Receptor
PDB id Resolution Class Description Source Keywords
3kfl 2 Å EC: 6.1.1.10 LEISHMANIA MAJOR METHIONYL-TRNA SYNTHETASE IN COMPLEX WITH METHIONYLADENYLATE AND PYROPHOSPHATE LEISHMANIA MAJOR LEISHMANIA PARASITE AMINOACYL-TRNA SYNTHETASE TRNA LIGASEMETRS METHIONINE TRANSLATION ATP-BINDING NUCLEOTIDE-BINSTRUCTURAL GENOMICS MSGPP LIGASE MEDICAL STRUCTURAL GENOPATHOGENIC PROTOZOA
Ref.: STRUCTURE OF LEISHMANIA MAJOR METHIONYL-TRNA SYNTHE COMPLEX WITH INTERMEDIATE PRODUCTS METHIONYLADENYLA PYROPHOSPHATE. BIOCHIMIE V. 93 570 2011
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
EDO A:811;
A:812;
A:813;
A:814;
A:815;
A:816;
A:817;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
none;
none;
 submit data
62.068 C2 H6 O2 C(CO)...
FMT A:821;
A:822;
A:823;
A:824;
 Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
 submit data
46.025 C H2 O2 C(=O)...
ME8 A:801;
 Valid;
 none;
 submit data
478.417 C15 H23 N6 O8 P S CSCC[...
MG A:803;
 Invalid;
 none;
 submit data
24.305 Mg [Mg+2...
POP A:802;
 Invalid;
 none;
 submit data
175.959 H2 O7 P2 O[P@@...
ZN A:804;
 Part of Protein;
 none;
 submit data
65.409 Zn [Zn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6SWX 1.95 Å EC: 6.1.1.10 LEISHMANIA MAJOR METHIONYL-TRNA SYNTHETASE IN COMPLEX WITH A ALLOSTERIC INHIBITOR LEISHMANIA MAJOR LEISHMANIA PARASITE AMINOACYL-TRNA SYNTHETASE TRNA LIGASEMETRS METHIONINE TRANSLATION ATP-BINDING NUCLEOTIDE-BINLIGASE DRUG DISCOVERY DUNDEE DRUG DISCOVERY UNIT
Ref.: DISCOVERY OF AN ALLOSTERIC BINDING SITE IN KINETOPL METHIONYL-TRNA SYNTHETASE. ACS INFECT DIS. V. 6 1044 2020
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 6SWX ic50 = 2.06 uM LWN C15 H14 F2 N6 O2 Cn1c2c(cn1....
2 3KFL - ME8 C15 H23 N6 O8 P S CSCC[C@@H]....
70% Homology Family (17)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 4ZT4 - 4RO C16 H15 Cl2 F2 N5 c1cc2c(nc1....
2 4MW1 - 44F C16 H20 Cl N3 O2 S COc1cc(cc(....
3 4MWE - 2EN C21 H26 Cl N3 O2 S C=CCc1cc(c....
4 4ZT5 - 4RN C17 H19 Cl2 N5 C[C@@H](CN....
5 4ZT7 - 4RC C18 H19 Cl2 F N6 c1cc(nc2c1....
6 4MVY - 387 C17 H19 Cl2 N3 O2 c1cc(cc(c1....
7 5J59 ic50 < 50 nM N93 C16 H16 Cl3 N5 CN(CCNCc1c....
8 4MWB - 2EK C13 H15 Cl2 N3 O S2 c1cscc1NC(....
9 5V49 ic50 < 50 nM 8WA C18 H19 Cl3 N6 CN(CCN[C@@....
10 4MW0 - 392 C17 H19 Cl2 N3 O2 c1ccc(c(c1....
11 4MW5 - 415 C18 H22 Cl N3 O2 COc1cc(cc(....
12 4ZT6 - 4RD C18 H18 Cl2 F N5 O c1cc(nc2c1....
13 4MW4 - MET C5 H11 N O2 S CSCC[C@@H]....
14 4MW2 - MET C5 H11 N O2 S CSCC[C@@H]....
15 4MWD - ACP C11 H18 N5 O12 P3 c1nc(c2c(n....
16 6SWX ic50 = 2.06 uM LWN C15 H14 F2 N6 O2 Cn1c2c(cn1....
17 3KFL - ME8 C15 H23 N6 O8 P S CSCC[C@@H]....
