Receptor
PDB id Resolution Class Description Source Keywords
1OBC 2.1 Å EC: 6.1.1.4 LEUCYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS COMPLEXED WITH A POST-TRANSFER EDITING SUBSTRATE ANALOGUE THERMUS THERMOPHILUS AMINOACYL-TRNA SYNTHETASE CLASS I AMINOACYL-TRNA SYNTHETASE ATP + L-LEUCINE + TRNA (LEU) -> AMP + PPI L- LEUCYL-TRNA(LEU) SYNTHETASE
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
LEU LMS A:1814;
Valid;
none;
submit data
460.492 n/a S(=O)...
NVA 2AD A:1815;
Valid;
none;
submit data
366.402 n/a O=C(N...
ZN A:1812;
A:1813;
Part of Protein;
Part of Protein;
none;
none;
submit data
65.409 Zn [Zn+2...
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: LEU LMS; Similar ligands found: 250
No: Ligand ECFP6 Tc MDL keys Tc
1 LEU LMS 1 1
2 NVA LMS 0.808989 0.954545
3 NSS 0.797753 0.942529
4 LSS 0.797753 0.988372
5 A5A 0.781609 0.930233
6 54H 0.764045 0.953488
7 VMS 0.764045 0.953488
8 TSB 0.755556 0.91954
9 52H 0.744444 0.942529
10 53H 0.736264 0.942529
11 SSA 0.733333 0.920455
12 G5A 0.727273 0.920455
13 5CA 0.717391 0.920455
14 DSZ 0.702128 0.920455
15 KAA 0.680412 0.89011
16 GSU 0.680412 0.920455
17 5AS 0.678161 0.877778
18 YSA 0.647059 0.920455
19 8X1 0.645833 0.89011
20 8PZ 0.621359 0.920455
21 P5A 0.613861 0.880435
22 LMS 0.609195 0.906977
23 WSA 0.6 0.931035
24 B1U 0.584906 0.851064
25 4YB 0.577982 0.9
26 649 0.571429 0.880435
27 8Q2 0.566372 0.89011
28 5AL 0.555556 0.784091
29 45A 0.554348 0.752809
30 ABM 0.554348 0.752809
31 DAL AMP 0.54902 0.784091
32 SON 0.547368 0.766667
33 A 0.538462 0.75
34 AMP 0.538462 0.75
35 A2D 0.537634 0.752809
36 3DH 0.533333 0.674157
37 8LH 0.529412 0.786517
38 9ZD 0.528846 0.788889
39 9ZA 0.528846 0.788889
40 BA3 0.526316 0.752809
41 M33 0.525773 0.764045
42 CA0 0.525773 0.755556
43 4AD 0.52381 0.797753
44 AP5 0.520833 0.752809
45 B4P 0.520833 0.752809
46 KG4 0.520408 0.755556
47 8LQ 0.519231 0.806818
48 AHX 0.518868 0.78022
49 TXA 0.518519 0.766667
50 SRA 0.516129 0.775281
51 PRX 0.515152 0.755556
52 GAP 0.514852 0.755556
53 8QN 0.514286 0.784091
54 48N 0.513043 0.76087
55 AOC 0.510638 0.674157
56 AP2 0.510417 0.747253
57 A12 0.510417 0.747253
58 AU1 0.510204 0.755556
59 ADX 0.510204 0.863636
60 8LE 0.509804 0.797753
61 PAJ 0.509434 0.791209
62 ADN 0.505882 0.670455
63 XYA 0.505882 0.670455
64 RAB 0.505882 0.670455
65 5CD 0.505747 0.659091
66 ADP 0.505155 0.752809
67 HEJ 0.50505 0.752809
68 50T 0.50505 0.725275
69 ATP 0.50505 0.752809
70 5X8 0.50505 0.704545
71 9K8 0.504587 0.755102
72 ADP MG 0.5 0.770115
73 AR6 0.5 0.752809
74 DTA 0.5 0.685393
75 AN2 0.5 0.764045
76 AQP 0.5 0.752809
77 SRP 0.5 0.786517
78 5FA 0.5 0.752809
79 SLU 0.5 0.868132
80 APR 0.5 0.752809
81 AT4 0.5 0.766667
82 AGS 0.49505 0.777778
83 SAP 0.49505 0.777778
84 AD9 0.49505 0.736264
85 5N5 0.494253 0.651685
86 NB8 0.490909 0.78022
87 PTJ 0.490909 0.8
88 ACP 0.49 0.755556
89 EP4 0.488889 0.696629
