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+2]...
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 6 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: 222
No: Ligand ECFP6 Tc MDL keys Tc
1 NVA LMS 1 1
2 LEU LMS 0.808989 0.954023
3 A5A 0.770115 0.941176
4 VMS 0.752809 0.91954
5 52H 0.752809 0.909091
6 54H 0.752809 0.91954
7 TSB 0.744444 0.930233
8 53H 0.744444 0.909091
9 SSA 0.741573 0.909091
10 NSS 0.728261 0.931035
11 LSS 0.728261 0.931818
12 5CA 0.725275 0.909091
13 GSU 0.723404 0.931035
14 DSZ 0.709677 0.909091
15 KAA 0.705263 0.9
16 G5A 0.696629 0.909091
17 5AS 0.686047 0.909091
18 YSA 0.653465 0.909091
19 WSA 0.62037 0.91954
20 P5A 0.62 0.89011
21 4YB 0.583333 0.910112
22 SON 0.553191 0.755556
23 AMP MG 0.549451 0.741573
24 649 0.548673 0.89011
25 5AL 0.545455 0.793103
26 A 0.544444 0.758621
27 AMP 0.544444 0.758621
28 ABM 0.543478 0.761364
29 3DH 0.539326 0.701149
30 DAL AMP 0.539216 0.793103
31 PRX 0.536082 0.804598
32 CA0 0.53125 0.764045
33 A2D 0.526882 0.761364
34 AHX 0.52381 0.769231
35 SRA 0.521739 0.784091
36 AOC 0.516129 0.681818
37 AP2 0.515789 0.736264
38 A12 0.515789 0.736264
39 BA3 0.515789 0.761364
40 ADX 0.515464 0.873563
41 AU1 0.515464 0.764045
42 ADP MG 0.515464 0.752809
43 M33 0.515464 0.772727
44 ADN 0.511905 0.678161
45 XYA 0.511905 0.678161
46 RAB 0.511905 0.678161
47 5CD 0.511628 0.666667
48 ADP 0.510417 0.761364
49 B4P 0.510417 0.761364
50 AP5 0.510417 0.761364
51 5X8 0.510204 0.693182
52 TXA 0.509259 0.775281
53 ARG AMP 0.508772 0.736842
54 AN2 0.505155 0.772727
55 GAP 0.504951 0.764045
56 SAM 0.504951 0.725275
57 ANP MG 0.504854 0.766667
58 SRP 0.504854 0.775281
59 S7M 0.504854 0.725275
60 8QN 0.504762 0.793103
61 XAH 0.504505 0.763441
62 SLU 0.504065 0.877778
63 NVA 2AD 0.5 0.735632
64 PAJ 0.5 0.76087
65 SA8 0.5 0.684783
66 4AD 0.5 0.786517
67 5N5 0.5 0.659091
68 1ZZ 0.495413 0.782609
69 ME8 0.495413 0.802198
70 ATP MG 0.49505 0.752809
71 ATP 0.494949 0.761364
72 50T 0.494949 0.733333
73 BEF ADP 0.494949 0.736264
74 ACP 0.494949 0.744444
75 ADP BEF 0.494949 0.736264
76 EP4 0.494382 0.666667
77 A4D 0.494253 0.678161
78 YLB 0.491525 0.784946
79 YLP 0.491379 0.765957
80 TYR AMP 0.491071 0.775281
81 MYR AMP 0.490909 0.782609
82 5SV 0.490566 0.769231
83 ANP 0.490196 0.764045
84 APC 0.49 0.736264
85 APR 0.49 0.761364
86 AR6 0.49 0.761364
87 5FA 0.49 0.761364
88 AQP 0.49 0.761364
89 DTA 0.488889 0.693182
90 M2T 0.488889 0.707865
91 LAD 0.486239 0.76087
92 AMO 0.485981 0.775281
93 0UM 0.485981 0.695652
94 AD9 0.485149 0.744444
95 AGS 0.485149 0.786517
96 ADV 0.485149 0.736264
97 RBY 0.485149 0.736264
98 ADP PO3 0.485149 0.77907
99 SAP 0.485149 0.786517
100 MTA 0.483516 0.701149
101 NB8 0.481818 0.769231
102 PTJ 0.481818 0.769231
103 DLL 0.481481 0.772727
104 SAH 0.480392 0.696629
105 SFG 0.48 0.681818
106 A3N 0.479167 0.637363
107 J7C 0.479167 0.663043
108 YLC 0.478992 0.763441
109 OAD 0.477064 0.784091
110 3UK 0.477064 0.764045
111 K15 0.477064 0.680851
112 OOB 0.476636 0.772727
