Receptor
PDB id Resolution Class Description Source Keywords
1WK8 1.7 Å EC: 6.1.1.5 ISOLEUCYL-TRNA SYNTHETASE EDITING DOMAIN COMPLEXED WITH THE PRE-TRANSFER EDITING SUBSTRATE ANALOGUE, VAL-AMS THERMUS THERMOPHILUS EDITING CP1 ISOLEUCYL-TRNA SYNTHETASE FIDELITY THERMUS THERMOPHILUS TRANSLATION AMINO ACID STRUCTURAL GENOMICSRIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE RSGI NPPSFA NATIONAL PROJECT ON PROTEIN STRUCTURAL AND FUNCTIONAL ANALYSES LIGASE
Ref.: STRUCTURAL BASIS FOR SUBSTRATE RECOGNITION BY THE EDITING DOMAIN OF ISOLEUCYL-TRNA SYNTHETASE J.MOL.BIOL. V. 359 901 2006
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
VMS B:999;
 Valid;
 none;
 submit data
445.451 C15 H23 N7 O7 S CC(C)...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1WK8 1.7 Å EC: 6.1.1.5 ISOLEUCYL-TRNA SYNTHETASE EDITING DOMAIN COMPLEXED WITH THE PRE-TRANSFER EDITING SUBSTRATE ANALOGUE, VAL-AMS THERMUS THERMOPHILUS EDITING CP1 ISOLEUCYL-TRNA SYNTHETASE FIDELITY THERMUS THERMOPHILUS TRANSLATION AMINO ACID STRUCTURAL GENOMICSRIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE RSGI NPPSFA NATIONAL PROJECT ON PROTEIN STRUCTURAL AND FUNCTIONAL ANALYSES LIGASE
Ref.: STRUCTURAL BASIS FOR SUBSTRATE RECOGNITION BY THE EDITING DOMAIN OF ISOLEUCYL-TRNA SYNTHETASE J.MOL.BIOL. V. 359 901 2006
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 1WK8 - VMS C15 H23 N7 O7 S CC(C)[C@@H....
2 1WNZ - 2VA C15 H23 N7 O4 CC(C)[C@@H....
3 1UE0 - VAL C5 H11 N O2 CC(C)[C@@H....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 1WK8 - VMS C15 H23 N7 O7 S CC(C)[C@@H....
2 1WNZ - 2VA C15 H23 N7 O4 CC(C)[C@@H....
3 1UE0 - VAL C5 H11 N O2 CC(C)[C@@H....
50% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 1WK8 - VMS C15 H23 N7 O7 S CC(C)[C@@H....
2 1WNZ - 2VA C15 H23 N7 O4 CC(C)[C@@H....
3 1UE0 - VAL C5 H11 N O2 CC(C)[C@@H....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: VMS; Similar ligands found: 309
No: Ligand ECFP6 Tc MDL keys Tc
1 54H 1 1
2 VMS 1 1
3 TSB 0.865854 0.963855
4 A5A 0.851852 0.97561
5 LSS 0.802326 0.964706
6 53H 0.8 0.987952
7 SSA 0.797619 0.918605
8 52H 0.788235 0.987952
9 DSZ 0.781609 0.918605
10 5CA 0.77907 0.918605
11 NSS 0.761364 0.918605
12 NVA LMS 0.752809 0.909091
13 KAA 0.736264 0.88764
14 GSU 0.736264 0.918605
15 G5A 0.729412 0.918605
16 8X1 0.7 0.88764
17 5AS 0.698795 0.918605
18 YSA 0.697917 0.918605
19 P5A 0.663158 0.877778
20 8PZ 0.653061 0.918605
21 LMS 0.646341 0.951219
22 WSA 0.644231 0.929412
23 B1U 0.613861 0.868132
24 5AL 0.602151 0.821429
25 8Q2 0.592593 0.88764