90 A4D 0.488636 0.670455
91 ARG AMP 0.486957 0.729167
92 XAH 0.486726 0.755319
93 OAD 0.486239 0.775281
94 5SV 0.485981 0.723404
95 ANP 0.485437 0.755556
96 APC 0.485149 0.747253
97 M2T 0.483516 0.738636
98 TYR AMP 0.482456 0.777778
99 AMO 0.481481 0.786517
100 ADP PO3 0.480392 0.770115
101 ADV 0.480392 0.747253
102 SA8 0.480392 0.677419
103 RBY 0.480392 0.747253
104 APC MG 0.480392 0.752809
105 ATP MG 0.480392 0.770115
106 NEC 0.479167 0.633333
107 MTA 0.478261 0.693182
108 3OD 0.477477 0.775281
109 ME8 0.477477 0.793478
110 1ZZ 0.477477 0.736842
111 DLL 0.477064 0.764045
112 A22 0.476636 0.744444
113 H1Q 0.475248 0.761364
114 MYR AMP 0.473214 0.736842
115 9X8 0.472727 0.777778
116 3UK 0.472727 0.755556
117 OOB 0.472222 0.764045
118 ADP VO4 0.471698 0.764045
119 VO4 ADP 0.471698 0.764045
120 S7M 0.471698 0.698925
121 TAT 0.471154 0.766667
122 ACQ 0.471154 0.755556
123 T99 0.471154 0.766667
124 6RE 0.46875 0.666667
125 WAQ 0.468468 0.75
126 LAD 0.468468 0.752688
127 ADQ 0.46789 0.736264
128 HQG 0.46729 0.744444
129 B5M 0.464912 0.758242
130 SXZ 0.464286 0.736264
131 00A 0.463636 0.731183
132 MAP 0.462963 0.73913
133 ADP ALF 0.462264 0.72043
134 ATF 0.462264 0.728261
135 ALF ADP 0.462264 0.72043
136 YLP 0.462185 0.739583
137 7MD 0.461538 0.755319
138 SAH 0.461538 0.688889
139 SAI 0.461538 0.663043
140 SFG 0.460784 0.674157
141 A3T 0.460784 0.693182
142 ADP BMA 0.459459 0.736264
143 A3N 0.459184 0.630435
144 J7C 0.459184 0.655914
145 25A 0.458716 0.752809
146 GEK 0.458716 0.722222
147 6YZ 0.457944 0.755556
148 SMM 0.457944 0.731183
149 DQV 0.457627 0.764045
150 SAM 0.457143 0.717391
151 9SN 0.45614 0.723404
152 PR8 0.455357 0.744681
153 B5V 0.455357 0.747253
154 OMR 0.454545 0.729167
155 TXE 0.454545 0.731183
156 GJV 0.454545 0.659574
157 A3R 0.454545 0.75
158 0UM 0.454545 0.670213
159 S4M 0.454545 0.677083
160 A1R 0.454545 0.75
161 7C5 0.452991 0.677419
162 EEM 0.45283 0.680851
163 COD 0.452381 0.789474
164 B5Y 0.452174 0.758242
165 FA5 0.452174 0.786517
166 YAP 0.452174 0.777778
167 NVA 2AD 0.451923 0.722222
168 FYA 0.451327 0.764045
169 MHZ 0.45098 0.670103
170 7MC 0.45082 0.757895
171 AP0 0.45082 0.723404
172 YLC 0.45082 0.755319
173 YLB 0.45082 0.757895
174 MAO 0.45 0.723404
175 A3G 0.44898 0.696629
176 DSH 0.44898 0.655914
177 25L 0.447368 0.744444
178 K15 0.446429 0.65625
179 NAI 0.446281 0.731183
180 OZV 0.445455 0.752809
181 TAD 0.445378 0.752688
182 GTA 0.445378 0.736842
183 F2R 0.444444 0.721649
184 AMP DBH 0.444444 0.717391
185 ZAS 0.443299 0.688889
186 A3S 0.441176 0.704545
187 A7D 0.441176 0.677778
188 JB6 0.438596 0.769231
189 BIS 0.438596 0.712766
190 KOY 0.438017 0.681319
191 GA7 0.436975 0.766667
192 CNA 0.436508 0.786517
193 AYB 0.436508 0.75
194 DND 0.434426 0.766667
195 TXD 0.434426 0.731183
196 NXX 0.434426 0.766667
197 4UW 0.434426 0.734043
198 6V0 0.434426 0.723404
199 NAX 0.434426 0.744681
