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 6 families.
1 3ZIU - LSS C16 H25 N7 O7 S CC(C)C[C@@....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: LSS; Similar ligands found: 226
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 54H 0.802326 0.964706
6 VMS 0.802326 0.964706
7 LEU LMS 0.797753 0.976744
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 0.931818
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 P5A 0.626263 0.89011
21 5AL 0.583333 0.793103
22 4YB 0.574074 0.910112
23 649 0.567568 0.89011
24 ABM 0.566667 0.761364
25 SON 0.55914 0.775281
26 AHX 0.558824 0.788889
27 AMP 0.550562 0.758621
28 A 0.550562 0.758621
29 5X8 0.547368 0.712644
30 SRP 0.54 0.795455
31 8QN 0.539216 0.793103
32 AMP MG 0.538462 0.722222
33 M33 0.536842 0.772727
34 CA0 0.536842 0.764045
35 XYA 0.536585 0.678161
36 RAB 0.536585 0.678161
37 ADN 0.536585 0.678161
38 A2D 0.532609 0.761364
39 DAL AMP 0.529412 0.772727
40 TXA 0.528302 0.775281
41 3DH 0.52809 0.681818
42 SRA 0.527473 0.784091
43 AN2 0.526316 0.772727
44 XAH 0.522936 0.763441
45 AOC 0.521739 0.681818
46 AP2 0.521277 0.755556
47 BA3 0.521277 0.761364
48 A12 0.521277 0.755556
49 ADX 0.520833 0.873563
50 AU1 0.520833 0.764045
51 SLU 0.520661 0.877778
52 SA8 0.520408 0.684783
53 AMO 0.519231 0.795455
54 5CD 0.517647 0.666667
55 B4P 0.515789 0.761364
56 ADP 0.515789 0.761364
57 AP5 0.515789 0.761364
58 SAH 0.515152 0.696629
59 ME8 0.514019 0.802198
60 NB8 0.514019 0.788889
61 PRX 0.510204 0.764045
62 GAP 0.51 0.744444
63 5N5 0.505882 0.659091
64 ADP MG 0.505155 0.733333
65 PAJ 0.504762 0.8
66 LAD 0.504673 0.76087
67 EP4 0.5 0.704545
68 ADP BEF 0.5 0.717391
69 A4D 0.5 0.678161
70 SFG 0.5 0.681818
71 BEF ADP 0.5 0.717391
72 ATP 0.5 0.761364
73 50T 0.5 0.733333
74 ACP 0.5 0.764045
75 7MD 0.495575 0.763441
76 S7M 0.495146 0.688172
77 SMM 0.495146 0.72043
78 SAM 0.49505 0.706522
79 ANP 0.49505 0.764045
80 AQP 0.494949 0.761364
81 APC 0.494949 0.755556
82 5FA 0.494949 0.761364
83 APR 0.494949 0.761364
84 AR6 0.494949 0.761364
85 A3S 0.494845 0.712644
86 6RE 0.494624 0.655914
87 M2T 0.494382 0.727273
88 DTA 0.494382 0.693182
89 4AD 0.490566 0.786517
90 EEM 0.490196 0.670213
91 AD9 0.49 0.744444
92 ADP PO3 0.49 0.758621
93 SAP 0.49 0.786517
94 RBY 0.49 0.755556
95 ADV 0.49 0.755556
96 AGS 0.49 0.786517
97 MTA 0.488889 0.701149
98 FA5 0.486486 0.795455
99 YAP 0.486486 0.786517
100 PTJ 0.486239 0.808989
101 SXZ 0.486239 0.744444
102 DLL 0.485981 0.772727
103 ATF 0.485437 0.736264
104 SAI 0.485149 0.67033
105 ATP MG 0.485149 0.733333
106 A3T 0.484848 0.701149
107 48N 0.482759 0.769231
108 YLP 0.482759 0.747368
109 OAD 0.481481 0.784091
110 3UK 0.481481 0.764045
111 OOB 0.481132 0.772727
112 VO4 ADP 0.480769 0.752809
113 ANP MG 0.480769 0.747253