26 4YB 0.590476 0.897727
27 LEU LMS 0.585859 0.886364
28 SON 0.577778 0.781609
29 QA7 0.57732 0.835294
30 8QN 0.571429 0.821429
31 AMP 0.569767 0.785714
32 A 0.569767 0.785714
33 649 0.568807 0.877778
34 ABM 0.568182 0.788235
35 45A 0.568182 0.788235
36 AMP MG 0.563218 0.77381
37 AHX 0.56 0.775281
38 8LH 0.556701 0.802326
39 BA3 0.555556 0.788235
40 9ZD 0.555556 0.825581
41 9ZA 0.555556 0.825581
42 CA0 0.554348 0.790698
43 8LE 0.552083 0.835294
44 A2D 0.550562 0.788235
45 B4P 0.549451 0.788235
46 AP5 0.549451 0.788235
47 KG4 0.548387 0.790698
48 5X8 0.548387 0.697674
49 3DH 0.546512 0.705882
50 DAL AMP 0.545455 0.8
51 SRA 0.545455 0.811765
52 8LQ 0.545455 0.802326
53 TXA 0.543689 0.802326
54 AN2 0.543478 0.8
55 SRP 0.540816 0.781609
56 AOC 0.539326 0.705882
57 A12 0.538462 0.761364
58 AP2 0.538462 0.761364
59 M33 0.537634 0.8
60 AU1 0.537634 0.790698
61 ADX 0.537634 0.904762
62 XYA 0.5375 0.702381
63 ADN 0.5375 0.702381
64 RAB 0.5375 0.702381
65 5CD 0.536585 0.690476
66 V2G 0.536082 0.775281
67 ADP 0.532609 0.788235
68 2VA 0.531915 0.75
69 9K8 0.528846 0.787234
70 ADP MG 0.526882 0.785714
71 ADP BEF 0.526882 0.785714
72 AT4 0.526882 0.802326
73 5FA 0.526316 0.788235
74 AQP 0.526316 0.788235
75 PRX 0.526316 0.770115
76 GAP 0.525773 0.770115
77 5N5 0.52439 0.682353
78 XAH 0.523364 0.75
79 MTA 0.523256 0.705882
80 SLU 0.521008 0.908046
81 SA8 0.520833 0.652174
82 PAJ 0.519608 0.806818
83 AMO 0.519608 0.781609
84 A4D 0.518072 0.702381
85 EP4 0.517647 0.709302
86 A3T 0.515789 0.72619
87 ATP 0.515789 0.788235
88 50T 0.515789 0.758621
89 ACP 0.515789 0.770115
90 HEJ 0.515789 0.788235
91 NB8 0.514286 0.775281
92 ME8 0.514286 0.769231
93 DTA 0.511628 0.717647
94 M2T 0.511628 0.732558
95 APC 0.510417 0.761364
96 AR6 0.510417 0.788235
97 APR 0.510417 0.788235
98 ANP 0.510204 0.790698
99 SAM 0.510204 0.673913
100 SMM 0.51 0.688172
101 7MD 0.509091 0.75
102 RBY 0.505155 0.761364
103 ADP PO3 0.505155 0.785714
104 ATP MG 0.505155 0.785714
105 APC MG 0.505155 0.767442
106 AGS 0.505155 0.813953
107 AD9 0.505155 0.770115
108 ADV 0.505155 0.761364
109 4AD 0.504854 0.772727
110 LAD 0.504762 0.747253
111 DLL 0.5 0.8
112 SFG 0.5 0.666667
113 ANP MG 0.5 0.8
114 H1Q 0.5 0.776471
115 BEF ADP 0.5 0.767442
116 SAI 0.5 0.655556
117 VO4 ADP 0.5 0.770115
118 PTJ 0.5 0.816092
119 SAH 0.5 0.681818
120 3OD 0.5 0.811765
121 48N 0.495575 0.775281
122 OAD 0.495238 0.811765
123 3UK 0.495238 0.790698
124 QXP 0.495146 0.840909
125 OOB 0.495146 0.8
126 S7M 0.49505 0.673913
127 T99 0.494949 0.802326
128 TAT 0.494949 0.802326
