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Receptor
PDB id Resolution Class Description Source Keywords
3PD5 2.29 Å EC: 6.1.1.3 CRYSTAL STRUCTURE OF THE EDITING DOMAIN OF THREONYL-TRNA SYN FROM PYROCOCCUS ABYSSI IN COMPLEX WITH AN ANALOG OF THREONYA DENYLATE PYROCOCCUS ABYSSI ALPHA/BETA FOLD DEACYLASE EDITING AMINOACYL-TRNA SYNTHETATRANSLATION LIGASE
Ref.: MECHANISTIC INSIGHTS INTO COGNATE SUBSTRATE DISCRIM DURING PROOFREADING IN TRANSLATION PROC.NATL.ACAD.SCI.USA 2010
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GOL A:500;
Invalid;
none;
submit data
92.094 C3 H8 O3 C(C(C...
TSB A:501;
B:502;
Valid;
Valid;
none;
none;
submit data
447.424 C14 H21 N7 O8 S C[C@H...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3PD2 1.86 Å EC: 6.1.1.3 CRYSTAL STRUCTURE OF THE EDITING DOMAIN OF THREONYL-TRNA SYN FROM PYROCOCCUS ABYSSI IN COMPLEX WITH SERYL-3'-AMINOADENOS PYROCOCCUS ABYSSI ALPHA/BETA FOLD DEACYLASE EDITING AMINOACYL-TRNA SYNTHETATRANSLATION LIGASE
Ref.: MECHANISTIC INSIGHTS INTO COGNATE SUBSTRATE DISCRIM DURING PROOFREADING IN TRANSLATION PROC.NATL.ACAD.SCI.USA V. 107 22117 2010
Members (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 7 families.
1 2HL0 - A3S C13 H19 N7 O5 c1nc(c2c(n....
2 2HKZ - SER C3 H7 N O3 C([C@@H](C....
3 4RRQ - A3S C13 H19 N7 O5 c1nc(c2c(n....
4 4RRR - A3T C14 H21 N7 O5 C[C@H]([C@....
5 3PD2 Kd = 3.4 uM A3S C13 H19 N7 O5 c1nc(c2c(n....
6 3PD4 Kd = 33.3 uM A3G C12 H17 N7 O4 c1nc(c2c(n....
7 2HL1 - A3S C13 H19 N7 O5 c1nc(c2c(n....
8 3PD3 Kd = 36.2 uM A3T C14 H21 N7 O5 C[C@H]([C@....
9 3PD5 - TSB C14 H21 N7 O8 S C[C@H]([C@....
70% Homology Family (11)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 2HL0 - A3S C13 H19 N7 O5 c1nc(c2c(n....
2 2HKZ - SER C3 H7 N O3 C([C@@H](C....
3 4RRQ - A3S C13 H19 N7 O5 c1nc(c2c(n....
4 4RRR - A3T C14 H21 N7 O5 C[C@H]([C@....
5 3PD2 Kd = 3.4 uM A3S C13 H19 N7 O5 c1nc(c2c(n....
6 3PD4 Kd = 33.3 uM A3G C12 H17 N7 O4 c1nc(c2c(n....
7 2HL1 - A3S C13 H19 N7 O5 c1nc(c2c(n....
8 3PD3 Kd = 36.2 uM A3T C14 H21 N7 O5 C[C@H]([C@....
9 3PD5 - TSB C14 H21 N7 O8 S C[C@H]([C@....
10 4RRF Kd = 555.6 uM A3S C13 H19 N7 O5 c1nc(c2c(n....
11 4RRG Kd = 3875.9 uM A3T C14 H21 N7 O5 C[C@H]([C@....
50% Homology Family (25)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 4RRK - A3T C14 H21 N7 O5 C[C@H]([C@....
2 4RR7 Kd = 1 uM A3S C13 H19 N7 O5 c1nc(c2c(n....
3 4RRH - A3S C13 H19 N7 O5 c1nc(c2c(n....
4 4RR8 Kd = 1 uM A3S C13 H19 N7 O5 c1nc(c2c(n....
5 4RRD Kd = 13.4 uM A3T C14 H21 N7 O5 C[C@H]([C@....
6 4RRC Kd = 13.4 uM A3T C14 H21 N7 O5 C[C@H]([C@....
7 4RRL - A3S C13 H19 N7 O5 c1nc(c2c(n....
8 4RR9 Kd = 1 uM A3S C13 H19 N7 O5 c1nc(c2c(n....
9 4RR6 Kd = 1 uM A3S C13 H19 N7 O5 c1nc(c2c(n....
