-->
Receptor
PDB id Resolution Class Description Source Keywords
5XET 2.38 Å EC: 6.1.1.10 CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS METHIONYL-TR SYNTHETASE BOUND BY METHIONYL-ADENYLATE (MET-AMP) MYCOBACTERIUM TUBERCULOSIS H37RA SYNTHETASE AMINOACYL-TRNA SYNTHETASE COMPLEX ATP LIGASE
Ref.: STRUCTURAL CHARACTERIZATION OF FREE-STATE AND PRODUCT-STATEMYCOBACTERIUM TUBERCULOSISMETHIONYL-TR SYNTHETASE REVEALS AN INDUCED-FIT LIGAND-RECOGNITIO MECHANISM. IUCRJ V. 5 478 2018
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MG C:605;
C:606;
C:604;
C:603;
C:607;
Part of Protein;
Invalid;
Invalid;
Part of Protein;
Invalid;
none;
none;
none;
none;
none;
submit data
24.305 Mg [Mg+2...
ME8 C:601;
Valid;
none;
submit data
478.417 C15 H23 N6 O8 P S CSCC[...
EDO C:602;
Invalid;
none;
submit data
62.068 C2 H6 O2 C(CO)...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5XET 2.38 Å EC: 6.1.1.10 CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS METHIONYL-TR SYNTHETASE BOUND BY METHIONYL-ADENYLATE (MET-AMP) MYCOBACTERIUM TUBERCULOSIS H37RA SYNTHETASE AMINOACYL-TRNA SYNTHETASE COMPLEX ATP LIGASE
Ref.: STRUCTURAL CHARACTERIZATION OF FREE-STATE AND PRODUCT-STATEMYCOBACTERIUM TUBERCULOSISMETHIONYL-TR SYNTHETASE REVEALS AN INDUCED-FIT LIGAND-RECOGNITIO MECHANISM. IUCRJ V. 5 478 2018
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 5XET - ME8 C15 H23 N6 O8 P S CSCC[C@@H]....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 2X1L - ADN C10 H13 N5 O4 c1nc(c2c(n....
2 5K0S ic50 = 0.006 uM 0OU C19 H19 Cl2 N3 O c1ccc2c(c1....
3 4PY2 ic50 = 0.272 uM 43E C15 H17 Cl2 N3 O S c1cscc1NC(....
4 5XET - ME8 C15 H23 N6 O8 P S CSCC[C@@H]....
50% Homology Family (20)
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 5XET - ME8 C15 H23 N6 O8 P S CSCC[C@@H]....
20 3KFL - ME8 C15 H23 N6 O8 P S CSCC[C@@H]....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: ME8; Similar ligands found: 322
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 YLC 0.688679 0.880952
14 YLB 0.688679 0.882353
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 ADP 0.644444 0.839506
25 AP5 0.644444 0.839506
26 B4P 0.644444 0.839506
27 AT4 0.637363 0.831325
28 PRX 0.634409 0.864198
29 WAQ 0.633663 0.878049
30 AMP 0.632184 0.8375
31 A 0.632184 0.8375
32 ADX 0.630435 0.784091
33 AHX 0.63 0.845238
34 DLL 0.63 0.875
35 ABM 0.629214 0.886076
36 AD9 0.62766 0.819277
37 TXA 0.627451 0.876543
38 1ZZ 0.627451 0.880952
39 OOB 0.626263 0.875
40 YLY 0.623932 0.894118
41 3UK 0.623762 0.864198
42 ATP 0.623656 0.839506
43 HEJ 0.623656 0.839506
44 50T 0.623656 0.807229
45 ACP 0.623656 0.841463