129 ACQ 0.494949 0.770115
130 6RE 0.494505 0.641304
131 PR8 0.490566 0.73913
132 A1R 0.490385 0.744444
133 EEM 0.49 0.638298
134 FA5 0.486239 0.781609
135 1ZZ 0.485981 0.75
136 FYA 0.485981 0.758621
137 00A 0.485714 0.764045
138 JNT 0.485714 0.770115
139 MAP 0.485437 0.772727
140 A22 0.485437 0.77907
141 ALF ADP 0.485149 0.733333
142 ATF 0.485149 0.761364
143 J7C 0.483871 0.648352
144 A3N 0.483871 0.659091
145 7MC 0.482759 0.752688
146 YLP 0.482456 0.734043
147 NWW 0.482353 0.650602
148 MYR AMP 0.481481 0.731183
149 9X8 0.481132 0.813953
150 5SV 0.480769 0.736264
151 25A 0.480769 0.788235
152 6YZ 0.480392 0.770115
153 A3S 0.479167 0.697674
154 S4M 0.478723 0.635417
155 GJV 0.478723 0.634409
156 9SN 0.477064 0.755556
157 WAQ 0.476636 0.764045
158 B5V 0.476636 0.781609
159 A3R 0.47619 0.744444
160 ADQ 0.47619 0.770115
161 0UM 0.47619 0.645161
162 HQG 0.475728 0.77907
163 MAO 0.473684 0.698925
164 DSH 0.473118 0.648352
165 NEC 0.473118 0.662791
166 B5Y 0.472727 0.793103
167 B5M 0.472727 0.793103
168 SXZ 0.472222 0.711111
169 YLC 0.470085 0.75
170 YLB 0.470085 0.734043
171 SO8 0.47 0.72093
172 ARG AMP 0.469027 0.705263
173 GA7 0.469027 0.761364
174 RRW 0.46789 0.930233
175 ZAS 0.467391 0.681818
176 K15 0.46729 0.631579
177 ADP BMA 0.46729 0.75
178 QXG 0.46729 0.831461
179 OZV 0.466667 0.788235
180 NAX 0.465517 0.73913
181 TAD 0.464912 0.766667
182 AMP DBH 0.464286 0.730337
183 A7D 0.463918 0.689655
184 R2V 0.462963 0.840909
185 F2R 0.46281 0.715789
186 RUZ 0.462264 0.895349
187 TYM 0.461538 0.781609
188 TXE 0.461538 0.764045
189 NWQ 0.461538 0.654762
190 LAQ 0.46087 0.769231
191 7C5 0.460177 0.707865
192 KMQ 0.459459 0.781609
193 MHZ 0.459184 0.645833
194 JB6 0.458716 0.784091
195 BIS 0.458716 0.744444
196 62X 0.457944 0.652632
197 5AD 0.457831 0.658537
198 A3G 0.457447 0.689655
199 LPA AMP 0.456897 0.75
200 KOY 0.456897 0.712644
201 4UU 0.45614 0.772727
202 AYB 0.454545 0.726316
203 25L 0.454545 0.77907
204 RSN 0.454545 0.885057
205 4UW 0.452991 0.766667
206 DND 0.452991 0.781609
207 TXD 0.452991 0.764045
208 6V0 0.452991 0.755556
209 GTA 0.452174 0.75
210 DQV 0.452174 0.8
211 4UV 0.451327 0.772727
212 J4G 0.449541 0.772727
213 ALF ADP 3PG 0.449153 0.728261
214 OMR 0.449153 0.741935
215 AF3 ADP 3PG 0.449153 0.728261
216 AHZ 0.448276 0.75
217 EO7 0.447917 0.906977
218 COD 0.447154 0.765957
219 YLA 0.446281 0.715789
220 L3W 0.445378 0.781609
221 NAD TDB 0.445378 0.788235
222 AP0 0.445378 0.755556
223 NAD IBO 0.445378 0.788235
224 CNA 0.442623 0.781609
225 N5O 0.442105 0.659091
