Receptor
PDB id Resolution Class Description Source Keywords
3HXU 2.1 Å EC: 6.1.1.7 CRYSTAL STRUCTURE OF CATALYTIC FRAGMENT OF E. COLI ALARS IN WITH ALASA ESCHERICHIA COLI AMINOACYL-TRNA SYNTHETASE LIGASE PROTEIN BIOSYNTHESIS NUCBINDING AMINO ACID-BINDING ATP-BINDING METAL-BINDING ZI
Ref.: PARADOX OF MISTRANSLATION OF SERINE FOR ALANINE CAU ALARS RECOGNITION DILEMMA. NATURE V. 462 808 2009
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
A5A A:442;
 Valid;
 none;
 submit data
417.398 C13 H19 N7 O7 S C[C@@...
BME A:445;
A:446;
 Invalid;
Invalid;
 none;
none;
 submit data
78.133 C2 H6 O S C(CS)...
EPE A:444;
 Invalid;
 none;
 submit data
238.305 C8 H18 N2 O4 S C1CN(...
HED A:443;
 Invalid;
 none;
 submit data
154.251 C4 H10 O2 S2 C(CSS...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3HXU 2.1 Å EC: 6.1.1.7 CRYSTAL STRUCTURE OF CATALYTIC FRAGMENT OF E. COLI ALARS IN WITH ALASA ESCHERICHIA COLI AMINOACYL-TRNA SYNTHETASE LIGASE PROTEIN BIOSYNTHESIS NUCBINDING AMINO ACID-BINDING ATP-BINDING METAL-BINDING ZI
Ref.: PARADOX OF MISTRANSLATION OF SERINE FOR ALANINE CAU ALARS RECOGNITION DILEMMA. NATURE V. 462 808 2009
Members (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 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....
70% Homology Family (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 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....
50% Homology Family (10)
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 1YFS - ALA C3 H7 N O2 C[C@@H](C(....
9 1YGB - SER C3 H7 N O3 C([C@@H](C....
10 1YFT - GLY C2 H5 N O2 C(C(=O)O)N
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: A5A; Similar ligands found: 246
No: Ligand ECFP6 Tc MDL keys Tc
1 A5A 1 1
2 54H 0.851852 0.97561
3 VMS 0.851852 0.97561
4 TSB 0.841463 0.987654
5 LSS 0.821429 0.941176
6 53H 0.819277 0.963855
7 SSA 0.817073 0.940476
8 52H 0.807229 0.963855
9 5CA 0.797619 0.940476
10 LEU LMS 0.781609 0.941176
11 DSZ 0.77907 0.940476
12 NVA LMS 0.770115 0.941176
13 NSS 0.758621 0.940476
14 KAA 0.752809 0.908046
15 GSU 0.752809 0.940476
16 G5A 0.746988 0.940476
17 YSA 0.731183 0.940476
18 5AS 0.716049 0.940476
19 WSA 0.673267 0.951807
20 P5A 0.659574 0.897727
21 5AL 0.633333 0.841463
22 4YB 0.617647 0.918605
23 SON 0.590909 0.8
24 AMP 0.583333 0.804878
25 A 0.583333 0.804878
26 ABM 0.581395 0.807229
27 649 0.579439 0.897727
28 AHX 0.571429 0.793103
29 AMP MG 0.569767 0.764706
30 5CD 0.56962 0.707317
31 8QN 0.56701 0.841463
32 CA0 0.566667 0.809524
33 A2D 0.563218 0.807229
34 5X8 0.56044 0.714286
35 3DH 0.559524 0.722892
36 SRA 0.55814 0.831325
37 5N5 0.556962 0.698795
38 DAL AMP 0.556701 0.819277
39 AN2 0.555556 0.819277
