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+2]...
NVA 2AD A:1815;
Valid;
none;
submit data
367.41 n/a O=C([...
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 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: LEU LMS; Similar ligands found: 218
No: Ligand ECFP6 Tc MDL keys Tc
1 LEU LMS 1 1
2 NVA LMS 0.808989 0.954023
3 LSS 0.797753 0.976744
4 A5A 0.781609 0.941176
5 VMS 0.764045 0.964706
6 54H 0.764045 0.964706
7 TSB 0.755556 0.930233
8 52H 0.744444 0.953488
9 53H 0.736264 0.953488
10 SSA 0.733333 0.909091
11 NSS 0.72043 0.931035
12 DSZ 0.72043 0.909091
13 5CA 0.717391 0.909091
14 GSU 0.697917 0.909091
15 G5A 0.688889 0.909091
16 KAA 0.680412 0.879121
17 5AS 0.659091 0.88764
18 YSA 0.647059 0.909091
19 WSA 0.614679 0.91954
20 P5A 0.613861 0.869565
21 SON 0.580645 0.755556
22 4YB 0.563636 0.888889
23 649 0.557522 0.869565
24 5AL 0.555556 0.793103
25 ABM 0.554348 0.761364
26 DAL AMP 0.54902 0.793103
27 AMP 0.538462 0.758621
28 A 0.538462 0.758621
29 AMP MG 0.526882 0.741573
30 AOC 0.526882 0.681818
31 CA0 0.525773 0.764045
32 M33 0.525773 0.772727
33 A2D 0.521277 0.761364
34 AHX 0.518868 0.769231
35 TXA 0.518519 0.775281
36 3DH 0.516484 0.681818
37 SRA 0.516129 0.784091
38 8QN 0.514286 0.793103
39 A12 0.510417 0.736264
40 BA3 0.510417 0.761364
41 AP2 0.510417 0.736264
42 ADX 0.510204 0.873563
43 AU1 0.510204 0.764045
44 XYA 0.505882 0.678161
45 ADN 0.505882 0.678161
46 RAB 0.505882 0.678161
47 5CD 0.505747 0.666667
48 ADP 0.505155 0.761364
49 B4P 0.505155 0.761364
50 AP5 0.505155 0.761364
51 5X8 0.50505 0.693182
52 GAP 0.5 0.764045
53 SLU 0.5 0.877778
54 PRX 0.5 0.764045
55 SRP 0.5 0.775281
56 AN2 0.5 0.772727
57 AMO 0.495327 0.775281
58 4AD 0.495327 0.786517
59 PAJ 0.495327 0.8
60 ADP MG 0.494949 0.752809
61 5N5 0.494253 0.659091
62 ARG AMP 0.491379 0.71875
63 NB8 0.490909 0.769231
64 ME8 0.490909 0.782609
65 BEF ADP 0.49 0.736264
66 ACP 0.49 0.744444
67 50T 0.49 0.733333
68 ADP BEF 0.49 0.736264
69 ATP 0.49 0.761364
70 EP4 0.488889 0.704545
71 A4D 0.488636 0.678161
72 TYR AMP 0.486726 0.775281
73 XAH 0.486726 0.744681
74 ANP 0.485437 0.764045
75 AR6 0.485149 0.761364
76 AQP 0.485149 0.761364
77 5FA 0.485149 0.761364
78 APR 0.485149 0.761364
79 APC 0.485149 0.736264
80 DTA 0.483516 0.693182
81 M2T 0.483516 0.747126
82 AD9 0.480392 0.744444
83 SAP 0.480392 0.786517
84 ADP PO3 0.480392 0.77907
85 ADV 0.480392 0.736264
86 SA8 0.480392 0.666667
87 RBY 0.480392 0.736264
88 AGS 0.480392 0.786517
89 7C5 0.478261 0.684783
90 MTA 0.478261 0.701149
91 PTJ 0.477477 0.808989
92 SXZ 0.477477 0.725275
93 DLL 0.477064 0.772727
94 ATP MG 0.475728 0.752809
95 48N 0.474576 0.75
96 7MD 0.474138 0.744681
97 OAD 0.472727 0.784091
98 3UK 0.472727 0.764045
99 OOB 0.472222 0.772727