46 B5V 0.617647 0.853659
47 5FA 0.617021 0.839506
48 AR6 0.617021 0.8625
49 AQP 0.617021 0.839506
50 APR 0.617021 0.8625
51 ANP 0.614583 0.819277
52 00A 0.613861 0.833333
53 SAP 0.610526 0.821429
54 AGS 0.610526 0.821429
55 B5Y 0.609524 0.865854
56 XAH 0.603774 0.837209
57 PR8 0.601942 0.869048
58 9SN 0.6 0.823529
59 DAL AMP 0.6 0.875
60 GAP 0.597938 0.841463
61 ACQ 0.597938 0.841463
62 AP2 0.597826 0.831325
63 A12 0.597826 0.831325
64 3OD 0.596154 0.8875
65 AU1 0.595745 0.819277
66 N0B 0.595041 0.83908
67 B5M 0.59434 0.865854
68 9ZA 0.594059 0.878049
69 9ZD 0.594059 0.878049
70 OAD 0.592233 0.8875
71 LAQ 0.590909 0.837209
72 SRA 0.588889 0.819277
73 A1R 0.588235 0.833333
74 ATF 0.585859 0.809524
75 4UV 0.583333 0.843373
76 6YZ 0.58 0.841463
77 5SV 0.578431 0.845238
78 9X8 0.576923 0.865854
79 ADQ 0.572816 0.841463
80 A22 0.568627 0.829268
81 SON 0.568421 0.876543
82 APC 0.56701 0.831325
83 FYA 0.566038 0.851852
84 T99 0.565657 0.831325
85 TAT 0.565657 0.831325
86 25A 0.563107 0.839506
87 ADV 0.561224 0.853659
88 RBY 0.561224 0.853659
89 MYR AMP 0.560748 0.858824
90 4UU 0.558559 0.843373
91 A3R 0.557692 0.833333
92 4UW 0.552632 0.857143
93 IOT 0.547009 0.829545
94 F2R 0.546219 0.83908
95 ADP PO3 0.545455 0.8375
96 48N 0.54386 0.86747
97 TXD 0.53913 0.833333
98 MAP 0.538462 0.8
99 BIS 0.537037 0.811765
100 TXE 0.534483 0.811765
101 SMM 0.533981 0.833333
102 80F 0.532787 0.83908
103 25L 0.53211 0.829268
104 ARG AMP 0.530973 0.827586
105 GA7 0.530973 0.853659
106 AFH 0.530973 0.813953
107 LPA AMP 0.530435 0.816092
108 LMS 0.526882 0.764045
109 TYR AMP 0.526786 0.865854
110 DQV 0.526316 0.851852
111 NAI 0.525862 0.811765
112 NAX 0.525862 0.847059
113 SAH 0.524752 0.8125
114 ALF ADP 0.524272 0.77907
115 ADP ALF 0.524272 0.77907
116 A5A 0.524272 0.786517
117 TSB 0.52381 0.777778
118 G3A 0.522124 0.802326
119 OMR 0.521368 0.870588
120 VO4 ADP 0.519231 0.829268
121 SSA 0.519231 0.78022
122 ADP VO4 0.519231 0.829268
123 7MD 0.517544 0.858824
124 G5P 0.517544 0.802326
125 AP0 0.516949 0.823529
126 MTA 0.516484 0.797468
127 EEM 0.514563 0.819277
128 VMS 0.514286 0.769231
129 54H 0.514286 0.769231
130 LSS 0.514019 0.802198
131 GTA 0.513043 0.816092
132 6V0 0.512821 0.802326
133 DND 0.512821 0.853659
134 NXX 0.512821 0.853659
135 BT5 0.512195 0.850575
136 XYA 0.511628 0.728395
137 RAB 0.511628 0.728395
138 ADN 0.511628 0.728395
139 5AS 0.510204 0.741935
140 5X8 0.51 0.810127
141 5CA 0.509434 0.78022
142 53H 0.509434 0.76087
143 M24 0.507937 0.804598
144 COD 0.504065 0.852273
145 GSU 0.5 0.820225
146 CNA 0.5 0.853659
147 SA8 0.5 0.839506
148 DSZ 0.5 0.8
149 KAA 0.5 0.774194
