Receptor
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
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
A3S A:500;
B:501;
Valid;
Valid;
none;
none;
Kd = 3.4 uM
353.334 C13 H19 N7 O5 c1nc(...
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 = 239.2 uM A3S C13 H19 N7 O5 c1nc(c2c(n....
11 4RRG Kd = 1538.5 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 = 239.2 uM A3S C13 H19 N7 O5 c1nc(c2c(n....
25 4RRG Kd = 1538.5 uM A3T C14 H21 N7 O5 C[C@H]([C@....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: A3S; Similar ligands found: 232
No: Ligand ECFP6 Tc MDL keys Tc
1 A3S 1 1
2 A3T 0.763158 0.953846
3 D3Y 0.743902 0.969697
4 A3G 0.716216 0.984615
5 3NZ 0.701149 0.927536
6 J4G 0.626374 0.815789
7 VRT 0.574713 0.941176
8 2VA 0.55814 0.925373
9 SSA 0.549451 0.771084
10 RAB 0.547945 0.953125
11 ADN 0.547945 0.953125
12 XYA 0.547945 0.953125
13 SO8 0.539326 0.911765
14 AHX 0.536842 0.842105
15 6RE 0.536585 0.847222
16 NVA 2AD 0.52809 0.927536
17 A4D 0.526316 0.923077
18 5CD 0.526316 0.878788
19 NWW 0.526316 0.859375
20 5X8 0.522727 0.910448
21 SRP 0.516129 0.851351
22 7D7 0.513514 0.835821
23 5N5 0.513158 0.923077
24 EEM 0.51087 0.813333
25 0UM 0.510417 0.849315
26 AMP 0.506024 0.808219
27 A 0.506024 0.808219
28 J7C 0.505882 0.859155
29 SFG 0.505618 0.895522
30 5CA 0.505263 0.771084
31 DTA 0.5 0.828571
32 GJV 0.5 0.835616
33 M2T 0.5 0.794521
34 LSS 0.494845 0.712644
35 SA8 0.494505 0.835616
36 N5O 0.494118 0.939394
37 NEC 0.494118 0.865672
38 3AM 0.493976 0.794521
39 GLU GMC 0.489583 0.876712
40 53H 0.489583 0.689655
41 A5A 0.489362 0.714286
42 SAI 0.48913 0.871429
43 SAH 0.48913 0.884058
44 7D5 0.487805 0.75
45 EP4 0.4875 0.816901
46 S7M 0.484211 0.813333
47 SAM 0.483871 0.813333
48 N5A 0.482759 0.909091
49 AMP MG 0.482353 0.819444
50 3DH 0.481928 0.84058
51 NWQ 0.481928 0.833333
52 5AD 0.48 0.815385
53 DSZ 0.479592 0.75
54 54H 0.479167 0.697674
55 VMS 0.479167 0.697674
56 5AL 0.478723 0.8
57 CA0 0.477778 0.813333
58 A3P 0.477273 0.783784
59 MTA 0.47561 0.84058
60 NB8 0.475248 0.818182
61 Y3J 0.474359 0.791045
62 QA7 0.474227 0.769231
63 TSB 0.474227 0.72619
64 KG4 0.472527 0.813333
65 ADP 0.47191 0.810811
66 A2D 0.471264 0.810811
67 ABM 0.471264 0.786667
68 45A 0.471264 0.786667
69 LMS 0.470588 0.710843
70 QQY 0.470588 0.736842
71 ZAS 0.470588 0.830986
72 SMM 0.46875 0.782051
73 8LH 0.46875 0.802632
74 SON 0.466667 0.802632
75 AN2 0.466667 0.8
76 KAA 0.465347 0.724138
77 GSU 0.465347 0.729412
78 OVE 0.465116 0.776316
79 SRA 0.465116 0.766234
80 AMO 0.464646 0.851351
81 2AM 0.464286 0.808219
82 52H 0.463918 0.689655
83 V2G 0.463158 0.794872
84 HZ2 0.462963 0.888889
85 AU1 0.461538 0.789474
86 A12 0.460674 0.802632
87 BA3 0.460674 0.810811
88 AP2 0.460674 0.802632
89 QQX 0.458824 0.727273
90 KL2 0.457831 0.756757
91 G5A 0.457447 0.75
92 XAH 0.457143 0.7875
93 KYE 0.457143 0.815789
94 YSA 0.457143 0.729412
95 ACP 0.456522 0.813333
96 ATP 0.456522 0.810811
97 HEJ 0.456522 0.810811
98 B4P 0.455556 0.810811
99 AP5 0.455556 0.810811
100 5AS 0.455556 0.689655
101 9ZA 0.454545 0.759494
102 9ZD 0.454545 0.759494
103 HY8 0.454545 0.888889
104 8QN 0.454545 0.8
105 A3N 0.454545 0.882353
106 ACK 0.453488 0.777778
107 ACQ 0.452632 0.813333
108 GAP 0.452632 0.813333
109 AQP 0.451613 0.810811
110 5FA 0.451613 0.810811
111 APC 0.451613 0.802632
112 LAD 0.45098 0.807692
113 AT4 0.450549 0.779221
114 ADP MG 0.450549 0.808219
115 A7D 0.450549 0.897059
116 ADP BEF 0.450549 0.808219
