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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 4 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 4 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 (11)
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 5V59 - 8X1 C14 H19 N7 O7 S c1nc(c2c(n....
9 1YFS - ALA C3 H7 N O2 C[C@@H](C(....
10 1YGB - SER C3 H7 N O3 C([C@@H](C....
11 1YFT - GLY C2 H5 N O2 C(C(=O)O)N
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: A5A; Similar ligands found: 258
No: Ligand ECFP6 Tc MDL keys Tc
1 A5A 1 1
2 VMS 0.851852 0.97561
3 54H 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 0.930233
11 DSZ 0.77907 0.940476
12 NVA LMS 0.770115 0.930233
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 8X1 0.696629 0.908046
20 WSA 0.673267 0.951807
21 8PZ 0.666667 0.940476
22 LMS 0.6625 0.975
23 P5A 0.659574 0.897727
24 5AL 0.633333 0.841463
25 4YB 0.617647 0.918605
26 8Q2 0.603774 0.908046
27 SON 0.590909 0.8
28 A 0.583333 0.804878
29 AMP 0.583333 0.804878
30 ABM 0.581395 0.807229
31 649 0.579439 0.897727
32 AHX 0.571429 0.793103
33 5CD 0.56962 0.707317
34 8QN 0.56701 0.841463
35 9ZA 0.56701 0.823529
36 9ZD 0.56701 0.823529
37 CA0 0.566667 0.809524
38 A2D 0.563218 0.807229
39 5X8 0.56044 0.714286
40 3DH 0.559524 0.722892
41 SRA 0.55814 0.831325
42 5N5 0.556962 0.698795
43 DAL AMP 0.556701 0.819277
44 AN2 0.555556 0.819277
45 TXA 0.554455 0.821429
46 SRP 0.552083 0.8
47 AOC 0.551724 0.722892
48 XYA 0.551282 0.719512
49 ADN 0.551282 0.719512
50 RAB 0.551282 0.719512
51 A12 0.550562 0.77907
52 BA3 0.550562 0.807229
53 AP2 0.550562 0.77907
54 ADX 0.549451 0.926829
55 M33 0.549451 0.819277
56 AU1 0.549451 0.809524
57 ADP 0.544444 0.807229
58 B4P 0.544444 0.807229
59 AP5 0.544444 0.807229
60 SLU 0.543103 0.929412
61 AT4 0.538462 0.821429
62 PRX 0.537634 0.788235
63 GAP 0.536842 0.788235
64 XAH 0.533333 0.766667
65 SA8 0.531915 0.666667
66 ADP PO3 0.531915 0.804878
67 A4D 0.530864 0.719512
68 EP4 0.53012 0.686047
69 PAJ 0.53 0.784091
70 AMO 0.53 0.8
71 50T 0.526882 0.776471
72 ACP 0.526882 0.788235
73 HEJ 0.526882 0.807229
74 ATP 0.526882 0.807229
75 ME8 0.524272 0.786517
76 NB8 0.524272 0.793103
77 9K8 0.524272 0.804348
78 M2T 0.52381 0.709302
79 DTA 0.52381 0.73494
80 5FA 0.521277 0.807229
81 AQP 0.521277 0.807229
82 APC 0.521277 0.77907
83 APR 0.521277 0.807229
84 AR6 0.521277 0.807229
85 ANP 0.520833 0.809524
86 7MD 0.518519 0.766667
87 MTA 0.517647 0.722892
88 AD9 0.515789 0.788235
89 AGS 0.515789 0.833333
90 ADV 0.515789 0.77907
91 RBY 0.515789 0.77907