150 AOC 0.5 0.753086
151 52H 0.5 0.76087
152 AF3 ADP 3PG 0.495798 0.813953
153 AHZ 0.495726 0.858824
154 JB6 0.495495 0.855422
155 NVA LMS 0.495413 0.813187
156 G5A 0.495146 0.78022
157 SFG 0.49505 0.775
158 5CD 0.494382 0.716049
159 T5A 0.491803 0.818182
160 ADJ 0.491803 0.827586
161 ADP BMA 0.490909 0.819277
162 SAM 0.490385 0.841463
163 2A5 0.490196 0.819277
164 3DH 0.489362 0.775
165 DTA 0.48913 0.722892
166 NAQ 0.488372 0.845238
167 UP5 0.487395 0.821429
168 TAD 0.487179 0.835294
169 AMP DBH 0.486957 0.797619
170 A A 0.486486 0.817073
171 NSS 0.486239 0.78022
172 6AD 0.485714 0.835294
173 PAP 0.485437 0.82716
174 A3D 0.484127 0.864198
175 5N5 0.483146 0.707317
176 SAI 0.480769 0.780488
177 NAE 0.48062 0.865854
178 NAD 0.48 0.851852
179 139 0.479675 0.804598
180 4TC 0.479339 0.823529
181 UPA 0.479339 0.811765
182 7MC 0.479339 0.860465
183 7D5 0.478723 0.761905
184 YSA 0.478261 0.78022
185 EP4 0.478261 0.756098
186 A4D 0.477778 0.728395
187 LEU LMS 0.477477 0.793478
188 S7M 0.476636 0.797619
189 A4P 0.47541 0.76087
190 7D3 0.474747 0.764706
191 M2T 0.473118 0.759036
192 0UM 0.472727 0.764706
193 PPS 0.471698 0.764045
194 ATR 0.471154 0.814815
195 7D4 0.470588 0.764706
196 A3P 0.47 0.8375
197 ATP A A A 0.469565 0.82716
198 9K8 0.469027 0.71875
199 62X 0.468468 0.790698
200 8X1 0.46789 0.774194
201 EAD 0.466165 0.825581
202 AR6 AR6 0.466102 0.839506
203 K15 0.464286 0.788235
204 GEK 0.463636 0.804878
205 P1H 0.463235 0.848837
206 ZID 0.462121 0.841463
207 A7D 0.460784 0.777778
208 P5A 0.460177 0.765957
209 6RE 0.459184 0.72093
210 A2R 0.458716 0.851852
211 8PZ 0.456897 0.78022
212 BTX 0.456693 0.83908
213 FB0 0.456522 0.844444
214 ITT 0.456311 0.792683
215 A2P 0.455446 0.825
216 ARU 0.455357 0.793103
217 DSH 0.454545 0.75
218 3AM 0.453608 0.802469
219 DZD 0.453125 0.835294
220 NDE 0.452555 0.831325
221 J7C 0.45 0.729412
222 ZAS 0.44898 0.705882
223 V3L 0.448598 0.8625
224 WSA 0.447154 0.788889
225 A3S 0.446602 0.765432
226 NAJ PZO 0.446154 0.781609
227 S4M 0.445545 0.770115
228 AMP NAD 0.445312 0.851852
229 SXZ 0.443478 0.819277
230 MAO 0.441176 0.845238
231 FDA 0.439716 0.771739
232 VRT 0.439252 0.792683
233 HFD 0.439252 0.8
234 A3T 0.438095 0.753086
235 NDC 0.435714 0.823529
236 IMO 0.435644 0.802469
237 A3N 0.435644 0.702381
238 6IA 0.435185 0.857143
239 0WD 0.434109 0.802326
240 NAJ PYZ 0.432836 0.747253
241 GJV 0.431373 0.712644
242 A5D 0.429907 0.722892
243 NVA 2AD 0.429907 0.783133
244 2AM 0.428571 0.792683
245 FNK 0.428571 0.784946
246 KB1 0.42735 0.744186
247 2SA 0.427273 0.876543
248 CAO 0.426471 0.815217
249 4YB 0.42623 0.802198
