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 CC(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 3HXW - SSA C13 H19 N7 O8 S c1nc(c2c(n....
3 3HXZ - A5A C13 H19 N7 O7 S CC(C(=O)NS....
4 3HXV - G5A C12 H17 N7 O7 S c1nc(c2c(n....
5 3HXY - ACP C11 H18 N5 O12 P3 c1nc(c2c(n....
6 3HY0 - G5A C12 H17 N7 O7 S c1nc(c2c(n....
7 3HXU - A5A C13 H19 N7 O7 S CC(C(=O)NS....
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 3HXW - SSA C13 H19 N7 O8 S c1nc(c2c(n....
3 3HXZ - A5A C13 H19 N7 O7 S CC(C(=O)NS....
4 3HXV - G5A C12 H17 N7 O7 S c1nc(c2c(n....
5 3HXY - ACP C11 H18 N5 O12 P3 c1nc(c2c(n....
6 3HY0 - G5A C12 H17 N7 O7 S c1nc(c2c(n....
7 3HXU - A5A C13 H19 N7 O7 S CC(C(=O)NS....
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 1YGB - SER C3 H7 N O3 C(C(C(=O)O....
2 1YFS - ALA C3 H7 N O2 CC(C(=O)O)....
3 1YFT - GLY C2 H5 N O2 C(C(=O)O)N
4 3HXX - ACP C11 H18 N5 O12 P3 c1nc(c2c(n....
5 3HXW - SSA C13 H19 N7 O8 S c1nc(c2c(n....
6 3HXZ - A5A C13 H19 N7 O7 S CC(C(=O)NS....
7 3HXV - G5A C12 H17 N7 O7 S c1nc(c2c(n....
8 3HXY - ACP C11 H18 N5 O12 P3 c1nc(c2c(n....
9 3HY0 - G5A C12 H17 N7 O7 S c1nc(c2c(n....
10 3HXU - A5A C13 H19 N7 O7 S CC(C(=O)NS....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: A5A; Similar ligands found: 208
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 0.941176
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 SON 0.590909 0.8
23 AMP 0.583333 0.804878
24 A 0.583333 0.804878
25 ABM 0.581395 0.807229
26 AHX 0.571429 0.793103
27 AMP MG 0.569767 0.764706
28 5CD 0.56962 0.707317
29 CA0 0.566667 0.809524
30 A2D 0.563218 0.807229
31 3DH 0.559524 0.722892
32 SRA 0.55814 0.831325
33 5N5 0.556962 0.698795
34 DAL AMP 0.556701 0.819277
35 TXA 0.554455 0.821429
36 SRP 0.552083 0.8
37 AOC 0.551724 0.722892
38 XYA 0.551282 0.719512
39 ADN 0.551282 0.719512
40 RAB 0.551282 0.719512
41 AP2 0.550562 0.77907
42 A12 0.550562 0.77907
43 BA3 0.550562 0.807229
44 M33 0.549451 0.819277
45 AU1 0.549451 0.809524
46 ADX 0.549451 0.926829
47 ADP 0.544444 0.807229
48 AP5 0.544444 0.807229
49 B4P 0.544444 0.807229
50 SLU 0.543103 0.929412
51 PRX 0.537634 0.788235
52 GAP 0.536842 0.788235
53 XAH 0.533333 0.766667
54 ADP MG 0.532609 0.776471
55 ADP PO3 0.531915 0.804878
56 SA8 0.531915 0.666667
57 A4D 0.530864 0.719512
58 EP4 0.53012 0.686047
59 PAJ 0.53 0.784091
60 AMO 0.53 0.8
61 ACP 0.526882 0.788235
62 BEF ADP 0.526882 0.758621
63 50T 0.526882 0.776471
64 ATP 0.526882 0.807229
65 ADP BEF 0.526882 0.758621
66 ATP MG 0.526316 0.776471
67 ME8 0.524272 0.786517
68 NB8 0.524272 0.793103
69 DTA 0.52381 0.73494
70 M2T 0.52381 0.709302
71 5FA 0.521277 0.807229
72 APC 0.521277 0.77907
73 APR 0.521277 0.807229
74 AQP 0.521277 0.807229
75 AR6 0.521277 0.807229