114 ADP VO4 0.480769 0.752809
115 TAT 0.480392 0.775281
116 ACQ 0.480392 0.764045
117 GJV 0.479167 0.648936
118 WAQ 0.477064 0.758242
119 0UM 0.476636 0.677419
120 ADQ 0.476636 0.744444
121 TYM 0.474576 0.795455
122 3OD 0.472727 0.784091
123 FYA 0.472727 0.772727
124 1ZZ 0.472727 0.744681
125 00A 0.472222 0.73913
126 A22 0.471698 0.752809
127 MAP 0.471698 0.747253
128 ALF ADP 0.471154 0.709677
129 ADP ALF 0.471154 0.709677
130 YLB 0.470588 0.765957
131 YLC 0.470588 0.763441
132 VRT 0.470588 0.719101
133 A3N 0.46875 0.637363
134 J7C 0.46875 0.663043
135 MYR AMP 0.468468 0.726316
136 K15 0.46789 0.663158
137 ADP BMA 0.46789 0.725275
138 5SV 0.46729 0.731183
139 25A 0.46729 0.761364
140 A7D 0.464646 0.685393
141 9SN 0.464286 0.731183
142 S4M 0.463918 0.666667
143 PR8 0.463636 0.752688
144 A1R 0.462963 0.758242
145 ARG AMP 0.461538 0.71875
146 MHZ 0.46 0.677083
147 MAO 0.459184 0.731183
148 62X 0.458716 0.684211
149 7MC 0.458333 0.765957
150 NEC 0.458333 0.640449
151 DSH 0.458333 0.663043
152 TYR AMP 0.45614 0.755556
153 2VA 0.455446 0.724138
154 AYB 0.455285 0.757895
155 TAD 0.452991 0.76087
156 ZAS 0.452632 0.677778
157 AMP DBH 0.452174 0.706522
158 NAD IBO 0.451613 0.786517
159 3NZ 0.45045 0.711111
160 7C5 0.448276 0.684783
161 YLA 0.447154 0.729167
162 BIS 0.446429 0.72043
163 JB6 0.446429 0.777778
164 AP0 0.446281 0.731183
165 D3Y 0.444444 0.696629
166 A3G 0.443299 0.704545
167 25L 0.442478 0.752809
168 SO8 0.442308 0.715909
169 5AD 0.44186 0.635294
170 6V0 0.441667 0.731183
171 S8M 0.440367 0.711111
172 4UV 0.439655 0.747253
173 IOT 0.439024 0.721649
174 OMR 0.438017 0.736842
175 TXE 0.438017 0.73913
176 LA8 ALF 3PG 0.438017 0.723404
177 ALF ADP 3PG 0.438017 0.723404
178 A A 0.4375 0.741573
179 AHZ 0.436975 0.726316
180 LAQ 0.436975 0.744681
181 COD 0.436508 0.797872
182 LPA AMP 0.433333 0.726316
183 4UU 0.432203 0.747253
184 AR6 AR6 0.432203 0.741573
185 CNA 0.432 0.775281
186 YLY 0.430769 0.757895
187 KB1 0.429825 0.642105
188 NXX 0.429752 0.755556
189 NAI 0.429752 0.73913
190 TXD 0.429752 0.73913
191 4UW 0.429752 0.741935
192 DND 0.429752 0.755556
193 NAX 0.429752 0.752688
194 GTA 0.428571 0.726316
195 KH3 0.428571 0.65625
196 GEK 0.427273 0.711111
197 3AM 0.427083 0.727273
198 AF3 ADP 3PG 0.42623 0.723404
199 ATP A A A 0.422414 0.75
200 Y3J 0.422222 0.602273
201 N0B 0.421053 0.729167
202 7D5 0.421053 0.692308
203 7D7 0.420455 0.617977
204 AFH 0.420168 0.723404
205 A5D 0.419048 0.693182
206 A2P 0.415842 0.747126
207 A3P 0.415842 0.758621
208 NAD 0.414062 0.772727
209 NAQ 0.413534 0.769231
210 594 0.412214 0.816327
211 G3A 0.411765 0.731183
212 V3L 0.411215 0.761364
213 6IA 0.411215 0.78022
214 G5P 0.408333 0.731183
215 A3D 0.407692 0.784091
216 AAT 0.407407 0.648936
217 UP5 0.406504 0.747253