10 4RRA Kd = 13.4 uM A3T C14 H21 N7 O5 C[C@H]([C@....
11 4RRB Kd = 13.4 uM A3T C14 H21 N7 O5 C[C@H]([C@....
12 4RRI - A3T C14 H21 N7 O5 C[C@H]([C@....
13 4RRJ - A3S C13 H19 N7 O5 c1nc(c2c(n....
14 4RRM - A3T C14 H21 N7 O5 C[C@H]([C@....
15 2HL0 - A3S C13 H19 N7 O5 c1nc(c2c(n....
16 2HKZ - SER C3 H7 N O3 C([C@@H](C....
17 4RRQ - A3S C13 H19 N7 O5 c1nc(c2c(n....
18 4RRR - A3T C14 H21 N7 O5 C[C@H]([C@....
19 3PD2 Kd = 3.4 uM A3S C13 H19 N7 O5 c1nc(c2c(n....
20 3PD4 Kd = 33.3 uM A3G C12 H17 N7 O4 c1nc(c2c(n....
21 2HL1 - A3S C13 H19 N7 O5 c1nc(c2c(n....
22 3PD3 Kd = 36.2 uM A3T C14 H21 N7 O5 C[C@H]([C@....
23 3PD5 - TSB C14 H21 N7 O8 S C[C@H]([C@....
24 4RRF Kd = 555.6 uM A3S C13 H19 N7 O5 c1nc(c2c(n....
25 4RRG Kd = 3875.9 uM A3T C14 H21 N7 O5 C[C@H]([C@....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: TSB; Similar ligands found: 258
No: Ligand ECFP6 Tc MDL keys Tc
1 TSB 1 1
2 VMS 0.865854 0.963855
3 54H 0.865854 0.963855
4 A5A 0.841463 0.987654
5 52H 0.8 0.952381
6 LSS 0.793103 0.930233
7 53H 0.790698 0.952381
8 SSA 0.788235 0.952381
9 5CA 0.770115 0.952381
10 LEU LMS 0.755556 0.91954
11 DSZ 0.752809 0.952381
12 NVA LMS 0.744444 0.91954
13 NSS 0.733333 0.952381
14 KAA 0.728261 0.897727
15 GSU 0.728261 0.929412
16 G5A 0.72093 0.929412
17 YSA 0.690722 0.929412
18 5AS 0.690476 0.929412
19 8X1 0.673913 0.897727
20 8PZ 0.646465 0.952381
21 P5A 0.639175 0.88764
22 LMS 0.638554 0.962963
23 WSA 0.638095 0.940476
24 8QN 0.631579 0.831325
25 5AL 0.612903 0.831325
26 SON 0.588889 0.790698
27 8Q2 0.587156 0.91954
28 4YB 0.584906 0.908046
29 TXA 0.584158 0.833333
30 AMP 0.581395 0.795181
31 A 0.581395 0.795181
32 ABM 0.579545 0.797619
33 A3T 0.576087 0.756098
34 AHX 0.57 0.804598
35 BA3 0.566667 0.819277
36 9ZA 0.565657 0.813953
37 9ZD 0.565657 0.813953
38 CA0 0.565217 0.821429
39 649 0.563636 0.88764
40 A2D 0.561798 0.819277
41 B4P 0.56044 0.819277
42 AP5 0.56044 0.819277
43 SRA 0.556818 0.821429
44 DAL AMP 0.555556 0.809524
45 AN2 0.554348 0.831325
46 SRP 0.55102 0.790698
47 A12 0.549451 0.790698
48 AP2 0.549451 0.790698
49 M33 0.548387 0.831325
50 AU1 0.548387 0.821429
51 ADX 0.548387 0.939024
52 PAJ 0.544554 0.795455
53 ADP 0.543478 0.819277
54 5X8 0.542553 0.705882
55 3DH 0.54023 0.714286
56 9K8 0.538462 0.795699
57 AT4 0.537634 0.833333
58 AQP 0.536842 0.819277
59 PRX 0.536842 0.77907
60 5FA 0.536842 0.819277
61 GAP 0.536082 0.77907
62 AOC 0.533333 0.714286
63 XAH 0.53271 0.758242
64 48N 0.531532 0.804598
65 ADN 0.530864 0.731707
66 XYA 0.530864 0.731707
67 RAB 0.530864 0.731707
68 5CD 0.53012 0.698795
69 SLU 0.529412 0.918605
70 AMO 0.529412 0.811765
71 ATP 0.526316 0.819277
72 50T 0.526316 0.788235
73 HEJ 0.526316 0.819277
74 ACP 0.526316 0.8
75 PTJ 0.52381 0.784091
76 NB8 0.52381 0.804598
77 ME8 0.52381 0.777778
78 APC 0.520833 0.790698
79 APR 0.520833 0.819277
80 AR6 0.520833 0.819277
81 ANP 0.520408 0.821429
