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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: 71
This union binding pocket(no: 1) in the query (biounit: 2v0c.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
1 1C4Q GLA GAL BGC None
2 3FC4 EDO 1.59453
3 1EU1 MGD 1.79487
4 5VLQ ANP 2.03735
5 5AHO TLA 2.08333
6 5G3U FDA 2.12766
7 4KRG OPE 2.36052
8 4P8K FAD 2.5
9 4P8K 38C 2.5
10 2GMH FAD 2.56849
11 5HCY 60D 2.71903
12 4KBA 1QM 2.71903
13 5K0A FAD 2.72727
14 3IT7 TLA 2.74725
15 4RL4 PPV 2.83019
16 3FXU TSU 2.95082
17 4OX5 DAL 3.20856
18 4X1Z FUC GAL NDG 3.31325
19 3COW 52H 3.32226
20 4U60 SIA 3.57143
21 5OFW 9TW 3.58744
22 5Z49 RUB 3.76569
23 3UG4 AHR 3.76984
24 3E1T FAD 3.90625
25 5YW5 ADE 3.91061
26 5KBZ 3B2 3.97878
27 5N53 8NB 4.10256
28 3KL3 GCU 4.2394
29 3S6X SIA GAL BGC 4.30769
30 2BOS GLA GAL GLC NBU 4.41176
31 2BOS GLA GAL GLC 4.41176
32 4HMT NNV 4.44444
33 4HMT FMN 4.44444
34 4YEF 4CQ 4.49438
35 2BP1 NDP 5.27778
36 6DZN AE3 5.30973
37 4OKE AMP 5.35714
38 4A34 FUL 5.44218
39 4HPP GLU 5.64334
40 3LAD FAD 5.67227
41 5ZHW DAL DAL 5.70175
42 3FSY SCA 5.72289
43 6A6A DAL 5.77778
44 1ONI BEZ 5.7971
45 1WLJ U5P 5.82011
46 4ZOH MCN 5.95238
47 3THR C2F 6.48464
48 1PNF NDG NAG 7.32484
49 2X3F APC 7.36842
50 5BSZ THM 7.6
51 3QDV NDG 7.69231
52 1I8T FAD 7.90191
53 1YOA FAD 8.80503
54 6E8I PTR 8.87574
55 1T3Q MCN 8.92857
56 2QZS 250 9.07216
57 2QZS ADP 9.07216
58 2QZS GLC 9.07216
59 3NTY 5P3 9.59752
60 1NML CIT 9.81595
61 2JLD ALA GLY GLY ALA ALA ALA ALA ALA 10
62 2BVE PH5 10.084
63 2V2V V12 12.9151
64 5C9P FUC 13.3858
65 3B2Q AES 13.4328
66 3B2Q ATP 13.4328
67 2PIE GLU LEU LYS TPO GLU ARG TYR 14.4928
68 1O9U ADZ 15.1429
69 2WFG ZZB 18.7739
70 1WK9 TSB 28.7671
71 1WK8 VMS 29.8969
Pocket No.: 2; Query (leader) PDB : 2V0C; Ligand: LEU LMS; Similar sites found with APoc: 80
This union binding pocket(no: 2) in the query (biounit: 2v0c.bio1) has 25 residues
No: Leader PDB Ligand Sequence Similarity
1 1WUW TSU None
2 5O0Z 9GB None
3 4JDR FAD 1.47679
4 4J75 TYM 1.71149
5 3JQA DX4 1.73611
6 4CMI M4V 1.73611
7 5Y0N ATP 1.83908
8 1FEC FAD 2.2449
9 4F5Z BEZ 2.34114
10 5N5U AMP 2.54777
11 1YID ATP 2.5641
12 5OCM 9RH 2.74914
13 1K4M NAD 2.8169
14 5GOO FRU 2.81996
15 1JIL 485 2.85714
16 3ND6 ATP 2.92398
17 4LZB URA 2.94118
18 1J09 GLU 2.99145
19 1J09 ATP 2.99145
20 2CYB TYR 3.09598
21 1R6T TYM 3.14465
22 2H29 DND 3.1746
23 2OWZ CIT 3.31325
24 3COW 52H 3.32226
25 4BCQ TJF 3.32226
26 2PID YSA 3.37079
27 1B09 PC 3.39806
28 1R6U TYM 3.43249
29 4MAF ADX 3.46535
30 1YUM NCN 3.71901
31 4TVD BGC 3.75854
32 1V59 FAD 3.76569
33 5HVJ ANP 3.80952
34 3HL4 CDC 3.81356
35 5ZDK ATP 4.0146
36 5I34 GDP 4.08163
37 1V47 ADX 4.29799
38 4GK9 MAN BMA MAN MAN MAN 4.30108
39 4NAT 2W5 4.375
40 4NAT ADP 4.375
41 5LLT DND 4.69484
42 1GPE FAD 4.77002
43 1BZL GCG 4.93827
44 1BZL FAD 4.93827
45 5OKT 9XK 5.09554
46 2J5B TYE 5.17241
47 1O6B ADP 5.32544
48 1F9A ATP 5.35714
49 5EY0 ILE 5.47445
50 4A91 GLU 5.7047
51 1KQN NAD 5.73477
52 5X3D 7XL 6.25
53 3C8Z 5CA 6.28019
54 1HFE CYS 6.50407
55 2Z49 AMG 6.94444
56 2X3F APC 7.36842
57 2QTR NXX 7.40741
58 4J56 FAD 7.89474
59 2CI5 HCS 8.09859
60 4LO6 SIA GAL 8.42105
61 5U8U FAD 8.73181
62 3AFH GSU 8.81148
63 2Q0L FAD 9.00322
64 4K55 H6P 9.67742
65 1LNX URI 9.87654
66 5DK4 5BX 11.2462
67 5DK4 ATP 11.2462
68 5V49 MET 13.4686
69 5V49 8WA 13.4686
70 5Y0T TAT 14.3529
71 1PFY MSP 14.7005
72 3KFL ME8 14.7163
73 2X1L ADN 15.2672
74 2X1L MET 15.2672
75 3UC5 ATP 15.2866
76 5XET ME8 15.3119
77 1N1D C2G 17.8295
78 5O0B 9FE 27.7778
79 3LQV ADE 28.2051
80 1JZS MRC 40.6821
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