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
459.484 n/a S(OC(...
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 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: LEU LMS; Similar ligands found: 268
No: Ligand ECFP6 Tc MDL keys Tc
1 LEU LMS 1 1
2 LSS 0.616162 0.920455
3 LMS 0.609195 0.840909
4 5AS 0.604396 0.815217
5 A5A 0.597938 0.863636
6 NVA LMS 0.594059 0.888889
7 VMS 0.585859 0.886364
8 54H 0.585859 0.886364
9 NSS 0.584158 0.876405
10 G5A 0.583333 0.855556
11 TSB 0.58 0.853933
12 DAL AMP 0.58 0.802326
13 ABM 0.571429 0.75
14 45A 0.571429 0.75
15 52H 0.57 0.876405
16 53H 0.564356 0.876405
17 5CA 0.564356 0.855556
18 SSA 0.56 0.855556
19 5AL 0.555556 0.781609
20 AMP MG 0.549451 0.776471
21 QA7 0.54902 0.816092
22 8LH 0.544554 0.784091
23 A 0.538462 0.747126
24 DSZ 0.538462 0.876405
25 AMP 0.538462 0.747126
26 4AD 0.538462 0.795455
27 KAA 0.537736 0.827957
28 A2D 0.537634 0.730337
29 8X1 0.533981 0.827957
30 8LQ 0.533981 0.804598
31 SRA 0.532609 0.752809
32 SON 0.53125 0.764045
33 GAP 0.53 0.772727
34 9ZD 0.528846 0.786517
35 8QN 0.528846 0.781609
36 9ZA 0.528846 0.786517
37 BA3 0.526316 0.730337
38 CA0 0.525773 0.752809
39 M33 0.525773 0.741573
40 ATP MG 0.525253 0.767442
41 ADP PO3 0.525253 0.767442
42 PAJ 0.52381 0.788889
43 GSU 0.523364 0.876405
44 B4P 0.520833 0.730337
45 ADP 0.520833 0.730337
46 AP5 0.520833 0.730337
47 KG4 0.520408 0.752809
48 50T 0.520408 0.722222
49 TXA 0.518519 0.764045
50 ADP MG 0.515464 0.767442
51 ADP BEF 0.515464 0.767442
52 AT4 0.515464 0.744444
53 PRX 0.515152 0.752809
54 SRP 0.514563 0.784091
55 YSA 0.513514 0.855556
56 AOC 0.510638 0.689655
57 A12 0.510417 0.725275
58 AP2 0.510417 0.725275
59 ADX 0.510204 0.8
60 AD9 0.51 0.714286
61 V2G 0.509804 0.758242
62 8LE 0.509804 0.795455
63 P5A 0.509259 0.819149
64 RAB 0.505882 0.686047
65 ADN 0.505882 0.686047
66 XYA 0.505882 0.686047
67 A4D 0.505747 0.686047
68 5CD 0.505747 0.674419
69 H1Q 0.50505 0.758621
70 HEJ 0.50505 0.730337
71 ATP 0.50505 0.730337
72 BEF ADP 0.504951 0.75
73 VO4 ADP 0.504854 0.733333
74 PTJ 0.504587 0.797753
75 8PZ 0.504505 0.855556
76 AQP 0.5 0.730337
77 APR 0.5 0.75
78 AR6 0.5 0.75
79 ARG AMP 0.5 0.763441
80 MYR AMP 0.5 0.752688
81 AN2 0.5 0.741573
82 5FA 0.5 0.730337
83 B1U 0.5 0.810526
84 3DH 0.5 0.689655
85 LAD 0.495413 0.75
86 AMO 0.495327 0.784091
87 AGS 0.49505 0.736264
88 APC MG 0.49505 0.75
89 AU1 0.494949 0.733333
90 5N5 0.494253 0.666667
91 ME8 0.490909 0.791209
92 9K8 0.490909 0.734694
93 1ZZ 0.490909 0.734043
94 ALF ADP 0.490385 0.717391
95 ANP MG 0.490385 0.761364
96 ACP 0.49 0.733333
97 EP4 0.488889 0.712644
98 OAD 0.486239 0.772727
99 5SV 0.485981 0.72043
100 OOB 0.485981 0.761364
101 T99 0.485437 0.744444
102 TAT 0.485437 0.744444
103 APC 0.485149 0.725275
104 M2T 0.483516 0.755814
105 DTA 0.483516 0.701149
106 WAQ 0.481818 0.747253
107 ADV 0.480392 0.744444
108 RBY 0.480392 0.744444
109 WSA 0.478992 0.865169
