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: 247
No: Ligand ECFP6 Tc MDL keys Tc
1 TSB 1 1
2 54H 0.865854 0.963855
3 VMS 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 0.930233
11 DSZ 0.752809 0.952381
12 NVA LMS 0.744444 0.930233
13 NSS 0.733333 0.952381
14 GSU 0.728261 0.929412
15 KAA 0.728261 0.897727
16 G5A 0.72093 0.929412
17 YSA 0.690722 0.929412
18 5AS 0.690476 0.929412
19 P5A 0.639175 0.88764
20 WSA 0.638095 0.940476
21 8QN 0.631579 0.831325
22 5AL 0.612903 0.831325
23 SON 0.588889 0.790698
24 4YB 0.584906 0.908046
25 TXA 0.584158 0.833333
26 AMP 0.581395 0.795181
27 A 0.581395 0.795181
28 ABM 0.579545 0.797619
29 A3T 0.576087 0.756098
30 AHX 0.57 0.804598
31 AMP MG 0.568182 0.755814
32 BA3 0.566667 0.819277
33 CA0 0.565217 0.821429
34 649 0.563636 0.88764
35 A2D 0.561798 0.819277
36 B4P 0.56044 0.819277
37 AP5 0.56044 0.819277
38 SRA 0.556818 0.821429
39 DAL AMP 0.555556 0.809524
40 AN2 0.554348 0.831325
41 SRP 0.55102 0.790698
42 AP2 0.549451 0.790698
43 A12 0.549451 0.790698
44 M33 0.548387 0.831325
45 ADX 0.548387 0.939024
46 AU1 0.548387 0.821429
47 PAJ 0.544554 0.795455
48 ADP 0.543478 0.819277
49 5X8 0.542553 0.705882
50 3DH 0.54023 0.714286
51 5FA 0.536842 0.819277
52 AQP 0.536842 0.819277
53 PRX 0.536842 0.77907
54 GAP 0.536082 0.77907
55 AOC 0.533333 0.714286
56 XAH 0.53271 0.758242
57 ADP MG 0.531915 0.767442
58 48N 0.531532 0.804598
59 ADN 0.530864 0.731707
60 RAB 0.530864 0.731707
61 XYA 0.530864 0.731707
62 5CD 0.53012 0.698795
63 SLU 0.529412 0.918605
64 AMO 0.529412 0.811765
65 50T 0.526316 0.788235
66 ATP 0.526316 0.819277
67 BEF ADP 0.526316 0.75
68 ACP 0.526316 0.8
69 ADP BEF 0.526316 0.75
70 PTJ 0.52381 0.784091
71 ME8 0.52381 0.777778
72 NB8 0.52381 0.804598
73 AR6 0.520833 0.819277
74 APR 0.520833 0.819277
75 APC 0.520833 0.790698
76 ANP 0.520408 0.821429
77 5N5 0.518072 0.710843
78 SAP 0.515464 0.845238
79 AD9 0.515464 0.8
80 SA8 0.515464 0.659341
81 ADV 0.515464 0.790698
82 RBY 0.515464 0.790698
83 AGS 0.515464 0.845238
84 ADP PO3 0.515464 0.795181
85 4AD 0.514563 0.802326
86 LAD 0.514286 0.755556
87 A4D 0.511905 0.731707
88 EP4 0.511628 0.678161
89 ATP MG 0.510204 0.767442
90 DLL 0.509615 0.809524
91 DTA 0.505747 0.72619
92 M2T 0.505747 0.701149
93 TAT 0.50505 0.833333
94 ACQ 0.50505 0.8
95 ANP MG 0.504951 0.781609
96 OOB 0.504854 0.809524
97 OAD 0.504762 0.843373
98 3UK 0.504762 0.8
99 7MD 0.504505 0.777778
100 MTA 0.5 0.714286
101 FA5 0.495413 0.790698
102 YAP 0.495413 0.781609
103 3OD 0.495327 0.843373
104 1ZZ 0.495327 0.758242
105 FYA 0.495327 0.767442
106 00A 0.495238 0.772727
107 MAP 0.495146 0.802326
108 A22 0.495146 0.809524
109 ATF 0.49505 0.790698
110 ALF ADP 0.49505 0.741573
111 ADP ALF 0.49505 0.741573
112 SAH 0.494949 0.689655
113 SFG 0.494845 0.674419
114 YLP 0.491228 0.741935
115 MYR AMP 0.490741 0.73913
116 25A 0.490385 0.797619
117 5SV 0.490385 0.744444
118 SMM 0.490196 0.677419
119 VO4 ADP 0.490196 0.788235
120 ADP VO4 0.490196 0.788235
121 S7M 0.490196 0.681319
122 SAM 0.49 0.681319
123 S4M 0.489362 0.642105
124 6RE 0.48913 0.648352
125 AMP DBH 0.486486 0.758621
126 9SN 0.486239 0.764045
127 PR8 0.485981 0.747253
128 WAQ 0.485981 0.772727
129 A1R 0.485714 0.772727
130 ADQ 0.485714 0.8
131 EEM 0.485149 0.645161
132 NEC 0.483871 0.690476
133 ARG AMP 0.482456 0.712766
134 JB6 0.481481 0.793103
135 SAI 0.48 0.662921
136 2VA 0.479592 0.738095
137 A3N 0.478723 0.686047
138 J7C 0.478723 0.655556
139 YLC 0.478632 0.758242
