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 10 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 10 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 (20)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 6YKW Ki = 1260.73 nM OVZ C25 H40 N6 O7 S CC(C)C[C@@....
2 6YKS Ki = 108.35 nM OVT C25 H39 N5 O7 S CC(C)C[C@@....
3 6Q8B - L3U C16 H26 N4 O9 S CC(C)C[C@@....
4 6YKT Ki = 387.66 nM OVN C21 H39 N5 O8 S CC(C)C[C@@....
5 6YKU Ki = 17.83 nM OVB C24 H34 F3 N5 O8 S CC(C)C[C@@....
6 6YKV Ki = 31.62 nM OVQ C22 H34 N6 O7 S CC(C)C[C@@....
7 7AP2 - RRW C19 H29 N5 O8 S CC(C)C[C@@....
8 6YKO Ki = 5.51 nM OW5 C28 H45 N5 O7 S CCCCCc1ccc....
9 6YKX Ki = 182.35 nM OW2 C26 H41 N7 O8 S CC(C)C[C@@....
10 6Q8A - HQ5 C15 H25 N5 O8 S CC(C)C[C@@....
11 6Q8C - LSU C15 H24 N4 O9 S CC(C)C[C@@....
12 6YKK Ki = 30.94 nM OVK C20 H30 N6 O7 S CC(C)C[C@@....
13 7A0P Ki = 31.28 nM QTW C25 H38 N6 O8 S CC(C)C[C@@....
14 6Q89 - LSS C16 H25 N7 O7 S CC(C)C[C@@....
15 6YKQ Ki = 52.36 nM OVW C25 H47 N5 O7 S CCCCCCCCc1....
16 6YKL Ki = 2.48 nM OVH C23 H35 N5 O7 S CC(C)C[C@@....
17 1OBC - NVA 2AD n/a n/a
18 1H3N - LEU LMS n/a n/a
19 2V0C - LEU LMS n/a n/a
20 1OBH - NVA LMS n/a n/a
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: NVA LMS; Similar ligands found: 284
No: Ligand ECFP6 Tc MDL keys Tc
1 NVA LMS 1 1
2 NSS 0.806818 0.942529
3 A5A 0.770115 0.930233
4 54H 0.752809 0.909091
5 52H 0.752809 0.898876
6 VMS 0.752809 0.909091
7 53H 0.744444 0.898876
8 TSB 0.744444 0.91954
9 SSA 0.741573 0.920455
10 LSS 0.728261 0.943182
11 5CA 0.725275 0.920455
12 G5A 0.715909 0.920455
13 DSZ 0.709677 0.920455
14 KAA 0.705263 0.911111
15 GSU 0.705263 0.942529
16 5AS 0.686047 0.898876
17 YSA 0.653465 0.920455
18 8X1 0.652632 0.911111
19 P5A 0.62 0.901099
20 LMS 0.616279 0.906977
21 8PZ 0.61165 0.920455
22 B1U 0.605769 0.851064
23 WSA 0.605505 0.931035
24 4YB 0.598131 0.921348
25 LEU LMS 0.594059 0.888889
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 45A 0.543478 0.752809
35 A2D 0.543478 0.752809
36 ABM 0.543478 0.752809
37 DAL AMP 0.539216 0.784091
38 QA7 0.539216 0.777778
39 AMP MG 0.538462 0.758621
40 PRX 0.536082 0.795455
41 BA3 0.531915 0.752809
42 ADX 0.53125 0.863636
43 CA0 0.53125 0.755556
44 V2G 0.53 0.76087
45 4AD 0.528846 0.797753
46 AP5 0.526316 0.752809
47 B4P 0.526316 0.752809
48 KG4 0.525773 0.755556
49 5X8 0.525773 0.704545
50 AHX 0.52381 0.78022
51 SRA 0.521739 0.775281
52 GAP 0.52 0.755556
53 8LH 0.519608 0.786517
54 9ZA 0.519231 0.769231
55 9ZD 0.519231 0.769231
56 AOC 0.516129 0.674157
57 A12 0.515789 0.747253
58 AP2 0.515789 0.747253
59 AU1 0.515464 0.755556
60 M33 0.515464 0.764045
61 8LE 0.514852 0.758242
62 ADN 0.511905 0.670455
63 XYA 0.511905 0.670455
64 RAB 0.511905 0.670455
65 5CD 0.511628 0.659091
66 ADP 0.510417 0.752809
67 ATP 0.510204 0.752809
68 HEJ 0.510204 0.752809
69 50T 0.510204 0.725275
70 8LQ 0.509615 0.806818