200 SO8 0.433962 0.707865
201 2VA 0.432692 0.715909
202 4UV 0.432203 0.73913
203 5AD 0.431818 0.627907
204 AF3 ADP 3PG 0.430894 0.734043
205 TYM 0.430894 0.786517
206 A A 0.429825 0.752809
207 LAQ 0.429752 0.736842
208 AHZ 0.429752 0.736842
209 LPA AMP 0.42623 0.736842
210 EO7 0.425743 0.866667
211 4UU 0.425 0.73913
212 AFH 0.425 0.715789
213 62X 0.424779 0.677083
214 A5D 0.424528 0.685393
215 80F 0.423077 0.739583
216 UP5 0.422764 0.73913
217 HY8 0.422764 0.645833
218 IOT 0.420635 0.714286
219 VRT 0.420561 0.711111
220 N5O 0.42 0.666667
221 NAJ PZO 0.419847 0.741935
222 3AM 0.418367 0.719101
223 NAQ 0.41791 0.78022
224 J4G 0.417391 0.777778
225 YLA 0.417323 0.721649
226 6IA 0.416667 0.771739
227 G3A 0.416667 0.723404
228 594 0.416667 0.808081
229 ATP A A A 0.415254 0.761364
230 ATP A 0.415254 0.761364
231 G5P 0.413223 0.723404
232 AR6 AR6 0.413223 0.752809
233 A4P 0.412698 0.69
234 N5A 0.411765 0.644444
235 6MZ 0.411765 0.741573
236 KH3 0.409836 0.649485
237 A2P 0.407767 0.738636
238 A3P 0.407767 0.75
239 NAD 0.407692 0.784091
240 NAJ PYZ 0.407407 0.71134
241 T5A 0.40625 0.739583
242 139 0.40625 0.726316
243 3NZ 0.405172 0.703297
244 UPA 0.404762 0.731183
245 4TC 0.404762 0.741935
246 N0B 0.404412 0.721649
247 YLY 0.402985 0.75
248 A3D 0.401515 0.795455
249 FB0 0.401408 0.73
250 AAT 0.4 0.642105
Ligand no: 2; Ligand: NVA 2AD; Similar ligands found: 172
No: Ligand ECFP6 Tc MDL keys Tc
1 NVA 2AD 1 1
2 VRT 0.78481 0.985507
3 2VA 0.725 0.887324
4 SO8 0.719512 0.928571
5 NVA LMS 0.546392 0.761364
6 A3T 0.533333 0.913043
7 A3S 0.52809 0.927536
8 A3G 0.505747 0.914286
9 RAB 0.5 0.884058
10 XYA 0.5 0.884058
11 ADN 0.5 0.884058
12 3DH 0.494118 0.833333
13 NEC 0.488636 0.857143
14 2AM 0.476744 0.75641
15 DTA 0.47619 0.773333
16 MTA 0.470588 0.833333
17 D3Y 0.47 0.901408
18 7D7 0.468354 0.777778
19 5X8 0.468085 0.847222
20 J7C 0.466667 0.826667
21 7D5 0.465116 0.703704
22 5CD 0.463415 0.816901
23 3NZ 0.461538 0.890411
24 J4G 0.461538 0.7875
25 0UM 0.460784 0.891892
26 A2P 0.456522 0.721519
27 DAL AMP 0.455446 0.794872
28 3AM 0.454545 0.74359
29 SAH 0.453608 0.849315
30 LEU LMS 0.451923 0.722222
31 5N5 0.451219 0.857143
32 GEK 0.45098 0.84
33 A2D 0.450549 0.759494
34 S7M 0.45 0.855263
35 A 0.449438 0.75641
36 AMP 0.449438 0.75641
37 PRX 0.447917 0.807692
38 EP4 0.447059 0.810811
39 AN2 0.446809 0.75
40 NSS 0.446602 0.727273
41 4AD 0.446602 0.810127
42 A4D 0.445783 0.857143
43 7D3 0.445652 0.707317
44 OVE 0.444444 0.728395
45 8LE 0.444444 0.743902
46 6RE 0.444444 0.84
47 5AL 0.444444 0.772152
48 SA8 0.443299 0.853333
49 ATR 0.443299 0.734177
50 7D4 0.442105 0.707317
51 CA0 0.442105 0.7625
52 M2T 0.44186 0.813333
53 BA3 0.44086 0.759494
54 A3P 0.44086 0.734177
55 A5A 0.44 0.693182
56 ATP 0.4375 0.759494
57 SFG 0.4375 0.859155
58 5AD 0.4375 0.782609
59 HEJ 0.4375 0.759494
60 KG4 0.4375 0.7625
61 8QN 0.436893 0.772152
