104
71 3OD 0.60396 0.946667
72 YLA 0.603604 0.86747
73 ADV 0.602151 0.934211
74 RBY 0.602151 0.934211
75 9ZA 0.602041 0.886076
76 9ZD 0.602041 0.886076
77 B5M 0.601942 0.897436
78 B5Y 0.601942 0.897436
79 9X8 0.6 0.897436
80 A3R 0.59596 0.910256
81 ADQ 0.59596 0.921053
82 NSS 0.59596 0.847059
83 4UU 0.59434 0.897436
84 SON 0.593407 0.934211
85 4UV 0.590476 0.897436
86 T99 0.589474 0.884615
87 TAT 0.589474 0.884615
88 NAI 0.587156 0.886076
89 25A 0.585859 0.894737
90 XAH 0.580952 0.865854
91 N0B 0.575 0.86747
92 FYA 0.572816 0.907895
93 4UW 0.572727 0.864198
94 G3A 0.570093 0.875
95 LAQ 0.568807 0.843373
96 ADP PO3 0.568421 0.918919
97 TXE 0.567568 0.886076
98 25L 0.567308 0.907895
99 G5P 0.564815 0.875
100 48N 0.563636 0.923077
101 YLY 0.563025 0.857143
102 AP0 0.5625 0.851852
103 DQV 0.559633 0.933333
104 NAX 0.558559 0.9
105 TXD 0.558559 0.886076
106 BIS 0.557692 0.8625
107 VO4 ADP 0.555556 0.907895
108 ADP VO4 0.555556 0.907895
109 OMR 0.553571 0.855422
110 IOT 0.552632 0.857143
111 MYR AMP 0.552381 0.843373
112 LMS 0.550562 0.788235
113 GA7 0.550459 0.884615
114 AFH 0.550459 0.8875
115 ALF ADP 0.545455 0.85
116 ADP ALF 0.545455 0.85
117 UP5 0.544643 0.897436
118 NXX 0.544643 0.96
119 DND 0.544643 0.96
120 6V0 0.544643 0.875
121 MAP 0.544554 0.873418
122 JB6 0.542857 0.8625
123 80F 0.537815 0.890244
124 M24 0.53719 0.853659
125 7MD 0.536364 0.9125
126 5AS 0.531915 0.744444
127 TAD 0.531532 0.8875
128 GTA 0.531532 0.865854
129 G5A 0.530612 0.804598
130 NVA LMS 0.528846 0.797753
131 F2R 0.525424 0.890244
132 LEU LMS 0.52381 0.797753
133 4TC 0.521739 0.898734
134 AOC 0.521739 0.779221
135 COD 0.521008 0.837209
136 A A 0.518868 0.894737
137 XYA 0.518072 0.8
138 ADN 0.518072 0.8
139 RAB 0.518072 0.8
140 5CD 0.517647 0.763158
141 CNA 0.516949 0.96
142 BT5 0.516667 0.857143
143 A5A 0.514852 0.790698
144 TSB 0.514563 0.802326
145 SSA 0.509804 0.825581
146 GEK 0.509615 0.810127
147 ADP BMA 0.509434 0.921053
148 UPA 0.508621 0.886076
149 T5A 0.508475 0.86747
150 139 0.508475 0.876543
151 ADJ 0.508475 0.855422
152 5N5 0.505882 0.776316
153 52H 0.504854 0.764045
154 VMS 0.504854 0.772727
155 54H 0.504854 0.772727
156 DSZ 0.504762 0.847059
157 AMP DBH 0.504505 0.896104
158 A4P 0.504274 0.825581
159 EAD 0.503937 0.876543
160 5CA 0.5 0.825581
161 AF3 ADP 3PG 0.5 0.8875
162 ATP A A A 0.5 0.906667
163 A4D 0.5 0.776316
164 8X1 0.5 0.777778
165 53H 0.5 0.764045
166 NAD 0.495868 0.933333
167 7MC 0.495726 0.890244
168 LPA AMP 0.495652 0.843373
