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: 247
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 0.964706
12 NSS 0.761364 0.918605
13 NVA LMS 0.752809 0.91954
14 GSU 0.736264 0.918605
15 KAA 0.736264 0.88764
16 G5A 0.729412 0.918605
17 5AS 0.698795 0.918605
18 YSA 0.697917 0.918605
19 P5A 0.663158 0.877778
20 WSA 0.644231 0.929412
21 5AL 0.602151 0.821429
22 4YB 0.590476 0.897727
23 SON 0.577778 0.781609
24 8QN 0.571429 0.821429
25 AMP 0.569767 0.785714
26 A 0.569767 0.785714
27 649 0.568807 0.877778
28 ABM 0.568182 0.788235
29 AHX 0.56 0.775281
30 AMP MG 0.556818 0.747126
31 BA3 0.555556 0.788235
32 CA0 0.554348 0.790698
33 A2D 0.550562 0.788235
34 AP5 0.549451 0.788235
35 B4P 0.549451 0.788235
36 5X8 0.548387 0.697674
37 3DH 0.546512 0.705882
38 SRA 0.545455 0.811765
39 DAL AMP 0.545455 0.8
40 TXA 0.543689 0.802326
41 AN2 0.543478 0.8
42 SRP 0.540816 0.781609
43 AOC 0.539326 0.705882
44 A12 0.538462 0.761364
45 AP2 0.538462 0.761364
46 AU1 0.537634 0.790698
47 ADX 0.537634 0.904762
48 M33 0.537634 0.8
49 XYA 0.5375 0.702381
50 RAB 0.5375 0.702381
51 ADN 0.5375 0.702381
52 5CD 0.536585 0.690476
53 ADP 0.532609 0.788235
54 2VA 0.531915 0.75
55 5FA 0.526316 0.788235
56 AQP 0.526316 0.788235
57 PRX 0.526316 0.770115
58 GAP 0.525773 0.770115
59 5N5 0.52439 0.682353
60 XAH 0.523364 0.75
61 MTA 0.523256 0.705882
62 ADP MG 0.521277 0.758621
63 SLU 0.521008 0.908046
64 SA8 0.520833 0.652174
65 AMO 0.519608 0.781609
66 PAJ 0.519608 0.806818
67 A4D 0.518072 0.702381
68 EP4 0.517647 0.709302
69 ACP 0.515789 0.770115
70 BEF ADP 0.515789 0.741573
71 ATP 0.515789 0.788235
72 A3T 0.515789 0.72619
73 50T 0.515789 0.758621
74 ADP BEF 0.515789 0.741573
75 NB8 0.514286 0.775281
76 ME8 0.514286 0.769231
77 M2T 0.511628 0.732558
78 DTA 0.511628 0.717647
79 APC 0.510417 0.761364
80 AR6 0.510417 0.788235
81 APR 0.510417 0.788235
82 ANP 0.510204 0.790698
83 SAM 0.510204 0.673913
84 SMM 0.51 0.688172
85 7MD 0.509091 0.75
86 ADV 0.505155 0.761364
87 ADP PO3 0.505155 0.785714
88 SAP 0.505155 0.813953
89 AGS 0.505155 0.813953
90 AD9 0.505155 0.770115
91 RBY 0.505155 0.761364
92 4AD 0.504854 0.772727
93 LAD 0.504762 0.747253
94 ATP MG 0.5 0.758621
95 DLL 0.5 0.8
96 SAI 0.5 0.655556
97 SAH 0.5 0.681818
98 3OD 0.5 0.811765
99 SFG 0.5 0.666667
100 PTJ 0.5 0.816092
101 48N 0.495575 0.775281
102 3UK 0.495238 0.790698
103 OAD 0.495238 0.811765
104 OOB 0.495146 0.8
105 ANP MG 0.49505 0.772727
106 S7M 0.49505 0.673913
107 ACQ 0.494949 0.770115
108 TAT 0.494949 0.802326
109 6RE 0.494505 0.641304
110 PR8 0.490566 0.73913
111 A1R 0.490385 0.744444
112 EEM 0.49 0.638298
113 FA5 0.486239 0.781609
114 YAP 0.486239 0.772727
115 1ZZ 0.485981 0.75
116 FYA 0.485981 0.758621
117 00A 0.485714 0.764045
118 MAP 0.485437 0.772727
119 A22 0.485437 0.77907
120 ATF 0.485149 0.761364
121 ADP ALF 0.485149 0.733333
122 ALF ADP 0.485149 0.733333
123 J7C 0.483871 0.648352
124 A3N 0.483871 0.659091
125 7MC 0.482759 0.752688
126 YLP 0.482456 0.734043
127 MYR AMP 0.481481 0.731183
128 25A 0.480769 0.788235
129 5SV 0.480769 0.736264
130 VO4 ADP 0.480392 0.77907
131 ADP VO4 0.480392 0.77907
132 A3S 0.479167 0.697674
133 S4M 0.478723 0.635417
134 GJV 0.478723 0.634409
135 9SN 0.477064 0.755556
136 WAQ 0.476636 0.764045
137 0UM 0.47619 0.645161
138 ADQ 0.47619 0.770115
139 MAO 0.473684 0.698925
140 ARG AMP 0.473684 0.705263
141 NEC 0.473118 0.662791
142 DSH 0.473118 0.648352
143 SXZ 0.472222 0.711111
144 YLC 0.470085 0.75
145 YLB 0.470085 0.734043
146 SO8 0.47 0.72093
147 TYR AMP 0.468468 0.761364
148 ZAS 0.467391 0.681818
149 ADP BMA 0.46729 0.75
150 K15 0.46729 0.631579
151 NAX 0.465517 0.73913
152 TAD 0.464912 0.766667
153 AMP DBH 0.464286 0.730337