50% Homology Family (21)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 2X1L - ADN C10 H13 N5 O4 c1nc(c2c(n....
2 4ZT4 - 4RO C16 H15 Cl2 F2 N5 c1cc2c(nc1....
3 4MW1 - 44F C16 H20 Cl N3 O2 S COc1cc(cc(....
4 4MWE - 2EN C21 H26 Cl N3 O2 S C=CCc1cc(c....
5 4ZT5 - 4RN C17 H19 Cl2 N5 C[C@@H](CN....
6 4ZT7 - 4RC C18 H19 Cl2 F N6 c1cc(nc2c1....
7 4MVY - 387 C17 H19 Cl2 N3 O2 c1cc(cc(c1....
8 5J59 ic50 < 50 nM N93 C16 H16 Cl3 N5 CN(CCNCc1c....
9 4MWB - 2EK C13 H15 Cl2 N3 O S2 c1cscc1NC(....
10 5V49 ic50 < 50 nM 8WA C18 H19 Cl3 N6 CN(CCN[C@@....
11 4MW0 - 392 C17 H19 Cl2 N3 O2 c1ccc(c(c1....
12 4MW5 - 415 C18 H22 Cl N3 O2 COc1cc(cc(....
13 4ZT6 - 4RD C18 H18 Cl2 F N5 O c1cc(nc2c1....
14 4MW4 - MET C5 H11 N O2 S CSCC[C@@H]....
15 4MW2 - MET C5 H11 N O2 S CSCC[C@@H]....
16 4MWD - ACP C11 H18 N5 O12 P3 c1nc(c2c(n....
17 6SWX ic50 = 2.06 uM LWN C15 H14 F2 N6 O2 Cn1c2c(cn1....
18 3KFL - ME8 C15 H23 N6 O8 P S CSCC[C@@H]....
19 5K0S ic50 = 0.006 uM 0OU C19 H19 Cl2 N3 O c1ccc2c(c1....
20 4PY2 ic50 = 0.272 uM 43E C15 H17 Cl2 N3 O S c1cscc1NC(....
21 5XET - ME8 C15 H23 N6 O8 P S CSCC[C@@H]....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: ME8; Similar ligands found: 365
No: Ligand ECFP6 Tc MDL keys Tc
1 ME8 1 1
2 SRP 0.795455 0.9
3 LAD 0.774194 0.879518
4 5AL 0.772727 0.898734
5 AMO 0.76087 0.9
6 8LH 0.736264 0.9
7 8QN 0.731183 0.898734
8 NB8 0.729167 0.86747
9 YLP 0.708738 0.860465
10 FA5 0.707071 0.9
11 PAJ 0.705263 0.857143
12 CA0 0.704545 0.864198
13 KG4 0.696629 0.864198
14 YLB 0.688679 0.882353
15 YLC 0.688679 0.880952
16 4AD 0.6875 0.888889
17 8LQ 0.684211 0.924051
18 8LE 0.677419 0.865854
19 PTJ 0.676768 0.86747
20 QA7 0.666667 0.888889
21 A2D 0.666667 0.839506
22 AYB 0.663636 0.872093
23 AN2 0.655556 0.829268
24 YLA 0.654545 0.83908
25 BA3 0.651685 0.839506
26 M33 0.648352 0.875
27 TYM 0.648148 0.9
28 B4P 0.644444 0.839506
29 AP5 0.644444 0.839506
30 ADP 0.644444 0.839506
31 AT4 0.637363 0.831325
32 PRX 0.634409 0.864198
33 WAQ 0.633663 0.878049
34 AMP 0.632184 0.8375
35 A 0.632184 0.8375
36 ADX 0.630435 0.784091
37 AHX 0.63 0.845238
38 DLL 0.63 0.875
39 45A 0.629214 0.886076
40 ABM 0.629214 0.886076
41 AD9 0.62766 0.819277
42 1ZZ 0.627451 0.880952
43 TXA 0.627451 0.876543
44 OOB 0.626263 0.875
45 AMP MG 0.625 0.825
46 YLY 0.623932 0.894118
47 3UK 0.623762 0.864198
48 HEJ 0.623656 0.839506
49 ACP 0.623656 0.841463
50 ATP 0.623656 0.839506
51 50T 0.623656 0.807229
52 B5V 0.617647 0.853659
53 5FA 0.617021 0.839506
54 AQP 0.617021 0.839506
55 APR 0.617021 0.8625
56 AR6 0.617021 0.8625
57 ANP 0.614583 0.819277
58 00A 0.613861 0.833333
59 AGS 0.610526 0.821429
60 B5Y 0.609524 0.865854
61 XAH 0.603774 0.837209
62 PR8 0.601942 0.869048
63 DAL AMP 0.6 0.875
