Receptor
PDB id Resolution Class Description Source Keywords
1OBH 2.2 Å EC: 6.1.1.4 LEUCYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS COMPLEXED WITH A PRE-TRANSFER EDITING SUBSTRATE ANALOGUE IN BOTH S YNTHETIC ACTIVE SITE AND EDITING SITE THERMUS THERMOPHILUS SYNTHETASE AMINOACYL-TRNA SYNTHETASE CLASS I AMINOACYL-TRNA SYNTHETASE ATP + L-LEUCINE + TRNA (LEU) -> AMP + PPI L- LEUCYL-TRNA(LEU)
Ref.: STRUCTURAL AND MECHANISTIC BASIS OF PRE- AND POSTTRANSFER EDITING BY LEUCYL-TRNA SYNTHETASE MOL.CELL V. 11 951 2003
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
NVA LMS A:1816;
A:1818;
Valid;
Valid;
none;
none;
submit data
446.465 n/a S(=O)...
SO4 A:1501;
A:1502;
A:1503;
A:1504;
A:1505;
A:1506;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
submit data
96.063 O4 S [O-]S...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2V0C 1.85 Å EC: 6.1.1.4 LEUCYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS COMPLEXED WITH A SULPHAMOYL ANALOGUE OF LEUCYL-ADENYLATE IN THE S YNTHETIC SITE AND AN ADDUCT OF AMP WITH 5-FLUORO-1,3- DI HYDRO-1-HYDROXY-2,1-BENZOXABOROLE (AN2690) IN THE EDI TING SIT THERMUS THERMOPHILUS LIGASE NUCLEOTIDE-BINDING PROTEIN BIOSYNTHESIS CLSS I AMINOACYL- TRNA SYNTHETASE ATP + L-LEUCINE + TRNA (LEU) GIVES AMP + PPI + L-LEUCYL-TRNA(LEU) AMINOACYL-TRNA SYNTHETASE ZINC ATP-BINDING METAL-BINDING
Ref.: AN ANTIFUNGAL AGENT INHIBITS AN AMINOACYL-TRNA SYNTHETASE BY TRAPPING TRNA IN THE EDITING SITE. SCIENCE V. 316 1759 2007
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 8 families.
1 1OBC - NVA 2AD n/a n/a
2 1H3N - LEU LMS n/a n/a
3 2V0C - LEU LMS n/a n/a
4 1OBH - NVA LMS n/a n/a
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 8 families.
1 1OBC - NVA 2AD n/a n/a
2 1H3N - LEU LMS n/a n/a
3 2V0C - LEU LMS n/a n/a
4 1OBH - NVA LMS n/a n/a
50% Homology Family (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 1OBC - NVA 2AD n/a n/a
2 1H3N - LEU LMS n/a n/a
3 2V0C - LEU LMS n/a n/a
4 1OBH - NVA LMS n/a n/a
5 6Q8B - L3U C16 H26 N4 O9 S CC(C)C[C@@....
6 6Q8A - HQ5 C15 H25 N5 O8 S CC(C)C[C@@....
7 6Q8C - LSU C15 H24 N4 O9 S CC(C)C[C@@....
8 6Q89 - LSS C16 H25 N7 O7 S CC(C)C[C@@....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: NVA LMS; Similar ligands found: 259
No: Ligand ECFP6 Tc MDL keys Tc
1 NVA LMS 1 1
2 LEU LMS 0.808989 0.954545
3 NSS 0.806818 0.942529
4 A5A 0.770115 0.930233
5 54H 0.752809 0.909091
6 VMS 0.752809 0.909091
7 52H 0.752809 0.898876
8 TSB 0.744444 0.91954
9 53H 0.744444 0.898876
10 SSA 0.741573 0.920455
11 LSS 0.728261 0.943182
12 5CA 0.725275 0.920455
13 G5A 0.715909 0.920455
14 DSZ 0.709677 0.920455
15 KAA 0.705263 0.911111
16 GSU 0.705263 0.942529
17 5AS 0.686047 0.898876
18 YSA 0.653465 0.920455
19 8X1 0.652632 0.911111
20 P5A 0.62 0.901099
21 LMS 0.616279 0.906977
22 8PZ 0.61165 0.920455
23 B1U 0.605769 0.851064
24 WSA 0.605505 0.931035
25 4YB 0.598131 0.921348
26 8Q2 0.557522 0.89011
27 3DH 0.556818 0.693182
28 SON 0.553191 0.766667
29 649 0.548673 0.901099
30 NVA 2AD 0.546392 0.761364
31 5AL 0.545455 0.784091
32 AMP 0.544444 0.75
