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)...
View in 3D viewer
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
Ligand no: 1; Ligand: VMS; Similar ligands found: 278
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 LEU LMS 0.764045 0.953488
12 NSS 0.761364 0.918605
13 NVA LMS 0.752809 0.909091
14 KAA 0.736264 0.88764
15 GSU 0.736264 0.918605
16 G5A 0.729412 0.918605
17 8X1 0.7 0.88764
18 5AS 0.698795 0.918605
19 YSA 0.697917 0.918605
20 P5A 0.663158 0.877778
21 8PZ 0.653061 0.918605
22 LMS 0.646341 0.951219
23 WSA 0.644231 0.929412
24 B1U 0.613861 0.868132
25 5AL 0.602151 0.821429
26 8Q2 0.592593 0.88764
27 4YB 0.590476 0.897727
28 SON 0.577778 0.781609
29 8QN 0.571429 0.821429
30 A 0.569767 0.785714
31 AMP 0.569767 0.785714
32 649 0.568807 0.877778
33 ABM 0.568182 0.788235
34 45A 0.568182 0.788235
35 AHX 0.56 0.775281
36 8LH 0.556701 0.802326
37 9ZA 0.555556 0.825581
38 BA3 0.555556 0.788235
39 9ZD 0.555556 0.825581
40 CA0 0.554348 0.790698
41 8LE 0.552083 0.835294
42 A2D 0.550562 0.788235
43 B4P 0.549451 0.788235
44 AP5 0.549451 0.788235
45 5X8 0.548387 0.697674
46 KG4 0.548387 0.790698
47 3DH 0.546512 0.705882
48 SRA 0.545455 0.811765
49 8LQ 0.545455 0.802326
50 DAL AMP 0.545455 0.8
51 TXA 0.543689 0.802326
52 AN2 0.543478 0.8
53 SRP 0.540816 0.781609
54 AOC 0.539326 0.705882
55 AP2 0.538462 0.761364
56 A12 0.538462 0.761364
57 ADX 0.537634 0.904762
58 AU1 0.537634 0.790698
59 M33 0.537634 0.8
60 XYA 0.5375 0.702381
61 ADN 0.5375 0.702381
62 RAB 0.5375 0.702381
63 5CD 0.536585 0.690476
64 ADP 0.532609 0.788235
65 2VA 0.531915 0.75
66 9K8 0.528846 0.787234
67 AT4 0.526882 0.802326
68 ADP MG 0.526882 0.785714
69 PRX 0.526316 0.770115
70 AQP 0.526316 0.788235
71 5FA 0.526316 0.788235
72 GAP 0.525773 0.770115
73 5N5 0.52439 0.682353
74 XAH 0.523364 0.75
75 MTA 0.523256 0.705882
76 SLU 0.521008 0.908046
77 SA8 0.520833 0.652174
78 PAJ 0.519608 0.806818
79 AMO 0.519608 0.781609
80 A4D 0.518072 0.702381
81 EP4 0.517647 0.709302
82 HEJ 0.515789 0.788235
83 50T 0.515789 0.758621
84 A3T 0.515789 0.72619
85 ACP 0.515789 0.770115
86 ATP 0.515789 0.788235
87 NB8 0.514286 0.775281
88 ME8 0.514286 0.769231
89 DTA 0.511628 0.717647
90 M2T 0.511628 0.732558
91 APR 0.510417 0.788235
92 AR6 0.510417 0.788235
93 APC 0.510417 0.761364
94 SAM 0.510204 0.673913
95 ANP 0.510204 0.790698
96 SMM 0.51 0.688172
97 7MD 0.509091 0.75
98 APC MG 0.505155 0.767442
99 SAP 0.505155 0.813953
100 ADV 0.505155 0.761364
101 ATP MG 0.505155 0.785714
102 AGS 0.505155 0.813953
103 ADP PO3 0.505155 0.785714
104 RBY 0.505155 0.761364
105 AD9 0.505155 0.770115
106 4AD 0.504854 0.772727
107 LAD 0.504762 0.747253
108 H1Q 0.5 0.776471
109 SFG 0.5 0.666667
110 DLL 0.5 0.8
111 3OD 0.5 0.811765
112 SAH 0.5 0.681818
113 SAI 0.5 0.655556
114 PTJ 0.5 0.816092
115 48N 0.495575 0.775281
116 3UK 0.495238 0.790698
117 OAD 0.495238 0.811765
118 OOB 0.495146 0.8
119 S7M 0.49505 0.673913
120 TAT 0.494949 0.802326
121 ACQ 0.494949 0.770115
122 T99 0.494949 0.802326
123 6RE 0.494505 0.641304
124 PR8 0.490566 0.73913
125 A1R 0.490385 0.744444
126 EEM 0.49 0.638298
127 FA5 0.486239 0.781609
128 YAP 0.486239 0.772727
129 FYA 0.485981 0.758621
130 1ZZ 0.485981 0.75
131 00A 0.485714 0.764045
132 MAP 0.485437 0.772727
133 A22 0.485437 0.77907
134 ALF ADP 0.485149 0.733333
135 ADP ALF 0.485149 0.733333
136 ATF 0.485149 0.761364
137 A3N 0.483871 0.659091
138 J7C 0.483871 0.648352
139 7MC 0.482759 0.752688
140 YLP 0.482456 0.734043
141 MYR AMP 0.481481 0.731183
142 9X8 0.481132 0.813953
143 25A 0.480769 0.788235
144 5SV 0.480769 0.736264