62 AP5 0.43617 0.759494
63 ADP 0.43617 0.759494
64 B4P 0.43617 0.759494
65 5AS 0.43617 0.688889
66 8LH 0.435644 0.797468
67 ABM 0.434783 0.759494
68 45A 0.434783 0.759494
69 SAM 0.434343 0.855263
70 LMS 0.433333 0.670455
71 AQP 0.43299 0.759494
72 5FA 0.43299 0.759494
73 A7D 0.431579 0.861111
74 AT4 0.431579 0.731707
75 52H 0.431373 0.67033
76 54H 0.431373 0.677778
77 A2R 0.431373 0.75
78 VMS 0.431373 0.677778
79 PPS 0.43 0.670455
80 EEM 0.43 0.855263
81 SXZ 0.429907 0.831169
82 ME8 0.429907 0.783133
83 1ZZ 0.429907 0.761905
84 3AD 0.428571 0.869565
85 AHX 0.428571 0.790123
86 SAP 0.428571 0.722892
87 PAP 0.428571 0.746835
88 3D1 0.428571 0.859155
89 3L1 0.428571 0.859155
90 AGS 0.428571 0.722892
91 A22 0.427184 0.75
92 53H 0.427184 0.67033
93 8LQ 0.427184 0.797468
94 TSB 0.427184 0.704545
95 ADX 0.427083 0.689655
96 M33 0.427083 0.772152
97 OAD 0.424528 0.78481
98 K15 0.424528 0.844156
99 NA7 0.424528 0.753086
100 SAI 0.424242 0.837838
101 G5A 0.424242 0.707865
102 DSH 0.423913 0.826667
103 N5O 0.423913 0.9
104 9ZA 0.423077 0.73494
105 5SV 0.423077 0.768293
106 9ZD 0.423077 0.73494
107 50T 0.42268 0.75
108 SMM 0.421569 0.822785
109 SRP 0.421569 0.797468
110 SSA 0.421569 0.727273
111 GAP 0.42 0.78481
112 V3L 0.42 0.7375
113 LSS 0.419048 0.711111
114 PAJ 0.419048 0.780488
115 AR6 0.418367 0.759494
116 APR 0.418367 0.759494
117 2A5 0.418367 0.7625
118 ACK 0.417582 0.727273
119 QQY 0.417582 0.691358
120 NB8 0.416667 0.768293
121 TXA 0.416667 0.775
122 PTJ 0.416667 0.746988
123 SON 0.416667 0.753086
124 Y3J 0.416667 0.736111
125 3OD 0.416667 0.78481
126 ARG AMP 0.415929 0.77381
127 DLL 0.415094 0.75
128 N5A 0.414894 0.871429
129 S4M 0.414894 0.822785
130 GJV 0.414894 0.828947
131 XAH 0.414414 0.761905
132 AD9 0.414141 0.740741
133 A5D 0.414141 0.773333
134 5CA 0.413462 0.727273
135 SRA 0.413043 0.719512
136 MYR AMP 0.412844 0.783133
137 0T1 0.412698 0.790698
138 AU1 0.412371 0.740741
139 9X8 0.411215 0.743902
140 AP2 0.410526 0.753086
141 A12 0.410526 0.753086
142 9SN 0.409091 0.705882
143 NPW 0.408333 0.761905
144 ACP 0.408163 0.7625
145 KAA 0.407407 0.703297
146 WAQ 0.407407 0.756098
147 GSU 0.407407 0.707865
148 LAD 0.407407 0.780488
149 PR8 0.407407 0.771084
150 YLB 0.40678 0.807229
151 QQX 0.406593 0.682927
152 TAT 0.405941 0.731707
153 3AT 0.405941 0.759494
154 T99 0.405941 0.731707
155 ACQ 0.405941 0.7625
156 ANP 0.405941 0.740741
157 DSZ 0.40566 0.707865
158 ADQ 0.40566 0.7625
159 AMO 0.40566 0.797468
160 48N 0.405172 0.768293
161 YLP 0.405172 0.785714
162 A3N 0.404255 0.821918
163 APC 0.40404 0.753086
164 HQG 0.403846 0.75
165 ZAS 0.402174 0.8
166 ADP MG 0.402062 0.779221
167 AAT 0.401961 0.805195
168 62X 0.401869 0.8
169 HY8 0.401709 0.855263
170 NAX 0.401709 0.771084
171 8X1 0.4 0.703297
172 KH3 0.4 0.857143
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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