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
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
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 3KFL - ME8 C15 H23 N6 O8 P S CSCC[C@@H]....
70% Homology Family (16)
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 3KFL - ME8 C15 H23 N6 O8 P S CSCC[C@@H]....
50% Homology Family (19)
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 5K0S ic50 = 0.006 uM 0OU C19 H19 Cl2 N3 O c1ccc2c(c1....
18 4PY2 ic50 = 0.272 uM 43E C15 H17 Cl2 N3 O S c1cscc1NC(....
19 3KFL - ME8 C15 H23 N6 O8 P S CSCC[C@@H]....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: ME8; Similar ligands found: 306
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 8QN 0.731183 0.898734
7 NB8 0.729167 0.86747
8 YLP 0.708738 0.860465
9 YAP 0.707071 0.888889
10 FA5 0.707071 0.9
11 PAJ 0.705263 0.857143
12 CA0 0.704545 0.864198
13 YLB 0.688679 0.882353
14 YLC 0.688679 0.880952
15 4AD 0.6875 0.888889
16 PTJ 0.676768 0.86747
17 A2D 0.666667 0.839506
18 AYB 0.663636 0.872093
19 AN2 0.655556 0.829268
20 YLA 0.654545 0.83908
21 BA3 0.651685 0.839506
22 M33 0.648352 0.875
23 TYM 0.648148 0.9
24 B4P 0.644444 0.839506
25 ADP 0.644444 0.839506
26 AP5 0.644444 0.839506
27 PRX 0.634409 0.864198
28 WAQ 0.633663 0.878049
29 A 0.632184 0.8375
30 AMP 0.632184 0.8375
31 ADX 0.630435 0.784091
32 AHX 0.63 0.845238
33 DLL 0.63 0.875
34 ABM 0.629214 0.886076
35 AD9 0.62766 0.819277
36 1ZZ 0.627451 0.880952
37 TXA 0.627451 0.876543
38 OOB 0.626263 0.875
39 YLY 0.623932 0.894118
40 3UK 0.623762 0.864198
41 ATP 0.623656 0.839506
42 50T 0.623656 0.807229
43 ACP 0.623656 0.841463
44 AMP MG 0.617977 0.795181
45 AR6 0.617021 0.8625
46 APR 0.617021 0.8625
47 AQP 0.617021 0.839506
48 5FA 0.617021 0.839506
49 ANP 0.614583 0.819277
50 00A 0.613861 0.833333
51 SAP 0.610526 0.821429
52 AGS 0.610526 0.821429
53 XAH 0.603774 0.837209
54 PR8 0.601942 0.869048
55 DAL AMP 0.6 0.875
56 9SN 0.6 0.823529
57 ACQ 0.597938 0.841463
58 GAP 0.597938 0.841463
59 A12 0.597826 0.831325
60 AP2 0.597826 0.831325
61 3OD 0.596154 0.8875
62 AU1 0.595745 0.819277
63 N0B 0.595041 0.83908
64 OAD 0.592233 0.8875
65 LAQ 0.590909 0.837209
66 SRA 0.588889 0.819277
67 A1R 0.588235 0.833333
68 ATF 0.585859 0.809524
69 4UV 0.583333 0.843373
70 5SV 0.578431 0.845238
71 ADQ 0.572816 0.841463
72 A22 0.568627 0.829268
73 SON 0.568421 0.876543
74 APC 0.56701 0.831325
75 FYA 0.566038 0.851852
76 TAT 0.565657 0.831325
77 25A 0.563107 0.839506
78 ADP MG 0.5625 0.807229
79 RBY 0.561224 0.853659
80 ADV 0.561224 0.853659
81 MYR AMP 0.560748 0.858824
82 4UU 0.558559 0.843373
83 ADP BEF 0.556701 0.788235