40 TXA 0.554455 0.821429
41 SRP 0.552083 0.8
42 AOC 0.551724 0.722892
43 RAB 0.551282 0.719512
44 ADN 0.551282 0.719512
45 XYA 0.551282 0.719512
46 AP2 0.550562 0.77907
47 BA3 0.550562 0.807229
48 A12 0.550562 0.77907
49 ADX 0.549451 0.926829
50 AU1 0.549451 0.809524
51 M33 0.549451 0.819277
52 ADP 0.544444 0.807229
53 B4P 0.544444 0.807229
54 AP5 0.544444 0.807229
55 SLU 0.543103 0.929412
56 PRX 0.537634 0.788235
57 GAP 0.536842 0.788235
58 XAH 0.533333 0.766667
59 ADP MG 0.532609 0.776471
60 SA8 0.531915 0.666667
61 ADP PO3 0.531915 0.804878
62 A4D 0.530864 0.719512
63 EP4 0.53012 0.686047
64 AMO 0.53 0.8
65 PAJ 0.53 0.784091
66 ADP BEF 0.526882 0.758621
67 ACP 0.526882 0.788235
68 BEF ADP 0.526882 0.758621
69 50T 0.526882 0.776471
70 ATP 0.526882 0.807229
71 ATP MG 0.526316 0.776471
72 NB8 0.524272 0.793103
73 ME8 0.524272 0.786517
74 M2T 0.52381 0.709302
75 DTA 0.52381 0.73494
76 AR6 0.521277 0.807229
77 AQP 0.521277 0.807229
78 5FA 0.521277 0.807229
79 APC 0.521277 0.77907
80 APR 0.521277 0.807229
81 ANP 0.520833 0.809524
82 7MD 0.518519 0.766667
83 MTA 0.517647 0.722892
84 AGS 0.515789 0.833333
85 AD9 0.515789 0.788235
86 RBY 0.515789 0.77907
87 ADV 0.515789 0.77907
88 SAP 0.515789 0.833333
89 4AD 0.514852 0.790698
90 LAD 0.514563 0.764045
91 A3T 0.510638 0.743902
92 SFG 0.510638 0.682353
93 SAH 0.510417 0.697674
94 MAP 0.51 0.790698
95 DLL 0.509804 0.819277
96 PTJ 0.509615 0.793103
97 6RE 0.505618 0.655556
98 TAT 0.505155 0.821429
99 SAM 0.505155 0.688889
100 ACQ 0.505155 0.788235
101 S7M 0.50505 0.688889
102 SMM 0.50505 0.684783
103 ANP MG 0.50505 0.790698
104 OOB 0.504951 0.819277
105 3UK 0.504854 0.809524
106 OAD 0.504854 0.831325
107 48N 0.504505 0.793103
108 EEM 0.5 0.652174
109 FA5 0.495327 0.8
110 YAP 0.495327 0.790698
111 3OD 0.495238 0.831325
112 1ZZ 0.495238 0.766667
113 FYA 0.495238 0.776471
114 00A 0.495146 0.781609
115 A22 0.49505 0.797619
116 ADP ALF 0.494949 0.75
117 ALF ADP 0.494949 0.75
118 ATF 0.494949 0.77907
119 SAI 0.494845 0.670455
120 J7C 0.494505 0.662921
121 A3N 0.494505 0.674419
122 YLP 0.491071 0.75
123 MYR AMP 0.490566 0.747253
124 25A 0.490196 0.807229
125 5SV 0.490196 0.752809
126 VO4 ADP 0.49 0.797619
127 ADP VO4 0.49 0.797619
128 A3S 0.489362 0.714286
129 S4M 0.48913 0.648936
130 GJV 0.48913 0.648352
131 9SN 0.485981 0.772727
132 WAQ 0.485714 0.781609
133 PR8 0.485714 0.755556
134 A1R 0.485437 0.761364
135 0UM 0.485437 0.659341
136 ADQ 0.485437 0.788235
137 MAO 0.483871 0.714286
138 DSH 0.483516 0.662921
139 NEC 0.483516 0.678571
140 ARG AMP 0.482143 0.72043
141 SXZ 0.481132 0.688889
142 2VA 0.479167 0.72619
143 YLB 0.478261 0.75
144 7MC 0.478261 0.769231
145 YLC 0.478261 0.766667