64 9SN 0.6 0.823529
65 GAP 0.597938 0.841463
66 ACQ 0.597938 0.841463
67 A12 0.597826 0.831325
68 AP2 0.597826 0.831325
69 3OD 0.596154 0.8875
70 AU1 0.595745 0.819277
71 N0B 0.595041 0.83908
72 B5M 0.59434 0.865854
73 9ZA 0.594059 0.878049
74 9ZD 0.594059 0.878049
75 OAD 0.592233 0.8875
76 LAQ 0.590909 0.837209
77 HQG 0.59 0.851852
78 SRA 0.588889 0.819277
79 A1R 0.588235 0.833333
80 ATF 0.585859 0.809524
81 4UV 0.583333 0.843373
82 6YZ 0.58 0.841463
83 5SV 0.578431 0.845238
84 9X8 0.576923 0.865854
85 V2G 0.575758 0.845238
86 ADQ 0.572816 0.841463
87 A22 0.568627 0.829268
88 ADP MG 0.568421 0.8375
89 ADP BEF 0.568421 0.8375
90 SON 0.568421 0.876543
91 JNT 0.567308 0.841463
92 APC 0.56701 0.831325
93 FYA 0.566038 0.851852
94 TAT 0.565657 0.831325
95 T99 0.565657 0.831325
96 25A 0.563107 0.839506
97 OZV 0.563107 0.839506
98 ADV 0.561224 0.853659
99 RBY 0.561224 0.853659
100 MYR AMP 0.560748 0.858824
101 4UU 0.558559 0.843373
102 A3R 0.557692 0.833333
103 4UW 0.552632 0.857143
104 IOT 0.547009 0.829545
105 F2R 0.546219 0.83908
106 APC MG 0.545455 0.817073
107 ATP MG 0.545455 0.8375
108 ADP PO3 0.545455 0.8375
109 48N 0.54386 0.86747
110 BEF ADP 0.54 0.817073
111 ANP MG 0.539216 0.829268
112 TXD 0.53913 0.833333
113 MAP 0.538462 0.8
114 BIS 0.537037 0.811765
115 KMQ 0.536364 0.876543
116 TXE 0.534483 0.811765
117 SMM 0.533981 0.833333
118 80F 0.532787 0.83908
119 25L 0.53211 0.829268
120 ARG AMP 0.530973 0.827586
121 AFH 0.530973 0.813953
122 GA7 0.530973 0.853659
123 LPA AMP 0.530435 0.816092
124 LMS 0.526882 0.764045
125 DQV 0.526316 0.851852
126 NAX 0.525862 0.847059
127 NAI 0.525862 0.811765
128 SAH 0.524752 0.8125
129 A5A 0.524272 0.786517
130 VO4 ADP 0.524272 0.819277
131 ALF ADP 0.524272 0.77907
132 TSB 0.52381 0.777778
133 G3A 0.522124 0.802326
134 OMR 0.521368 0.870588
135 SSA 0.519231 0.78022
136 G5P 0.517544 0.802326
137 7MD 0.517544 0.858824
138 L3W 0.516949 0.831325
139 AP0 0.516949 0.823529
140 MTA 0.516484 0.797468
141 EEM 0.514563 0.819277
142 VMS 0.514286 0.769231
143 54H 0.514286 0.769231
144 LSS 0.514019 0.802198
145 GTA 0.513043 0.816092
146 6V0 0.512821 0.802326
147 DND 0.512821 0.853659
148 BT5 0.512195 0.850575
149 XYA 0.511628 0.728395
150 RAB 0.511628 0.728395
151 ADN 0.511628 0.728395
152 5AS 0.510204 0.741935
153 5X8 0.51 0.810127
154 53H 0.509434 0.76087
155 5CA 0.509434 0.78022
156 M24 0.507937 0.804598
157 COD 0.504065 0.852273
158 GSU 0.5 0.820225
159 52H 0.5 0.76087
160 CNA 0.5 0.853659
161 DSZ 0.5 0.8
162 AOC 0.5 0.753086
163 KAA 0.5 0.774194
164 SA8 0.5 0.839506
165 ALF ADP 3PG 0.495798 0.813953
166 AF3 ADP 3PG 0.495798 0.813953
167 AHZ 0.495726 0.858824
168 JB6 0.495495 0.855422
169 NVA LMS 0.495413 0.813187
170 G5A 0.495146 0.78022