92 SAP 0.515789 0.833333
93 4AD 0.514852 0.790698
94 LAD 0.514563 0.764045
95 SFG 0.510638 0.682353
96 A3T 0.510638 0.743902
97 SAH 0.510417 0.697674
98 MAP 0.51 0.790698
99 DLL 0.509804 0.819277
100 PTJ 0.509615 0.793103
101 6RE 0.505618 0.655556
102 T99 0.505155 0.821429
103 TAT 0.505155 0.821429
104 SAM 0.505155 0.688889
105 ACQ 0.505155 0.788235
106 S7M 0.50505 0.688889
107 SMM 0.50505 0.684783
108 OOB 0.504951 0.819277
109 3UK 0.504854 0.809524
110 OAD 0.504854 0.831325
111 48N 0.504505 0.793103
112 EEM 0.5 0.652174
113 YAP 0.495327 0.790698
114 FA5 0.495327 0.8
115 1ZZ 0.495238 0.766667
116 3OD 0.495238 0.831325
117 FYA 0.495238 0.776471
118 00A 0.495146 0.781609
119 A22 0.49505 0.797619
120 ADP ALF 0.494949 0.75
121 ALF ADP 0.494949 0.75
122 ATF 0.494949 0.77907
123 SAI 0.494845 0.670455
124 J7C 0.494505 0.662921
125 A3N 0.494505 0.674419
126 YLP 0.491071 0.75
127 MYR AMP 0.490566 0.747253
128 9X8 0.490385 0.833333
129 5SV 0.490196 0.752809
130 25A 0.490196 0.807229
131 ADP VO4 0.49 0.797619
132 6YZ 0.49 0.788235
133 VO4 ADP 0.49 0.797619
134 A3S 0.489362 0.714286
135 GJV 0.48913 0.648352
136 S4M 0.48913 0.648936
137 9SN 0.485981 0.772727
138 PR8 0.485714 0.755556
139 B5V 0.485714 0.8
140 WAQ 0.485714 0.781609
141 0UM 0.485437 0.659341
142 ADQ 0.485437 0.788235
143 A1R 0.485437 0.761364
144 MAO 0.483871 0.714286
145 DSH 0.483516 0.662921
146 NEC 0.483516 0.678571
147 B5Y 0.481481 0.811765
148 B5M 0.481481 0.811765
149 SXZ 0.481132 0.688889
150 2VA 0.479167 0.72619
151 YLB 0.478261 0.75
152 YLC 0.478261 0.766667
153 7MC 0.478261 0.769231
154 ZAS 0.477778 0.697674
155 ARG AMP 0.477477 0.72043
156 4UU 0.477477 0.790698
157 ADP BMA 0.47619 0.767442
158 K15 0.47619 0.645161
159 A7D 0.473684 0.705882
160 TAD 0.473214 0.784091
161 AMP DBH 0.472727 0.747126
162 4UV 0.472727 0.790698
163 TYR AMP 0.472727 0.770115
164 A3R 0.471154 0.761364
165 F2R 0.470588 0.731183
166 TXE 0.469565 0.781609
167 TYM 0.469565 0.8
168 5AD 0.469136 0.675
169 MHZ 0.46875 0.659574
170 7C5 0.468468 0.724138
171 A3G 0.467391 0.705882
172 BIS 0.46729 0.761364
173 JB6 0.46729 0.802326
174 62X 0.466667 0.631579
175 SO8 0.464646 0.717647
176 GA7 0.464286 0.77907
177 25L 0.462963 0.797619
178 AYB 0.462185 0.741935
179 TXD 0.46087 0.781609
180 6V0 0.46087 0.772727
181 4UW 0.46087 0.784091
182 DQV 0.460177 0.819277
183 A A 0.457944 0.785714
184 EO7 0.457447 0.928571
185 OMR 0.456897 0.758242
186 LAQ 0.45614 0.786517
187 AHZ 0.45614 0.766667
188 ATP A A A 0.454545 0.795181
189 COD 0.454545 0.744681
190 YLA 0.453782 0.731183