146 ZAS 0.477778 0.697674
147 4UU 0.477477 0.790698
148 TYR AMP 0.477064 0.77907
149 ADP BMA 0.47619 0.767442
150 K15 0.47619 0.645161
151 A7D 0.473684 0.705882
152 TAD 0.473214 0.784091
153 AMP DBH 0.472727 0.747126
154 4UV 0.472727 0.790698
155 TYM 0.469565 0.8
156 TXE 0.469565 0.781609
157 5AD 0.469136 0.675
158 MHZ 0.46875 0.659574
159 7C5 0.468468 0.724138
160 A3G 0.467391 0.705882
161 JB6 0.46729 0.802326
162 BIS 0.46729 0.761364
163 62X 0.466667 0.631579
164 SO8 0.464646 0.717647
165 25L 0.462963 0.797619
166 AYB 0.462185 0.741935
167 TXD 0.46087 0.781609
168 4UW 0.46087 0.784091
169 6V0 0.46087 0.772727
170 NAD IBO 0.458333 0.790698
171 A A 0.457944 0.785714
172 LA8 ALF 3PG 0.456897 0.744444
173 OMR 0.456897 0.758242
174 ALF ADP 3PG 0.456897 0.744444
175 LAQ 0.45614 0.786517
176 AHZ 0.45614 0.766667
177 ATP A A A 0.454545 0.795181
178 COD 0.454545 0.744681
179 YLA 0.453782 0.731183
180 LPA AMP 0.452174 0.766667
181 3AM 0.450549 0.771084
182 VRT 0.45 0.701149
183 DND 0.448276 0.8
184 NAX 0.448276 0.755556
185 NXX 0.448276 0.8
186 GEK 0.447619 0.712644
187 KH3 0.447368 0.638298
188 GTA 0.447368 0.766667
189 Y3J 0.447059 0.638554
190 7D7 0.445783 0.654762
191 IOT 0.445378 0.723404
192 AF3 ADP 3PG 0.444444 0.744444
193 3NZ 0.444444 0.712644
194 7D5 0.444444 0.732558
195 AP0 0.440678 0.772727
196 A5D 0.44 0.73494
197 AFH 0.438596 0.744444
198 AR6 AR6 0.438596 0.785714
199 D3Y 0.438095 0.697674
200 CNA 0.438017 0.8
201 A2P 0.4375 0.792683
202 A3P 0.4375 0.804878
203 YLY 0.436508 0.741935
204 KB1 0.436364 0.641304
205 NAI 0.435897 0.781609
206 S8M 0.433962 0.712644
207 2A5 0.43 0.747126
208 G3A 0.429825 0.772727
209 NAQ 0.429688 0.793103
210 AAT 0.427184 0.648352
211 G5P 0.426087 0.772727
212 A3D 0.424 0.831325
213 2AM 0.423913 0.761905
214 UP5 0.423729 0.790698
215 NAD 0.419355 0.819277
216 T5A 0.418033 0.75
217 6IA 0.417476 0.725275
218 V3L 0.417476 0.807229
219 594 0.417323 0.821053
220 4TC 0.416667 0.772727
221 UPA 0.416667 0.781609
222 BT5 0.416 0.741935
223 N0B 0.415385 0.731183
224 PPS 0.413462 0.903614
225 A4P 0.413223 0.715789
226 7D3 0.412371 0.735632
227 FB0 0.411765 0.704082
228 PAP 0.411765 0.795181
229 ATR 0.411765 0.783133
230 NVA 2AD 0.411765 0.678161
231 NAE 0.410853 0.811765
232 OVE 0.410526 0.776471
233 7D4 0.41 0.735632
234 2SA 0.409524 0.77907
235 NAJ PZO 0.409449 0.772727
236 A6D 0.409091 0.7
237 3AD 0.409091 0.707317
238 4TA 0.408 0.73913
239 139 0.406504 0.755556
240 ADJ 0.406504 0.72043
241 DZD 0.404762 0.764045
242 AMP NAD 0.40458 0.8
243 BS5 0.403226 0.787234
244 67D 0.403226 0.896552
245 IMO 0.402062 0.771084
246 A2R 0.401869 0.797619