110 MTA 0.478261 0.709302
111 FA5 0.477876 0.784091
112 3OD 0.477477 0.772727
113 NB8 0.477477 0.777778
114 00A 0.477064 0.728261
115 AHX 0.477064 0.758242
116 5X8 0.475248 0.741176
117 AP0 0.475 0.702128
118 YLP 0.474576 0.736842
119 48N 0.474576 0.777778
120 3UK 0.472727 0.752809
121 9X8 0.472727 0.755556
122 ADP BMA 0.472727 0.752809
123 GEK 0.472222 0.738636
124 SMM 0.471698 0.766667
125 ACQ 0.471154 0.733333
126 SAM 0.471154 0.752809
127 ANP 0.471154 0.733333
128 NAI 0.470588 0.709677
129 4YB 0.470085 0.857143
130 A1R 0.46789 0.728261
131 HQG 0.46729 0.741573
132 649 0.466667 0.819149
133 OMR 0.466667 0.726316
134 EEM 0.466667 0.714286
135 SA8 0.466019 0.711111
136 B5M 0.464912 0.755556
137 MAO 0.464646 0.72043
138 NEC 0.463918 0.647727
139 JNT 0.463636 0.733333
140 DLL 0.463636 0.761364
141 A22 0.462963 0.722222
142 8Q2 0.46281 0.827957
143 YLB 0.46281 0.755319
144 ATF 0.462264 0.706522
145 XAH 0.46087 0.734043
146 SFG 0.460784 0.709302
147 6YZ 0.457944 0.733333
148 S7M 0.457944 0.733333
149 DQV 0.457627 0.741573
150 NWW 0.455556 0.635294
151 PR8 0.455357 0.741935
152 B5V 0.455357 0.744444
153 ADQ 0.454545 0.733333
154 AF3 ADP 3PG 0.454545 0.75
155 A3R 0.454545 0.728261
156 S4M 0.454545 0.691489
157 TXE 0.454545 0.709677
158 ALF ADP 3PG 0.454545 0.75
159 AHZ 0.453782 0.752688
160 6RE 0.453608 0.7
161 ATP A A A 0.452174 0.758621
162 B5Y 0.452174 0.755556
163 ATP A 0.452174 0.758621
164 FYA 0.451327 0.761364
165 JB6 0.451327 0.747253
166 MHZ 0.45098 0.666667
167 YLC 0.45082 0.752688
168 NAD IBO 0.45082 0.770115
169 NAD TDB 0.45082 0.770115
170 L3W 0.45082 0.725275
171 MAP 0.449541 0.717391
172 A3G 0.44898 0.712644
173 AYB 0.448 0.747368
174 SAH 0.447619 0.724138
175 SAI 0.447619 0.696629
176 A3T 0.446602 0.709302
177 QXP 0.445455 0.744681
178 OZV 0.445455 0.730337
179 25A 0.445455 0.730337
180 80F 0.445312 0.736842
181 A3N 0.444444 0.644444
182 J7C 0.444444 0.688889
183 F2R 0.444444 0.736842
184 9SN 0.443478 0.72043
185 ZAS 0.443299 0.724138
186 TYM 0.442623 0.784091
187 NAJ PZO 0.44186 0.73913
188 0UM 0.441441 0.703297
189 A7D 0.441176 0.693182
190 COD 0.440945 0.768421
191 GJV 0.44 0.692308
192 KMQ 0.439655 0.744444
193 NAQ 0.439394 0.758242
194 SXZ 0.438596 0.752809
195 BIS 0.438596 0.691489
196 LPA AMP 0.438017 0.752688
197 7MD 0.436975 0.752688
198 GA7 0.436975 0.764045
199 25L 0.434783 0.722222
200 4UW 0.434426 0.731183
201 TXD 0.434426 0.709677
202 DND 0.434426 0.764045
203 DSH 0.434343 0.67033
204 K15 0.433628 0.688172
205 QXG 0.433628 0.736842
206 TAD 0.433333 0.731183
207 AMP DBH 0.432203 0.752809
208 4UV 0.432203 0.736264
209 5AD 0.431818 0.642857
210 SLU 0.430769 0.806452
211 R2V 0.429825 0.744681
212 LAQ 0.429752 0.734043
213 7C5 0.428571 0.711111
214 YLA 0.428571 0.71875
215 NAJ PYZ 0.428571 0.708333
216 7MC 0.427419 0.755319
217 A3S 0.427184 0.72093
218 CNA 0.425197 0.764045
219 4UU 0.425 0.736264
220 AR6 AR6 0.425 0.770115