145 VO4 ADP 0.480392 0.77907
146 ADP VO4 0.480392 0.77907
147 6YZ 0.480392 0.770115
148 A3S 0.479167 0.697674
149 GJV 0.478723 0.634409
150 S4M 0.478723 0.635417
151 9SN 0.477064 0.755556
152 WAQ 0.476636 0.764045
153 B5V 0.476636 0.781609
154 ADQ 0.47619 0.770115
155 A3R 0.47619 0.744444
156 0UM 0.47619 0.645161
157 HQG 0.475728 0.77907
158 MAO 0.473684 0.698925
159 DSH 0.473118 0.648352
160 NEC 0.473118 0.662791
161 B5Y 0.472727 0.793103
162 B5M 0.472727 0.793103
163 SXZ 0.472222 0.711111
164 YLB 0.470085 0.734043
165 YLC 0.470085 0.75
166 SO8 0.47 0.72093
167 GA7 0.469027 0.761364
168 ARG AMP 0.469027 0.705263
169 ZAS 0.467391 0.681818
170 K15 0.46729 0.631579
171 ADP BMA 0.46729 0.75
172 OZV 0.466667 0.788235
173 NAX 0.465517 0.73913
174 TAD 0.464912 0.766667
175 AMP DBH 0.464286 0.730337
176 TYR AMP 0.464286 0.752809
177 A7D 0.463918 0.689655
178 F2R 0.46281 0.715789
179 TXE 0.461538 0.764045
180 TYM 0.461538 0.781609
181 LAQ 0.46087 0.769231
182 7C5 0.460177 0.707865
183 MHZ 0.459184 0.645833
184 JB6 0.458716 0.784091
185 BIS 0.458716 0.744444
186 62X 0.457944 0.652632
187 5AD 0.457831 0.658537
188 A3G 0.457447 0.689655
189 LPA AMP 0.456897 0.75
190 KOY 0.456897 0.712644
191 4UU 0.45614 0.772727
192 25L 0.454545 0.77907
193 AYB 0.454545 0.726316
194 6V0 0.452991 0.755556
195 NXX 0.452991 0.781609
196 TXD 0.452991 0.764045
197 4UW 0.452991 0.766667
198 DND 0.452991 0.781609
199 DQV 0.452174 0.8
200 GTA 0.452174 0.75
201 4UV 0.451327 0.772727
202 A A 0.449541 0.767442
203 J4G 0.449541 0.772727
204 AF3 ADP 3PG 0.449153 0.728261
205 OMR 0.449153 0.741935
206 AHZ 0.448276 0.75
207 EO7 0.447917 0.906977
208 COD 0.447154 0.765957
209 YLA 0.446281 0.715789
210 AP0 0.445378 0.755556
211 CNA 0.442623 0.781609
212 N5O 0.442105 0.659091
213 VRT 0.441176 0.685393
214 YLY 0.440945 0.726316
215 3AM 0.44086 0.752941
216 NAI 0.440678 0.764045
217 GEK 0.439252 0.696629
218 IOT 0.438017 0.708333
219 Y3J 0.436782 0.623529
220 3NZ 0.436364 0.696629
221 7D7 0.435294 0.639535
222 7D5 0.434783 0.715909
223 G3A 0.434783 0.755556
224 T5A 0.434426 0.734043
225 ATP A 0.433628 0.776471
226 ATP A A A 0.433628 0.776471
227 N5A 0.43299 0.636364
228 NVA 2AD 0.431373 0.677778
229 A5D 0.431373 0.717647
230 AR6 AR6 0.431034 0.767442
231 G5P 0.431034 0.755556
232 AFH 0.431034 0.728261
233 D3Y 0.429907 0.681818
234 A4P 0.429752 0.701031
235 A3D 0.428571 0.811765
236 UP5 0.428571 0.772727
237 A3P 0.428571 0.785714
238 A2P 0.428571 0.77381
239 KB1 0.428571 0.62766
240 KH3 0.42735 0.625
241 S8M 0.425926 0.696629
242 AMP NAD 0.424 0.77907
243 NAD 0.424 0.8
244 HZ2 0.423729 0.638298
245 NAQ 0.423077 0.795455
246 594 0.421875 0.804124
247 BT5 0.420635 0.726316
248 N0B 0.419847 0.715789
249 AAT 0.419048 0.634409
250 6MZ 0.418367 0.776471
251 80F 0.417323 0.734043
252 HY8 0.416667 0.638298
253 3AD 0.41573 0.690476
254 2AM 0.414894 0.744186
255 4TA 0.412698 0.723404
256 ADJ 0.41129 0.705263
257 139 0.41129 0.73913
258 4TC 0.409836 0.755556
259 UPA 0.409836 0.764045
260 6IA 0.409524 0.747253
261 V3L 0.409524 0.788235
262 DZD 0.409449 0.747253
263 BS5 0.408 0.770833
264 2A5 0.407767 0.730337
265 Z5A 0.406015 0.71875
266 FB0 0.405797 0.707071
267 PPS 0.40566 0.882353
268 NAE 0.40458 0.793103
269 7D3 0.40404 0.719101
270 ATR 0.403846 0.764706
271 PAP 0.403846 0.776471
272 NAJ PZO 0.403101 0.755556
273 CC5 0.402299 0.698795
274 OVE 0.402062 0.758621
275 7D4 0.401961 0.719101
276 2SA 0.401869 0.761364
277 A6D 0.401786 0.684783
278 BTX 0.401575 0.734043
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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