Receptor
PDB id Resolution Class Description Source Keywords
3PD4 2.4 Å EC: 6.1.1.3 CRYSTAL STRUCTURE OF THE EDITING DOMAIN OF THREONYL-TRNA SYN FROM PYROCOCCUS ABYSSI IN COMPLEX WITH GLYCYL-3'-AMINOADENO 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
A3G A:500;
B:501;
Valid;
Valid;
none;
none;
Kd = 33.3 uM
323.308 C12 H17 N7 O4 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: A3G; Similar ligands found: 254
No: Ligand ECFP6 Tc MDL keys Tc
1 A3G 1 1
2 A3S 0.716216 0.984615
3 A3T 0.697368 0.939394
4 D3Y 0.623529 0.955224
5 3NZ 0.588889 0.914286
6 RAB 0.588235 0.938462
7 XYA 0.588235 0.938462
8 ADN 0.588235 0.938462
9 5N5 0.571429 0.938462
10 NWW 0.56338 0.846154
11 5CD 0.56338 0.865672
12 G5A 0.552941 0.761905
13 6RE 0.551282 0.861111
14 A4D 0.541667 0.909091
15 A 0.538462 0.797297
16 AMP 0.538462 0.797297
17 J4G 0.537634 0.805195
18 J7C 0.5375 0.873239
19 M2T 0.533333 0.783784
20 DTA 0.533333 0.816901
21 N5A 0.530864 0.924242
22 7D7 0.528571 0.823529
23 3AM 0.525641 0.783784
24 NEC 0.525 0.880597
25 N5O 0.525 0.954545
26 EP4 0.52 0.830986
27 2VA 0.517647 0.911765
28 5AD 0.514286 0.80303
29 3DH 0.512821 0.828571
30 NWQ 0.512821 0.820895
31 SRA 0.5125 0.75641
32 AMP MG 0.5125 0.808219
33 GJV 0.512195 0.849315
34 MTA 0.506494 0.828571
35 A3P 0.506024 0.773333
36 CA0 0.505882 0.802632
37 NVA 2AD 0.505747 0.914286
38 7D5 0.5 0.74026
39 45A 0.5 0.776316
40 ADP 0.5 0.8
41 VRT 0.5 0.927536
42 A2D 0.5 0.8
43 ABM 0.5 0.776316
44 SO8 0.5 0.898551
45 LMS 0.5 0.702381
46 KG4 0.5 0.802632
47 ZAS 0.5 0.84507
48 5X8 0.5 0.897059
49 SON 0.494118 0.792208
50 S4M 0.493976 0.794872
51 OVE 0.493827 0.766234
52 2AM 0.493671 0.797297
53 HQG 0.48913 0.789474
54 V2G 0.488889 0.807692
55 AU1 0.488372 0.779221
56 A12 0.488095 0.792208
57 AP2 0.488095 0.792208
58 BA3 0.488095 0.8
59 DSH 0.487805 0.873239
60 Y3J 0.486486 0.779412
61 ACP 0.482759 0.802632
62 HEJ 0.482759 0.8
63 ATP 0.482759 0.8
64 SFG 0.482759 0.882353
65 B4P 0.482353 0.8
66 5AS 0.482353 0.701149
67 AP5 0.482353 0.8
68 A3N 0.481928 0.897059
69 3AD 0.48 0.923077
70 ACQ 0.477778 0.802632
71 GAP 0.477778 0.826667
72 APC 0.477273 0.792208
73 5FA 0.477273 0.8
74 AQP 0.477273 0.8
75 ADP MG 0.476744 0.797297
76 AN2 0.476744 0.789474
77 ADP BEF 0.476744 0.797297
78 AT4 0.476744 0.769231
79 PAJ 0.473684 0.775
80 EEM 0.472527 0.802632
81 5AL 0.472527 0.789474
82 8LE 0.472527 0.759494
83 PAP 0.47191 0.786667
84 AGS 0.47191 0.759494
85 SA8 0.47191 0.849315
86 MHZ 0.471264 0.78481
87 ADX 0.471264 0.722892
88 M33 0.471264 0.789474
89 A2P 0.470588 0.76
90 AOC 0.46988 0.855072
91 QQX 0.469136 0.717949
92 AHX 0.46875 0.831169
93 KL2 0.468354 0.746667
94 QA7 0.468085 0.759494
95 A5A 0.467391 0.705882
96 SAH 0.466667 0.871429
97 SAI 0.466667 0.859155
98 50T 0.465909 0.789474
99 QQY 0.463415 0.727273
100 ACK 0.463415 0.767123
101 9ZA 0.463158 0.75
102 9ZD 0.463158 0.75
103 SSA 0.462366 0.761905
104 8LH 0.462366 0.792208
105 SRP 0.462366 0.84
106 6YZ 0.462366 0.802632
107 S7M 0.462366 0.802632
108 ANP 0.461538 0.779221
109 TAT 0.461538 0.769231
110 T99 0.461538 0.769231
111 SAM 0.461538 0.802632
112 PRX 0.460674 0.75641
113 APR 0.460674 0.8
114 AR6 0.460674 0.8
115 NWZ 0.460674 0.873239
116 7D3 0.458824 0.74359
117 KYB 0.458333 0.826667
118 0UM 0.458333 0.863014
119 54H 0.457447 0.689655
120 VMS 0.457447 0.689655
121 52H 0.457447 0.681818
122 PPS 0.456522 0.702381
123 ADP PO3 0.455556 0.797297
124 AD9 0.455556 0.779221
125 ADV 0.455556 0.792208
126 RBY 0.455556 0.792208
127 APC MG 0.455556 0.776316
128 ATP MG 0.455556 0.797297