71 9K8 0.509259 0.773196
72 TXA 0.509259 0.766667
73 DTA 0.505618 0.685393
74 ADP MG 0.505155 0.770115
75 AT4 0.505155 0.766667
76 ADP BEF 0.505155 0.770115
77 AN2 0.505155 0.764045
78 5FA 0.50505 0.752809
79 APR 0.50505 0.752809
80 AQP 0.50505 0.752809
81 AR6 0.50505 0.752809
82 SRP 0.504854 0.786517
83 5SV 0.504762 0.76087
84 QXP 0.504762 0.804348
85 8QN 0.504762 0.784091
86 XAH 0.504505 0.774194
87 ARG AMP 0.504425 0.747368
88 SLU 0.504065 0.868132
89 5N5 0.5 0.651685
90 MTA 0.5 0.693182
91 AGS 0.5 0.777778
92 SA8 0.5 0.695652
93 PAJ 0.5 0.752688
94 AD9 0.5 0.736264
95 NB8 0.495413 0.78022
96 ME8 0.495413 0.813187
97 1ZZ 0.495413 0.774194
98 ANP MG 0.495146 0.784091
99 SAH 0.49505 0.707865
100 ACP 0.494949 0.755556
101 J7C 0.494737 0.673913
102 EP4 0.494382 0.659341
103 A4D 0.494253 0.670455
104 48N 0.491379 0.76087
105 MYR AMP 0.490909 0.774194
106 OAD 0.490741 0.775281
107 3UK 0.490741 0.755556
108 QXG 0.490741 0.795699
109 S7M 0.490385 0.736264
110 ANP 0.490196 0.755556
111 APC 0.49 0.747253
112 M2T 0.488889 0.7
113 9SN 0.486486 0.723404
114 LAD 0.486239 0.771739
115 0UM 0.485981 0.706522
116 AMO 0.485981 0.786517
117 ATP MG 0.485149 0.770115
118 ADP PO3 0.485149 0.770115
119 ADV 0.485149 0.747253
120 APC MG 0.485149 0.752809
121 RBY 0.485149 0.747253
122 NEC 0.484211 0.651685
123 PTJ 0.481818 0.76087
124 3OD 0.481818 0.775281
125 DLL 0.481481 0.764045
126 JNT 0.481481 0.755556
127 A22 0.481132 0.744444
128 SAI 0.480392 0.681319
129 VRT 0.480392 0.75
130 BEF ADP 0.480392 0.752809
131 H1Q 0.48 0.761364
132 SFG 0.48 0.693182
133 YLB 0.478992 0.795699
134 YLP 0.478632 0.776596
135 9X8 0.477064 0.777778
136 K15 0.477064 0.691489
137 GEK 0.476636 0.741573
138 OOB 0.476636 0.764045
139 SMM 0.47619 0.731183
140 ACQ 0.475728 0.755556
141 TAT 0.475728 0.766667
142 SAM 0.475728 0.736264
143 T99 0.475728 0.766667
144 A7D 0.474747 0.696629
145 6RE 0.473684 0.684783
146 R2V 0.472727 0.804348
147 WAQ 0.472727 0.769231
148 B5V 0.472727 0.747253
149 PR8 0.472727 0.763441
150 ADQ 0.472222 0.736264
151 HQG 0.471698 0.744444
152 EEM 0.471154 0.698925
153 OMR 0.470588 0.765957
154 B5M 0.469027 0.758242
155 DSH 0.46875 0.673913
156 SXZ 0.468468 0.717391
157 00A 0.46789 0.731183
158 MAP 0.46729 0.73913
159 ALF ADP 0.466667 0.72043
160 VO4 ADP 0.466667 0.755556
161 ATF 0.466667 0.728261
162 7MD 0.465517 0.774194
163 A3N 0.463918 0.630435
164 AYB 0.463415 0.787234
165 25A 0.462963 0.752809
166 6YZ 0.462264 0.755556
167 NAX 0.462185 0.763441
168 AMP DBH 0.46087 0.717391
169 NWW 0.460674 0.62069
170 F2R 0.459677 0.739583
171 S4M 0.459184 0.694737
172 GJV 0.459184 0.677419
173 A3R 0.458716 0.75
174 RUZ 0.458716 0.897727
175 A1R 0.458716 0.75
176 TXE 0.458333 0.731183
177 7C5 0.456897 0.677419
178 B5Y 0.45614 0.758242
179 KMQ 0.45614 0.747253
180 FA5 0.45614 0.786517
181 BIS 0.455357 0.731183
182 FYA 0.455357 0.764045
183 JB6 0.455357 0.788889
