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Receptor
PDB id Resolution Class Description Source Keywords
1X55 1.8 Å EC: 6.1.1.22 CRYSTAL STRUCTURE OF ASPARAGINYL-TRNA SYNTHETASE FROM PYROCO HORIKOSHII COMPLEXED WITH ASPARAGINYL-ADENYLATE ANALOGUE 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
MG A:2001;
A:2002;
Part of Protein;
Part of Protein;
none;
none;
submit data
24.305 Mg [Mg+2...
NSS A:3002;
Valid;
none;
submit data
461.43 C14 H21 N8 O8 S c1nc(...
PO4 A:3001;
Invalid;
none;
submit data
94.971 O4 P [O-]P...
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: NSS; Similar ligands found: 239
No: Ligand ECFP6 Tc MDL keys Tc
1 NSS 1 1
2 NVA LMS 0.806818 0.942529
3 LEU LMS 0.797753 0.942529
4 54H 0.761364 0.918605
5 VMS 0.761364 0.918605
6 A5A 0.758621 0.940476
7 SSA 0.75 0.97619
8 52H 0.741573 0.908046
9 DSZ 0.736264 0.97619
10 53H 0.733333 0.908046
11 5CA 0.733333 0.97619
12 TSB 0.733333 0.952381
13 G5A 0.724138 0.952941
14 LSS 0.717391 0.931035
15 KAA 0.694737 0.920455
16 GSU 0.694737 0.952941
17 5AS 0.674419 0.886364
18 YSA 0.66 0.952941
19 8X1 0.659574 0.920455
20 P5A 0.642857 0.910112
21 8PZ 0.633663 0.97619
22 LMS 0.623529 0.939759
23 WSA 0.611111 0.964286
24 4AD 0.59596 0.847059
25 8Q2 0.576577 0.942529
26 4YB 0.574074 0.931035
27 SON 0.55914 0.793103
28 649 0.553571 0.910112
29 A 0.550562 0.776471
30 AMP 0.550562 0.776471
31 A2D 0.549451 0.8
32 BA3 0.537634 0.8
33 CA0 0.536842 0.802326
34 5AL 0.535354 0.790698
35 ABM 0.532609 0.758621
36 B4P 0.531915 0.8
37 AP5 0.531915 0.8
38 DAL AMP 0.529412 0.790698
39 AHX 0.528846 0.827586
40 3DH 0.52809 0.678161
41 SRA 0.527473 0.802326
42 GAP 0.525253 0.781609
43 AOC 0.521739 0.697674
44 A12 0.521277 0.793103
45 AP2 0.521277 0.793103
46 ADX 0.520833 0.916667
47 AU1 0.520833 0.802326
48 ADN 0.518072 0.714286
49 XYA 0.518072 0.714286
50 RAB 0.518072 0.714286
51 5CD 0.517647 0.682353
52 ADP 0.515789 0.8
53 ATP 0.515464 0.8
54 HEJ 0.515464 0.8
55 5X8 0.515464 0.729412
56 50T 0.515464 0.770115
57 NB8 0.514019 0.827586
58 AN2 0.510417 0.811765
59 AT4 0.510417 0.813953
60 PRX 0.510204 0.741573
61 APR 0.510204 0.8
62 AR6 0.510204 0.8
63 5FA 0.510204 0.8
64 AQP 0.510204 0.8
65 SRP 0.509804 0.813953
66 9ZD 0.509615 0.775281
67 9ZA 0.509615 0.775281
68 ARG AMP 0.508929 0.752688
69 SLU 0.508197 0.897727
70 5N5 0.505882 0.694118
71 M33 0.505155 0.790698
72 SAP 0.50505 0.825581
73 AD9 0.50505 0.781609
74 AGS 0.50505 0.825581
75 PAJ 0.504762 0.758242
76 AMO 0.504762 0.835294
77 TXA 0.5 0.793103
78 ACP 0.5 0.802326
79 A4D 0.5 0.714286
80 9K8 0.5 0.760417
81 XAH 0.495495 0.78022
82 8QN 0.495238 0.790698
83 ANP 0.49505 0.802326
84 APC 0.494949 0.793103
85 DTA 0.494382 0.709302
86 TYR AMP 0.491071 0.804598
87 RBY 0.49 0.793103
88 ADP PO3 0.49 0.797619
89 ADV 0.49 0.793103
90 ME8 0.486239 0.78022
91 PTJ 0.486239 0.747253
92 DLL 0.485981 0.790698
93 A22 0.485714 0.790698
94 SAI 0.485149 0.685393
95 EP4 0.483146 0.644444
96 48N 0.482759 0.786517
97 7MD 0.482456 0.8
98 OAD 0.481481 0.802326
99 9X8 0.481481 0.804598
100 3UK 0.481481 0.781609
101 OOB 0.481132 0.790698
102 5SV 0.481132 0.709677
103 ADP VO4 0.480769 0.790698
104 VO4 ADP 0.480769 0.790698
105 S7M 0.480769 0.703297
106 TAT 0.480392 0.813953
107 T99 0.480392 0.813953
108 ACQ 0.480392 0.802326
109 6RE 0.478723 0.688889
110 M2T 0.477778 0.685393
111 WAQ 0.477064 0.775281
112 LAD 0.477064 0.777778
113 PR8 0.477064 0.769231
