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Receptor
PDB id Resolution Class Description Source Keywords
3ZIU 2.07 Å EC: 6.1.1.4 CRYSTAL STRUCTURE OF MYCOPLASMA MOBILE LEUCYL-TRNA SYNTHETASE WITH LEU-AMS IN THE ACTIVE SITE MYCOPLASMA MOBILE LIGASE
Ref.: LEUCYL-TRNA SYNTHETASE EDITING DOMAIN FUNCTIONS AS MOLECULAR RHEOSTAT TO CONTROL CODON AMBIGUITY IN MY PATHOGENS. PROC.NATL.ACAD.SCI.USA V. 110 3817 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GOL A:1643;
A:1641;
B:1579;
B:1578;
B:1577;
A:1642;
B:1580;
A:1639;
B:1581;
A:1640;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
LSS B:1576;
A:1638;
Valid;
Valid;
none;
none;
submit data
459.477 C16 H25 N7 O7 S CC(C)...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3ZIU 2.07 Å EC: 6.1.1.4 CRYSTAL STRUCTURE OF MYCOPLASMA MOBILE LEUCYL-TRNA SYNTHETASE WITH LEU-AMS IN THE ACTIVE SITE MYCOPLASMA MOBILE LIGASE
Ref.: LEUCYL-TRNA SYNTHETASE EDITING DOMAIN FUNCTIONS AS MOLECULAR RHEOSTAT TO CONTROL CODON AMBIGUITY IN MY PATHOGENS. PROC.NATL.ACAD.SCI.USA V. 110 3817 2013
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 7 families.
1 3ZIU - LSS C16 H25 N7 O7 S CC(C)C[C@@....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 7 families.
1 3ZIU - LSS C16 H25 N7 O7 S CC(C)C[C@@....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 3ZIU - LSS C16 H25 N7 O7 S CC(C)C[C@@....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: LSS; Similar ligands found: 240
No: Ligand ECFP6 Tc MDL keys Tc
1 LSS 1 1
2 SSA 0.833333 0.931035
3 A5A 0.821429 0.941176
4 5CA 0.813953 0.931035
5 VMS 0.802326 0.964706
6 54H 0.802326 0.964706
7 LEU LMS 0.797753 0.988372
8 DSZ 0.795455 0.931035
9 TSB 0.793103 0.930233
10 53H 0.772727 0.953488
11 KAA 0.769231 0.9
12 GSU 0.769231 0.931035
13 52H 0.761364 0.953488
14 YSA 0.729167 0.931035
15 NVA LMS 0.728261 0.943182
16 NSS 0.717391 0.931035
17 G5A 0.704545 0.931035
18 WSA 0.68932 0.94186
19 5AS 0.674419 0.88764
20 8X1 0.659574 0.9
21 8PZ 0.65 0.931035
22 P5A 0.626263 0.89011
23 LMS 0.623529 0.917647
24 8Q2 0.590909 0.9
25 5AL 0.583333 0.793103
26 4YB 0.574074 0.910112
27 649 0.567568 0.89011
28 ABM 0.566667 0.761364
29 SON 0.55914 0.775281
30 AHX 0.558824 0.788889
31 A 0.550562 0.758621
32 AMP 0.550562 0.758621
33 5X8 0.547368 0.712644
34 SRP 0.54 0.795455
35 8QN 0.539216 0.793103
36 9ZD 0.539216 0.797753
37 9ZA 0.539216 0.797753
38 CA0 0.536842 0.764045
39 M33 0.536842 0.772727
40 RAB 0.536585 0.678161
41 ADN 0.536585 0.678161
42 XYA 0.536585 0.678161
43 A2D 0.532609 0.761364
44 DAL AMP 0.529412 0.772727
45 TXA 0.528302 0.775281
46 3DH 0.52809 0.681818
47 SRA 0.527473 0.784091
48 AN2 0.526316 0.772727
49 XAH 0.522936 0.763441
50 AOC 0.521739 0.681818
51 A12 0.521277 0.755556
52 AP2 0.521277 0.755556
53 BA3 0.521277 0.761364
54 AU1 0.520833 0.764045
55 ADX 0.520833 0.873563
56 SLU 0.520661 0.877778
57 SA8 0.520408 0.684783
58 AMO 0.519231 0.795455
59 5CD 0.517647 0.666667
60 ADP 0.515789 0.761364
61 AP5 0.515789 0.761364
62 B4P 0.515789 0.761364
63 SAH 0.515152 0.696629
64 NB8 0.514019 0.788889
65 ME8 0.514019 0.802198
66 AT4 0.510417 0.775281
67 PRX 0.510204 0.764045
68 GAP 0.51 0.744444
69 5N5 0.505882 0.659091
70 PAJ 0.504762 0.8
71 LAD 0.504673 0.76087
72 9K8 0.5 0.762887