250 NA7 0.426087 0.831325
251 A3G 0.425743 0.756098
252 NEC 0.425743 0.686747
253 S8M 0.424779 0.783133
254 2VA 0.424528 0.73494
255 A G 0.423077 0.790698
256 4TA 0.423077 0.806818
257 G A A A 0.423077 0.781609
258 1HE 0.422535 0.866667
259 5AD 0.422222 0.683544
260 3AT 0.422018 0.839506
261 7C5 0.421488 0.752941
262 8Q2 0.420635 0.755319
263 U A G G 0.419847 0.790698
264 TXP 0.418605 0.823529
265 AAT 0.418182 0.712644
266 6FA 0.416667 0.797753
267 COS 0.416058 0.824176
268 OVE 0.415842 0.785714
269 ODP 0.415385 0.793103
270 NJP 0.415385 0.821429
271 PGS 0.415094 0.770115
272 MHZ 0.415094 0.781609
273 0T1 0.414815 0.822222
274 KH3 0.414634 0.77907
275 AV2 0.414414 0.77381
276 SO8 0.412844 0.746988
277 AVV 0.412281 0.802326
278 SOP 0.411348 0.844444
279 DAT 0.411215 0.807229
280 FAD 0.410959 0.806818
281 SFD 0.410959 0.72
282 FAS 0.410959 0.806818
283 NDP 0.410853 0.802326
284 NPW 0.410853 0.837209
285 ETB 0.410448 0.873563
286 DCA 0.410448 0.822222
287 3NZ 0.410256 0.783133
288 ACO 0.410072 0.835165
289 F0P 0.409449 0.77381
290 DTP 0.409091 0.807229
291 1VU 0.408451 0.815217
292 NZQ 0.407692 0.813953
293 P5F 0.406452 0.782609
294 Z5A 0.405797 0.76087
295 30N 0.405797 0.773196
296 2MC 0.405594 0.789474
297 COA 0.404412 0.842697
298 FYN 0.404255 0.842697
299 Y3J 0.404255 0.646341
300 3KK 0.404255 0.824176
301 C2R 0.40404 0.804878
302 AMZ 0.40404 0.792683
303 GGZ 0.403509 0.741573
304 D3Y 0.403509 0.746988
305 U A 0.402985 0.811765
306 BCO 0.402778 0.824176
307 A1S 0.402778 0.865169
308 IVC 0.402778 0.833333
309 3HC 0.402778 0.833333
310 MLC 0.402778 0.844444
311 7D7 0.402174 0.662651
312 A A A 0.401709 0.829268
313 A6D 0.401709 0.67033
314 649 0.401575 0.765957
315 COK 0.401408 0.824176
316 OXK 0.401408 0.844444
317 71V 0.4 0.790698
318 62F 0.4 0.795455
319 CAA 0.4 0.833333
320 FCX 0.4 0.815217
321 FAM 0.4 0.804348
322 6C6 0.4 0.831325
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5XET; Ligand: ME8; Similar sites found with APoc: 151
This union binding pocket(no: 1) in the query (biounit: 5xet.bio1) has 26 residues
No: Leader PDB Ligand Sequence Similarity
1 3UOY FAD 0.94518
2 3UOY NAP 0.94518
3 3NRR D16 1.16505
4 1KC7 PPR 1.51229
5 3TY3 GGG 1.63934
6 2OG2 MLI 1.67131
7 2GKS ADP 1.70132
8 2VVG ADP 1.71429
9 4TQK NAG 1.97044
10 3AFH GSU 2.04918
11 5C9P FUC 2.09974
12 3HL4 CDC 2.11864
13 5FAG PPI 2.19512
14 1JJ7 ADP 2.30769
15 3IB1 IMN 2.31884
16 5ZDK ATP 2.45747
17 5WS9 OXL 2.52632
18 1GPM AMP 2.6465
19 3LM9 ADP 2.64901
20 3ITJ CIT 2.66272
21 4J75 TYM 2.68949
22 4MAF ADX 2.72277
23 2DPY ADP 2.73973
24 3EWA ANP 2.79503
25 3LRE ADP 2.8169
26 5TSH ADP 2.83554
