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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
Ligand no: 1; Ligand: VMS; Similar ligands found: 258
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 5AL 0.602151 0.821429
25 8Q2 0.592593 0.88764
26 4YB 0.590476 0.897727
27 SON 0.577778 0.781609
28 8QN 0.571429 0.821429
29 AMP 0.569767 0.785714
30 A 0.569767 0.785714
31 649 0.568807 0.877778
32 ABM 0.568182 0.788235
33 AHX 0.56 0.775281
34 9ZD 0.555556 0.825581
35 BA3 0.555556 0.788235
36 9ZA 0.555556 0.825581
37 CA0 0.554348 0.790698
38 A2D 0.550562 0.788235
39 AP5 0.549451 0.788235
40 B4P 0.549451 0.788235
41 5X8 0.548387 0.697674
42 3DH 0.546512 0.705882
43 DAL AMP 0.545455 0.8
44 SRA 0.545455 0.811765
45 TXA 0.543689 0.802326
46 AN2 0.543478 0.8
47 SRP 0.540816 0.781609
48 AOC 0.539326 0.705882
49 AP2 0.538462 0.761364
50 A12 0.538462 0.761364
51 AU1 0.537634 0.790698
52 ADX 0.537634 0.904762
53 M33 0.537634 0.8
54 XYA 0.5375 0.702381
55 ADN 0.5375 0.702381
56 RAB 0.5375 0.702381
57 5CD 0.536585 0.690476
58 ADP 0.532609 0.788235
59 2VA 0.531915 0.75
60 9K8 0.528846 0.787234
61 AT4 0.526882 0.802326
62 5FA 0.526316 0.788235
63 PRX 0.526316 0.770115
64 AQP 0.526316 0.788235
65 GAP 0.525773 0.770115
66 5N5 0.52439 0.682353
67 XAH 0.523364 0.75
68 MTA 0.523256 0.705882
69 SLU 0.521008 0.908046
70 SA8 0.520833 0.652174
71 PAJ 0.519608 0.806818
72 AMO 0.519608 0.781609
73 A4D 0.518072 0.702381
74 EP4 0.517647 0.709302
75 HEJ 0.515789 0.788235
76 ACP 0.515789 0.770115
77 A3T 0.515789 0.72619
78 ATP 0.515789 0.788235
79 50T 0.515789 0.758621
80 NB8 0.514286 0.775281
81 ME8 0.514286 0.769231
82 DTA 0.511628 0.717647
83 M2T 0.511628 0.732558
84 APC 0.510417 0.761364
85 APR 0.510417 0.788235
86 AR6 0.510417 0.788235
87 SAM 0.510204 0.673913
88 ANP 0.510204 0.790698
89 SMM 0.51 0.688172
90 7MD 0.509091 0.75
91 SAP 0.505155 0.813953
92 AGS 0.505155 0.813953
93 ADV 0.505155 0.761364
94 ADP PO3 0.505155 0.785714
95 RBY 0.505155 0.761364
96 AD9 0.505155 0.770115
97 4AD 0.504854 0.772727
98 LAD 0.504762 0.747253
99 SAI 0.5 0.655556
100 PTJ 0.5 0.816092
101 SAH 0.5 0.681818
102 SFG 0.5 0.666667
103 3OD 0.5 0.811765
104 DLL 0.5 0.8
105 48N 0.495575 0.775281
106 OAD 0.495238 0.811765
107 3UK 0.495238 0.790698
108 OOB 0.495146 0.8
109 S7M 0.49505 0.673913
110 T99 0.494949 0.802326
111 ACQ 0.494949 0.770115
112 TAT 0.494949 0.802326
113 6RE 0.494505 0.641304
114 PR8 0.490566 0.73913
115 A1R 0.490385 0.744444
116 EEM 0.49 0.638298
117 YAP 0.486239 0.772727
118 FA5 0.486239 0.781609
119 FYA 0.485981 0.758621
120 1ZZ 0.485981 0.75
121 00A 0.485714 0.764045
122 A22 0.485437 0.77907
123 MAP 0.485437 0.772727
124 ALF ADP 0.485149 0.733333
125 ADP ALF 0.485149 0.733333
126 ATF 0.485149 0.761364
127 J7C 0.483871 0.648352
128 A3N 0.483871 0.659091
