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 = 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: A3G; Similar ligands found: 218
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 5CD 0.56338 0.865672
11 G5A 0.552941 0.761905
12 6RE 0.551282 0.861111
13 A4D 0.541667 0.909091
14 A 0.538462 0.797297
15 AMP 0.538462 0.797297
16 J7C 0.5375 0.873239
17 DTA 0.533333 0.816901
18 M2T 0.533333 0.783784
19 7D7 0.528571 0.823529
20 3AM 0.525641 0.783784
21 NEC 0.525 0.880597
22 EP4 0.52 0.830986
23 2VA 0.517647 0.911765
24 5AD 0.514286 0.80303
25 3DH 0.512821 0.828571
26 SRA 0.5125 0.75641
27 GJV 0.512195 0.849315
28 MTA 0.506494 0.828571
29 A3P 0.506024 0.773333
30 CA0 0.505882 0.802632
31 NVA 2AD 0.505747 0.914286
32 VRT 0.5 0.927536
33 ABM 0.5 0.776316
34 A2D 0.5 0.8
35 LMS 0.5 0.702381
36 7D5 0.5 0.74026
37 5X8 0.5 0.897059
38 SO8 0.5 0.898551
39 ADP 0.5 0.8
40 ZAS 0.5 0.84507
41 SON 0.494118 0.792208
42 S4M 0.493976 0.794872
43 OVE 0.493827 0.766234
44 2AM 0.493671 0.797297
45 AU1 0.488372 0.779221
46 A12 0.488095 0.792208
47 BA3 0.488095 0.8
48 AP2 0.488095 0.792208
49 DSH 0.487805 0.873239
50 Y3J 0.486486 0.779412
51 ATP 0.482759 0.8
52 HEJ 0.482759 0.8
53 SFG 0.482759 0.882353
54 ACP 0.482759 0.802632
55 B4P 0.482353 0.8
56 AP5 0.482353 0.8
57 5AS 0.482353 0.701149
58 A3N 0.481928 0.897059
59 3AD 0.48 0.923077
60 GAP 0.477778 0.826667
61 ACQ 0.477778 0.802632
62 AQP 0.477273 0.8
63 APC 0.477273 0.792208
64 5FA 0.477273 0.8
65 AN2 0.476744 0.789474
66 AT4 0.476744 0.769231
67 PAJ 0.473684 0.775
68 5AL 0.472527 0.789474
69 EEM 0.472527 0.802632
70 PAP 0.47191 0.786667
71 SAP 0.47191 0.759494
72 AGS 0.47191 0.759494
73 SA8 0.47191 0.849315
74 ADX 0.471264 0.722892
75 M33 0.471264 0.789474
76 MHZ 0.471264 0.78481
77 A2P 0.470588 0.76
78 AOC 0.46988 0.855072
79 QQX 0.469136 0.717949
80 AHX 0.46875 0.831169
81 A5A 0.467391 0.705882
82 SAI 0.466667 0.859155
83 SAH 0.466667 0.871429
84 50T 0.465909 0.789474
85 ACK 0.463415 0.767123
86 QQY 0.463415 0.727273
87 9ZD 0.463158 0.75
88 9ZA 0.463158 0.75
89 SRP 0.462366 0.84
90 6YZ 0.462366 0.802632
91 S7M 0.462366 0.802632
92 SSA 0.462366 0.761905
93 ANP 0.461538 0.779221
94 TAT 0.461538 0.769231
95 T99 0.461538 0.769231
96 SAM 0.461538 0.802632
97 APR 0.460674 0.8
98 PRX 0.460674 0.75641
99 AR6 0.460674 0.8
100 7D3 0.458824 0.74359
101 0UM 0.458333 0.863014
102 52H 0.457447 0.681818
103 VMS 0.457447 0.689655
104 54H 0.457447 0.689655
105 PPS 0.456522 0.702381
106 ADP PO3 0.455556 0.797297
107 ADV 0.455556 0.792208
108 AD9 0.455556 0.779221
109 RBY 0.455556 0.792208
110 NB8 0.454545 0.807692
111 SXZ 0.454545 0.802632
112 PTJ 0.454545 0.740741
113 TXA 0.454545 0.792208
114 DLL 0.453608 0.789474
115 MAO 0.453488 0.78481