171 SFG 0.49505 0.775
172 5CD 0.494382 0.716049
173 D4F 0.492188 0.837209
174 T5A 0.491803 0.818182
175 ADJ 0.491803 0.827586
176 ADP BMA 0.490909 0.819277
177 LEU LMS 0.490909 0.791209
178 SAM 0.490385 0.841463
179 2A5 0.490196 0.819277
180 3DH 0.489362 0.775
181 DTA 0.48913 0.722892
182 NAQ 0.488372 0.845238
183 UP5 0.487395 0.821429
184 TAD 0.487179 0.835294
185 AMP DBH 0.486957 0.797619
186 NSS 0.486239 0.78022
187 6AD 0.485714 0.835294
188 PAP 0.485437 0.82716
189 A3D 0.484127 0.864198
190 5N5 0.483146 0.707317
191 SAI 0.480769 0.780488
192 NAE 0.48062 0.865854
193 NAD 0.48 0.851852
194 139 0.479675 0.804598
195 4TC 0.479339 0.823529
196 7MC 0.479339 0.860465
197 UPA 0.479339 0.811765
198 7D5 0.478723 0.761905
199 EP4 0.478261 0.756098
200 YSA 0.478261 0.78022
201 A4D 0.477778 0.728395
202 S7M 0.476636 0.797619
203 A4P 0.47541 0.76087
204 7D3 0.474747 0.764706
205 J4G 0.473214 0.9125
206 M2T 0.473118 0.759036
207 0UM 0.472727 0.764706
208 PPS 0.471698 0.764045
209 ATR 0.471154 0.814815
210 7D4 0.470588 0.764706
211 A3P 0.47 0.8375
212 ATP A 0.469565 0.82716
213 ATP A A A 0.469565 0.82716
214 9K8 0.469027 0.71875
215 62X 0.468468 0.790698
216 8X1 0.46789 0.774194
217 EAD 0.466165 0.825581
218 AR6 AR6 0.466102 0.839506
219 H1Q 0.466019 0.804878
220 K15 0.464286 0.788235
221 GEK 0.463636 0.804878
222 P1H 0.463235 0.848837
223 ZID 0.462121 0.841463
224 NWW 0.461538 0.675
225 A7D 0.460784 0.777778
226 P5A 0.460177 0.765957
227 6RE 0.459184 0.72093
228 A2R 0.458716 0.851852
229 8PZ 0.456897 0.78022
230 BTX 0.456693 0.83908
231 FB0 0.456522 0.844444
232 ITT 0.456311 0.792683
233 A2P 0.455446 0.825
234 ARU 0.455357 0.793103
235 NAD TDB 0.455285 0.839506
236 NAD IBO 0.455285 0.839506
237 DSH 0.454545 0.75
238 3AM 0.453608 0.802469
239 DZD 0.453125 0.835294
240 NDE 0.452555 0.831325
241 J7C 0.45 0.729412
242 ZAS 0.44898 0.705882
243 V3L 0.448598 0.8625
244 WSA 0.447154 0.788889
245 A3S 0.446602 0.765432
246 NAJ PZO 0.446154 0.781609
247 S4M 0.445545 0.770115
248 6MZ 0.445545 0.85
249 AMP NAD 0.445312 0.851852
250 SXZ 0.443478 0.819277
251 MAO 0.441176 0.845238
252 B1U 0.440678 0.704082
253 FDA 0.439716 0.771739
254 VRT 0.439252 0.792683
255 HFD 0.439252 0.8
256 JSQ 0.439252 0.8
257 A3T 0.438095 0.753086
258 NDC 0.435714 0.823529
259 IMO 0.435644 0.802469
260 A3N 0.435644 0.702381
261 6IA 0.435185 0.857143
262 0WD 0.434109 0.802326
263 NAJ PYZ 0.432836 0.747253
264 NO7 0.432432 0.788235
265 GJV 0.431373 0.712644
266 OZP 0.430894 0.77381
267 KOY 0.430894 0.780488
268 A5D 0.429907 0.722892
269 NVA 2AD 0.429907 0.783133
270 2AM 0.428571 0.792683
271 FNK 0.428571 0.784946
272 KYE 0.428571 0.738636
273 KB1 0.42735 0.744186
274 2SA 0.427273 0.876543
275 CAO 0.426471 0.815217