129 PTJ 0.454545 0.740741
130 TXA 0.454545 0.792208
131 SXZ 0.454545 0.802632
132 NB8 0.454545 0.807692
133 DLL 0.453608 0.789474
134 MAO 0.453488 0.78481
135 8X1 0.452632 0.735632
136 GLU GMC 0.452632 0.864865
137 TSB 0.452632 0.717647
138 DAL AMP 0.452632 0.789474
139 5CA 0.452632 0.761905
140 KY2 0.452632 0.826667
141 8LQ 0.452632 0.792208
142 53H 0.452632 0.681818
143 ATF 0.451613 0.769231
144 ANP MG 0.451613 0.766234
145 BEF ADP 0.450549 0.776316
146 H1Q 0.449438 0.786667
147 LEU LMS 0.44898 0.712644
148 QXP 0.447917 0.746988
149 8QN 0.447917 0.789474
150 OOB 0.447917 0.789474
151 SMM 0.446809 0.772152
152 V47 0.446809 0.84058
153 CC5 0.445946 0.907692
154 V3L 0.445652 0.776316
155 NX8 0.445652 0.887324
156 R2V 0.444444 0.746988
157 2A5 0.444444 0.779221
158 PR8 0.444444 0.810127
159 LAD 0.444444 0.820513
160 KAA 0.444444 0.735632
161 DSZ 0.443299 0.741176
162 LSS 0.443299 0.704545
163 AMO 0.443299 0.84
164 NSS 0.443299 0.741176
165 4AD 0.443299 0.828947
166 A7D 0.443182 0.884058
167 3L1 0.441558 0.910448
168 3D1 0.441558 0.910448
169 AAT 0.44086 0.849315
170 ATR 0.43956 0.773333
171 A5D 0.43956 0.816901
172 NVA LMS 0.438776 0.696629
173 00A 0.438776 0.75
174 7D4 0.438202 0.74359
175 A22 0.4375 0.789474
176 MAP 0.4375 0.759494
177 XAH 0.436893 0.8
178 KYE 0.436893 0.828947
179 VO4 ADP 0.43617 0.75641
180 ALF ADP 0.43617 0.7375
181 OAD 0.434343 0.802632
182 ADP BMA 0.434343 0.802632
183 QXG 0.434343 0.738095
184 3UK 0.434343 0.779221
185 CUU 0.433333 0.8
186 25A 0.43299 0.776316
187 GEK 0.43299 0.835616
188 WAQ 0.43 0.772152
189 B5V 0.43 0.769231
190 P5A 0.43 0.727273
191 GSU 0.43 0.72093
192 HZ2 0.429907 0.902778
193 A1R 0.428571 0.842105
194 ADQ 0.428571 0.802632
195 0XU 0.428571 0.855072
196 SP1 0.428571 0.730769
197 RP1 0.428571 0.730769
198 8PZ 0.427184 0.741176
199 YLP 0.425926 0.780488
200 ME8 0.425743 0.756098
201 3OD 0.425743 0.802632
202 1ZZ 0.425743 0.714286
203 9K8 0.425743 0.659341
204 ARG AMP 0.424528 0.790123
205 7MD 0.424528 0.822785
206 62X 0.424242 0.794872
207 YSA 0.423077 0.72093
208 HY8 0.422018 0.902778
209 MYR AMP 0.421569 0.714286
210 CMP 0.420455 0.780822
211 2BA 0.420455 0.77027
212 K15 0.42 0.815789
213 9X8 0.42 0.759494
214 OZV 0.418367 0.8
215 5SV 0.418367 0.719512
216 9SN 0.417476 0.740741
217 KY8 0.415842 0.849315
218 K2K 0.415842 0.887324
219 7C5 0.415094 0.8
220 3AT 0.414894 0.8
221 YLB 0.414414 0.780488
222 A3R 0.414141 0.842105
223 FA5 0.413462 0.815789
224 B5M 0.413462 0.759494
225 B5Y 0.413462 0.759494
226 5F1 0.4125 0.811594
227 A2R 0.412371 0.789474
228 FYA 0.411765 0.813333
229 JNT 0.41 0.826667
230 J7V 0.409836 0.712644
231 B1U 0.409524 0.645161
232 NAX 0.409091 0.7875
233 KY5 0.407767 0.873239
234 KB1 0.407767 0.837838
235 25L 0.407767 0.789474
236 KH3 0.407407 0.828947
237 KXW 0.407407 0.875
238 4YB 0.407407 0.704545
239 101 0.406977 0.763158
240 AV2 0.40625 0.730769
241 NA7 0.405941 0.792208
242 A6D 0.405941 0.725
243 4UV 0.40566 0.759494
244 COD 0.405172 0.77381
245 AHZ 0.40367 0.714286
246 DCA 0.403361 0.764706
247 ETB 0.403361 0.77381
248 DA 0.402299 0.763158
249 D5M 0.402299 0.763158
250 7MC 0.401786 0.802469
251 YLC 0.401786 0.8
252 U4Y 0.4 0.835616
253 ARJ 0.4 0.861538
254 AFX 0.4 0.75
Similar Ligands (3D)
Ligand no: 1; Ligand: A3G; Similar ligands found: 9
No: Ligand Similarity coefficient
1 3GP 0.9375
2 T3P 0.9156
3 103 0.9146
4 C3P 0.9108
5 U3P 0.9079
6 UMF 0.9042
7 UM3 0.8976
8 NOS 0.8689
9 DBM 0.8610
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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