169 2A5 0.494949 0.871795
170 6RE 0.494624 0.765432
171 3DH 0.494505 0.734177
172 M2T 0.494382 0.719512
173 DTA 0.494382 0.746835
174 NAQ 0.492063 0.875
175 P5A 0.490741 0.769231
176 LSS 0.490566 0.786517
177 A2R 0.490385 0.933333
178 ATR 0.49 0.893333
179 PAP 0.49 0.906667
180 ITT 0.489796 0.868421
181 7D4 0.489796 0.835443
182 A3P 0.489583 0.893333
183 P1H 0.48855 0.855422
184 A3D 0.487805 0.921053
185 AHZ 0.486957 0.843373
186 9K8 0.486239 0.72043
187 5X8 0.484848 0.815789
188 J7C 0.484211 0.753086
189 NAJ PZO 0.483871 0.851852
190 BTX 0.483607 0.845238
191 7D5 0.483516 0.810127
192 EP4 0.483146 0.716049
193 AR6 AR6 0.482456 0.92
194 SMM 0.480769 0.752941
195 S7M 0.480769 0.759036
196 DZD 0.479675 0.8875
197 7D3 0.479167 0.835443
198 KAA 0.477064 0.777778
199 GSU 0.477064 0.825581
200 ZID 0.476562 0.921053
201 PPS 0.475728 0.809524
202 A2P 0.474227 0.88
203 NEC 0.473684 0.730769
204 8PZ 0.473214 0.825581
205 3AM 0.473118 0.855263
206 MTA 0.472527 0.734177
207 NAE 0.472441 0.897436
208 ARU 0.472222 0.797619
209 AMP NAD 0.471545 0.933333
210 0WD 0.471545 0.875
211 2SA 0.471154 0.96
212 HFD 0.470588 0.873418
213 SFG 0.47 0.802632
214 YSA 0.469027 0.804598
215 NAJ PYZ 0.46875 0.811765
216 A3N 0.46875 0.746835
217 V3L 0.466019 0.92
218 SAM 0.466019 0.759036
219 GJV 0.463918 0.756098
220 S4M 0.463918 0.693182
221 EEM 0.461538 0.759036
222 6AD 0.461538 0.841463
223 SA8 0.460784 0.756098
224 G A A A 0.459677 0.851852
225 FB0 0.459259 0.808989
226 NDP 0.459016 0.875
227 DSH 0.458333 0.731707
228 SAH 0.456311 0.794872
229 SAI 0.456311 0.78481
230 NDE 0.455224 0.909091
231 NA7 0.454545 0.909091
232 IMO 0.453608 0.855263
233 ZAS 0.452632 0.772152
234 3AT 0.451923 0.92
235 DTP 0.451923 0.883117
236 6IA 0.451923 0.819277
237 6FA 0.449275 0.845238
238 A G 0.448 0.8625
239 2AM 0.446809 0.868421
240 NVA 2AD 0.446602 0.810127
241 U A G G 0.444444 0.8625
242 MAO 0.444444 0.764706
243 NZQ 0.443548 0.8875
244 A3G 0.443299 0.828947
245 DAT 0.441176 0.883117
246 FNK 0.440559 0.808989
247 AVV 0.440367 0.875
248 NJP 0.44 0.922078
249 ODP 0.44 0.8875
250 WSA 0.438017 0.813953
251 NDC 0.437956 0.875
252 U A 0.4375 0.886076
253 7DT 0.436893 0.906667
254 0UM 0.436364 0.746988
255 7C5 0.435897 0.8
256 A7D 0.435644 0.759494
257 A3S 0.435644 0.84
258 7DD 0.435644 0.906667
259 NPW 0.435484 0.888889
260 8Q2 0.434426 0.797753
261 OVE 0.43299 0.835443
262 A5D 0.432692 0.746835
263 FAD 0.432624 0.855422
264 FAS 0.432624 0.855422
265 TXP 0.432 0.875
266 FDA 0.431655 0.816092