84 BEF ADP 0.556701 0.788235
85 4UW 0.552632 0.857143
86 IOT 0.547009 0.829545
87 TYR AMP 0.545455 0.853659
88 ADP PO3 0.545455 0.8375
89 48N 0.54386 0.86747
90 ATP MG 0.54 0.807229
91 TXD 0.53913 0.833333
92 MAP 0.538462 0.8
93 BIS 0.537037 0.811765
94 ARG AMP 0.535088 0.827586
95 TXE 0.534483 0.811765
96 ANP MG 0.533981 0.8
97 SMM 0.533981 0.833333
98 25L 0.53211 0.829268
99 AFH 0.530973 0.813953
100 LPA AMP 0.530435 0.816092
101 NAI 0.525862 0.811765
102 NAX 0.525862 0.847059
103 SAH 0.524752 0.8125
104 ADP ALF 0.524272 0.77907
105 ALF ADP 0.524272 0.77907
106 A5A 0.524272 0.786517
107 TSB 0.52381 0.777778
108 G3A 0.522124 0.802326
109 OMR 0.521368 0.870588
110 SSA 0.519231 0.78022
111 ADP VO4 0.519231 0.829268
112 VO4 ADP 0.519231 0.829268
113 G5P 0.517544 0.802326
114 7MD 0.517544 0.858824
115 AP0 0.516949 0.823529
116 MTA 0.516484 0.797468
117 EEM 0.514563 0.819277
118 54H 0.514286 0.769231
119 VMS 0.514286 0.769231
120 LSS 0.514019 0.802198
121 GTA 0.513043 0.816092
122 NXX 0.512821 0.853659
123 DND 0.512821 0.853659
124 6V0 0.512821 0.802326
125 BT5 0.512195 0.850575
126 XYA 0.511628 0.728395
127 RAB 0.511628 0.728395
128 ADN 0.511628 0.728395
129 5AS 0.510204 0.741935
130 5X8 0.51 0.810127
131 53H 0.509434 0.76087
132 5CA 0.509434 0.78022
133 M24 0.507937 0.804598
134 COD 0.504065 0.852273
135 CNA 0.5 0.853659
136 AOC 0.5 0.753086
137 SA8 0.5 0.839506
138 DSZ 0.5 0.8
139 52H 0.5 0.76087
140 GSU 0.5 0.820225
141 KAA 0.5 0.774194
142 LA8 ALF 3PG 0.495798 0.813953
143 AF3 ADP 3PG 0.495798 0.813953
144 ALF ADP 3PG 0.495798 0.813953
145 AHZ 0.495726 0.858824
146 JB6 0.495495 0.855422
147 NVA LMS 0.495413 0.802198
148 G5A 0.495146 0.78022
149 SFG 0.49505 0.775
150 5CD 0.494382 0.716049
151 T5A 0.491803 0.818182
152 ADJ 0.491803 0.827586
153 ADP BMA 0.490909 0.819277
154 LEU LMS 0.490909 0.782609
155 SAM 0.490385 0.841463
156 2A5 0.490196 0.819277
157 3DH 0.489362 0.775
158 DTA 0.48913 0.722892
159 NAQ 0.488372 0.845238
160 UP5 0.487395 0.821429
161 TAD 0.487179 0.835294
162 AMP DBH 0.486957 0.797619
163 A A 0.486486 0.817073
164 NSS 0.486239 0.78022
165 6AD 0.485714 0.835294
166 PAP 0.485437 0.82716
167 A3D 0.484127 0.864198
168 5N5 0.483146 0.707317
169 SAI 0.480769 0.780488
170 NAE 0.48062 0.865854
171 NAD 0.48 0.851852
172 139 0.479675 0.804598
173 7MC 0.479339 0.860465
174 UPA 0.479339 0.811765
175 4TC 0.479339 0.823529
176 7D5 0.478723 0.761905
177 EP4 0.478261 0.756098
178 YSA 0.478261 0.78022
179 A4D 0.477778 0.728395
180 S7M 0.476636 0.797619
181 A4P 0.47541 0.76087
182 7D3 0.474747 0.764706
183 M2T 0.473118 0.759036
184 0UM 0.472727 0.764706