82 5N5 0.518072 0.710843
83 SA8 0.515464 0.659341
84 ADV 0.515464 0.790698
85 SAP 0.515464 0.845238
86 RBY 0.515464 0.790698
87 AGS 0.515464 0.845238
88 AD9 0.515464 0.8
89 ADP PO3 0.515464 0.795181
90 4AD 0.514563 0.802326
91 LAD 0.514286 0.755556
92 A4D 0.511905 0.731707
93 EP4 0.511628 0.678161
94 DLL 0.509615 0.809524
95 M2T 0.505747 0.701149
96 DTA 0.505747 0.72619
97 T99 0.50505 0.833333
98 ACQ 0.50505 0.8
99 TAT 0.50505 0.833333
100 OOB 0.504854 0.809524
101 3UK 0.504762 0.8
102 OAD 0.504762 0.843373
103 7MD 0.504505 0.777778
104 MTA 0.5 0.714286
105 YAP 0.495413 0.781609
106 FA5 0.495413 0.790698
107 1ZZ 0.495327 0.758242
108 3OD 0.495327 0.843373
109 FYA 0.495327 0.767442
110 00A 0.495238 0.772727
111 MAP 0.495146 0.802326
112 A22 0.495146 0.809524
113 ALF ADP 0.49505 0.741573
114 ADP ALF 0.49505 0.741573
115 ATF 0.49505 0.790698
116 SAH 0.494949 0.689655
117 SFG 0.494845 0.674419
118 YLP 0.491228 0.741935
119 MYR AMP 0.490741 0.73913
120 9X8 0.490566 0.845238
121 25A 0.490385 0.797619
122 5SV 0.490385 0.744444
123 SMM 0.490196 0.677419
124 ADP VO4 0.490196 0.788235
125 VO4 ADP 0.490196 0.788235
126 S7M 0.490196 0.681319
127 6YZ 0.490196 0.8
128 SAM 0.49 0.681319
129 S4M 0.489362 0.642105
130 6RE 0.48913 0.648352
131 AMP DBH 0.486486 0.758621
132 9SN 0.486239 0.764045
133 WAQ 0.485981 0.772727
134 PR8 0.485981 0.747253
135 B5V 0.485981 0.790698
136 ADQ 0.485714 0.8
137 A3R 0.485714 0.772727
138 A1R 0.485714 0.772727
139 EEM 0.485149 0.645161
140 NEC 0.483871 0.690476
141 B5Y 0.481818 0.802326
142 B5M 0.481818 0.802326
143 JB6 0.481481 0.793103
144 SAI 0.48 0.662921
145 2VA 0.479592 0.738095
146 J7C 0.478723 0.655556
147 A3N 0.478723 0.686047
148 7MC 0.478632 0.78022
149 YLC 0.478632 0.758242
150 YLB 0.478632 0.741935
151 GA7 0.477876 0.790698
152 ARG AMP 0.477876 0.712766
153 ADP BMA 0.476636 0.77907
154 A3S 0.474227 0.72619
155 A7D 0.474227 0.697674
156 TAD 0.473684 0.795455
157 GJV 0.473684 0.641304
158 TYR AMP 0.473214 0.761364
159 0UM 0.471698 0.652174
160 F2R 0.471074 0.741935
161 TYM 0.470085 0.790698
162 AF3 ADP 3PG 0.470085 0.736264
163 LAQ 0.469565 0.777778
164 7C5 0.469027 0.715909
165 MAO 0.46875 0.706522
166 DSH 0.468085 0.655556
167 BIS 0.46789 0.772727
168 SXZ 0.46789 0.681319
169 COD 0.467213 0.755319
170 LPA AMP 0.465517 0.758242
171 SO8 0.465347 0.729412
172 25L 0.463636 0.809524
173 K15 0.462963 0.638298
174 AYB 0.46281 0.734043
175 ZAS 0.462366 0.689655
176 GTA 0.46087 0.777778
177 DQV 0.46087 0.831325
178 4UV 0.460177 0.781609
179 A A 0.458716 0.776471
180 OMR 0.457627 0.769231
181 TXE 0.457627 0.793103
182 AHZ 0.456897 0.758242
183 YLA 0.454545 0.723404
184 MHZ 0.454545 0.652632
185 AP0 0.453782 0.784091
186 62X 0.453704 0.625
187 A3G 0.452632 0.717647
188 5AD 0.452381 0.666667
189 AFH 0.452174 0.755556
190 4UU 0.452174 0.781609
191 3AM 0.451613 0.761905
192 NAX 0.449153 0.766667
193 6V0 0.449153 0.784091