73 ACP 0.5 0.764045
74 EP4 0.5 0.704545
75 50T 0.5 0.733333
76 SFG 0.5 0.681818
77 ATP 0.5 0.761364
78 A4D 0.5 0.678161
79 HEJ 0.5 0.761364
80 7MD 0.495575 0.763441
81 SMM 0.495146 0.72043
82 S7M 0.495146 0.688172
83 SAM 0.49505 0.706522
84 ANP 0.49505 0.764045
85 AQP 0.494949 0.761364
86 AR6 0.494949 0.761364
87 5FA 0.494949 0.761364
88 APR 0.494949 0.761364
89 APC 0.494949 0.755556
90 A3S 0.494845 0.712644
91 6RE 0.494624 0.655914
92 M2T 0.494382 0.727273
93 DTA 0.494382 0.693182
94 4AD 0.490566 0.786517
95 EEM 0.490196 0.670213
96 AGS 0.49 0.786517
97 RBY 0.49 0.755556
98 ADV 0.49 0.755556
99 AD9 0.49 0.744444
100 ADP PO3 0.49 0.758621
101 SAP 0.49 0.786517
102 MTA 0.488889 0.701149
103 FA5 0.486486 0.795455
104 YAP 0.486486 0.786517
105 SXZ 0.486239 0.744444
106 PTJ 0.486239 0.808989
107 DLL 0.485981 0.772727
108 ATF 0.485437 0.736264
109 SAI 0.485149 0.67033
110 A3T 0.484848 0.701149
111 YLP 0.482759 0.747368
112 48N 0.482759 0.769231
113 3UK 0.481481 0.764045
114 OAD 0.481481 0.784091
115 OOB 0.481132 0.772727
116 VO4 ADP 0.480769 0.752809
117 ADP VO4 0.480769 0.752809
118 T99 0.480392 0.775281
119 TAT 0.480392 0.775281
120 ACQ 0.480392 0.764045
121 GJV 0.479167 0.648936
122 WAQ 0.477064 0.758242
123 0UM 0.476636 0.677419
124 ADQ 0.476636 0.744444
125 TYM 0.474576 0.795455
126 B5M 0.473214 0.766667
127 3OD 0.472727 0.784091
128 1ZZ 0.472727 0.744681
129 FYA 0.472727 0.772727
130 00A 0.472222 0.73913
131 MAP 0.471698 0.747253
132 A22 0.471698 0.752809
133 ADP ALF 0.471154 0.709677
134 ALF ADP 0.471154 0.709677
135 YLC 0.470588 0.763441
136 YLB 0.470588 0.765957
137 VRT 0.470588 0.719101
138 ARG AMP 0.469565 0.71875
139 A3N 0.46875 0.637363
140 J7C 0.46875 0.663043
141 MYR AMP 0.468468 0.726316
142 K15 0.46789 0.663158
143 ADP BMA 0.46789 0.725275
144 9X8 0.46789 0.786517
145 25A 0.46729 0.761364
146 5SV 0.46729 0.731183
147 6YZ 0.466667 0.764045
148 A7D 0.464646 0.685393
149 9SN 0.464286 0.731183
150 S4M 0.463918 0.666667
151 B5V 0.463636 0.755556
152 PR8 0.463636 0.752688
153 F2R 0.463415 0.729167
154 A1R 0.462963 0.758242
155 B5Y 0.460177 0.766667
156 MHZ 0.46 0.677083
157 MAO 0.459184 0.731183
158 62X 0.458716 0.684211
159 DSH 0.458333 0.663043
160 7MC 0.458333 0.765957
161 NEC 0.458333 0.640449
162 2VA 0.455446 0.724138
163 AYB 0.455285 0.757895
164 DQV 0.452991 0.772727
165 TAD 0.452991 0.76087
166 ZAS 0.452632 0.677778
167 TYR AMP 0.452174 0.766667
168 AMP DBH 0.452174 0.706522
169 3NZ 0.45045 0.711111
170 A3R 0.449541 0.758242
171 7C5 0.448276 0.684783
172 YLA 0.447154 0.729167
173 JB6 0.446429 0.777778
174 BIS 0.446429 0.72043
175 AP0 0.446281 0.731183
176 GA7 0.444444 0.775281
177 D3Y 0.444444 0.696629
178 A3G 0.443299 0.704545
179 25L 0.442478 0.752809
180 SO8 0.442308 0.715909
181 5AD 0.44186 0.635294
182 6V0 0.441667 0.731183
183 S8M 0.440367 0.711111
184 4UV 0.439655 0.747253
185 IOT 0.439024 0.721649
186 TXE 0.438017 0.73913
187 OMR 0.438017 0.736842
188 A A 0.4375 0.741573
189 LAQ 0.436975 0.744681
190 AHZ 0.436975 0.726316
191 COD 0.436508 0.797872
192 EO7 0.434343 0.876405
193 LPA AMP 0.433333 0.726316
194 AR6 AR6 0.432203 0.741573
195 4UU 0.432203 0.747253
196 CNA 0.432 0.775281
197 YLY 0.430769 0.757895
198 KB1 0.429825 0.642105
199 4UW 0.429752 0.741935
