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 7 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 7 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 (4)
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
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: NVA LMS; Similar ligands found: 239
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 VMS 0.752809 0.909091
6 54H 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 WSA 0.605505 0.931035
24 4YB 0.598131 0.921348
25 8Q2 0.557522 0.89011
26 3DH 0.556818 0.693182
27 SON 0.553191 0.766667
28 649 0.548673 0.901099
29 NVA 2AD 0.546392 0.761364
30 5AL 0.545455 0.784091
31 A 0.544444 0.75
32 AMP 0.544444 0.75
33 ABM 0.543478 0.752809
34 A2D 0.543478 0.752809
35 DAL AMP 0.539216 0.784091
36 PRX 0.536082 0.795455
37 BA3 0.531915 0.752809
38 CA0 0.53125 0.755556
39 ADX 0.53125 0.863636
40 4AD 0.528846 0.797753
41 AP5 0.526316 0.752809
42 B4P 0.526316 0.752809
43 5X8 0.525773 0.704545
44 AHX 0.52381 0.78022
45 SRA 0.521739 0.775281
46 GAP 0.52 0.755556
47 9ZA 0.519231 0.769231
48 9ZD 0.519231 0.769231
49 AOC 0.516129 0.674157
50 AP2 0.515789 0.747253
51 A12 0.515789 0.747253
52 M33 0.515464 0.764045
53 AU1 0.515464 0.755556
54 RAB 0.511905 0.670455
55 ADN 0.511905 0.670455
56 XYA 0.511905 0.670455
57 5CD 0.511628 0.659091
58 ADP 0.510417 0.752809
59 50T 0.510204 0.725275
60 ATP 0.510204 0.752809
61 HEJ 0.510204 0.752809
62 9K8 0.509259 0.773196
63 TXA 0.509259 0.766667
64 DTA 0.505618 0.685393
65 AN2 0.505155 0.764045
66 AT4 0.505155 0.766667
67 AQP 0.50505 0.752809
68 AR6 0.50505 0.752809
69 APR 0.50505 0.752809
70 5FA 0.50505 0.752809
71 SRP 0.504854 0.786517
72 5SV 0.504762 0.76087
73 8QN 0.504762 0.784091
74 XAH 0.504505 0.774194
75 ARG AMP 0.504425 0.747368
76 SLU 0.504065 0.868132
77 SA8 0.5 0.695652
78 MTA 0.5 0.693182
79 PAJ 0.5 0.752688
80 5N5 0.5 0.651685
81 AD9 0.5 0.736264
82 AGS 0.5 0.777778
83 SAP 0.5 0.777778
84 ME8 0.495413 0.813187
85 NB8 0.495413 0.78022
86 1ZZ 0.495413 0.774194
87 SAH 0.49505 0.707865
88 ACP 0.494949 0.755556
89 J7C 0.494737 0.673913
90 EP4 0.494382 0.659341
91 A4D 0.494253 0.670455
92 48N 0.491379 0.76087
93 MYR AMP 0.490909 0.774194
94 3UK 0.490741 0.755556
95 OAD 0.490741 0.775281
96 S7M 0.490385 0.736264
97 ANP 0.490196 0.755556
98 APC 0.49 0.747253
99 M2T 0.488889 0.7
100 TYR AMP 0.486726 0.777778
101 9SN 0.486486 0.723404
102 LAD 0.486239 0.771739
103 0UM 0.485981 0.706522
104 AMO 0.485981 0.786517
105 RBY 0.485149 0.747253
106 ADV 0.485149 0.747253
107 ADP PO3 0.485149 0.770115
108 NEC 0.484211 0.651685
109 3OD 0.481818 0.775281
110 PTJ 0.481818 0.76087
111 DLL 0.481481 0.764045
112 A22 0.481132 0.744444
113 SAI 0.480392 0.681319
114 VRT 0.480392 0.75
115 SFG 0.48 0.693182
116 YLB 0.478992 0.795699
117 YLP 0.478632 0.776596
118 K15 0.477064 0.691489
119 9X8 0.477064 0.777778
120 OOB 0.476636 0.764045
121 GEK 0.476636 0.741573
122 SMM 0.47619 0.731183
123 VO4 ADP 0.47619 0.764045
124 ADP VO4 0.47619 0.764045
125 ACQ 0.475728 0.755556
126 SAM 0.475728 0.736264