276 KXW 0.42623 0.752941
277 4YB 0.42623 0.802198
278 NA7 0.426087 0.831325
279 O02 0.425926 0.802326
280 NEC 0.425743 0.686747
281 A3G 0.425743 0.756098
282 S8M 0.424779 0.783133
283 QXP 0.424779 0.709677
284 2VA 0.424528 0.73494
285 CUU 0.424528 0.839506
286 4TA 0.423077 0.806818
287 1HE 0.422535 0.866667
288 5AD 0.422222 0.683544
289 3AT 0.422018 0.839506
290 7C5 0.421488 0.752941
291 8Q2 0.420635 0.755319
292 K3K 0.420168 0.717647
293 38V 0.419118 0.795455
294 TXP 0.418605 0.823529
295 AAT 0.418182 0.712644
296 6FA 0.416667 0.797753
297 COS 0.416058 0.824176
298 HY8 0.416 0.755814
299 OVE 0.415842 0.785714
300 ODP 0.415385 0.793103
301 NJP 0.415385 0.821429
302 MHZ 0.415094 0.781609
303 PGS 0.415094 0.770115
304 0T1 0.414815 0.822222
305 KH3 0.414634 0.77907
306 AV2 0.414414 0.77381
307 NWQ 0.414141 0.7
308 QXG 0.413793 0.702128
309 K3E 0.413223 0.709302
310 SO8 0.412844 0.746988
311 AVV 0.412281 0.802326
312 SOP 0.411348 0.844444
313 HZ2 0.41129 0.755814
314 DAT 0.411215 0.807229
315 FAS 0.410959 0.806818
316 SFD 0.410959 0.72
317 FAD 0.410959 0.806818
318 NPW 0.410853 0.837209
319 NDP 0.410853 0.802326
320 V47 0.410714 0.7625
321 ETB 0.410448 0.873563
322 DCA 0.410448 0.822222
323 R2V 0.410256 0.709677
324 3NZ 0.410256 0.783133
325 ACO 0.410072 0.835165
326 Q2M 0.409449 0.755814
327 Q34 0.409449 0.719101
328 F0P 0.409449 0.77381
329 DTP 0.409091 0.807229
330 1VU 0.408451 0.815217
331 NZQ 0.407692 0.813953
332 P5F 0.406452 0.782609
333 Z5A 0.405797 0.76087
334 30N 0.405797 0.773196
335 2MC 0.405594 0.789474
336 K2H 0.405172 0.738095
337 LQJ 0.404959 0.817073
338 COA 0.404412 0.842697
339 3KK 0.404255 0.824176
340 FYN 0.404255 0.842697
341 Y3J 0.404255 0.646341
342 AMZ 0.40404 0.792683
343 C2R 0.40404 0.804878
344 D3Y 0.403509 0.746988
345 GGZ 0.403509 0.741573
346 PLP AAD 0.402985 0.793478
347 IVC 0.402778 0.833333
348 BCO 0.402778 0.824176
349 3HC 0.402778 0.833333
350 A1S 0.402778 0.865169
351 MLC 0.402778 0.844444
352 7D7 0.402174 0.662651
353 A6D 0.401709 0.67033
354 649 0.401575 0.765957
355 N37 0.401575 0.759036
356 Q2P 0.401515 0.719101
357 OXK 0.401408 0.844444
358 COK 0.401408 0.824176
359 FME ARG THR GLY ASN ALA ASP ND7 0.401198 0.868132
360 62F 0.4 0.795455
361 CAA 0.4 0.833333
362 6C6 0.4 0.831325
363 71V 0.4 0.790698
364 FAM 0.4 0.804348
365 FCX 0.4 0.815217
Similar Ligands (3D)
Ligand no: 1; Ligand: ME8; Similar ligands found: 5
No: Ligand Similarity coefficient
1 MSP 0.9838
2 MOD 0.9696
3 L3U 0.8771
4 GDP 0.8672
5 TYR AMP 0.8540
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6SWX; Ligand: LWN; 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: 6swx.bio1) has 41 residues
No: Leader PDB Ligand Sequence Similarity
APoc FAQ
Feedback