113 SMM 0.47619 0.72043
114 TAT 0.475728 0.775281
115 ACQ 0.475728 0.744444
116 AYB 0.47541 0.776596
117 GJV 0.474227 0.666667
118 6RE 0.473684 0.673913
119 9SN 0.473214 0.731183
120 WAQ 0.472727 0.758242
121 EEM 0.471154 0.688172
122 NEC 0.46875 0.659091
123 3OD 0.468468 0.784091
124 00A 0.46789 0.73913
125 MAP 0.46729 0.747253
126 A22 0.46729 0.752809
127 ATF 0.466667 0.736264
128 ALF ADP 0.466667 0.728261
129 ADP ALF 0.466667 0.728261
130 48N 0.466102 0.75
131 VRT 0.466019 0.738636
132 SAI 0.466019 0.67033
133 7MD 0.465517 0.763441
134 ADP BMA 0.463636 0.744444
135 25A 0.462963 0.761364
136 VO4 ADP 0.462264 0.772727
137 ADP VO4 0.462264 0.772727
138 AMP DBH 0.46087 0.725275
139 A7D 0.46 0.685393
140 PR8 0.459459 0.752688
141 S4M 0.459184 0.684211
142 ADQ 0.458716 0.744444
143 OMR 0.458333 0.774194
144 YAP 0.45614 0.766667
145 FA5 0.45614 0.775281
146 JB6 0.455357 0.777778
147 BIS 0.455357 0.73913
148 FYA 0.455357 0.752809
149 SXZ 0.455357 0.706522
150 MAO 0.454545 0.731183
151 7MC 0.454545 0.765957
152 DSH 0.453608 0.663043
153 A3T 0.45098 0.701149
154 GEK 0.449541 0.730337
155 KH3 0.449153 0.673684
156 ZAS 0.447917 0.696629
157 TYM 0.446281 0.775281
158 TXE 0.446281 0.73913
159 A3S 0.445545 0.693182
160 A1R 0.445455 0.73913
161 7C5 0.444444 0.684783
162 YLA 0.443548 0.729167
163 62X 0.441441 0.649485
164 MHZ 0.441176 0.677083
165 A3G 0.438776 0.685393
166 25L 0.438596 0.752809
167 SO8 0.438095 0.715909
168 NAX 0.438017 0.752688
169 TAD 0.436975 0.741935
170 GTA 0.436975 0.744681
171 5AD 0.436782 0.635294
172 4UV 0.435897 0.747253
173 IOT 0.435484 0.721649
174 LA8 ALF 3PG 0.434426 0.723404
175 ALF ADP 3PG 0.434426 0.723404
176 A A 0.433628 0.761364
177 LAQ 0.433333 0.763441
178 AHZ 0.433333 0.763441
179 COD 0.433071 0.760417
180 LPA AMP 0.429752 0.763441
181 4UU 0.428571 0.747253
182 YLY 0.427481 0.757895
183 4UW 0.42623 0.741935
184 NAI 0.42623 0.73913
185 DND 0.42623 0.775281
186 NXX 0.42623 0.775281
187 TXD 0.42623 0.73913
188 6V0 0.42623 0.731183
189 NAD IBO 0.425197 0.766667
190 2VA 0.423077 0.685393
191 AF3 ADP 3PG 0.422764 0.723404
192 3AM 0.42268 0.727273
193 AP0 0.419355 0.731183
194 ATP A A A 0.418803 0.770115
195 Y3J 0.417582 0.602273
196 CNA 0.417323 0.795455
197 AR6 AR6 0.416667 0.761364
198 AFH 0.416667 0.705263
199 A5D 0.415094 0.693182
200 UP5 0.414634 0.747253
201 KB1 0.413793 0.642105
202 A3P 0.411765 0.758621
203 A2P 0.411765 0.747126
204 S8M 0.410714 0.711111
205 NAQ 0.410448 0.788889
206 3NZ 0.408696 0.692308
207 G3A 0.408333 0.731183
208 UPA 0.408 0.73913
209 4TC 0.408 0.731183
210 6IA 0.407407 0.741935
211 N0B 0.407407 0.729167
212 G5P 0.404959 0.731183
213 A3D 0.40458 0.804598
214 FB0 0.404255 0.72
215 AAT 0.40367 0.648936
216 7D5 0.402062 0.692308
217 D3Y 0.401786 0.677778
218 NAJ PZO 0.401515 0.75
219 A6D 0.4 0.680851
220 7D7 0.4 0.617977
221 NAD 0.4 0.793103
222 OVE 0.4 0.733333
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2V0C; Ligand: ANZ; Similar sites found: 24