117 NSS 0.45 0.75
118 3AD 0.45 0.9375
119 PAJ 0.45 0.78481
120 7D3 0.449438 0.753247
121 S4M 0.449438 0.782051
122 8LE 0.447917 0.769231
123 PAP 0.446809 0.797297
124 ME8 0.446602 0.765432
125 M33 0.445652 0.8
126 MHZ 0.445652 0.772152
127 ADX 0.445652 0.731707
128 NVA LMS 0.445545 0.704545
129 DLL 0.445545 0.8
130 62X 0.445545 0.782051
131 ARG AMP 0.444444 0.777778
132 7MD 0.444444 0.810127
133 8LQ 0.444444 0.802632
134 A2P 0.444444 0.77027
135 DAL AMP 0.444444 0.8
136 ATF 0.443299 0.779221
137 AOC 0.443182 0.867647
138 DSH 0.443182 0.859155
139 BEF ADP 0.442105 0.786667
140 K15 0.441176 0.802632
141 50T 0.44086 0.8
142 QXP 0.44 0.73494
143 6YZ 0.438776 0.813333
144 T99 0.4375 0.779221
145 TAT 0.4375 0.779221
146 ANP 0.4375 0.789474
147 R2V 0.436893 0.73494
148 NWZ 0.43617 0.859155
149 PRX 0.43617 0.766234
150 2A5 0.43617 0.789474
151 APR 0.43617 0.810811
152 AR6 0.43617 0.810811
153 4AD 0.435644 0.84
154 HQG 0.434343 0.8
155 FA5 0.433962 0.826667
156 PPS 0.43299 0.710843
157 FYA 0.432692 0.824324
158 PTJ 0.432692 0.75
159 TXA 0.432692 0.802632
160 YLP 0.432432 0.768293
161 3D1 0.432099 0.924242
162 3L1 0.432099 0.924242
163 AGS 0.431579 0.769231
164 APC MG 0.431579 0.786667
165 ATP MG 0.431579 0.808219
166 ADV 0.431579 0.802632
167 ADP PO3 0.431579 0.808219
168 AD9 0.431579 0.789474
169 RBY 0.431579 0.802632
170 JNT 0.431373 0.837838
171 7D4 0.430108 0.753247
172 8X1 0.43 0.724138
173 MAO 0.428571 0.772152
174 ANP MG 0.428571 0.776316
175 KB1 0.428571 0.824324
176 KXW 0.427273 0.861111
177 KH3 0.427273 0.815789
178 QXG 0.427184 0.72619
179 LEU LMS 0.427184 0.72093
180 OOB 0.425743 0.8
181 GEK 0.425743 0.847222
182 H1Q 0.425532 0.797297
183 WSA 0.424779 0.738095
184 V47 0.424242 0.852941
185 WAQ 0.423077 0.782051
186 NX8 0.42268 0.873239
187 V3L 0.42268 0.786667
188 ADQ 0.421569 0.813333
189 A1R 0.421569 0.828947
190 KYB 0.421569 0.813333
191 YLC 0.421053 0.7875
192 0XU 0.421053 0.867647
193 YLB 0.421053 0.768293
194 8PZ 0.420561 0.75
195 48N 0.419643 0.794872
196 SXZ 0.419048 0.813333
197 CC5 0.417722 0.921875
198 00A 0.417476 0.759494
199 ATR 0.416667 0.783784
200 A5D 0.416667 0.828571
201 MAP 0.415842 0.769231
202 A22 0.415842 0.8
203 KY2 0.415842 0.813333
204 F2R 0.415254 0.790123
205 ALF ADP 0.414141 0.746835
206 VO4 ADP 0.414141 0.766234
207 ADP BMA 0.413462 0.813333
208 3UK 0.413462 0.789474
209 OAD 0.413462 0.813333
210 25A 0.411765 0.786667
211 CUU 0.410526 0.810811
212 YLA 0.410256 0.768293
213 P5A 0.409524 0.715909
214 B5V 0.409524 0.779221
215 PR8 0.409524 0.797468
216 SFB 0.408696 0.744186
217 B5M 0.407407 0.769231
218 AYB 0.40678 0.759036
219 3OD 0.40566 0.813333
220 9K8 0.40566 0.666667
221 1ZZ 0.40566 0.722892
222 5F1 0.404762 0.823529
223 RP1 0.404494 0.74026
224 SP1 0.404494 0.74026
225 AAT 0.40404 0.835616
226 EU9 0.403509 0.73494
227 MYR AMP 0.401869 0.722892
228 DQV 0.401786 0.824324
229 TYM 0.4 0.826667
230 9X8 0.4 0.769231
231 A6D 0.4 0.734177
232 AV2 0.4 0.74026
Similar Ligands (3D)
Ligand no: 1; Ligand: A3S; Similar ligands found: 7
No: Ligand Similarity coefficient
1 3GP 0.9055
2 101 0.9011
3 103 0.8898
4 TMP 0.8725
5 EV7 0.8723
6 T3P 0.8601
7 DG 0.8581
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: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 3pd2.bio1) has 46 residues
No: Leader PDB Ligand Sequence Similarity
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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