221 AFH 0.425 0.712766
222 62X 0.424779 0.709677
223 NVA 2AD 0.424528 0.738636
224 6V0 0.422764 0.702128
225 NAX 0.422764 0.723404
226 UP5 0.422764 0.717391
227 NWQ 0.42268 0.639535
228 GTA 0.421488 0.734043
229 IOT 0.420635 0.729167
230 AMP NAD 0.418605 0.781609
231 4TA 0.418605 0.744681
232 NAD 0.418605 0.761364
233 3AM 0.418367 0.715909
234 V47 0.418182 0.678161
235 139 0.417323 0.705263
236 G3A 0.416667 0.72043
237 K3K 0.415254 0.659341
238 N0B 0.414815 0.71875
239 KOY 0.414634 0.696629
240 YLY 0.413534 0.747368
241 G5P 0.413223 0.72043
242 Y3J 0.413043 0.609195
243 A3D 0.412214 0.772727
244 EO7 0.411765 0.804348
245 HY8 0.41129 0.677419
246 A5D 0.411215 0.701149
247 KY2 0.410714 0.659574
248 NAE 0.410448 0.775281
249 KH3 0.409836 0.680851
250 KXW 0.409836 0.673913
251 EAD 0.408759 0.723404
252 A6D 0.408696 0.706522
253 K3E 0.408333 0.652174
254 A3P 0.407767 0.727273
255 SO8 0.407407 0.724138
256 T5A 0.40625 0.71875
257 ADJ 0.40625 0.690722
258 N5O 0.405941 0.681818
259 2VA 0.40566 0.732558
260 3NZ 0.405172 0.719101
261 UPA 0.404762 0.709677
262 4TC 0.404762 0.72043
263 DZD 0.40458 0.712766
264 6IA 0.40367 0.769231
265 A4P 0.401575 0.686869
266 Z5A 0.40146 0.739583
267 KYE 0.4 0.680851
268 AAT 0.4 0.655914
Ligand no: 2; Ligand: NVA 2AD; Similar ligands found: 185
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 ADN 0.5 0.884058
11 XYA 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 NWW 0.463415 0.797101
24 J4G 0.461538 0.7875
25 3NZ 0.461538 0.890411
26 0UM 0.460784 0.891892
27 A2P 0.456522 0.721519
28 QA7 0.455446 0.765432
29 DAL AMP 0.455446 0.794872
30 3AM 0.454545 0.74359
31 SAH 0.453608 0.849315
32 5N5 0.451219 0.857143
33 GEK 0.45098 0.84
34 A2D 0.450549 0.759494
35 S7M 0.45 0.855263
36 A 0.449438 0.75641
37 AMP 0.449438 0.75641
38 PRX 0.447917 0.807692
39 EP4 0.447059 0.810811
40 AN2 0.446809 0.75
41 NSS 0.446602 0.727273
42 4AD 0.446602 0.810127
43 A4D 0.445783 0.857143
44 7D3 0.445652 0.707317
45 8LE 0.444444 0.743902
46 6RE 0.444444 0.84
47 OVE 0.444444 0.728395
48 5AL 0.444444 0.772152
49 ATR 0.443299 0.734177
50 SA8 0.443299 0.853333
51 NWQ 0.443182 0.8
52 CA0 0.442105 0.7625
53 7D4 0.442105 0.707317
54 M2T 0.44186 0.813333
55 GLU GMC 0.441176 0.893333
56 BA3 0.44086 0.759494
57 A3P 0.44086 0.734177
58 A5A 0.44 0.693182
59 5AD 0.4375 0.782609
60 HEJ 0.4375 0.759494
61 KG4 0.4375 0.7625
62 SFG 0.4375 0.859155
63 ATP 0.4375 0.759494
64 8QN 0.436893 0.772152
65 5AS 0.43617 0.688889
66 B4P 0.43617 0.759494
67 ADP 0.43617 0.759494
68 AP5 0.43617 0.759494
69 8LH 0.435644 0.797468
70 ABM 0.434783 0.759494
71 45A 0.434783 0.759494
72 SAM 0.434343 0.855263
73 LMS 0.433333 0.670455
74 5FA 0.43299 0.759494
75 AQP 0.43299 0.759494
76 A7D 0.431579 0.861111
77 AT4 0.431579 0.731707
78 52H 0.431373 0.67033
79 VMS 0.431373 0.677778
80 A2R 0.431373 0.75
81 54H 0.431373 0.677778
82 PPS 0.43 0.670455
83 V2G 0.43 0.746988
84 EEM 0.43 0.855263