This union binding pocket(no: 1) in the query (biounit: 2v0c.bio1) has 20 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3K8L CEY 0.006532 0.42777 1.9432
2 4P8K 38C 0.03915 0.40151 2.5
3 5HCY 60D 0.02204 0.4074 2.71903
4 4KBA 1QM 0.01604 0.40417 2.71903
5 3IT7 TLA 0.005148 0.4375 2.74725
6 4RL4 PPV 0.00267 0.45452 2.83019
7 4X1Z FUC GAL NDG 0.01805 0.40897 3.31325
8 4U60 SIA 0.03017 0.40125 3.57143
9 5KBZ 3B2 0.01715 0.40577 3.97878
10 5N53 8NB 0.006595 0.429 4.10256
11 3KL3 GCU 0.003005 0.45566 4.2394
12 3S6X SIA GAL BGC 0.004035 0.44041 4.30769
13 2BOS GLA GAL GLC NBU 0.00698 0.42981 4.41176
14 2BOS GLA GAL GLC 0.01142 0.41666 4.41176
15 4HPP GLU 0.01299 0.4146 5.64334
16 3LAD FAD 0.02307 0.40731 5.67227
17 1I8T FAD 0.02697 0.40136 7.90191
18 2BVE PH5 0.01277 0.40594 10.084
19 3B2Q ATP 0.008628 0.4065 13.4328
20 2PIE GLU LEU LYS TPO GLU ARG TYR 0.02104 0.40309 14.4928
21 1O9U ADZ 0.0254 0.40498 15.1429
22 2WFG ZZB 0.00000002314 0.64404 18.7739
23 1WK9 TSB 0.00000004895 0.59749 28.7671
24 1WK8 VMS 0.00000006125 0.58428 29.8969
Pocket No.: 2; Query (leader) PDB : 2V0C; Ligand: LEU LMS; Similar sites found: 45
This union binding pocket(no: 2) in the query (biounit: 2v0c.bio1) has 25 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1WUW TSU 0.002701 0.45927 None
2 4J75 TYM 0.0000009602 0.56076 1.71149
3 3JQA DX4 0.02263 0.41666 1.73611
4 4CMI M4V 0.01437 0.40331 1.73611
5 4F5Z BEZ 0.01363 0.42074 2.34114
6 1YID ATP 0.0005379 0.40075 2.5641
7 1K4M NAD 0.001001 0.4148 2.8169
8 1JIL 485 0.000207 0.4697 2.85714
9 1J09 GLU 0.001045 0.41654 2.99145
10 1J09 ATP 0.00145 0.41078 2.99145
11 2CYB TYR 0.01412 0.42429 3.09598
12 1R6T TYM 0.000006661 0.44435 3.14465
13 2H29 DND 0.0003689 0.40852 3.1746
14 4BCQ TJF 0.02418 0.40358 3.32226
15 2PID YSA 0.00005111 0.4633 3.37079
16 1R6U TYM 0.00003244 0.49162 3.43249
17 1YUM NCN 0.003147 0.40152 3.71901
18 1V59 FAD 0.01557 0.40389 3.76569
19 5HVJ ANP 0.03292 0.40286 3.80952
20 3HL4 CDC 0.0004347 0.45583 3.81356
21 1V47 ADX 0.00107 0.41515 4.29799
22 4NAT ADP 0.009636 0.43286 4.375
23 4NAT 2W5 0.002246 0.43286 4.375
24 5LLT DND 0.004706 0.41198 4.69484
25 1H3F TYE 0.00726 0.43536 5.09259
26 1O6B ADP 0.004566 0.4403 5.32544
27 1F9A ATP 0.003786 0.41537 5.35714
28 4A91 GLU 0.0001103 0.53822 5.7047
29 1KQN NAD 0.004004 0.41621 5.73477
30 3C8Z 5CA 0.00000001863 0.64374 6.28019
31 2X3F APC 0.000006987 0.48687 7.36842
32 2QTR NXX 0.0002696 0.41902 7.40741
33 2CI5 HCS 0.02957 0.40424 8.09859
34 3AFH GSU 0.000001343 0.5774 8.81148
35 3WCS MAN NAG 0.03282 0.40076 9.44882
36 5V49 8WA 0.000005637 0.53814 13.4686
37 5V49 MET 0.0001202 0.40764 13.4686
38 1PFY MSP 0.000000004887 0.63201 14.7005
39 3KFL ME8 0.0000001471 0.56579 14.7163
40 2X1L ADN 0.000001164 0.59534 15.2672
41 2X1L MET 0.0002034 0.51981 15.2672
42 3UC5 ATP 0.01206 0.40334 15.2866
43 1N1D C2G 0.0003548 0.44091 17.8295
44 3LQV ADE 0.02017 0.43015 28.2051
45 1JZS MRC 0.00002947 0.51154 40.6821
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