114 ADQ 0.476636 0.781609
115 SA8 0.475248 0.663043
116 DSH 0.473684 0.677778
117 NEC 0.473684 0.655172
118 3OD 0.472727 0.802326
119 1ZZ 0.472727 0.723404
120 MTA 0.472527 0.678161
121 00A 0.472222 0.755556
122 MAP 0.471698 0.784091
123 ALF ADP 0.471154 0.744444
124 ATF 0.471154 0.772727
125 ADP ALF 0.471154 0.744444
126 SAH 0.470588 0.712644
127 SFG 0.47 0.697674
128 J7C 0.46875 0.677778
129 A3N 0.46875 0.670455
130 MYR AMP 0.468468 0.723404
131 25A 0.46729 0.77907
132 GEK 0.46729 0.747126
133 6YZ 0.466667 0.802326
134 NAX 0.466102 0.788889
135 9SN 0.464286 0.747253
136 GJV 0.463918 0.681319
137 B5V 0.463636 0.772727
138 A1R 0.462963 0.795455
139 A3R 0.462963 0.795455
140 TXE 0.462185 0.775281
141 7C5 0.46087 0.7
142 FA5 0.460177 0.813953
143 YAP 0.460177 0.804598
144 FYA 0.459459 0.790698
145 7MC 0.458333 0.782609
146 YLB 0.458333 0.744681
147 YLP 0.457627 0.744681
148 25L 0.455357 0.790698
149 ADP BMA 0.454545 0.781609
150 TAD 0.452991 0.797753
151 SMM 0.45283 0.698925
152 ZAS 0.452632 0.712644
153 AMP DBH 0.452174 0.761364
154 SAM 0.451923 0.703297
155 A A 0.45045 0.77907
156 OMR 0.45 0.734043
157 A7D 0.45 0.701149
158 A3S 0.45 0.75
159 AF3 ADP 3PG 0.45 0.758242
160 0UM 0.449541 0.655914
161 S4M 0.44898 0.663158
162 EEM 0.447619 0.666667
163 B5Y 0.447368 0.764045
164 B5M 0.447368 0.764045
165 NVA 2AD 0.446602 0.727273
166 BIS 0.446429 0.755556
167 SXZ 0.446429 0.684783
168 JB6 0.446429 0.795455
169 MAO 0.444444 0.709677
170 A3G 0.443299 0.741176
171 DND 0.441667 0.813953
172 NXX 0.441667 0.813953
173 NAI 0.441667 0.775281
174 TXD 0.441667 0.775281
175 6V0 0.441667 0.766667
176 K15 0.441441 0.642105
177 A3T 0.441176 0.717647
178 DQV 0.440678 0.811765
179 GTA 0.440678 0.76087
180 F2R 0.44 0.763441
181 4UV 0.439655 0.764045
182 TYM 0.438017 0.813953
183 LAQ 0.436975 0.76087
184 COD 0.436508 0.757895
185 ATP A A A 0.434783 0.788235
186 YLC 0.434426 0.76087
187 EO7 0.434343 0.896552
188 LPA AMP 0.433333 0.76087
189 AR6 AR6 0.432203 0.77907
190 4UU 0.432203 0.764045
191 AFH 0.432203 0.758242
192 AYB 0.432 0.736842
193 MHZ 0.431373 0.65625
194 UP5 0.429752 0.784091
195 IOT 0.427419 0.736842
196 2VA 0.427184 0.701149
197 3AM 0.427083 0.744186
198 5AD 0.425287 0.630952
199 AHZ 0.425 0.741935
200 YLA 0.424 0.744681
201 G3A 0.423729 0.766667
202 AP0 0.422764 0.747253
203 Y3J 0.422222 0.616279
204 CNA 0.420635 0.835294
205 GA7 0.420168 0.772727
206 G5P 0.420168 0.766667
207 62X 0.419643 0.628866
208 A4P 0.419355 0.729167
209 A5D 0.419048 0.709302
210 80F 0.418605 0.782609
211 4UW 0.418033 0.73913
212 A2P 0.415842 0.764706
213 A3P 0.415842 0.776471
214 NAJ PZO 0.415385 0.766667
215 VRT 0.415094 0.715909
216 SO8 0.415094 0.693182
217 139 0.412698 0.769231
218 4TC 0.41129 0.786517
219 UPA 0.41129 0.775281
220 V3L 0.411215 0.77907
221 N0B 0.410448 0.744681
222 AAT 0.407407 0.663043
223 7D5 0.40625 0.707865
224 D3Y 0.405405 0.732558
225 KB1 0.405172 0.655914
226 KH3 0.404959 0.635417
227 7D7 0.404494 0.632184
228 2SA 0.40367 0.813953
229 NAD 0.403101 0.811765
230 AMP NAD 0.403101 0.790698
231 NAJ PYZ 0.402985 0.734043
232 NAQ 0.402985 0.766667
233 2AM 0.402062 0.755814
234 S8M 0.401786 0.727273
235 T5A 0.401575 0.763441
236 ADJ 0.401575 0.734043
237 594 0.401515 0.833333
238 3NZ 0.4 0.727273
239 BT5 0.4 0.755319
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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