127 TAT 0.475728 0.766667
128 T99 0.475728 0.766667
129 A7D 0.474747 0.696629
130 6RE 0.473684 0.684783
131 PR8 0.472727 0.763441
132 WAQ 0.472727 0.769231
133 B5V 0.472727 0.747253
134 ADQ 0.472222 0.736264
135 EEM 0.471154 0.698925
136 OMR 0.470588 0.765957
137 B5M 0.469027 0.758242
138 DSH 0.46875 0.673913
139 SXZ 0.468468 0.717391
140 00A 0.46789 0.731183
141 MAP 0.46729 0.73913
142 ALF ADP 0.466667 0.72043
143 ADP ALF 0.466667 0.72043
144 ATF 0.466667 0.728261
145 7MD 0.465517 0.774194
146 A3N 0.463918 0.630435
147 AYB 0.463415 0.787234
148 25A 0.462963 0.752809
149 6YZ 0.462264 0.755556
150 NAX 0.462185 0.763441
151 AMP DBH 0.46087 0.717391
152 F2R 0.459677 0.739583
153 GJV 0.459184 0.677419
154 S4M 0.459184 0.694737
155 A3R 0.458716 0.75
156 A1R 0.458716 0.75
157 TXE 0.458333 0.731183
158 7C5 0.456897 0.677419
159 YAP 0.45614 0.777778
160 FA5 0.45614 0.786517
161 B5Y 0.45614 0.758242
162 FYA 0.455357 0.764045
163 BIS 0.455357 0.731183
164 JB6 0.455357 0.788889
165 YLC 0.454545 0.774194
166 7MC 0.454545 0.776596
167 MAO 0.454545 0.741935
168 25L 0.451327 0.744444
169 A3T 0.45098 0.693182
170 ADP BMA 0.45045 0.736264
171 DQV 0.449153 0.764045
172 GTA 0.449153 0.736842
173 ZAS 0.447917 0.688889
174 IOT 0.447154 0.731959
175 A3S 0.445545 0.704545
176 COD 0.444444 0.770833
177 62X 0.441441 0.659794
178 MHZ 0.441176 0.6875
179 A3G 0.438776 0.696629
180 SO8 0.438095 0.707865
181 NXX 0.438017 0.766667
182 TXD 0.438017 0.731183
183 NAI 0.438017 0.731183
184 DND 0.438017 0.766667
185 6V0 0.438017 0.723404
186 KH3 0.436975 0.684211
187 TAD 0.436975 0.752688
188 2VA 0.436893 0.677778
189 5AD 0.436782 0.627907
190 4UV 0.435897 0.73913
191 AF3 ADP 3PG 0.434426 0.734043
192 TYM 0.434426 0.786517
193 A A 0.433628 0.752809
194 AHZ 0.433333 0.755319
195 LAQ 0.433333 0.755319
196 YLA 0.432 0.739583
197 AP0 0.430894 0.723404
198 EO7 0.43 0.866667
199 LPA AMP 0.429752 0.755319
200 A5D 0.428571 0.685393
201 AFH 0.428571 0.715789
202 CNA 0.428571 0.786517
203 GA7 0.428571 0.766667
204 4UU 0.428571 0.73913
205 80F 0.426357 0.739583
206 4UW 0.42623 0.734043
207 UP5 0.42623 0.73913
208 S8M 0.423423 0.722222
209 3AM 0.42268 0.719101
210 G3A 0.420168 0.723404
211 ATP A A A 0.418803 0.761364
212 N0B 0.41791 0.739583
213 G5P 0.416667 0.723404
214 AAT 0.416667 0.659574
215 AR6 AR6 0.416667 0.752809
216 YLY 0.416667 0.768421
217 A4P 0.416 0.69
218 A3D 0.415385 0.795455
219 KB1 0.413793 0.652632
220 A6D 0.412281 0.673684
221 NAJ PZO 0.412214 0.741935
222 A3P 0.411765 0.75
223 A2P 0.411765 0.738636
224 NAQ 0.410448 0.78022
225 T5A 0.409449 0.739583
226 139 0.409449 0.726316
227 3NZ 0.408696 0.703297
228 UPA 0.408 0.731183
229 4TC 0.408 0.741935
230 6IA 0.407407 0.752688
231 FB0 0.404255 0.73
232 PPS 0.40367 0.842697
233 7D5 0.402062 0.684783
234 D3Y 0.401786 0.688889
235 AMP NAD 0.4 0.764045
236 NAJ PYZ 0.4 0.71134
237 NAD 0.4 0.784091
238 7D7 0.4 0.611111
239 4TA 0.4 0.747368
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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