100 ANP MG 0.471698 0.766667
101 S7M 0.471698 0.688172
102 SAM 0.471154 0.706522
103 TAT 0.471154 0.775281
104 ACQ 0.471154 0.744444
105 AMP DBH 0.469565 0.725275
106 GJV 0.469388 0.648936
107 6RE 0.46875 0.655914
108 LAD 0.468468 0.741935
109 1ZZ 0.464286 0.744681
110 3OD 0.464286 0.784091
111 00A 0.463636 0.73913
112 MAP 0.462963 0.747253
113 A22 0.462963 0.752809
114 7MC 0.46281 0.747368
115 ATF 0.462264 0.736264
116 ALF ADP 0.462264 0.728261
117 ADP ALF 0.462264 0.728261
118 YLP 0.462185 0.729167
119 SAH 0.461538 0.677778
120 SFG 0.460784 0.662921
121 A3T 0.460784 0.701149
122 MYR AMP 0.460177 0.744681
123 ADP BMA 0.459459 0.744444
124 A3N 0.459184 0.637363
125 J7C 0.459184 0.645161
126 5SV 0.458716 0.731183
127 25A 0.458716 0.761364
128 ADP VO4 0.457944 0.772727
129 SMM 0.457944 0.72043
130 VO4 ADP 0.457944 0.772727
131 9SN 0.45614 0.731183
132 WAQ 0.455357 0.73913
133 PR8 0.455357 0.734043
134 S4M 0.454545 0.666667
135 ADQ 0.454545 0.744444
136 EEM 0.45283 0.670213
137 FA5 0.452174 0.775281
138 YAP 0.452174 0.766667
139 FYA 0.451327 0.752809
140 MHZ 0.45098 0.659794
141 YLC 0.45082 0.744681
142 YLB 0.45082 0.747368
143 MAO 0.45 0.712766
144 NEC 0.44898 0.640449
145 DSH 0.44898 0.645161
146 AYB 0.448 0.739583
147 SAI 0.447619 0.652174
148 TAD 0.445378 0.741935
149 NAD IBO 0.444444 0.806818
150 ZAS 0.443299 0.696629
151 TYM 0.442623 0.775281
152 A A 0.442478 0.761364
153 LAQ 0.441667 0.744681
154 0UM 0.441441 0.659574
155 A1R 0.441441 0.73913
156 A3S 0.441176 0.693182
157 A7D 0.441176 0.666667
158 YLA 0.44 0.71134
159 JB6 0.438596 0.758242
160 BIS 0.438596 0.72043
161 LPA AMP 0.438017 0.744681
162 25L 0.434783 0.752809
163 A3G 0.434343 0.685393
164 K15 0.433628 0.645833
165 GTA 0.433333 0.744681
166 2VA 0.432692 0.724138
167 4UV 0.432203 0.747253
168 5AD 0.431818 0.635294
169 OMR 0.430894 0.736842
170 LA8 ALF 3PG 0.430894 0.723404
171 TXE 0.430894 0.73913
172 ALF ADP 3PG 0.430894 0.723404
173 AHZ 0.429752 0.744681
174 COD 0.429688 0.778947
175 AP0 0.427419 0.731183
176 ATP A A A 0.42735 0.770115
177 CNA 0.425197 0.795455
178 AR6 AR6 0.425 0.761364
179 4UU 0.425 0.747253
180 62X 0.424779 0.666667
181 NVA 2AD 0.424528 0.696629
182 4UW 0.422764 0.741935
183 6V0 0.422764 0.731183
184 TXD 0.422764 0.73913
185 NXX 0.422764 0.775281
186 NAX 0.422764 0.734043
187 NAI 0.422764 0.73913
188 DND 0.422764 0.775281
189 IOT 0.420635 0.704082
190 SO8 0.420561 0.715909
191 GEK 0.419643 0.711111
192 AF3 ADP 3PG 0.419355 0.723404
193 NAD 0.418605 0.793103
194 3AM 0.418367 0.727273
195 NAQ 0.41791 0.788889
196 G3A 0.416667 0.731183
197 6IA 0.416667 0.76087
198 N0B 0.414815 0.71134
199 YLY 0.413534 0.739583
200 G5P 0.413223 0.731183
201 AFH 0.413223 0.705263
202 Y3J 0.413043 0.602273