116 TSB 0.452632 0.717647
117 8X1 0.452632 0.735632
118 53H 0.452632 0.681818
119 5CA 0.452632 0.761905
120 DAL AMP 0.452632 0.789474
121 ATF 0.451613 0.769231
122 LEU LMS 0.44898 0.696629
123 OOB 0.447917 0.789474
124 8QN 0.447917 0.789474
125 SMM 0.446809 0.772152
126 CC5 0.445946 0.907692
127 V3L 0.445652 0.776316
128 LAD 0.444444 0.820513
129 PR8 0.444444 0.810127
130 KAA 0.444444 0.735632
131 2A5 0.444444 0.779221
132 DSZ 0.443299 0.741176
133 AMO 0.443299 0.84
134 LSS 0.443299 0.704545
135 4AD 0.443299 0.828947
136 NSS 0.443299 0.741176
137 A7D 0.443182 0.884058
138 3D1 0.441558 0.910448
139 3L1 0.441558 0.910448
140 AAT 0.44086 0.849315
141 A5D 0.43956 0.816901
142 ATR 0.43956 0.773333
143 NVA LMS 0.438776 0.696629
144 00A 0.438776 0.75
145 7D4 0.438202 0.74359
146 A22 0.4375 0.789474
147 MAP 0.4375 0.759494
148 XAH 0.436893 0.8
149 ADP ALF 0.43617 0.7375
150 ALF ADP 0.43617 0.7375
151 ADP BMA 0.434343 0.802632
152 OAD 0.434343 0.802632
153 3UK 0.434343 0.779221
154 GEK 0.43299 0.835616
155 25A 0.43299 0.776316
156 ADP VO4 0.431579 0.766234
157 VO4 ADP 0.431579 0.766234
158 B5V 0.43 0.769231
159 P5A 0.43 0.727273
160 WAQ 0.43 0.772152
161 GSU 0.43 0.72093
162 RP1 0.428571 0.730769
163 SP1 0.428571 0.730769
164 A1R 0.428571 0.842105
165 0XU 0.428571 0.855072
166 ADQ 0.428571 0.802632
167 8PZ 0.427184 0.741176
168 YLP 0.425926 0.780488
169 ME8 0.425743 0.756098
170 1ZZ 0.425743 0.714286
171 9K8 0.425743 0.659341
172 3OD 0.425743 0.802632
173 ARG AMP 0.424528 0.790123
174 7MD 0.424528 0.822785
175 62X 0.424242 0.794872
176 YSA 0.423077 0.72093
177 MYR AMP 0.421569 0.714286
178 2BA 0.420455 0.77027
179 CMP 0.420455 0.780822
180 K15 0.42 0.815789
181 9X8 0.42 0.759494
182 A A A 0.42 0.789474
183 5SV 0.418367 0.719512
184 9SN 0.417476 0.740741
185 7C5 0.415094 0.8
186 3AT 0.414894 0.8
187 YLB 0.414414 0.780488
188 A3R 0.414141 0.842105
189 B5Y 0.413462 0.759494
190 B5M 0.413462 0.759494
191 YAP 0.413462 0.805195
192 FA5 0.413462 0.815789
193 5F1 0.4125 0.811594
194 A2R 0.412371 0.789474
195 FYA 0.411765 0.813333
196 J7V 0.409836 0.712644
197 NAX 0.409091 0.7875
198 25L 0.407767 0.789474
199 KB1 0.407767 0.837838
200 4YB 0.407407 0.704545
201 KH3 0.407407 0.828947
202 101 0.406977 0.763158
203 AV2 0.40625 0.730769
204 A6D 0.405941 0.725
205 NA7 0.405941 0.792208
206 TYR AMP 0.40566 0.805195
207 4UV 0.40566 0.759494
208 COD 0.405172 0.77381
209 AHZ 0.40367 0.714286
210 DCA 0.403361 0.764706
211 ETB 0.403361 0.77381
212 DA 0.402299 0.763158
213 D5M 0.402299 0.763158
214 A A 0.401961 0.776316
215 YLC 0.401786 0.8
216 7MC 0.401786 0.802469
217 AFX 0.4 0.75
218 ARJ 0.4 0.861538
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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