194 NXX 0.449153 0.811765
195 TXD 0.449153 0.793103
196 4UW 0.449153 0.775281
197 DND 0.449153 0.811765
198 IOT 0.446281 0.715789
199 7D5 0.445652 0.724138
200 G3A 0.443478 0.784091
201 EO7 0.443299 0.917647
202 ATP A A A 0.442478 0.785714
203 G5P 0.439655 0.784091
204 AR6 AR6 0.439655 0.776471
205 CNA 0.439024 0.811765
206 A3P 0.438776 0.795181
207 A2P 0.438776 0.783133
208 YLY 0.4375 0.734043
209 NAI 0.436975 0.793103
210 UP5 0.436975 0.802326
211 VRT 0.436893 0.712644
212 A3D 0.436508 0.821429
213 GEK 0.435185 0.704545
214 3NZ 0.432432 0.724138
215 Y3J 0.431818 0.630952
216 T5A 0.430894 0.76087
217 NAQ 0.430769 0.784091
218 7D7 0.430233 0.647059
219 BT5 0.428571 0.734043
220 A5D 0.427184 0.72619
221 NVA 2AD 0.427184 0.704545
222 A4P 0.42623 0.726316
223 D3Y 0.425926 0.709302
224 2AM 0.425532 0.77381
225 80F 0.425197 0.76087
226 KB1 0.424779 0.634409
227 KH3 0.423729 0.631579
228 FB0 0.423358 0.714286
229 S8M 0.422018 0.704545
230 AMP NAD 0.420635 0.788235
231 NAD 0.420635 0.809524
232 ADJ 0.419355 0.731183
233 6IA 0.419048 0.717391
234 V3L 0.419048 0.797619
235 594 0.418605 0.8125
236 4TC 0.418033 0.784091
237 UPA 0.418033 0.793103
238 2A5 0.417476 0.758621
239 N0B 0.416667 0.723404
240 AAT 0.415094 0.641304
241 PPS 0.415094 0.915663
242 7D3 0.414141 0.747126
243 PAP 0.413462 0.807229
244 ATR 0.413462 0.795181
245 OVE 0.412371 0.788235
246 NAE 0.412214 0.802326
247 7D4 0.411765 0.747126
248 2SA 0.411215 0.790698
249 NAJ PZO 0.410853 0.764045
250 BTX 0.409449 0.741935
251 4TA 0.409449 0.731183
252 139 0.408 0.766667
253 IXN 0.407407 0.84375
254 J1D 0.40625 0.708738
255 DZD 0.40625 0.775281
256 BS5 0.404762 0.797872
257 590 0.404412 0.822917
258 A2R 0.40367 0.809524
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3PD2; Ligand: A3S; Similar sites found with APoc: 34
This union binding pocket(no: 1) in the query (biounit: 3pd2.bio1) has 46 residues
No: Leader PDB Ligand Sequence Similarity
1 5H4S RAM None
2 3M2W L8I None
3 1ZEA DVA DPR GLY DSN DGN DHI DTY DAS DSN None
4 5AHW CMP 1.36054
5 1DCP HBI 1.92308
6 4NBI D3Y 2.04082
7 1P9P SAH 2.04082
8 4CNE SAH 2.04082
9 4JAL SAH 2.72109
10 4R2M ANP 2.72109
11 5T63 ALA ALA ALA ALA 3.40136
12 6EMU SAM 3.40136
13 5LPB ADP 4.08163
14 4MCC 21X 4.7619
15 4YJK URA 5.44218
16 1GPM AMP 5.44218
17 1OBD AMP 6.12245
18 1SQL GUN 6.16438
19 1CT9 AMP 6.80272
20 2YY8 SAM 6.80272
21 5A7Y SAH 8.84354
22 1NU4 MLA 9.27835
23 1R6B ADP 9.52381
24 4FXQ G9L 10.2041
25 4FK7 P34 10.2041
26 2ZX2 RAM 11.5646
27 5Y4R C2E 11.7241
28 5CGE 51F 12.2449
29 5YW5 ADE 13.6054
30 3HGM ATP 14.2857
31 3FD5 AP2 15.6463
32 1O94 AMP 19.0476
33 3IWD M2T 20.9677
34 1L0I PSR 24.359
Pocket No.: 2; Query (leader) PDB : 3PD2; Ligand: A3S; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 3pd2.bio1) has 46 residues
No: Leader PDB Ligand Sequence Similarity
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