191 LPA AMP 0.452174 0.766667
192 3AM 0.450549 0.771084
193 VRT 0.45 0.701149
194 NAX 0.448276 0.755556
195 NXX 0.448276 0.8
196 DND 0.448276 0.8
197 GEK 0.447619 0.712644
198 KH3 0.447368 0.638298
199 GTA 0.447368 0.766667
200 Y3J 0.447059 0.638554
201 7D7 0.445783 0.654762
202 IOT 0.445378 0.723404
203 7D5 0.444444 0.732558
204 AF3 ADP 3PG 0.444444 0.744444
205 3NZ 0.444444 0.712644
206 AP0 0.440678 0.772727
207 NVA 2AD 0.44 0.693182
208 A5D 0.44 0.73494
209 AR6 AR6 0.438596 0.785714
210 AFH 0.438596 0.744444
211 D3Y 0.438095 0.697674
212 CNA 0.438017 0.8
213 A3P 0.4375 0.804878
214 A2P 0.4375 0.792683
215 YLY 0.436508 0.741935
216 KB1 0.436364 0.641304
217 NAI 0.435897 0.781609
218 S8M 0.433962 0.712644
219 2A5 0.43 0.747126
220 G3A 0.429825 0.772727
221 NAQ 0.429688 0.793103
222 AAT 0.427184 0.648352
223 G5P 0.426087 0.772727
224 A3D 0.424 0.831325
225 80F 0.424 0.75
226 2AM 0.423913 0.761905
227 UP5 0.423729 0.790698
228 NAD 0.419355 0.819277
229 AMP NAD 0.419355 0.797619
230 T5A 0.418033 0.75
231 6IA 0.417476 0.725275
232 V3L 0.417476 0.807229
233 594 0.417323 0.821053
234 4TC 0.416667 0.772727
235 UPA 0.416667 0.781609
236 BT5 0.416 0.741935
237 N0B 0.415385 0.731183
238 PPS 0.413462 0.903614
239 A4P 0.413223 0.715789
240 7D3 0.412371 0.735632
241 PAP 0.411765 0.795181
242 ATR 0.411765 0.783133
243 FB0 0.411765 0.704082
244 NAE 0.410853 0.811765
245 OVE 0.410526 0.776471
246 7D4 0.41 0.735632
247 2SA 0.409524 0.77907
248 NAJ PZO 0.409449 0.772727
249 A6D 0.409091 0.7
250 3AD 0.409091 0.707317
251 4TA 0.408 0.73913
252 139 0.406504 0.755556
253 ADJ 0.406504 0.72043
254 DZD 0.404762 0.764045
255 67D 0.403226 0.896552
256 BS5 0.403226 0.787234
257 IMO 0.402062 0.771084
258 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 with APoc: 149
This union binding pocket(no: 1) in the query (biounit: 3hxu.bio1) has 24 residues
No: Leader PDB Ligand Sequence Similarity
1 4RD0 GDP 1.20482
2 4YDQ HFG 1.36054
3 4YDQ ANP 1.36054
4 2E4G TRP 1.36054
5 5KJW 53C 1.40515
6 3E9I XAH 1.5873
7 1MJT ITU 1.72911
8 5VAD 91Y 1.81406
9 5VAD PRO 1.81406
10 6E1Q CFA 1.81406
11 5O9W AKG 1.90736
12 3MF2 AMP 2.02312
13 2H12 OAA 2.06422
14 1X54 4AD 2.07373
15 3E7S AT2 2.08817
16 2QPU QPU 2.22222
17 1QHO MAL 2.26757
18 3A5Y KAA 2.31884
19 12AS AMP 2.42424
20 4CM9 YGL 2.43056
21 6F1J EDG 2.46154
22 5VKM GAL SIA 2.46914
23 2J3M PRI 2.49433
24 2J3M ATP 2.49433
25 1WLE SRP 2.49433
26 1E1O LYS 2.49433
27 3SAO DBH 2.5
28 3A5Z KAA 2.6178
29 4HWT 1B2 2.66344
30 4RF7 ARG 2.72109
31 1G51 AMO 2.75862
32 3G1Z AMP 2.76074