184 YLC 0.454545 0.774194
185 7MC 0.454545 0.776596
186 MAO 0.454545 0.741935
187 25L 0.451327 0.744444
188 RRW 0.451327 0.910112
189 A3T 0.45098 0.693182
190 ADP BMA 0.45045 0.736264
191 OZV 0.449541 0.752809
192 GTA 0.449153 0.736842
193 DQV 0.449153 0.764045
194 ZAS 0.447917 0.688889
195 IOT 0.447154 0.731959
196 ALF ADP 3PG 0.446281 0.734043
197 A3S 0.445545 0.704545
198 COD 0.444444 0.770833
199 NWQ 0.442105 0.625
200 KOY 0.441667 0.7
201 62X 0.441441 0.659794
202 MHZ 0.441176 0.6875
203 KY2 0.440367 0.645833
204 A3G 0.438776 0.696629
205 RSN 0.438596 0.88764
206 SO8 0.438095 0.707865
207 6V0 0.438017 0.723404
208 DND 0.438017 0.766667
209 NAI 0.438017 0.731183
210 TXD 0.438017 0.731183
211 TAD 0.436975 0.752688
212 KH3 0.436975 0.684211
213 2VA 0.436893 0.677778
214 5AD 0.436782 0.627907
215 4UV 0.435897 0.73913
216 V47 0.435185 0.681818
217 TYM 0.434426 0.786517
218 AF3 ADP 3PG 0.434426 0.734043
219 J4G 0.433628 0.797753
220 AHZ 0.433333 0.755319
221 LAQ 0.433333 0.755319
222 YLA 0.432 0.739583
223 L3W 0.430894 0.747253
224 AP0 0.430894 0.723404
225 EO7 0.43 0.866667
226 U4Y 0.429752 0.703297
227 LPA AMP 0.429752 0.755319
228 AFH 0.428571 0.715789
229 4UU 0.428571 0.73913
230 GA7 0.428571 0.766667
231 CNA 0.428571 0.786517
232 A5D 0.428571 0.685393
233 KYE 0.42735 0.649485
234 80F 0.426357 0.739583
235 4UW 0.42623 0.734043
236 UP5 0.42623 0.73913
237 KXW 0.425 0.659574
238 N5O 0.424242 0.685393
239 S8M 0.423423 0.722222
240 3AM 0.42268 0.719101
241 K2K 0.421053 0.648936
242 G3A 0.420168 0.723404
243 KYB 0.419643 0.645833
244 NAD IBO 0.419355 0.772727
245 NAD TDB 0.419355 0.772727
246 ATP A 0.418803 0.761364
247 K3K 0.418803 0.645161
248 ATP A A A 0.418803 0.761364
249 N0B 0.41791 0.739583
250 YLY 0.416667 0.768421
251 G5P 0.416667 0.723404
252 AAT 0.416667 0.659574
253 AR6 AR6 0.416667 0.752809
254 A4P 0.416 0.69
255 N5A 0.415842 0.662921
256 6MZ 0.415842 0.741573
257 A3D 0.415385 0.795455
258 HY8 0.414634 0.663158
259 KB1 0.413793 0.652632
260 RRB 0.413223 0.88764
261 A6D 0.412281 0.673684
262 NAJ PZO 0.412214 0.741935
263 A2P 0.411765 0.738636
264 K3E 0.411765 0.638298
265 A3P 0.411765 0.75
266 NAQ 0.410448 0.78022
267 HZ2 0.409836 0.663158
268 139 0.409449 0.726316
269 T5A 0.409449 0.739583
270 3NZ 0.408696 0.703297
271 4TC 0.408 0.741935
272 UPA 0.408 0.731183
273 6IA 0.407407 0.752688
274 FB0 0.404255 0.73
275 PPS 0.40367 0.842697
276 EU9 0.403226 0.71134
277 7D5 0.402062 0.684783
278 D3Y 0.401786 0.688889
279 KY5 0.401709 0.655914
280 4TA 0.4 0.747368
281 7D7 0.4 0.611111
282 AMP NAD 0.4 0.764045
283 NAD 0.4 0.784091
284 NAJ PYZ 0.4 0.71134
Similar Ligands (3D)
Ligand no: 1; Ligand: NVA LMS; Similar ligands found: 4
No: Ligand Similarity coefficient
1 MSP 0.9377
2 L3U 0.9310
3 MOD 0.9223
4 GDP 0.8600
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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