85 SXZ 0.429907 0.831169
86 1ZZ 0.429907 0.761905
87 ME8 0.429907 0.783133
88 3D1 0.428571 0.859155
89 AGS 0.428571 0.722892
90 AMP MG 0.428571 0.789474
91 3AD 0.428571 0.869565
92 AHX 0.428571 0.790123
93 3L1 0.428571 0.859155
94 PAP 0.428571 0.746835
95 A22 0.427184 0.75
96 TSB 0.427184 0.704545
97 8LQ 0.427184 0.797468
98 53H 0.427184 0.67033
99 M33 0.427083 0.772152
100 ADX 0.427083 0.689655
101 OAD 0.424528 0.78481
102 K15 0.424528 0.844156
103 NA7 0.424528 0.753086
104 QXG 0.424528 0.685393
105 LEU LMS 0.424528 0.738636
106 G5A 0.424242 0.707865
107 SAI 0.424242 0.837838
108 DSH 0.423913 0.826667
109 N5O 0.423913 0.9
110 9ZD 0.423077 0.73494
111 9ZA 0.423077 0.73494
112 5SV 0.423077 0.768293
113 50T 0.42268 0.75
114 SMM 0.421569 0.822785
115 SSA 0.421569 0.727273
116 SRP 0.421569 0.797468
117 KL2 0.420455 0.708861
118 GAP 0.42 0.78481
119 V3L 0.42 0.7375
120 LSS 0.419048 0.711111
121 PAJ 0.419048 0.780488
122 2A5 0.418367 0.7625
123 AR6 0.418367 0.759494
124 APR 0.418367 0.759494
125 QQY 0.417582 0.691358
126 ACK 0.417582 0.727273
127 TXA 0.416667 0.775
128 3OD 0.416667 0.78481
129 Y3J 0.416667 0.736111
130 NB8 0.416667 0.768293
131 PTJ 0.416667 0.746988
132 SON 0.416667 0.753086
133 ARG AMP 0.415929 0.77381
134 DLL 0.415094 0.75
135 N5A 0.414894 0.871429
136 S4M 0.414894 0.822785
137 GJV 0.414894 0.828947
138 XAH 0.414414 0.761905
139 A5D 0.414141 0.773333
140 AD9 0.414141 0.740741
141 5CA 0.413462 0.727273
142 SRA 0.413043 0.719512
143 MYR AMP 0.412844 0.783133
144 0T1 0.412698 0.790698
145 AU1 0.412371 0.740741
146 9X8 0.411215 0.743902
147 AP2 0.410526 0.753086
148 A12 0.410526 0.753086
149 QXP 0.409524 0.693182
150 9SN 0.409091 0.705882
151 NPW 0.408333 0.761905
152 ACP 0.408163 0.7625
153 CUU 0.408163 0.759494
154 V47 0.407767 0.819444
155 GSU 0.407407 0.707865
156 KAA 0.407407 0.703297
157 PR8 0.407407 0.771084
158 WAQ 0.407407 0.756098
159 LAD 0.407407 0.780488
160 YLB 0.40678 0.807229
161 QQX 0.406593 0.682927
162 ACQ 0.405941 0.7625
163 T99 0.405941 0.731707
164 3AT 0.405941 0.759494
165 ANP 0.405941 0.740741
166 TAT 0.405941 0.731707
167 DSZ 0.40566 0.707865
168 ADQ 0.40566 0.7625
169 AMO 0.40566 0.797468
170 48N 0.405172 0.768293
171 YLP 0.405172 0.785714
172 A3N 0.404255 0.821918
173 APC 0.40404 0.753086
174 NWZ 0.40404 0.826667
175 HQG 0.403846 0.75
176 ZAS 0.402174 0.8
177 ADP MG 0.402062 0.779221
178 ADP BEF 0.402062 0.779221
179 AAT 0.401961 0.805195
180 62X 0.401869 0.8
181 JNT 0.401869 0.78481
182 HY8 0.401709 0.855263
183 NAX 0.401709 0.771084
184 8X1 0.4 0.703297
185 KH3 0.4 0.857143
Similar Ligands (3D)
Ligand no: 1; Ligand: LEU LMS; Similar ligands found: 3
No: Ligand Similarity coefficient
1 MSP 0.9460
2 L3U 0.9442
3 MOD 0.9404
Ligand no: 2; Ligand: NVA 2AD; Similar ligands found: 1
No: Ligand Similarity coefficient
1 2GP 0.8660
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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