27 2AWN ADP 2.83554
28 3QPB URA 2.83554
29 4LAE NAP 2.99401
30 4LAE 1VM 2.99401
31 5Z5I XYP 3.02457
32 5DK4 5BX 3.03951
33 5DK4 ATP 3.03951
34 1N1D C2G 3.10078
35 1V47 ADX 3.15186
36 1R6T TYM 3.21361
37 1XP8 AGS 3.27869
38 4A91 GLU 3.3557
39 2YGM GLA NAG GAL FUC 3.38983
40 4TVD BGC 3.40265
41 1D4D SIN 3.40265
42 6E0D XXX 3.40426
43 2GDJ ANP 3.40909
44 1R6U TYM 3.43249
45 5GLN XYP XYP XYP 3.48837
46 1G6H ADP 3.50195
47 1KQN NAD 3.58423
48 2G50 PYR 3.59168
49 1XF1 CIT 3.59168
50 5LX6 78P 3.66492
51 4U00 ADP 3.68852
52 2XZ9 PYR 3.7037
53 2H29 DND 3.7037
54 2OBM ADP 3.7464
55 1K4M NAD 3.75587
56 1Q19 SSC 3.77734
57 2F2T 5IQ 3.96975
58 4UP4 GAL NAG 3.99003
59 3EYK EYK 4.06977
60 2HZL PYR 4.10959
61 5T52 NGA 4.13223
62 5Y0N ATP 4.13793
63 1VBH PEP 4.15879
64 3NOJ PYR 4.20168
65 1W6F ISZ 4.31655
66 4NTO 1PW 4.34783
67 4WBD CIT 4.34783
68 1NXJ TLA 4.37158
69 5Y0Q APC 4.37788
70 4PEG 5GP 4.44444
71 1J09 GLU 4.48718
72 1J09 ATP 4.48718
73 2V5K OXM 4.52962
74 4CFS HQD 4.52962
75 3FIU POP 4.53686
76 5WXU FLC 4.5929
77 1AOE GW3 4.6875
78 1AOE NDP 4.6875
79 4G05 JZ3 4.73186
80 1JIL 485 4.7619
81 2PID YSA 4.77528
82 3THR C2F 4.77816
83 5JDI 6JO 4.91493
84 2Y65 ADP 4.93151
85 4B5W PYR 5.07812
86 3UC5 ATP 5.10397
87 1NC4 DOF 5.11628
88 1NC2 DOE 5.11628
89 3MKN DNB 5.37975
90 5N5U AMP 5.41401
91 2ZR9 DTP 5.44413
92 3HQP OXL 5.48204
93 4IP7 FLC 5.48204
94 4F8L AES 5.51724
95 4KCT PYR 5.61122
96 5LLT DND 5.6338
97 4GNC ASO 5.68562
98 1B0U ATP 5.72519
99 1T0S BML 5.81395
100 2CBZ ATP 5.86011
101 2Z49 AMG 5.86011
102 2KIN ADP 6
103 6F5W KG1 6.04915
104 1YQT ADP 6.04915
105 5YV5 ADP 6.04915
106 5O74 GDP 6.09137
107 1T5C ADP 6.42722
108 2HK9 SKM 6.54545
109 1XMV ADP 6.74157
110 2B6N ALA PRO THR 6.83453
111 4URN NOV 7.11111
112 2PHX MAN MAN 7.14286
113 1Q8Q MAN MMA 7.14286
114 5XJD 87L 7.27273
115 5EXE 5SR 7.32484
116 2X3F APC 7.7193
117 1ZGA HMK 7.84314
118 2VWT PYR 7.86517
119 2QTR NXX 7.93651
120 3DOO SKM 7.94224
121 3C8Z 5CA 7.97101
122 1U72 MTX 8.06452
123 1U72 NDP 8.06452
124 4JX1 CAM 8.43373
125 6CHP F0Y 8.69565
126 4YDS ATP 8.77193
127 1FNZ A2G 9.2827
128 4XUB 43D 9.40171
129 1O6B ADP 9.46746
130 2D2F ADP 9.6
131 5Y0T TAT 9.88235
132 3COW 52H 10.299
133 4NAT 2W5 10.625
134 4RFM 3P6 10.9023
135 3ND6 ATP 11.1111
136 1ZEI CRS 11.3208
137 1WHT BZS 11.7647
138 2PS1 ORO 11.9469
139 5C9J DAO 12.0996
140 3ZIA ADP 12.6984
141 5X3D 7XL 13.75
142 1EXF GLY 14.0496
143 2BS5 BGC GAL FUC 14.4444
144 2V0C LEU LMS 15.3119
145 1RV0 NDG 15.625
146 1HBK MYR 15.7303
147 5TVF PUT 16.4706
148 4DN8 BMA 16.6667
149 6FTB M0E 18.5714
150 1JZS MRC 20.794
151 3ZIU LSS 33.0813
APoc FAQ
Feedback