33 A 0.544444 0.75
34 A2D 0.543478 0.752809
35 45A 0.543478 0.752809
36 ABM 0.543478 0.752809
37 DAL AMP 0.539216 0.784091
38 PRX 0.536082 0.795455
39 BA3 0.531915 0.752809
40 CA0 0.53125 0.755556
41 ADX 0.53125 0.863636
42 4AD 0.528846 0.797753
43 B4P 0.526316 0.752809
44 AP5 0.526316 0.752809
45 5X8 0.525773 0.704545
46 KG4 0.525773 0.755556
47 AHX 0.52381 0.78022
48 SRA 0.521739 0.775281
49 GAP 0.52 0.755556
50 8LH 0.519608 0.786517
51 9ZA 0.519231 0.769231
52 9ZD 0.519231 0.769231
53 AOC 0.516129 0.674157
54 AP2 0.515789 0.747253
55 A12 0.515789 0.747253
56 AU1 0.515464 0.755556
57 M33 0.515464 0.764045
58 8LE 0.514852 0.758242
59 XYA 0.511905 0.670455
60 ADN 0.511905 0.670455
61 RAB 0.511905 0.670455
62 5CD 0.511628 0.659091
63 ADP 0.510417 0.752809
64 ATP 0.510204 0.752809
65 50T 0.510204 0.725275
66 HEJ 0.510204 0.752809
67 8LQ 0.509615 0.806818
68 9K8 0.509259 0.773196
69 TXA 0.509259 0.766667
70 DTA 0.505618 0.685393
71 AN2 0.505155 0.764045
72 AT4 0.505155 0.766667
73 ADP MG 0.505155 0.770115
74 APR 0.50505 0.752809
75 5FA 0.50505 0.752809
76 AR6 0.50505 0.752809
77 AQP 0.50505 0.752809
78 SRP 0.504854 0.786517
79 5SV 0.504762 0.76087
80 8QN 0.504762 0.784091
81 XAH 0.504505 0.774194
82 ARG AMP 0.504425 0.747368
83 SLU 0.504065 0.868132
84 SAP 0.5 0.777778
85 MTA 0.5 0.693182
86 PAJ 0.5 0.752688
87 5N5 0.5 0.651685
88 AD9 0.5 0.736264
89 AGS 0.5 0.777778
90 SA8 0.5 0.695652
91 1ZZ 0.495413 0.774194
92 ME8 0.495413 0.813187
93 NB8 0.495413 0.78022
94 SAH 0.49505 0.707865
95 ACP 0.494949 0.755556
96 J7C 0.494737 0.673913
97 EP4 0.494382 0.659341
98 A4D 0.494253 0.670455
99 48N 0.491379 0.76087
100 MYR AMP 0.490909 0.774194
101 3UK 0.490741 0.755556
102 OAD 0.490741 0.775281
103 S7M 0.490385 0.736264
104 ANP 0.490196 0.755556
105 APC 0.49 0.747253
106 M2T 0.488889 0.7
107 TYR AMP 0.486726 0.777778
108 9SN 0.486486 0.723404
109 LAD 0.486239 0.771739
110 0UM 0.485981 0.706522
111 AMO 0.485981 0.786517
112 ADP PO3 0.485149 0.770115
113 RBY 0.485149 0.747253
114 ATP MG 0.485149 0.770115
115 APC MG 0.485149 0.752809
116 ADV 0.485149 0.747253
117 NEC 0.484211 0.651685
118 3OD 0.481818 0.775281
119 PTJ 0.481818 0.76087
120 DLL 0.481481 0.764045
121 A22 0.481132 0.744444
122 SAI 0.480392 0.681319
123 VRT 0.480392 0.75
124 SFG 0.48 0.693182
125 H1Q 0.48 0.761364
126 YLB 0.478992 0.795699
127 YLP 0.478632 0.776596
128 9X8 0.477064 0.777778
129 K15 0.477064 0.691489
130 OOB 0.476636 0.764045
131 GEK 0.476636 0.741573
132 VO4 ADP 0.47619 0.764045
133 SMM 0.47619 0.731183
134 ADP VO4 0.47619 0.764045
135 ACQ 0.475728 0.755556
136 T99 0.475728 0.766667
137 TAT 0.475728 0.766667
138 SAM 0.475728 0.736264
139 A7D 0.474747 0.696629
140 6RE 0.473684 0.684783
141 B5V 0.472727 0.747253
142 PR8 0.472727 0.763441
143 WAQ 0.472727 0.769231
144 ADQ 0.472222 0.736264
145 HQG 0.471698 0.744444
146 EEM 0.471154 0.698925
147 OMR 0.470588 0.765957
148 B5M 0.469027 0.758242
149 DSH 0.46875 0.673913
150 SXZ 0.468468 0.717391
151 00A 0.46789 0.731183
152 MAP 0.46729 0.73913
153 ATF 0.466667 0.728261
154 ALF ADP 0.466667 0.72043
