Receptor
PDB id Resolution Class Description Source Keywords
2HL1 2.25 Å EC: 6.1.1.3 CRYSTAL STRUCTURE OF THE EDITING DOMAIN OF THREONYL-TRNA SYNTHETASE FROM PYROCOCCUS ABYSSI IN COMPLEX WITH SERYL-3'-A MINOADENOSINE PYROCOCCUS ABYSSI TRANSLATION EDITING AMINOACYL-TRNA SYNTHETASE ENZYME MECHANISM ENANTIOSELECTIVITY LIGASE
Ref.: POST-TRANSFER EDITING MECHANISM OF A D-AMINOACYL-TRNA DEACYLASE-LIKE DOMAIN IN THREONYL-TRNA SYNTHETASE FROM ARCHAEA EMBO J. V. 25 4152 2006
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;
submit data
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 = 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: A3S; Similar ligands found: 191
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 VRT 0.574713 0.941176
7 2VA 0.55814 0.925373
8 SSA 0.549451 0.771084
9 RAB 0.547945 0.953125
10 XYA 0.547945 0.953125
11 ADN 0.547945 0.953125
12 SO8 0.539326 0.911765
13 AHX 0.536842 0.842105
14 6RE 0.536585 0.847222
15 A4D 0.526316 0.923077
16 5CD 0.526316 0.878788
17 5X8 0.522727 0.910448
18 SRP 0.516129 0.851351
19 7D7 0.513514 0.835821
20 5N5 0.513158 0.923077
21 EEM 0.51087 0.813333
22 0UM 0.510417 0.849315
23 AMP 0.506024 0.808219
24 A 0.506024 0.808219
25 J7C 0.505882 0.859155
26 SFG 0.505618 0.895522
27 5CA 0.505263 0.771084
28 GJV 0.5 0.835616
29 M2T 0.5 0.794521
30 DTA 0.5 0.828571
31 LSS 0.494845 0.712644
32 SA8 0.494505 0.835616
33 NEC 0.494118 0.865672
34 3AM 0.493976 0.794521
35 53H 0.489583 0.689655
36 A5A 0.489362 0.714286
37 SAI 0.48913 0.871429
38 SAH 0.48913 0.884058
39 7D5 0.487805 0.75
40 EP4 0.4875 0.816901
41 S7M 0.484211 0.813333
42 SAM 0.483871 0.813333
43 3DH 0.481928 0.84058
44 5AD 0.48 0.815385
45 DSZ 0.479592 0.75
46 54H 0.479167 0.697674
47 VMS 0.479167 0.697674
48 5AL 0.478723 0.8
49 CA0 0.477778 0.813333
50 A3P 0.477273 0.783784
51 AMP MG 0.476744 0.786667
52 MTA 0.47561 0.84058
53 NB8 0.475248 0.818182
54 Y3J 0.474359 0.791045
55 TSB 0.474227 0.72619
56 ADP 0.47191 0.810811
57 A2D 0.471264 0.810811
58 ABM 0.471264 0.786667
59 QQY 0.470588 0.736842
60 ZAS 0.470588 0.830986
61 SMM 0.46875 0.782051
62 AN2 0.466667 0.8
63 SON 0.466667 0.802632
64 KAA 0.465347 0.724138
65 GSU 0.465347 0.729412
66 SRA 0.465116 0.766234
67 OVE 0.465116 0.776316
68 AMO 0.464646 0.851351
69 2AM 0.464286 0.808219
70 52H 0.463918 0.689655
71 AU1 0.461538 0.789474
72 AP2 0.460674 0.802632
73 BA3 0.460674 0.810811
74 A12 0.460674 0.802632
75 QQX 0.458824 0.727273
76 G5A 0.457447 0.75
77 XAH 0.457143 0.7875
78 YSA 0.457143 0.729412
79 ATP 0.456522 0.810811
80 ACP 0.456522 0.813333
81 AP5 0.455556 0.810811
82 5AS 0.455556 0.689655
83 B4P 0.455556 0.810811
84 A3N 0.454545 0.882353
85 8QN 0.454545 0.8
86 ACK 0.453488 0.777778
87 ACQ 0.452632 0.813333
88 GAP 0.452632 0.813333