76 ANP 0.520833 0.809524
77 7MD 0.518519 0.766667
78 MTA 0.517647 0.722892
79 AGS 0.515789 0.833333
80 RBY 0.515789 0.77907
81 ADV 0.515789 0.77907
82 AD9 0.515789 0.788235
83 SAP 0.515789 0.833333
84 4AD 0.514852 0.790698
85 LAD 0.514563 0.764045
86 SFG 0.510638 0.682353
87 A3T 0.510638 0.743902
88 SAH 0.510417 0.697674
89 MAP 0.51 0.790698
90 DLL 0.509804 0.819277
91 PTJ 0.509615 0.793103
92 SAM 0.505155 0.688889
93 ACQ 0.505155 0.788235
94 TAT 0.505155 0.821429
95 ANP MG 0.50505 0.790698
96 S7M 0.50505 0.688889
97 SMM 0.50505 0.684783
98 OAD 0.504854 0.831325
99 EEM 0.5 0.652174
100 YAP 0.495327 0.790698
101 FA5 0.495327 0.8
102 FYA 0.495238 0.776471
103 3OD 0.495238 0.831325
104 1ZZ 0.495238 0.766667
105 00A 0.495146 0.781609
106 A22 0.49505 0.797619
107 ATF 0.494949 0.77907
108 ADP ALF 0.494949 0.75
109 ALF ADP 0.494949 0.75
110 SAI 0.494845 0.670455
111 A3N 0.494505 0.674419
112 YLP 0.491071 0.75
113 MYR AMP 0.490566 0.747253
114 25A 0.490196 0.807229
115 ADP VO4 0.49 0.797619
116 A3S 0.489362 0.714286
117 S4M 0.48913 0.648936
118 PR8 0.485714 0.755556
119 A1R 0.485437 0.761364
120 ADQ 0.485437 0.788235
121 0UM 0.485437 0.659341
122 MAO 0.483871 0.714286
123 NEC 0.483516 0.678571
124 DSH 0.483516 0.662921
125 2VA 0.479167 0.72619
126 YLC 0.478261 0.766667
127 YLB 0.478261 0.75
128 7MC 0.478261 0.769231
129 ZAS 0.477778 0.697674
130 K15 0.47619 0.645161
131 ADP BMA 0.47619 0.767442
132 A7D 0.473684 0.705882
133 TAD 0.473214 0.784091
134 AMP DBH 0.472727 0.747126
135 TYM 0.469565 0.8
136 5AD 0.469136 0.675
137 MHZ 0.46875 0.659574
138 A3G 0.467391 0.705882
139 BIS 0.46729 0.761364
140 25L 0.462963 0.797619
141 AYB 0.462185 0.741935
142 TXD 0.46087 0.781609
143 NAD IBO 0.458333 0.790698
144 LA8 ALF 3PG 0.456897 0.744444
145 ALF ADP 3PG 0.456897 0.744444
146 AHZ 0.45614 0.766667
147 LAQ 0.45614 0.786517
148 ATP A A A 0.454545 0.795181
149 COD 0.454545 0.744681
150 YLA 0.453782 0.731183
151 PA7 0.452632 0.647727
152 LPA AMP 0.452174 0.766667
153 3AM 0.450549 0.771084
154 DND 0.448276 0.8
155 NAX 0.448276 0.755556
156 NXX 0.448276 0.8
157 GEK 0.447619 0.712644
158 GTA 0.447368 0.766667
159 KH3 0.447368 0.638298
160 IOT 0.445378 0.723404
161 AF3 ADP 3PG 0.444444 0.744444
162 3NZ 0.444444 0.712644
163 AP0 0.440678 0.772727
164 A5D 0.44 0.73494
165 AR6 AR6 0.438596 0.785714
166 AFH 0.438596 0.744444
167 D3Y 0.438095 0.697674
168 CNA 0.438017 0.8
169 A2P 0.4375 0.792683
170 A3P 0.4375 0.804878
171 YLY 0.436508 0.741935
172 NAI 0.435897 0.781609
173 2A5 0.43 0.747126
174 G3A 0.429825 0.772727
175 NAQ 0.429688 0.793103
176 AAT 0.427184 0.648352
177 G5P 0.426087 0.772727
178 A3D 0.424 0.831325
179 2AM 0.423913 0.761905
180 UP5 0.423729 0.790698
181 NAD 0.419355 0.819277