129 7MC 0.482759 0.752688
130 YLP 0.482456 0.734043
131 MYR AMP 0.481481 0.731183
132 9X8 0.481132 0.813953
133 25A 0.480769 0.788235
134 5SV 0.480769 0.736264
135 VO4 ADP 0.480392 0.77907
136 6YZ 0.480392 0.770115
137 ADP VO4 0.480392 0.77907
138 A3S 0.479167 0.697674
139 S4M 0.478723 0.635417
140 GJV 0.478723 0.634409
141 9SN 0.477064 0.755556
142 WAQ 0.476636 0.764045
143 B5V 0.476636 0.781609
144 A3R 0.47619 0.744444
145 ADQ 0.47619 0.770115
146 0UM 0.47619 0.645161
147 MAO 0.473684 0.698925
148 NEC 0.473118 0.662791
149 DSH 0.473118 0.648352
150 B5Y 0.472727 0.793103
151 B5M 0.472727 0.793103
152 SXZ 0.472222 0.711111
153 YLB 0.470085 0.734043
154 YLC 0.470085 0.75
155 SO8 0.47 0.72093
156 GA7 0.469027 0.761364
157 ARG AMP 0.469027 0.705263
158 ZAS 0.467391 0.681818
159 K15 0.46729 0.631579
160 ADP BMA 0.46729 0.75
161 NAX 0.465517 0.73913
162 TAD 0.464912 0.766667
163 AMP DBH 0.464286 0.730337
164 TYR AMP 0.464286 0.752809
165 A7D 0.463918 0.689655
166 F2R 0.46281 0.715789
167 TXE 0.461538 0.764045
168 TYM 0.461538 0.781609
169 LAQ 0.46087 0.769231
170 7C5 0.460177 0.707865
171 MHZ 0.459184 0.645833
172 JB6 0.458716 0.784091
173 BIS 0.458716 0.744444
174 62X 0.457944 0.652632
175 5AD 0.457831 0.658537
176 A3G 0.457447 0.689655
177 LPA AMP 0.456897 0.75
178 4UU 0.45614 0.772727
179 25L 0.454545 0.77907
180 AYB 0.454545 0.726316
181 4UW 0.452991 0.766667
182 6V0 0.452991 0.755556
183 TXD 0.452991 0.764045
184 NXX 0.452991 0.781609
185 DND 0.452991 0.781609
186 GTA 0.452174 0.75
187 DQV 0.452174 0.8
188 4UV 0.451327 0.772727
189 A A 0.449541 0.767442
190 OMR 0.449153 0.741935
191 AF3 ADP 3PG 0.449153 0.728261
192 AHZ 0.448276 0.75
193 EO7 0.447917 0.906977
194 COD 0.447154 0.765957
195 YLA 0.446281 0.715789
196 AP0 0.445378 0.755556
197 CNA 0.442623 0.781609
198 VRT 0.441176 0.685393
199 YLY 0.440945 0.726316
200 3AM 0.44086 0.752941
201 NAI 0.440678 0.764045
202 GEK 0.439252 0.696629
203 IOT 0.438017 0.708333
204 Y3J 0.436782 0.623529
205 3NZ 0.436364 0.696629
206 7D7 0.435294 0.639535
207 7D5 0.434783 0.715909
208 G3A 0.434783 0.755556
209 T5A 0.434426 0.734043
210 ATP A A A 0.433628 0.776471
211 A5D 0.431373 0.717647
212 NVA 2AD 0.431373 0.677778
213 AR6 AR6 0.431034 0.767442
214 G5P 0.431034 0.755556
215 AFH 0.431034 0.728261
216 D3Y 0.429907 0.681818
217 A4P 0.429752 0.701031
218 KB1 0.428571 0.62766
219 UP5 0.428571 0.772727
220 A3P 0.428571 0.785714
221 A2P 0.428571 0.77381
222 A3D 0.428571 0.811765
223 KH3 0.42735 0.625
224 S8M 0.425926 0.696629
225 NAD 0.424 0.8
226 AMP NAD 0.424 0.77907
227 NAQ 0.423077 0.795455
228 594 0.421875 0.804124
229 BT5 0.420635 0.726316
230 N0B 0.419847 0.715789
231 AAT 0.419048 0.634409
232 80F 0.417323 0.734043
233 3AD 0.41573 0.690476
234 2AM 0.414894 0.744186