89 5FA 0.451613 0.810811
90 APC 0.451613 0.802632
91 AQP 0.451613 0.810811
92 LAD 0.45098 0.807692
93 A7D 0.450549 0.897059
94 PAJ 0.45 0.78481
95 NSS 0.45 0.75
96 3AD 0.45 0.9375
97 7D3 0.449438 0.753247
98 S4M 0.449438 0.782051
99 PAP 0.446809 0.797297
100 NVA 2AD 0.446809 0.884058
101 ME8 0.446602 0.765432
102 ADP MG 0.445652 0.776316
103 MHZ 0.445652 0.772152
104 M33 0.445652 0.8
105 ADX 0.445652 0.731707
106 NVA LMS 0.445545 0.693182
107 62X 0.445545 0.782051
108 DLL 0.445545 0.8
109 7MD 0.444444 0.810127
110 A2P 0.444444 0.77027
111 DAL AMP 0.444444 0.8
112 ATF 0.443299 0.779221
113 DSH 0.443182 0.859155
114 AOC 0.443182 0.867647
115 LEU LMS 0.441176 0.693182
116 K15 0.441176 0.802632
117 BEF ADP 0.44086 0.75641
118 50T 0.44086 0.8
119 ADP BEF 0.44086 0.75641
120 ANP 0.4375 0.789474
121 TAT 0.4375 0.779221
122 APR 0.43617 0.810811
123 AR6 0.43617 0.810811
124 2A5 0.43617 0.789474
125 PRX 0.43617 0.766234
126 4AD 0.435644 0.84
127 FA5 0.433962 0.826667
128 YAP 0.433962 0.815789
129 PPS 0.43299 0.710843
130 TXA 0.432692 0.802632
131 FYA 0.432692 0.824324
132 PTJ 0.432692 0.75
133 YLP 0.432432 0.768293
134 3D1 0.432099 0.924242
135 3L1 0.432099 0.924242
136 AGS 0.431579 0.769231
137 ADV 0.431579 0.802632
138 RBY 0.431579 0.802632
139 SAP 0.431579 0.769231
140 AD9 0.431579 0.789474
141 ADP PO3 0.431579 0.808219
142 7D4 0.430108 0.753247
143 MAO 0.428571 0.772152
144 KB1 0.428571 0.824324
145 KH3 0.427273 0.815789
146 ATP MG 0.427083 0.776316
147 OOB 0.425743 0.8
148 GEK 0.425743 0.847222
149 WSA 0.424779 0.738095
150 ANP MG 0.424242 0.746835
151 WAQ 0.423077 0.782051
152 V3L 0.42268 0.786667
153 ADQ 0.421569 0.813333
154 A1R 0.421569 0.828947
155 YLC 0.421053 0.7875
156 YLB 0.421053 0.768293
157 0XU 0.421053 0.867647
158 48N 0.419643 0.794872
159 SXZ 0.419048 0.813333
160 CC5 0.417722 0.921875
161 00A 0.417476 0.759494
162 ATR 0.416667 0.783784
163 A5D 0.416667 0.828571
164 A22 0.415842 0.8
165 MAP 0.415842 0.769231
166 ALF ADP 0.414141 0.746835
167 ADP ALF 0.414141 0.746835
168 3UK 0.413462 0.789474
169 OAD 0.413462 0.813333
170 ADP BMA 0.413462 0.813333
171 25A 0.411765 0.786667
172 ARG AMP 0.410714 0.777778
173 YLA 0.410256 0.768293
174 ADP VO4 0.41 0.776316
175 VO4 ADP 0.41 0.776316
176 PR8 0.409524 0.797468
177 P5A 0.409524 0.715909
178 SFB 0.408696 0.744186
179 AYB 0.40678 0.759036
180 1ZZ 0.40566 0.722892
181 3OD 0.40566 0.813333
182 5F1 0.404762 0.823529
183 SP1 0.404494 0.74026
184 RP1 0.404494 0.74026
185 AAT 0.40404 0.835616
186 TYR AMP 0.40367 0.802632
187 MYR AMP 0.401869 0.722892
188 AV2 0.4 0.74026
189 A A A 0.4 0.8
190 A6D 0.4 0.734177
191 TYM 0.4 0.826667
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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