267 GGZ 0.431193 0.785714
268 AV2 0.429907 0.846154
269 K15 0.428571 0.729412
270 6C6 0.428571 0.860759
271 4YB 0.428571 0.806818
272 A3T 0.427184 0.802632
273 5AD 0.425287 0.706667
274 4TA 0.425197 0.855422
275 DCA 0.423077 0.827586
276 SFD 0.422535 0.739583
277 Y3J 0.422222 0.688312
278 SXZ 0.421053 0.759036
279 C2R 0.421053 0.881579
280 AMZ 0.421053 0.868421
281 AAT 0.420561 0.714286
282 62X 0.419643 0.712644
283 A U 0.419355 0.873418
284 1DG 0.41791 0.875
285 DG1 0.41791 0.875
286 FAY 0.417808 0.865854
287 MHZ 0.417476 0.704545
288 PGS 0.417476 0.839506
289 0T1 0.416667 0.827586
290 A A A 0.415929 0.907895
291 PO4 PO4 A A A A PO4 0.415929 0.88
292 71V 0.415842 0.839506
293 RFL 0.414966 0.825581
294 649 0.414634 0.769231
295 6K6 0.414414 0.857143
296 DA 0.414141 0.857143
297 D5M 0.414141 0.857143
298 NMN AMP PO4 0.414062 0.873418
299 ETB 0.412214 0.837209
300 62F 0.410959 0.843373
301 P5F 0.407895 0.848837
302 AMX 0.407407 0.837209
303 Z5A 0.407407 0.804598
304 COA 0.406015 0.827586
305 KB1 0.405172 0.746988
306 7D7 0.404494 0.705128
307 9JJ 0.403974 0.865854
308 A6D 0.403509 0.709302
309 V1N 0.403361 0.894737
310 XNP 0.403101 0.853659
311 F2N 0.402597 0.818182
312 VRT 0.401869 0.797468
313 GP3 0.401869 0.875
314 SO8 0.401869 0.772152
315 2VA 0.4 0.782051
316 FA9 0.4 0.86747
317 3NZ 0.4 0.810127
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: 159
This union binding pocket(no: 1) in the query (biounit: 1x54.bio1) has 26 residues
No: Leader PDB Ligand Sequence Similarity
1 6CS9 PIO None
2 1WUW TSU None
3 3E4O SIN 0.655738
4 4HWS 1B3 1.45985
5 3ERR AMP 1.6129
6 4ZS4 ATP 1.62866
7 5DMZ ADP 1.64384
8 1SES AHX 1.66271
9 1SES AMP 1.66271
10 5E6O TRP GLU GLU LEU 1.69492
11 5W75 SUC 1.78571
12 2CDO GAL AAL GAL AAL GAL AAL 1.875
13 2Z3U CRR 1.88235
14 5V59 8X1 2.07373
15 3HXU A5A 2.07373
16 5VAD 91Y 2.07373
17 2X1L ADN 2.07373
18 2VL1 GLY GLY 2.07373
19 4DBH OXL 2.08333
20 4KBA 1QM 2.1148
21 6FOG OXL 2.23214
22 5XIO ANP 2.30415
23 3IAL PR8 2.30415
24 4YDQ HFG 2.30415
25 4YDQ ANP 2.30415
26 2I4O ATP 2.30415
27 4WOE ADP 2.30415
28 1YFS ALA 2.30415
29 5XIO HFG 2.30415
30 5YJS SAL 2.30769
31 5LHT TIH 2.38095
32 5G48 1FL 2.40642
33 1F5F DHT 2.43902
34 1IA9 ANP 2.5
35 2J3M PRI 2.53456
36 2J3M ATP 2.53456
37 5A1S FLC 2.53456
38 3UW5 MAA CHG PRO 0DQ 2.58621
39 4L9Z OXL 2.65487
40 2ART LPA AMP 2.67176
41 1NXJ TLA 2.73224
42 5KJW 53C 2.8103
43 1M5W DXP 2.88066
44 3TEG DAH 2.89157
45 5XIJ ANP 2.99539
46 5XIJ 873 2.99539
47 5LUN OGA 3.125