182 T5A 0.418033 0.75
183 6IA 0.417476 0.725275
184 V3L 0.417476 0.807229
185 UPA 0.416667 0.781609
186 4TC 0.416667 0.772727
187 BT5 0.416 0.741935
188 N0B 0.415385 0.731183
189 PPS 0.413462 0.903614
190 A4P 0.413223 0.715789
191 PAP 0.411765 0.795181
192 FB0 0.411765 0.704082
193 ATR 0.411765 0.783133
194 NVA 2AD 0.411765 0.678161
195 NAE 0.410853 0.811765
196 OVE 0.410526 0.776471
197 2SA 0.409524 0.77907
198 NAJ PZO 0.409449 0.772727
199 3AD 0.409091 0.707317
200 A6D 0.409091 0.7
201 4TA 0.408 0.73913
202 139 0.406504 0.755556
203 ADJ 0.406504 0.72043
204 DZD 0.404762 0.764045
205 AMP NAD 0.40458 0.8
206 BS5 0.403226 0.787234
207 IMO 0.402062 0.771084
208 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)
1 3A5Z KAA 0.000000002268 0.68014
2 3A5Z KAA 0.00000000175 0.67668
3 2XGT NSS 0.000000005489 0.65868
4 3A5Y KAA 0.000000004016 0.65576
5 4CS4 AXZ 0.00000003727 0.6556
6 3A5Y KAA 0.000000005653 0.65257
7 4CS4 ANP 0.00000002596 0.65214
8 3E9I XAH 0.00000001755 0.64247
9 3E9I XAH 0.00000003222 0.63129
10 1X54 4AD 0.00000001906 0.63063
11 2J3M PRI 0.00000001957 0.62733
12 3NEM AMO 0.00000002958 0.62538
13 4H2X G5A 0.00000006813 0.6245
14 2J3M ATP 0.00000002106 0.62308
15 1SES AHX 0.0000003619 0.60819
16 4H2V AMP 0.00000004061 0.60371
17 3QO8 SSA 0.0000004879 0.60227
18 3MF2 AMP 0.00000007405 0.60063
19 1G51 AMO 0.0000001371 0.59999
20 3REU ATP 0.00000001389 0.59393
21 2CJ9 SSA 0.00000004493 0.58768
22 3G1Z AMP 0.000000001555 0.58352
23 1E1O LYS 0.0000003228 0.58201
24 1WLE SRP 0.0000001477 0.5657
25 3IAL PR8 0.0000006128 0.56291
26 12AS AMP 0.00000126 0.55955
27 3NEM ATP 0.00000001191 0.55399
28 3BJU ATP 0.00000006292 0.54929
29 1B7Y FYA 0.000002171 0.54744
30 3BJU ATP 0.00000008173 0.54583
31 3BJU ATP 0.00000008173 0.54583
32 1SES AMP 0.0000341 0.54541
33 4H2W AMP 0.0000001765 0.54524
34 2I4O ATP 0.00000005011 0.53323
35 2I4O ATP 0.00000007703 0.52877
36 4H2W 5GP 0.000001175 0.52266
37 3UH0 TSB 0.00001111 0.51348
38 2CJA ATP 0.000009158 0.48843
39 4HWS 1B3 0.00001499 0.48504
40 1SS4 GSH 0.000599 0.45715
41 1SS4 GSH 0.000599 0.45715
42 3ERR AMP 0.00004007 0.45086
43 4DZ1 DAL 0.005931 0.44132
44 4HWT 1B2 0.0002957 0.43893
45 2WMC MGP 0.005452 0.43849
46 2QHV OC9 0.005412 0.4349
47 3TEG DAH 0.0009069 0.42818
48 4GID 0GH 0.02371 0.42225
49 3VMG 9CA 0.009018 0.41516
50 1UY4 XYP XYP XYP XYP 0.01502 0.41271
51 3T4L ZEA 0.001646 0.40623
52 3PNA CMP 0.02105 0.40512
53 3PNA CMP 0.02105 0.40512
54 3PNA CMP 0.02109 0.40509
55 1M83 ATP 0.01407 0.40501
56 3MEH THP 0.01487 0.40472
57 3LL5 IPE 0.0115 0.40182
58 3LL5 ADP 0.0115 0.40182
59 3E7S AT2 0.03037 0.40163
60 3LL5 ADP 0.01194 0.40112
61 1L7P SEP 0.02546 0.40093
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