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3HXU; Ligand: A5A; Similar sites found: 61
This union binding pocket(no: 1) in the query (biounit: 3hxu.bio1) has 24 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3E9I XAH 0.00000001755 0.64247 1.5873
2 5VAD 91Y 0.000004486 0.46666 1.81406
3 5VAD PRO 0.001877 0.44312 1.81406
4 3MF2 AMP 0.00000007405 0.60063 2.02312
5 1X54 4AD 0.00000001906 0.63063 2.07373
6 3E7S AT2 0.03037 0.40163 2.08817
7 3A5Y KAA 0.000000005653 0.65257 2.31884
8 12AS AMP 0.00000126 0.55955 2.42424
9 2J3M PRI 0.00000001957 0.62733 2.49433
10 2J3M ATP 0.00000002106 0.62308 2.49433
11 1E1O LYS 0.0000003228 0.58201 2.49433
12 1WLE SRP 0.0000001477 0.5657 2.49433
13 3A5Z KAA 0.00000000175 0.67668 2.6178
14 4HWT 1B2 0.0002957 0.43893 2.66344
15 1G51 AMO 0.0000001371 0.59999 2.75862
16 3G1Z AMP 0.000000001555 0.58352 2.76074
17 2JLD ALA GLY GLY ALA ALA ALA ALA ALA 0.02867 0.40473 2.85714
18 5LUN OGA 0.01772 0.40486 3.125
19 1B7Y FYA 0.000002171 0.54744 3.1746
20 2I4O ATP 0.00000007703 0.52877 3.1746
21 2XGT NSS 0.000000005489 0.65868 3.21839
22 1SS4 GSH 0.000599 0.45715 3.26797
23 3REU ATP 0.00000001389 0.59393 3.40136
24 3MEH THP 0.01487 0.40472 3.4965
25 3TEG DAH 0.0009069 0.42818 3.61446
26 4H2V AMP 0.00000004061 0.60371 3.63636
27 4CS4 AXZ 0.00000003727 0.6556 3.64964
28 4CS4 ANP 0.00000002596 0.65214 3.64964
29 5EOO CIT 0.02028 0.41752 3.77358
30 5F6U 5VK 0.009324 0.41775 3.82166
31 2WMC MGP 0.005452 0.43849 3.93258
32 3BJU ATP 0.00000008173 0.54583 4.08163
33 4GID 0GH 0.02465 0.42225 4.12371
34 3QO8 SSA 0.0000004879 0.60227 4.30839
35 4DZ1 DAL 0.005931 0.44132 4.6332
36 2CJ9 SSA 0.00000004493 0.58768 4.7619
37 2CJA ATP 0.000009158 0.48843 4.7619
38 2QHV OC9 0.005412 0.4349 4.7619
39 3LL5 IPE 0.0115 0.40182 4.81928
40 3LL5 ADP 0.01194 0.40112 4.81928
41 3IAL PR8 0.0000006128 0.56291 5.21542
42 3UH0 TSB 0.00001111 0.51348 5.21542
43 1SES AHX 0.0000003619 0.60819 5.46318
44 1SES AMP 0.0000341 0.54541 5.46318
45 1L7P SEP 0.02546 0.40093 5.6872
46 4H2X G5A 0.00000006813 0.6245 5.82524
47 4H2W AMP 0.0000001765 0.54524 5.82524
48 4H2W 5GP 0.000001175 0.52266 5.82524
49 3ERR AMP 0.00004007 0.45086 6.12245
50 3NEM AMO 0.00000002958 0.62538 6.16438
51 3NEM ATP 0.00000001191 0.55399 6.16438
52 3T4L ZEA 0.001646 0.40623 7.40741
53 4WOE ADP 0.001394 0.47314 8.39002
54 5D9G GLU ASN LEU TYR PHE GLN 0.02504 0.40129 8.94309
55 3PNA CMP 0.02105 0.40512 9.09091
56 4HWS 1B3 0.00001791 0.43095 9.73236
57 5L2J 70E 0.002909 0.4526 10.2041
58 5L2J 6UL 0.002719 0.4526 10.2041
59 3VMG 9CA 0.009018 0.41516 11.3043
60 5F7U GLC GLC 0.01222 0.41964 12.2449
61 1UY4 XYP XYP XYP XYP 0.01502 0.41271 14.4828
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