140 YLB 0.478632 0.741935
141 7MC 0.478632 0.78022
142 TYR AMP 0.477477 0.770115
143 ADP BMA 0.476636 0.77907
144 A3S 0.474227 0.72619
145 A7D 0.474227 0.697674
146 TAD 0.473684 0.795455
147 GJV 0.473684 0.641304
148 0UM 0.471698 0.652174
149 ALF ADP 3PG 0.470085 0.736264
150 TYM 0.470085 0.790698
151 AF3 ADP 3PG 0.470085 0.736264
152 LA8 ALF 3PG 0.470085 0.736264
153 LAQ 0.469565 0.777778
154 7C5 0.469027 0.715909
155 MAO 0.46875 0.706522
156 DSH 0.468085 0.655556
157 BIS 0.46789 0.772727
158 SXZ 0.46789 0.681319
159 COD 0.467213 0.755319
160 LPA AMP 0.465517 0.758242
161 SO8 0.465347 0.729412
162 25L 0.463636 0.809524
163 K15 0.462963 0.638298
164 AYB 0.46281 0.734043
165 ZAS 0.462366 0.689655
166 GTA 0.46087 0.777778
167 4UV 0.460177 0.781609
168 NAD IBO 0.459016 0.781609
169 A A 0.458716 0.776471
170 TXE 0.457627 0.793103
171 OMR 0.457627 0.769231
172 AHZ 0.456897 0.758242
173 MHZ 0.454545 0.652632
174 YLA 0.454545 0.723404
175 AP0 0.453782 0.784091
176 62X 0.453704 0.625
177 A3G 0.452632 0.717647
178 5AD 0.452381 0.666667
179 AFH 0.452174 0.755556
180 4UU 0.452174 0.781609
181 3AM 0.451613 0.761905
182 TXD 0.449153 0.793103
183 4UW 0.449153 0.775281
184 6V0 0.449153 0.784091
185 NAX 0.449153 0.766667
186 NXX 0.449153 0.811765
187 DND 0.449153 0.811765
188 IOT 0.446281 0.715789
189 7D5 0.445652 0.724138
190 G3A 0.443478 0.784091
191 ATP A A A 0.442478 0.785714
192 G5P 0.439655 0.784091
193 AR6 AR6 0.439655 0.776471
194 CNA 0.439024 0.811765
195 A2P 0.438776 0.783133
196 A3P 0.438776 0.795181
197 YLY 0.4375 0.734043
198 NAI 0.436975 0.793103
199 UP5 0.436975 0.802326
200 VRT 0.436893 0.712644
201 A3D 0.436508 0.821429
202 GEK 0.435185 0.704545
203 3NZ 0.432432 0.724138
204 Y3J 0.431818 0.630952
205 T5A 0.430894 0.76087
206 NAQ 0.430769 0.784091
207 7D7 0.430233 0.647059
208 BT5 0.428571 0.734043
209 A5D 0.427184 0.72619
210 A4P 0.42623 0.726316
211 D3Y 0.425926 0.709302
212 2AM 0.425532 0.77381
213 KB1 0.424779 0.634409
214 KH3 0.423729 0.631579
215 FB0 0.423358 0.714286
216 S8M 0.422018 0.704545
217 NAD 0.420635 0.809524
218 ADJ 0.419355 0.731183
219 V3L 0.419048 0.797619
220 6IA 0.419048 0.717391
221 594 0.418605 0.8125
222 4TC 0.418033 0.784091
223 UPA 0.418033 0.793103
224 2A5 0.417476 0.758621
225 N0B 0.416667 0.723404
226 PPS 0.415094 0.915663
227 AAT 0.415094 0.641304
228 7D3 0.414141 0.747126
229 ATR 0.413462 0.795181
230 PAP 0.413462 0.807229
231 OVE 0.412371 0.788235
232 NAE 0.412214 0.802326
233 7D4 0.411765 0.747126
234 2SA 0.411215 0.790698
235 NAJ PZO 0.410853 0.764045
236 4TA 0.409449 0.731183
237 BTX 0.409449 0.741935
238 NAJ PYZ 0.409091 0.766667
239 139 0.408 0.766667
240 IXN 0.407407 0.84375
241 J1D 0.40625 0.708738
242 DZD 0.40625 0.775281
243 AMP NAD 0.406015 0.790698
244 BS5 0.404762 0.797872
245 590 0.404412 0.822917
246 A2R 0.40367 0.809524
247 NVA 2AD 0.4 0.689655
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3PD2; Ligand: A3S; Similar sites found: 4
This union binding pocket(no: 1) in the query (biounit: 3pd2.bio1) has 46 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4NBI D3Y 0.0000042 0.40202 2.04082
2 1GPM AMP 0.01869 0.43287 5.44218
3 2BLF MSS 0.01602 0.41148 10.2041
4 3FD5 AP2 0.02141 0.40841 15.6463
Pocket No.: 2; Query (leader) PDB : 3PD2; Ligand: A3S; Similar sites found: 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 P-value (APoc) PS_Score (APoc) Sequence Similarity
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