155 ADP ALF 0.466667 0.72043
156 7MD 0.465517 0.774194
157 A3N 0.463918 0.630435
158 AYB 0.463415 0.787234
159 25A 0.462963 0.752809
160 6YZ 0.462264 0.755556
161 NAX 0.462185 0.763441
162 AMP DBH 0.46087 0.717391
163 F2R 0.459677 0.739583
164 GJV 0.459184 0.677419
165 S4M 0.459184 0.694737
166 A1R 0.458716 0.75
167 A3R 0.458716 0.75
168 TXE 0.458333 0.731183
169 7C5 0.456897 0.677419
170 FA5 0.45614 0.786517
171 B5Y 0.45614 0.758242
172 YAP 0.45614 0.777778
173 FYA 0.455357 0.764045
174 BIS 0.455357 0.731183
175 JB6 0.455357 0.788889
176 YLC 0.454545 0.774194
177 MAO 0.454545 0.741935
178 7MC 0.454545 0.776596
179 25L 0.451327 0.744444
180 A3T 0.45098 0.693182
181 ADP BMA 0.45045 0.736264
182 OZV 0.449541 0.752809
183 DQV 0.449153 0.764045
184 GTA 0.449153 0.736842
185 ZAS 0.447917 0.688889
186 IOT 0.447154 0.731959
187 A3S 0.445545 0.704545
188 COD 0.444444 0.770833
189 KOY 0.441667 0.7
190 62X 0.441441 0.659794
191 MHZ 0.441176 0.6875
192 A3G 0.438776 0.696629
193 SO8 0.438095 0.707865
194 DND 0.438017 0.766667
195 NAI 0.438017 0.731183
196 NXX 0.438017 0.766667
197 TXD 0.438017 0.731183
198 6V0 0.438017 0.723404
199 TAD 0.436975 0.752688
200 KH3 0.436975 0.684211
201 2VA 0.436893 0.677778
202 5AD 0.436782 0.627907
203 4UV 0.435897 0.73913
204 AF3 ADP 3PG 0.434426 0.734043
205 TYM 0.434426 0.786517
206 J4G 0.433628 0.797753
207 A A 0.433628 0.752809
208 AHZ 0.433333 0.755319
209 LAQ 0.433333 0.755319
210 YLA 0.432 0.739583
211 AP0 0.430894 0.723404
212 EO7 0.43 0.866667
213 LPA AMP 0.429752 0.755319
214 GA7 0.428571 0.766667
215 4UU 0.428571 0.73913
216 A5D 0.428571 0.685393
217 CNA 0.428571 0.786517
218 AFH 0.428571 0.715789
219 80F 0.426357 0.739583
220 4UW 0.42623 0.734043
221 UP5 0.42623 0.73913
222 N5O 0.424242 0.685393
223 S8M 0.423423 0.722222
224 3AM 0.42268 0.719101
225 G3A 0.420168 0.723404
226 ATP A A A 0.418803 0.761364
227 ATP A 0.418803 0.761364
228 N0B 0.41791 0.739583
229 YLY 0.416667 0.768421
230 G5P 0.416667 0.723404
231 AAT 0.416667 0.659574
232 AR6 AR6 0.416667 0.752809
233 A4P 0.416 0.69
234 N5A 0.415842 0.662921
235 6MZ 0.415842 0.741573
236 A3D 0.415385 0.795455
237 HY8 0.414634 0.663158
238 KB1 0.413793 0.652632
239 A6D 0.412281 0.673684
240 NAJ PZO 0.412214 0.741935
241 A3P 0.411765 0.75
242 A2P 0.411765 0.738636
243 NAQ 0.410448 0.78022
244 HZ2 0.409836 0.663158
245 T5A 0.409449 0.739583
246 139 0.409449 0.726316
247 3NZ 0.408696 0.703297
248 4TC 0.408 0.741935
249 UPA 0.408 0.731183
250 6IA 0.407407 0.752688
251 FB0 0.404255 0.73
252 PPS 0.40367 0.842697
253 7D5 0.402062 0.684783
254 D3Y 0.401786 0.688889
255 AMP NAD 0.4 0.764045
256 NAJ PYZ 0.4 0.71134
257 4TA 0.4 0.747368
258 7D7 0.4 0.611111
259 NAD 0.4 0.784091
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2V0C; Ligand: ANZ; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 2v0c.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 2V0C; Ligand: LEU LMS; 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: 2v0c.bio1) has 25 residues
No: Leader PDB Ligand Sequence Similarity
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