33 4ZTD ALA GLY ALA GLY ALA 2.7668
34 2JLD AG1 2.85714
35 2JLD ALA GLY GLY ALA ALA ALA ALA ALA 2.85714
36 1GJW GLC 2.94785
37 3R6K FUC GAL GLA 2.95082
38 2FN1 PYR 2.97483
39 4IEN GDP 3.06748
40 4DFU QUE 3.10559
41 5LUN OGA 3.125
42 1B7Y FYA 3.1746
43 2I4O ATP 3.1746
44 5G48 1FL 3.20856
45 2XGT NSS 3.21839
46 1SS4 GSH 3.26797
47 3QSB 743 3.27869
48 4MOB ADP 3.31325
49 2BVE PH5 3.36134
50 1I7E IBS 3.39623
51 3REU ATP 3.40136
52 5XIJ ANP 3.40136
53 5XIJ 873 3.40136
54 4ZDM GLY 3.44828
55 3MEH THP 3.4965
56 3CBC DBS 3.53535
57 3QPB URA 3.5461
58 3TEG DAH 3.61446
59 5XIO ANP 3.62812
60 5XIO HFG 3.62812
61 4H2V AMP 3.63636
62 4CS4 ANP 3.64964
63 4CS4 AXZ 3.64964
64 5EOO CIT 3.77358
65 1GT4 UNA 3.77358
66 4BTV RB3 3.77907
67 5F6U 5VK 3.82166
68 3KVY URA 3.8835
69 2WMC MGP 3.93258
70 4HNN LYS 4.04624
71 1LSH PLD 4.07523
72 3BJU ATP 4.08163
73 4YRI 4JH 4.08163
74 2VL1 GLY GLY 4.08163
75 2G36 TRP 4.11765
76 2QHS OCA 4.21941
77 3QO8 SSA 4.30839
78 2AGC DAO 4.32099
79 3QRC SCR 4.4586
80 3AKI AH8 4.53515
81 2PNC CLU 4.53515
82 1F9V ADP 4.61095
83 4DZ1 DAL 4.6332
84 5DYO FLU 4.71698
85 2CJ9 SSA 4.7619
86 2CJA ATP 4.7619
87 2QHV OC9 4.7619
88 3UEC ALA ARG TPO LYS 4.79452
89 3LL5 IPE 4.81928
90 3LL5 ADP 4.81928
91 3GD8 GOL 4.93274
92 1VRP ADP 4.98688
93 3IAL PR8 5.21542
94 3UH0 TSB 5.21542
95 5FPE 3TR 5.42636
96 4C2C ALA ALA ALA 5.44218
97 1SES AHX 5.46318
98 1SES AMP 5.46318
99 1L7P SEP 5.6872
100 1UPR 4IP 5.69106
101 4H2X G5A 5.82524
102 4H2W AMP 5.82524
103 4H2W 5GP 5.82524
104 3ERR AMP 6.12245
105 3NEM AMO 6.16438
106 3NEM ATP 6.16438
107 3QXV MTX 6.34921
108 3H0L ADP 6.38298
109 6GNO XDI 6.66667
110 5H4S RAM 6.69014
111 3G2Y GF4 6.84411
112 2YKL NLD 7.07547
113 5YJS SAL 7.17949
114 3T4L ZEA 7.40741
115 6DW2 HD4 7.45098
116 1DCP HBI 7.69231
117 4K55 H6P 8.06452
118 5CIC 51R 8.33333
119 4WOE ADP 8.39002
120 3BIB PSF 8.62069
121 1M5W DXP 8.64198
122 2ART LPA AMP 8.77863
123 1UNQ 4IP 8.8
124 2Z3U CRR 8.94118
125 5D9G GLU ASN LEU TYR PHE GLN 8.94309
126 3PNA CMP 9.09091
127 2AG4 OLA 9.14634
128 5HWV MBN 9.23077
129 3TW1 AHN 9.2827
130 5VM6 9EG 9.48905
131 1PVS 7HP 9.57447
132 4HWS 1B3 9.73236
133 5WL1 CUY 10.101
134 5WL1 D3D 10.101
135 2HJ4 PNZ 10.3704
136 2RBK VN4 11.1111
137 1I7Q PYR 11.1111
138 4NPL AKG 11.2
139 3VMG 9CA 11.3043
140 4IAW LIZ 11.7021
141 1ECM TSA 11.9266
142 5F7U GLC GLC 12.2449
143 4V1F BQ1 12.7907
144 3ZXE PGZ 14.2857
145 3HCH RSM 14.3836
146 6FA4 D1W 14.4509
147 1UY4 XYP XYP XYP XYP 14.4828
148 4OGQ 7PH 14.7059
149 4OCT AKG 16.6667
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