185 PPS 0.471698 0.764045
186 ATR 0.471154 0.814815
187 7D4 0.470588 0.764706
188 A3P 0.47 0.8375
189 ATP A A A 0.469565 0.82716
190 62X 0.468468 0.790698
191 EAD 0.466165 0.825581
192 AR6 AR6 0.466102 0.839506
193 K15 0.464286 0.788235
194 GEK 0.463636 0.804878
195 P1H 0.463235 0.848837
196 ZID 0.462121 0.841463
197 A7D 0.460784 0.777778
198 NAD IBO 0.460317 0.821429
199 P5A 0.460177 0.765957
200 6RE 0.459184 0.72093
201 A2R 0.458716 0.851852
202 BTX 0.456693 0.83908
203 FB0 0.456522 0.844444
204 ITT 0.456311 0.792683
205 A2P 0.455446 0.825
206 ARU 0.455357 0.793103
207 DSH 0.454545 0.75
208 3AM 0.453608 0.802469
209 DZD 0.453125 0.835294
210 NDE 0.452555 0.831325
211 J7C 0.45 0.729412
212 ZAS 0.44898 0.705882
213 V3L 0.448598 0.8625
214 WSA 0.447154 0.788889
215 A3S 0.446602 0.765432
216 NAJ PZO 0.446154 0.781609
217 S4M 0.445545 0.770115
218 SXZ 0.443478 0.819277
219 MAO 0.441176 0.845238
220 FDA 0.439716 0.771739
221 VRT 0.439252 0.792683
222 A3T 0.438095 0.753086
223 NDC 0.435714 0.823529
224 IMO 0.435644 0.802469
225 A3N 0.435644 0.702381
226 6IA 0.435185 0.857143
227 0WD 0.434109 0.802326
228 GJV 0.431373 0.712644
229 A5D 0.429907 0.722892
230 AMP NAD 0.42963 0.853659
231 2AM 0.428571 0.792683
232 FNK 0.428571 0.784946
233 KB1 0.42735 0.744186
234 2SA 0.427273 0.876543
235 CAO 0.426471 0.815217
236 4YB 0.42623 0.802198
237 NA7 0.426087 0.831325
238 NEC 0.425743 0.686747
239 A3G 0.425743 0.756098
240 S8M 0.424779 0.783133
241 2VA 0.424528 0.73494
242 4TA 0.423077 0.806818
243 G A A A 0.423077 0.781609
244 1HE 0.422535 0.866667
245 5AD 0.422222 0.683544
246 NAJ PYZ 0.422222 0.784091
247 3AT 0.422018 0.839506
248 7C5 0.421488 0.752941
249 U A G G 0.419847 0.790698
250 TXP 0.418605 0.823529
251 AAT 0.418182 0.712644
252 6FA 0.416667 0.797753
253 COS 0.416058 0.824176
254 OVE 0.415842 0.785714
255 NJP 0.415385 0.821429
256 ODP 0.415385 0.793103
257 MHZ 0.415094 0.781609
258 PGS 0.415094 0.770115
259 0T1 0.414815 0.822222
260 KH3 0.414634 0.77907
261 AV2 0.414414 0.77381
262 SO8 0.412844 0.746988
263 AVV 0.412281 0.802326
264 SOP 0.411348 0.844444
265 DAT 0.411215 0.807229
266 FAS 0.410959 0.806818
267 FAD 0.410959 0.806818
268 SFD 0.410959 0.72
269 NPW 0.410853 0.837209
270 NDP 0.410853 0.802326
271 ETB 0.410448 0.873563
272 DCA 0.410448 0.822222
273 3NZ 0.410256 0.783133
274 ACO 0.410072 0.835165
275 DTP 0.409091 0.807229
276 1VU 0.408451 0.815217
277 NZQ 0.407692 0.813953
278 P5F 0.406452 0.782609
279 30N 0.405797 0.773196
280 Z5A 0.405797 0.76087
281 2MC 0.405594 0.789474
282 COA 0.404412 0.842697
283 FYN 0.404255 0.842697
284 3KK 0.404255 0.824176
285 Y3J 0.404255 0.646341