235 4TA 0.412698 0.723404
236 139 0.41129 0.73913
237 ADJ 0.41129 0.705263
238 UPA 0.409836 0.764045
239 4TC 0.409836 0.755556
240 V3L 0.409524 0.788235
241 6IA 0.409524 0.747253
242 DZD 0.409449 0.747253
243 BS5 0.408 0.770833
244 2A5 0.407767 0.730337
245 Z5A 0.406015 0.71875
246 FB0 0.405797 0.707071
247 PPS 0.40566 0.882353
248 NAE 0.40458 0.793103
249 7D3 0.40404 0.719101
250 ATR 0.403846 0.764706
251 PAP 0.403846 0.776471
252 NAJ PZO 0.403101 0.755556
253 CC5 0.402299 0.698795
254 OVE 0.402062 0.758621
255 7D4 0.401961 0.719101
256 2SA 0.401869 0.761364
257 A6D 0.401786 0.684783
258 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: 95
This union binding pocket(no: 1) in the query (biounit: 1wk8.bio2) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 2BOS GLA GAL GLC NBU None
2 1NNU NAD 2.06186
3 1NNU TCT 2.06186
4 3WDM ADN 2.57732
5 3LCC SAH 2.57732
6 1X1T NAD 2.57732
7 5K6A NAP 2.57732
8 3JQ7 NAP 2.57732
9 5EIN NAP 2.57732
10 4CLR NAP 2.57732
11 2P3V SRT 2.57732
12 1D1T NAD 2.57732
13 4CLO NAP 2.57732
14 2C91 NAP 2.57732
15 3JQB NAP 2.57732
16 6E8I PTR 2.95858
17 4RDN 6MD 2.99401
18 1QFY FAD 3.09278
19 1QFY NAP 3.09278
20 2O07 MTA 3.09278
21 3C3N FMN 3.09278
22 5W7M SAH 3.09278
23 1FND A2P 3.09278
24 1FND FAD 3.09278
25 2O07 SPD 3.09278
26 5XWC 8GL 3.60825
27 5XWC NAP 3.60825
28 5XWC 2IT 3.60825
29 1EU1 GLC 3.60825
30 3DRG ARG PRO PRO GLY PHE SER PRO PHE ALA 4.12371
31 2RC5 FAD 4.12371
32 1LLU NAD 4.12371
33 1X7D NAD 4.63918
34 4UYW H1S 4.63918
35 3VYW SAM 4.63918
36 4QVB F42 4.7619
37 2HNK SAH 5.02092
38 2AMT 1AA 5.03145
39 4LHD GLY 5.15464
40 5W8E ADE 5.15464
41 1EWY FAD 5.15464
42 5IKH 6BW 5.15464
43 1PVN MZP 5.15464
44 5H5J FAD 5.15464
45 3S6X SIA GAL BGC 5.6701
46 5BUK FAD 5.6701
47 3THR C2F 5.6701
48 5LOG SAH 5.6701
49 6BQ6 TER 5.6701
50 5W7K SAH 5.6701
51 5YW5 ADE 6.14525
52 5GUD NDP 6.18557
53 5GUD 2IT 6.18557
54 4W6Z 8ID 6.70103
55 1SM4 FAD 6.70103
56 1USF FMN 6.74157
57 1USF NAP 6.74157
58 3VET CP 7.2165
59 3VET TOY 7.2165
60 3VET ADP 7.2165
61 4RL4 PPV 7.2165
62 3MHP FAD 7.69231
63 1T9M FMN 7.73196
64 1SJD NPG 7.73196
65 1VBO MAN MAN MAN 7.73196
66 3BGD SAH 7.73196
67 5L3R GCP 7.73196
68 4QTB 38Z 7.73196
69 1PNF NDG NAG 8.24742
70 3PNL ADP 8.76289
71 3FPF TNA 8.76289
72 3FPF MTA 8.76289
73 1U3U NAD 8.76289
74 1U3U BNF 8.76289
75 3B6R CRN 9.27835
76 3NB0 G6P 9.27835
77 5AHO TLA 9.27835
78 5LXT GTP 9.79381
79 4HMT FMN 11.3402
80 4HMT NNV 11.3402
81 5T0K SAM 11.3402
82 4M1U MBG A2G 11.4286
83 3NZW BOC TY5 ALA RE0 ABN 13.4021
84 5KOK SAH 13.4021
85 5AHW CMP 14.966
86 5Y6Q FAD 17.9012
87 5Y6Q MCN 17.9012
88 5AGR A52 20.1031
89 5FOM A2H 21.134
90 4K47 WMP 22.3958
91 1WK9 TSB 28.0822
92 2V0C ANZ 29.8969
93 2AJH MET 34.0206
94 2WFG ZZB 38.1443
95 3SWC SAH 41.6667
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