218 NAJ PZO 0.40458 0.731183
219 A6D 0.403509 0.663158
220 NAJ PYZ 0.402985 0.734043
221 2AM 0.402062 0.719101
222 T5A 0.401575 0.747368
223 4TC 0.4 0.75
224 UPA 0.4 0.73913
225 BT5 0.4 0.739583
226 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: 54
This union binding pocket(no: 1) in the query (biounit: 3ziu.bio1) has 25 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1JIL 485 0.0005135 0.45272 1.66667
2 4J75 TYM 0.0000002178 0.58743 1.71149
3 4RF7 ARG 0.01675 0.40598 1.88383
4 2PID YSA 0.00003857 0.46675 1.96629
5 3COW 52H 0.00000576 0.41197 1.99336
6 5G3R NAG 0.01224 0.42316 2.27273
7 1V47 ADX 0.0005619 0.4259 2.29226
8 3AFH GSU 0.000002711 0.56372 2.45902
9 1J09 GLU 0.000362 0.43454 2.77778
10 1J09 ATP 0.000726 0.42361 2.77778
11 1JPA ANP 0.00421 0.42687 2.88462
12 2CI5 HCS 0.02024 0.41571 3.16901
13 3ALT MLB 0.01507 0.42389 3.18471
14 1YUM NCN 0.0006869 0.42686 3.30579
15 4LZB URA 0.04669 0.40198 3.36134
16 3HL4 CDC 0.0009118 0.44199 3.38983
17 4GVF NDG 0.00907 0.4208 3.4384
18 4GVF NAG 0.00907 0.4208 3.4384
19 1H3F TYE 0.005003 0.44534 3.47222
20 4MAF ADX 0.001019 0.40355 3.71287
21 3BJE URA 0.02594 0.40478 3.72493
22 1UA4 BGC 0.02483 0.40299 3.95604
23 1UA4 GLC 0.02483 0.40299 3.95604
24 1KQN NAD 0.00613 0.40839 4.6595
25 2QTR NXX 0.0000813 0.42183 4.7619
26 2JFV FLC 0.03727 0.40147 4.811
27 4A91 GLU 0.0005338 0.49348 5.03356
28 1K4M NAD 0.0004162 0.42869 5.16432
29 2H29 DND 0.000176 0.4185 5.82011
30 4PTN PYR 0.03061 0.40456 5.8309
31 3CV3 UDP 0.005231 0.41628 6.15764
32 1WUW TSU 0.03087 0.40048 6.66667
33 1R6T TYM 0.000004056 0.45139 6.7086
34 1YID ATP 0.0007599 0.46843 7.12251
35 1R6U TYM 0.00001927 0.49168 7.32265
36 3C8Z 5CA 0.0000000189 0.64348 8.21256
37 5V49 MET 0.0001979 0.50908 8.30258
38 5V49 8WA 0.00001117 0.45429 8.30258
39 3EW2 BTN 0.01924 0.40863 9.62963
40 1N1D C2G 0.001581 0.41475 10.0775
41 1F9A ATP 0.002289 0.42479 11.3095
42 1PFY MSP 0.00000001031 0.61946 11.6152
43 2X3F APC 0.000004671 0.49269 12.2807
44 1RVV INI 0.02041 0.40733 12.3377
45 5HVJ ANP 0.03235 0.40292 13.0159
46 4NAT ADP 0.008805 0.43471 13.125
47 4NAT 2W5 0.002035 0.43471 13.125
48 3UC5 ATP 0.01402 0.40031 14.0127
49 1O6B ADP 0.003937 0.44355 15.3846
50 3LQV ADE 0.02378 0.42507 15.3846
51 1JZS MRC 0.00009266 0.4897 18.5243
52 2X1L ADN 0.000001947 0.58486 20.4198
53 2X1L MET 0.0003252 0.50782 20.4198
54 3KFL ME8 0.0000001499 0.56634 29.9645
Pocket No.: 2; Query (leader) PDB : 3ZIU; Ligand: LSS; Similar sites found: 3
This union binding pocket(no: 2) in the query (biounit: 3ziu.bio2) has 25 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3QPB URA 0.02984 0.40057 3.19149
2 1YOA FMN 0.009027 0.41187 5.03145
3 1XMV ADP 0.01502 0.40607 11.5169
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