200 DND 0.429752 0.755556
201 NXX 0.429752 0.755556
202 TXD 0.429752 0.73913
203 NAX 0.429752 0.752688
204 NAI 0.429752 0.73913
205 80F 0.429688 0.747368
206 GTA 0.428571 0.726316
207 KH3 0.428571 0.65625
208 GEK 0.427273 0.711111
209 3AM 0.427083 0.727273
210 AF3 ADP 3PG 0.42623 0.723404
211 ATP A A A 0.422414 0.75
212 Y3J 0.422222 0.602273
213 N0B 0.421053 0.729167
214 7D5 0.421053 0.692308
215 7D7 0.420455 0.617977
216 AFH 0.420168 0.723404
217 A5D 0.419048 0.693182
218 NVA 2AD 0.419048 0.711111
219 A2P 0.415842 0.747126
220 A3P 0.415842 0.758621
221 NAD 0.414062 0.772727
222 NAQ 0.413534 0.769231
223 594 0.412214 0.816327
224 G3A 0.411765 0.731183
225 6IA 0.411215 0.78022
226 V3L 0.411215 0.761364
227 G5P 0.408333 0.731183
228 A3D 0.407692 0.784091
229 AAT 0.407407 0.648936
230 UP5 0.406504 0.747253
231 NAJ PZO 0.40458 0.731183
232 A6D 0.403509 0.663158
233 AMP NAD 0.403101 0.752809
234 2AM 0.402062 0.719101
235 T5A 0.401575 0.747368
236 BT5 0.4 0.739583
237 F0P 0.4 0.666667
238 4TC 0.4 0.75
239 UPA 0.4 0.73913
240 DZD 0.4 0.741935
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3ZIU; Ligand: LSS; Similar sites found with APoc: 78
This union binding pocket(no: 1) in the query (biounit: 3ziu.bio1) has 25 residues
No: Leader PDB Ligand Sequence Similarity
1 5Y0T TAT 1.17647
2 5VLQ ANP 1.52801
3 1KY8 NAP 1.59681
4 2Z49 AMG 1.62037
5 1JIL 485 1.66667
6 4J75 TYM 1.71149
7 4RF7 ARG 1.88383
8 2PID YSA 1.96629
9 3COW 52H 1.99336
10 5G3R NAG 2.27273
11 1V47 ADX 2.29226
12 3AFH GSU 2.45902
13 2J5B TYE 2.58621
14 5ZDK ATP 2.73723
15 1J09 GLU 2.77778
16 1J09 ATP 2.77778
17 1JPA ANP 2.88462
18 2CI5 HCS 3.16901
19 3ALT MLB 3.18471
20 1YUM NCN 3.30579
21 4LZB URA 3.36134
22 3HL4 CDC 3.38983
23 4GVF NDG 3.4384
24 4GVF NAG 3.4384
25 5Y0N ATP 3.44828
26 5Y0Q APC 3.45622
27 1FEC FAD 3.46939
28 5XDT MB3 3.57143
29 4MAF ADX 3.71287
30 3BJE URA 3.72493
31 6CHP F0Y 3.72671
32 5X3D 7XL 3.75
33 1UA4 BGC 3.95604
34 1UA4 GLC 3.95604
35 4JDR FAD 4.00844
36 1KQN NAD 4.6595
37 2QTR NXX 4.7619
38 2JFV FLC 4.811
39 4A91 GLU 5.03356
40 1K4M NAD 5.16432
41 1HFE CYS 5.65149
42 2H29 DND 5.82011
43 4PTN PYR 5.8309
44 2WPB ZZI 5.92105
45 3CV3 UDP 6.15764
46 1WUW TSU 6.66667
47 1R6T TYM 6.7086
48 5LLT DND 7.04225
49 1YID ATP 7.12251
50 1R6U TYM 7.32265
51 5DK4 ATP 7.59878
52 5DK4 5BX 7.59878
53 4P86 5GP 8.19672
54 3C8Z 5CA 8.21256
55 5V49 8WA 8.30258
56 5V49 MET 8.30258
57 3EW2 BTN 9.62963
58 1N1D C2G 10.0775
59 5N5U AMP 11.1465
60 1F9A ATP 11.3095
61 1PFY MSP 11.6152
62 2X3F APC 12.2807
63 1RVV INI 12.3377
64 5O0B 9FE 12.963
65 5HVJ ANP 13.0159
66 4NAT 2W5 13.125
67 4NAT ADP 13.125
68 3UC5 ATP 14.0127
69 1B09 PC 14.0777
70 1O6B ADP 15.3846
71 3LQV ADE 15.3846
72 1JZS MRC 18.5243
73 2F5Z FAD 20.3125
74 2X1L ADN 20.4198
75 2X1L MET 20.4198
76 3ND6 ATP 22.2222
77 3KFL ME8 29.9645
78 5XET ME8 33.0813
Pocket No.: 2; Query (leader) PDB : 3ZIU; Ligand: LSS; Similar sites found with APoc: 7
This union binding pocket(no: 2) in the query (biounit: 3ziu.bio2) has 25 residues
No: Leader PDB Ligand Sequence Similarity
1 3QPB URA 3.19149
2 2Q0L FAD 3.85852
3 1BZL GCG 4.52675
4 1BZL FAD 4.52675
5 3FXU TSU 4.59016
6 1YOA FMN 5.03145
7 1XMV ADP 11.5169
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