154 A7D 0.463918 0.689655
155 NAD IBO 0.46281 0.813953
156 TXE 0.461538 0.764045
157 TYM 0.461538 0.781609
158 LAQ 0.46087 0.769231
159 7C5 0.460177 0.707865
160 MHZ 0.459184 0.645833
161 JB6 0.458716 0.784091
162 BIS 0.458716 0.744444
163 62X 0.457944 0.652632
164 5AD 0.457831 0.658537
165 A3G 0.457447 0.689655
166 LPA AMP 0.456897 0.75
167 4UU 0.45614 0.772727
168 AYB 0.454545 0.726316
169 25L 0.454545 0.77907
170 6V0 0.452991 0.755556
171 TXD 0.452991 0.764045
172 DND 0.452991 0.781609
173 4UW 0.452991 0.766667
174 NXX 0.452991 0.781609
175 GTA 0.452174 0.75
176 4UV 0.451327 0.772727
177 A A 0.449541 0.767442
178 OMR 0.449153 0.741935
179 LA8 ALF 3PG 0.449153 0.728261
180 ALF ADP 3PG 0.449153 0.728261
181 AF3 ADP 3PG 0.449153 0.728261
182 AHZ 0.448276 0.75
183 COD 0.447154 0.765957
184 YLA 0.446281 0.715789
185 AP0 0.445378 0.755556
186 CNA 0.442623 0.781609
187 VRT 0.441176 0.685393
188 YLY 0.440945 0.726316
189 3AM 0.44086 0.752941
190 NAI 0.440678 0.764045
191 GEK 0.439252 0.696629
192 IOT 0.438017 0.708333
193 Y3J 0.436782 0.623529
194 3NZ 0.436364 0.696629
195 7D7 0.435294 0.639535
196 G3A 0.434783 0.755556
197 7D5 0.434783 0.715909
198 T5A 0.434426 0.734043
199 ATP A A A 0.433628 0.776471
200 A5D 0.431373 0.717647
201 AFH 0.431034 0.728261
202 G5P 0.431034 0.755556
203 AR6 AR6 0.431034 0.767442
204 D3Y 0.429907 0.681818
205 A4P 0.429752 0.701031
206 A3P 0.428571 0.785714
207 A3D 0.428571 0.811765
208 UP5 0.428571 0.772727
209 A2P 0.428571 0.77381
210 KB1 0.428571 0.62766
211 KH3 0.42735 0.625
212 S8M 0.425926 0.696629
213 NAD 0.424 0.8
214 NAQ 0.423077 0.795455
215 594 0.421875 0.804124
216 BT5 0.420635 0.726316
217 N0B 0.419847 0.715789
218 AAT 0.419048 0.634409
219 3AD 0.41573 0.690476
220 2AM 0.414894 0.744186
221 4TA 0.412698 0.723404
222 ADJ 0.41129 0.705263
223 139 0.41129 0.73913
224 4TC 0.409836 0.755556
225 UPA 0.409836 0.764045
226 6IA 0.409524 0.747253
227 V3L 0.409524 0.788235
228 DZD 0.409449 0.747253
229 AMP NAD 0.409091 0.781609
230 BS5 0.408 0.770833
231 2A5 0.407767 0.730337
232 Z5A 0.406015 0.71875
233 FB0 0.405797 0.707071
234 PPS 0.40566 0.882353
235 NAE 0.40458 0.793103
236 7D3 0.40404 0.719101
237 ATR 0.403846 0.764706
238 NVA 2AD 0.403846 0.662921
239 PAP 0.403846 0.776471
240 NAJ PZO 0.403101 0.755556
241 CC5 0.402299 0.698795
242 OVE 0.402062 0.758621
243 7D4 0.401961 0.719101
244 2SA 0.401869 0.761364
245 A6D 0.401786 0.684783
246 BTX 0.401575 0.734043
247 NAJ PYZ 0.401515 0.758242
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1WK8; Ligand: VMS; Similar sites found: 25
This union binding pocket(no: 1) in the query (biounit: 1wk8.bio2) has 16 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2BOS GLA GAL GLC NBU 0.007139 0.4212 None
2 3IT7 TLA 0.0156 0.40534 2.74725
3 4RDN 6MD 0.01543 0.40387 2.99401
4 1QFY FAD 0.02904 0.40904 3.09278
5 1QFY NAP 0.02904 0.40904 3.09278
6 1EU1 GLC 0.001868 0.40493 3.60825
7 4UYW H1S 0.006999 0.4048 4.63918
8 2AMT 1AA 0.02019 0.40647 5.03145
9 5H5J FAD 0.01606 0.4019 5.15464
10 3S6X SIA GAL BGC 0.0007307 0.46956 5.6701
11 4W6Z 8ID 0.04258 0.40037 6.70103
12 4RL4 PPV 0.003023 0.44549 7.2165
13 3MHP FAD 0.01695 0.40076 7.69231
14 1VBO MAN MAN MAN 0.01211 0.40456 7.73196
15 3PNL ADP 0.01597 0.4071 8.76289
16 3B6R CRN 0.02004 0.41663 9.27835
17 5AHO TLA 0.01899 0.40901 9.27835
18 4M1U MBG A2G 0.0229 0.40087 11.4286
19 5AHW CMP 0.01455 0.40015 14.966
20 5AGR A52 0.0000003541 0.56766 20.1031
21 4K47 WMP 0.000004518 0.5641 22.3958
22 1WK9 TSB 0.000008027 0.54904 28.0822
23 2V0C ANZ 0.00000006125 0.58428 29.8969
24 2AJH MET 0.0000009142 0.61442 34.0206
25 2WFG ZZB 0.000002171 0.58845 38.1443
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