226 VRT 0.441176 0.685393
227 YLY 0.440945 0.726316
228 3AM 0.44086 0.752941
229 NAI 0.440678 0.764045
230 GEK 0.439252 0.696629
231 V47 0.438095 0.694118
232 IOT 0.438017 0.708333
233 Y3J 0.436782 0.623529
234 3NZ 0.436364 0.696629
235 7D7 0.435294 0.639535
236 7D5 0.434783 0.715909
237 G3A 0.434783 0.755556
238 T5A 0.434426 0.734043
239 ATP A 0.433628 0.776471
240 ATP A A A 0.433628 0.776471
241 N5A 0.43299 0.636364
242 A5D 0.431373 0.717647
243 NVA 2AD 0.431373 0.677778
244 G5P 0.431034 0.755556
245 AR6 AR6 0.431034 0.767442
246 AFH 0.431034 0.728261
247 D3Y 0.429907 0.681818
248 KYE 0.429825 0.625
249 A4P 0.429752 0.701031
250 A3P 0.428571 0.785714
251 A2P 0.428571 0.77381
252 A3D 0.428571 0.811765
253 UP5 0.428571 0.772727
254 EU9 0.428571 0.670103
255 KB1 0.428571 0.62766
256 KH3 0.42735 0.625
257 KXW 0.42735 0.634409
258 S8M 0.425926 0.696629
259 NAD 0.424 0.8
260 AMP NAD 0.424 0.77907
261 HZ2 0.423729 0.638298
262 K2K 0.423423 0.623656
263 NAQ 0.423077 0.795455
264 NX8 0.423077 0.623656
265 594 0.421875 0.804124
266 K3K 0.421053 0.674157
267 BT5 0.420635 0.726316
268 N0B 0.419847 0.715789
269 AAT 0.419048 0.634409
270 6MZ 0.418367 0.776471
271 80F 0.417323 0.734043
272 KY2 0.416667 0.621053
273 HY8 0.416667 0.638298
274 3AD 0.41573 0.690476
275 D4F 0.415385 0.75
276 RRB 0.415254 0.885057
277 2AM 0.414894 0.744186
278 K3E 0.413793 0.666667
279 4TA 0.412698 0.723404
280 139 0.41129 0.73913
281 ADJ 0.41129 0.705263
282 UPA 0.409836 0.764045
283 4TC 0.409836 0.755556
284 Q34 0.409836 0.608247
285 Q2M 0.409836 0.638298
286 V3L 0.409524 0.788235
287 6IA 0.409524 0.747253
288 DZD 0.409449 0.747253
289 KYB 0.409091 0.621053
290 U4Y 0.408333 0.677778
291 BS5 0.408 0.770833
292 2A5 0.407767 0.730337
293 NWZ 0.407767 0.612903
294 Z5A 0.406015 0.71875
295 FB0 0.405797 0.707071
296 PPS 0.40566 0.882353
297 NAE 0.40458 0.793103
298 7D3 0.40404 0.719101
299 ATR 0.403846 0.764706
300 PAP 0.403846 0.776471
301 NAJ PZO 0.403101 0.755556
302 CC5 0.402299 0.698795
303 OVE 0.402062 0.758621
304 7D4 0.401961 0.719101
305 2SA 0.401869 0.761364
306 A6D 0.401786 0.684783
307 BTX 0.401575 0.734043
308 Q2P 0.401575 0.608247
309 Q2V 0.4 0.62766
Similar Ligands (3D)
Ligand no: 1; Ligand: VMS; Similar ligands found: 0
No: Ligand Similarity coefficient
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1WK8; Ligand: VMS; 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: 1wk8.bio2) has 16 residues
No: Leader PDB Ligand Sequence Similarity
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