Receptor
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
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ANZ A:1817;
Valid;
none;
submit data
480.129 C17 H17 B F N5 O8 P [B@@-...
LEU LMS A:1501;
Valid;
none;
submit data
459.484 n/a S(OC(...
SO4 A:1818;
A:1819;
A:1820;
A:1821;
A:1822;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
submit data
96.063 O4 S [O-]S...
ZN A:1815;
A:1816;
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: ANZ; Similar ligands found: 63
No: Ligand ECFP6 Tc MDL keys Tc
1 ANZ 1 1
2 ZZB 0.711712 0.936709
3 WMP 0.649573 0.945946
4 7D5 0.489796 0.7875
5 A3P 0.480769 0.820513
6 AMP 0.475248 0.820513
7 A 0.475248 0.820513
8 A2H 0.46875 0.851852
9 A52 0.464567 0.825
10 A2P 0.45283 0.831169
11 TM1 0.45 0.77907
12 38Y 0.44697 0.878049
13 AV2 0.438596 0.846154
14 7D3 0.429907 0.768293
15 PAP 0.428571 0.810127
16 D5M 0.424528 0.7875
17 DA 0.424528 0.7875
18 3AM 0.423077 0.807692
19 ADP 0.422018 0.8
20 J4G 0.421488 0.761905
21 A2D 0.420561 0.8
22 45A 0.420561 0.777778
23 ABM 0.420561 0.777778
24 APC 0.419643 0.771084
25 PPS 0.417391 0.727273
26 LQJ 0.416 0.822785
27 8LQ 0.415254 0.75
28 GGZ 0.415254 0.744186
29 AMP MG 0.415094 0.807692
30 CA0 0.414414 0.759036
31 7D4 0.414414 0.768293
32 2AM 0.413462 0.820513
33 A12 0.412844 0.771084
34 BA3 0.412844 0.8
35 AP2 0.412844 0.771084
36 9SN 0.41129 0.851852
37 ATP 0.410714 0.8
38 KG4 0.410714 0.759036
39 CUU 0.410714 0.8
40 HEJ 0.410714 0.8
41 B5V 0.409836 0.792683
42 AP5 0.409091 0.8
43 B4P 0.409091 0.8
44 V3L 0.408696 0.8
45 B5M 0.408 0.783133
46 AQP 0.40708 0.8
47 2A5 0.40708 0.759036
48 5FA 0.40708 0.8
49 ADP MG 0.405405 0.797468
50 SON 0.405405 0.771084
51 ADP BEF 0.405405 0.797468
52 AT4 0.405405 0.771084
53 AN2 0.405405 0.790123
54 5AL 0.405172 0.768293
55 ATR 0.403509 0.820513
56 SRA 0.401869 0.780488
57 M33 0.401786 0.768293
58 AU1 0.401786 0.780488
59 ADX 0.401786 0.707865
60 ATF 0.401709 0.8375
61 8QN 0.4 0.768293
62 OOB 0.4 0.790123
63 25A 0.4 0.822785
Ligand no: 2; 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
Similar Ligands (3D)
Ligand no: 1; Ligand: ANZ; Similar ligands found: 0
No: Ligand Similarity coefficient
Ligand no: 2; Ligand: LEU LMS; Similar ligands found: 3
No: Ligand Similarity coefficient
1 MSP 0.9460
2 L3U 0.9442
3 MOD 0.9404
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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