203 A3D 0.412214 0.804598
204 A5D 0.411215 0.693182
205 OVE 0.41 0.733333
206 KH3 0.409836 0.639175
207 A3P 0.407767 0.758621
208 A2P 0.407767 0.747126
209 VRT 0.407407 0.7
210 T5A 0.40625 0.729167
211 594 0.406015 0.79798
212 3NZ 0.405172 0.692308
213 V3L 0.40367 0.761364
214 A4P 0.401575 0.69697
215 FB0 0.401408 0.72
216 NAE 0.4 0.806818
217 AAT 0.4 0.631579
218 UP5 0.4 0.747253
Ligand no: 2; Ligand: NVA 2AD; Similar ligands found: 90
No: Ligand ECFP6 Tc MDL keys Tc
1 NVA 2AD 1 1
2 VRT 0.516129 0.942029
3 RAB 0.5 0.867647
4 NVA LMS 0.5 0.735632
5 XYA 0.5 0.867647
6 ADN 0.5 0.867647
7 3AM 0.471264 0.75
8 SO8 0.46875 0.913043
9 7D7 0.468354 0.785714
10 2VA 0.468085 0.871429
11 5CD 0.463415 0.8
12 OVE 0.460674 0.75641
13 2AM 0.45977 0.786667
14 5AD 0.455696 0.791045
15 A3G 0.455556 0.871429
16 NEC 0.455556 0.867647
17 MTA 0.453488 0.816901
18 A3T 0.452632 0.897059
19 5N5 0.451219 0.84058
20 EP4 0.447059 0.794521
21 A3S 0.446809 0.884058
22 A4D 0.445783 0.84058
23 SA8 0.443299 0.813333
24 3DH 0.443182 0.816901
25 DTA 0.44186 0.756757
26 M2T 0.44186 0.797297
27 A3P 0.44086 0.74026
28 5X8 0.4375 0.805556
29 SFG 0.4375 0.816901
30 S7M 0.435644 0.815789
31 SAM 0.434343 0.815789
32 AMP 0.433333 0.74026
33 A 0.433333 0.74026
34 0UM 0.432692 0.851351
35 7D5 0.431818 0.708861
36 SON 0.431579 0.716049
37 EEM 0.43 0.815789
38 5AL 0.43 0.75641
39 DAL AMP 0.427184 0.779221
40 GLU GMC 0.427184 0.821918
41 A2P 0.425532 0.75
42 LEU LMS 0.424528 0.696629
43 K15 0.424528 0.805195
44 SAI 0.424242 0.797297
45 SAH 0.424242 0.808219
46 SMM 0.421569 0.78481
47 5AS 0.421053 0.674157
48 J7C 0.419355 0.786667
49 ABM 0.419355 0.74359
50 PRX 0.418367 0.792208
51 ZAS 0.417582 0.783784
52 ACK 0.417582 0.756757
53 QQY 0.417582 0.717949
54 52H 0.417476 0.655556
55 Y3J 0.416667 0.742857
56 S4M 0.414894 0.78481
57 PAP 0.414141 0.753247
58 AGS 0.414141 0.707317
59 SAP 0.414141 0.707317
60 6RE 0.413043 0.8
61 CA0 0.412371 0.746835
62 KH3 0.412281 0.818182
63 3AD 0.411765 0.852941
64 A5A 0.411765 0.678161
65 BA3 0.410526 0.74359
66 GEK 0.409524 0.8
67 AMP MG 0.408602 0.74359
68 50T 0.408163 0.734177
69 ATP 0.408163 0.74359
70 QQX 0.406593 0.708861
71 B4P 0.40625 0.74359
72 ADP 0.40625 0.74359
73 AP5 0.40625 0.74359
74 V3L 0.405941 0.721519
75 A2D 0.404255 0.74359
76 5FA 0.40404 0.74359
77 AQP 0.40404 0.74359
78 VMS 0.403846 0.662921
79 54H 0.403846 0.662921
80 A7D 0.402062 0.819444
81 AN2 0.402062 0.734177
82 PPS 0.401961 0.674419
83 AHX 0.401869 0.753086
84 62X 0.401869 0.7625
85 GJV 0.4 0.789474
86 53H 0.4 0.655556
87 D3Y 0.4 0.859155
88 TSB 0.4 0.689655
89 7D3 0.4 0.7125
90 ATR 0.4 0.763158
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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