286 AMZ 0.40404 0.792683
287 C2R 0.40404 0.804878
288 GGZ 0.403509 0.741573
289 D3Y 0.403509 0.746988
290 3HC 0.402778 0.833333
291 A1S 0.402778 0.865169
292 IVC 0.402778 0.833333
293 MLC 0.402778 0.844444
294 BCO 0.402778 0.824176
295 7D7 0.402174 0.662651
296 A A A 0.401709 0.829268
297 A6D 0.401709 0.67033
298 649 0.401575 0.765957
299 COK 0.401408 0.824176
300 OXK 0.401408 0.844444
301 FCX 0.4 0.815217
302 71V 0.4 0.790698
303 62F 0.4 0.795455
304 CAA 0.4 0.833333
305 FAM 0.4 0.804348
306 6C6 0.4 0.831325
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3KFL; Ligand: ME8; Similar sites found: 50
This union binding pocket(no: 1) in the query (biounit: 3kfl.bio1) has 27 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2PID YSA 0.0001443 0.45377 1.1236
2 1M2W MTL 0.01878 0.41729 1.21704
3 4OE4 NAD 0.006589 0.4114 1.59574
4 3AFH GSU 0.000001206 0.5023 1.84426
5 2Z49 AMG 0.03005 0.41242 1.85185
6 2JHP GUN 0.03093 0.40227 1.86335
7 4MAF ADX 0.0007607 0.40095 1.9802
8 4XH0 ADP 0.01195 0.42879 2.23325
9 4CFS HQD 0.01952 0.40345 3.13589
10 1J09 GLU 0.00004231 0.45984 3.4188
11 1J09 ATP 0.00006703 0.45144 3.4188
12 2AF6 BRU 0.04053 0.40077 3.87597
13 4OKS 2T9 0.01904 0.41176 4.09483
14 4XFM THE 0.02927 0.40813 4.09483
15 4BWL MN9 0.03049 0.40613 4.60526
16 1JIL 485 0.006674 0.40784 4.7619
17 2GKS ADP 0.004174 0.41339 4.94506
18 2CYB TYR 0.02774 0.40477 4.95356
19 4RW3 SHV 0.02542 0.41125 4.96689
20 5G4R LF1 0.03717 0.40067 5.08475
21 1KQN NAD 0.001063 0.43386 5.37634
22 4J75 TYM 0.0000004671 0.56206 5.86797
23 1V47 ADX 0.0005077 0.42043 6.01719
24 5T52 NGA 0.03022 0.40143 6.19835
25 1EXF GLY 0.005663 0.45626 6.61157
26 1K4M NAD 0.0004374 0.43528 7.04225
27 2H29 DND 0.0006477 0.40786 7.40741
28 3VSV XYS 0.03728 0.40315 7.62411
29 4A91 GLU 0.00008724 0.52146 8.38926
30 1R6T TYM 0.00000422 0.45741 8.80503
31 3UC5 ATP 0.002818 0.43563 8.9172
32 5LLT DND 0.001473 0.40066 9.38967
33 1R6U TYM 0.000008656 0.50242 9.61098
34 3COW 52H 0.0000005149 0.44981 9.63455
35 1N1D C2G 0.00102 0.4174 10.0775
36 3DGY 2GP 0.03104 0.40607 10.3093
37 5IGL BMF 0.01408 0.42709 10.3226
38 1NC4 DOF 0.02411 0.41367 10.6977
39 2X3F APC 0.00001088 0.50749 11.5789
40 1JZS MRC 0.0000001111 0.6232 12.9433
41 1XDN ATP 0.01385 0.40702 12.9964
42 1O6B ADP 0.01786 0.41319 13.0178
43 4NAT ADP 0.0197 0.41342 14.375
44 4NAT 2W5 0.004688 0.41342 14.375
45 2V0C LEU LMS 0.0000001471 0.56579 14.7163
46 3C8Z 5CA 0.0000008497 0.57719 15.2174
47 3B6C SDN 0.03524 0.40191 17.094
48 5ABU GTG 0.0264 0.40908 18.5714
49 3ZIU LSS 0.0000001499 0.56634 29.9645
50 2QTR NXX 0.00003443 0.44048 34.3915
Feedback