48 3SAO DBH 3.125
49 5F7J ADE 3.125
50 4M69 ANP 3.18021
51 4IAW LIZ 3.19149
52 4M3P HCS 3.20197
53 3UH0 TSB 3.22581
54 5F7U GLC GLC 3.22581
55 3TW1 AHN 3.37553
56 3NZ1 3NY 3.44828
57 1GPM AMP 3.45622
58 2VDF OCT 3.55731
59 5EJL C2E 3.62903
60 6MJ7 ARG 3.63636
61 4OYA 1VE 3.68664
62 1HXD BTN 3.73832
63 5H2U 1N1 3.74532
64 3TAO PGH 3.74532
65 5XDT MB3 3.8961
66 2RDE C2E 3.98406
67 1B7Y FYA 4
68 3FIU AMP 4.01606
69 2W5P CL8 4.02685
70 3MF2 AMP 4.04624
71 3QO8 SSA 4.14747
72 3A7R LAQ 4.1543
73 2HJ4 PNZ 4.15512
74 2QHS OCA 4.21941
75 6E1Q CFA 4.37788
76 3A16 PXO 4.55764
77 4B2D SER 4.60829
78 2G50 ALA 4.60829
79 2WCU FUC 4.69799
80 2QHV OC9 4.7619
81 5XVG 8FX 4.77816
82 6CA4 MLI 4.8
83 1SW0 PGA 4.83871
84 1W96 S1A 4.83871
85 3GD8 GOL 4.93274
86 1CZA G6P 5.06912
87 4HWT 1B2 5.08475
88 4MOB ADP 5.12048
89 5K6A 6QT 5.20833
90 4YRI 4JH 5.29954
91 5AHN IMP 5.29954
92 5OQW A4E 5.51181
93 4RF7 ARG 5.52995
94 5WHT SIA GAL 5.7971
95 5WHT SIA GAL GLC 5.7971
96 5WHT SIA 5.7971
97 5HWV MBN 6.15385
98 2JK0 ASP 6.15385
99 4ONT SIA GAL BGC 6.20155
100 2OJW ADP 6.25
101 4JZ8 CIT 6.30915
102 1WLJ U5P 6.34921
103 4RHS SIA SIA GAL 6.55738
104 3WWX DIA 6.59026
105 5T8U LPA 6.66667
106 2CYC TYR 6.66667
107 4NAE 1GP 6.66667
108 2CJA ATP 6.68203
109 5DBX ANP 6.70732
110 5YSN 5AD 6.77966
111 2RHQ GAX 6.80272
112 2CJ9 SSA 7.14286
113 4CS4 ANP 7.29927
114 4CS4 AXZ 7.29927
115 2ZTG A5A 7.37327
116 4ZTD ALA GLY ALA GLY ALA 7.50988
117 1QDS PGA 7.56972
118 2GQS C2R 7.59494
119 1WLE SRP 7.60369
120 3T4L ZEA 7.77778
121 4Y24 TD2 7.79221
122 1RZX ACE VAL LYS GLU SER LEU VAL 8.16327
123 4P83 U5P 8.24176
124 5F6U 5VK 8.28025
125 5DYO FLU 8.49057
126 5WBF LAC 8.51852
127 3UW4 MAA CHG PRO 0DQ 8.69565
128 2E5A LAQ 8.93372
129 3HUN ZZ7 8.98618
130 2WOR 2AN 9
131 12AS AMP 9.09091
132 4DS0 A2G GAL NAG FUC 9.20245
133 4H2X G5A 10.6796
134 4H2W AMP 10.6796
135 4H2W 5GP 10.6796
136 3QX9 ATP 10.8696
137 3F5A SIA GAL NAG 10.9756
138 4P86 5GP 11.4754
139 3CM2 X23 11.5385
140 4H2V AMP 11.8182
141 3EFS BTN 12.8755
142 3IWD M2T 13.2353
143 1O6B ADP 14.2012
144 3AXK NDP 14.7287
145 6FA4 D1W 15.0289
146 3H0L ADP 15.9574
147 6DZN AE3 16.4319
148 1UPR 4IP 18.6992
149 2G30 ALA ALA PHE 25
150 3BJU ATP 29.9539
151 3G08 FEE 31.3131
152 3ZIA ADP 31.746
153 3A5Y KAA 34.4928
154 1G51 AMO 35.2535
155 3A5Z KAA 36.2805
156 3G1Z AMP 36.8098
157 3REU ATP 41.8367
158 1E1O LYS 44.0092
159 3E9I XAH 47.4654
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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