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Receptor
PDB id Resolution Class Description Source Keywords
3HXW 1.93 Å EC: 6.1.1.7 CRYSTAL STRUCTURE OF CATALYTIC FRAGMENT OF E. COLI ALARS IN WITH SERSA 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
EPE A:443;
Invalid;
none;
submit data
238.305 C8 H18 N2 O4 S C1CN(...
HED A:444;
A:445;
A:446;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
154.251 C4 H10 O2 S2 C(CSS...
SSA A:442;
Valid;
none;
submit data
433.397 C13 H19 N7 O8 S c1nc(...
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: SSA; Similar ligands found: 256
No: Ligand ECFP6 Tc MDL keys Tc
1 SSA 1 1
2 5CA 0.876543 1
3 DSZ 0.833333 0.97619
4 LSS 0.833333 0.931035
5 A5A 0.817073 0.940476
6 53H 0.809524 0.908046
7 KAA 0.804598 0.942529
8 GSU 0.804598 0.952941
9 VMS 0.797619 0.918605
10 54H 0.797619 0.918605
11 TSB 0.788235 0.952381
12 52H 0.776471 0.908046
13 YSA 0.76087 0.952941
14 NSS 0.75 0.97619
15 NVA LMS 0.741573 0.920455
16 G5A 0.738095 0.97619
17 LEU LMS 0.733333 0.920455
18 WSA 0.7 0.964286
19 8X1 0.688889 0.942529
20 5AS 0.686747 0.908046
21 8PZ 0.659794 0.97619
22 LMS 0.654321 0.939759
23 P5A 0.652632 0.931818
24 AHX 0.631579 0.848837
25 8Q2 0.598131 0.942529
26 4YB 0.596154 0.931035
27 SRP 0.595745 0.835294
28 649 0.588785 0.910112
29 SON 0.58427 0.793103
30 A 0.576471 0.776471
31 AMP 0.576471 0.776471
32 5AL 0.574468 0.790698
33 5X8 0.571429 0.729412
34 BA3 0.561798 0.8
35 CA0 0.56044 0.802326
36 ABM 0.556818 0.758621
37 A2D 0.556818 0.8
38 B4P 0.555556 0.8
39 AP5 0.555556 0.8
40 SRA 0.551724 0.802326
41 AN2 0.549451 0.811765
42 A3S 0.549451 0.771084
43 AOC 0.545455 0.697674
44 AP2 0.544444 0.793103
45 A12 0.544444 0.793103
46 XYA 0.544304 0.73494
47 RAB 0.544304 0.73494
48 ADN 0.544304 0.73494
49 ADX 0.543478 0.916667
50 AU1 0.543478 0.802326
51 5CD 0.54321 0.682353
52 XAH 0.542857 0.8
53 AMO 0.54 0.835294
54 SLU 0.538462 0.897727
55 ADP 0.538462 0.8
56 HEJ 0.537634 0.8
57 ATP 0.537634 0.8
58 SAH 0.536842 0.712644
59 3DH 0.534884 0.678161
60 NB8 0.533981 0.827586
61 AT4 0.532609 0.813953
62 AQP 0.531915 0.8
63 5FA 0.531915 0.8
64 GAP 0.53125 0.781609
65 5N5 0.530864 0.714286
66 9ZA 0.53 0.775281
67 9ZD 0.53 0.775281
68 8QN 0.53 0.790698
69 M33 0.526882 0.790698
70 SA8 0.526316 0.663043
71 AGS 0.526316 0.825581
72 SAP 0.526316 0.825581
73 A4D 0.52439 0.73494
74 LAD 0.524272 0.797753
75 50T 0.521277 0.770115
76 ACP 0.521277 0.802326
77 SFG 0.521277 0.697674
78 DAL AMP 0.52 0.770115
79 DLL 0.519608 0.790698
80 ME8 0.519231 0.78022
81 TXA 0.519231 0.793103
82 DTA 0.517647 0.709302
83 AR6 0.515789 0.8
84 PRX 0.515789 0.741573
85 APC 0.515789 0.793103
86 APR 0.515789 0.8
87 TAT 0.515464 0.813953
88 ANP 0.515464 0.802326
89 T99 0.515464 0.813953
90 OOB 0.514852 0.790698
91 3UK 0.514563 0.781609
92 7MD 0.513761 0.820225
93 ADP PO3 0.510417 0.776471
94 RBY 0.510417 0.793103
95 ADV 0.510417 0.793103
96 AD9 0.510417 0.781609
97 4AD 0.509804 0.825581
98 PAJ 0.509804 0.777778
99 0UM 0.509804 0.673913
100 EP4 0.505882 0.644444
101 SAI 0.505155 0.685393
102 ATF 0.50505 0.772727
103 00A 0.504854 0.755556
104 9K8 0.504762 0.760417
105 FA5 0.504673 0.813953
106 YAP 0.504673 0.804598
107 ACQ 0.5 0.802326
108 SAM 0.5 0.684783
109 SMM 0.5 0.680851
110 A7D 0.5 0.72093
111 S7M 0.5 0.684783
112 M2T 0.5 0.666667
113 6YZ 0.5 0.802326
114 6RE 0.5 0.688889
115 9SN 0.495327 0.747253
116 WAQ 0.495238 0.775281
117 B5V 0.495238 0.772727
118 EEM 0.494949 0.648936
119 MTA 0.494253 0.678161
120 FYA 0.490566 0.790698
121 PTJ 0.490566 0.747253
122 MAP 0.490196 0.784091
123 A22 0.490196 0.790698
124 ADP ALF 0.49 0.725275
125 ALF ADP 0.49 0.725275
126 A3N 0.48913 0.689655
127 J7C 0.48913 0.696629
128 YLP 0.486726 0.763441
129 ARG AMP 0.486486 0.752688
130 K15 0.485714 0.642105
131 OAD 0.485714 0.802326
132 25A 0.485437 0.77907
133 ADP VO4 0.485149 0.770115
134 VO4 ADP 0.485149 0.770115
135 GJV 0.483871 0.681319
136 PR8 0.481132 0.788889
137 ADQ 0.480769 0.802326
138 A1R 0.480769 0.816092
139 DSH 0.478261 0.696629
140 TYM 0.478261 0.813953
141 B5Y 0.477064 0.764045
142 B5M 0.477064 0.764045
143 1ZZ 0.476636 0.723404
144 BIS 0.476636 0.755556
145 3OD 0.476636 0.802326
146 62X 0.47619 0.628866
147 A3T 0.474227 0.738095
148 YLB 0.474138 0.763441
149 YLC 0.474138 0.78022
150 48N 0.473684 0.786517
151 ZAS 0.472527 0.693182
152 MYR AMP 0.472222 0.705263
153 25L 0.472222 0.790698
154 9X8 0.471698 0.804598
155 ADP BMA 0.471698 0.781609
156 5SV 0.471154 0.709677
157 TYR AMP 0.468468 0.784091
158 AMP DBH 0.468468 0.741573
159 S4M 0.468085 0.663158
160 A3R 0.466667 0.816092
161 F2R 0.466667 0.782609
162 7C5 0.464286 0.7
163 MAO 0.463158 0.709677
164 JB6 0.462963 0.795455
165 SXZ 0.462963 0.684783
166 NEC 0.462366 0.674419
167 A3G 0.462366 0.761905
168 YLA 0.462185 0.763441
169 7MC 0.461538 0.802198
170 VRT 0.46 0.735632
171 KB1 0.458716 0.655914
172 AYB 0.458333 0.755319
173 TAD 0.45614 0.797753
174 DQV 0.45614 0.811765
175 4UV 0.455357 0.764045
176 IOT 0.453782 0.755319
177 A A 0.453704 0.758621
178 TXE 0.452991 0.775281
179 EO7 0.452632 0.896552
180 LAQ 0.452174 0.76087
181 MHZ 0.44898 0.673684
182 LPA AMP 0.448276 0.741935
183 D3Y 0.447619 0.752941
184 4UU 0.447368 0.764045
185 GA7 0.447368 0.793103
186 AFH 0.447368 0.777778
187 5AD 0.445783 0.630952
188 3AM 0.445652 0.764706
189 6V0 0.444444 0.766667
190 TXD 0.444444 0.775281
191 NAX 0.444444 0.788889
192 DND 0.444444 0.793103
193 2VA 0.444444 0.72093
194 NXX 0.444444 0.793103
195 KH3 0.443478 0.652632
196 GTA 0.443478 0.741935
197 S8M 0.443396 0.727273
198 GEK 0.443396 0.727273
199 Y3J 0.44186 0.616279
200 OMR 0.440678 0.734043
201 AF3 ADP 3PG 0.440678 0.73913
202 7D7 0.440476 0.651163
203 3NZ 0.440367 0.747126
204 AHZ 0.439655 0.723404
205 7D5 0.43956 0.727273
206 COD 0.439024 0.776596
207 G3A 0.438596 0.766667
208 ATP A A A 0.4375 0.767442
209 594 0.436508 0.833333
210 A5D 0.435644 0.709302
211 AR6 AR6 0.434783 0.758621
212 G5P 0.434783 0.766667
213 BS5 0.434426 0.83871
214 N0B 0.434109 0.763441
215 YLY 0.433071 0.755319
216 A2P 0.43299 0.764706
217 A3P 0.43299 0.776471
218 NAI 0.432203 0.775281
219 UP5 0.432203 0.784091
220 4UW 0.432203 0.73913
221 80F 0.432 0.782609
222 SO8 0.431373 0.712644
223 BT5 0.424 0.755319
224 AAT 0.423077 0.681319
225 CNA 0.422764 0.813953
226 NVA 2AD 0.421569 0.727273
227 A4P 0.421488 0.747368
228 7D4 0.42 0.75
229 2AM 0.419355 0.776471
230 NAD 0.416 0.790698
231 AMP NAD 0.416 0.770115
232 T5A 0.414634 0.763441
233 V3L 0.413462 0.77907
234 4TC 0.413223 0.786517
235 AP0 0.413223 0.747253
236 UPA 0.413223 0.795455
237 2A5 0.411765 0.781609
238 590 0.410448 0.84375
239 PPS 0.409524 0.894118
240 A3D 0.409449 0.781609
241 7D3 0.408163 0.75
242 PAP 0.407767 0.788235
243 ATR 0.407767 0.776471
244 NAJ PZO 0.40625 0.747253
245 OVE 0.40625 0.790698
246 2SA 0.40566 0.813953
247 A6D 0.405405 0.677419
248 BTX 0.404762 0.763441
249 NAQ 0.40458 0.747253
250 3AD 0.404494 0.722892
251 139 0.403226 0.788889
252 ADJ 0.403226 0.734043
253 F0P 0.401639 0.681319
254 DZD 0.401575 0.777778
255 M24 0.4 0.75
256 67D 0.4 0.909091
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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