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: 209
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 ADN 0.588235 0.938462
7 RAB 0.588235 0.938462
8 XYA 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 AMP MG 0.506173 0.776316
30 A3P 0.506024 0.773333
31 CA0 0.505882 0.802632
32 A2D 0.5 0.8
33 5X8 0.5 0.897059
34 ZAS 0.5 0.84507
35 7D5 0.5 0.74026
36 ABM 0.5 0.776316
37 ADP 0.5 0.8
38 VRT 0.5 0.927536
39 SO8 0.5 0.898551
40 SON 0.494118 0.792208
41 S4M 0.493976 0.794872
42 OVE 0.493827 0.766234
43 2AM 0.493671 0.797297
44 AU1 0.488372 0.779221
45 BA3 0.488095 0.8
46 A12 0.488095 0.792208
47 AP2 0.488095 0.792208
48 DSH 0.487805 0.873239
49 Y3J 0.486486 0.779412
50 ATP 0.482759 0.8
51 ACP 0.482759 0.802632
52 SFG 0.482759 0.882353
53 5AS 0.482353 0.701149
54 AP5 0.482353 0.8
55 B4P 0.482353 0.8
56 A3N 0.481928 0.897059
57 3AD 0.48 0.923077
58 GAP 0.477778 0.826667
59 ACQ 0.477778 0.802632
60 AQP 0.477273 0.8
61 5FA 0.477273 0.8
62 APC 0.477273 0.792208
63 AN2 0.476744 0.789474
64 PAJ 0.473684 0.775
65 EEM 0.472527 0.802632
66 5AL 0.472527 0.789474
67 SA8 0.47191 0.849315
68 SAP 0.47191 0.759494
69 AGS 0.47191 0.759494
70 PAP 0.47191 0.786667
71 ADP MG 0.471264 0.766234
72 MHZ 0.471264 0.78481
73 M33 0.471264 0.789474
74 ADX 0.471264 0.722892
75 A2P 0.470588 0.76
76 AOC 0.46988 0.855072
77 QQX 0.469136 0.717949
78 AHX 0.46875 0.831169
79 A5A 0.467391 0.705882
80 SAH 0.466667 0.871429
81 SAI 0.466667 0.859155
82 ADP BEF 0.465909 0.746835
83 50T 0.465909 0.789474
84 BEF ADP 0.465909 0.746835
85 QQY 0.463415 0.727273
86 ACK 0.463415 0.767123
87 SSA 0.462366 0.761905
88 SRP 0.462366 0.84
89 S7M 0.462366 0.802632
90 ANP 0.461538 0.779221
91 SAM 0.461538 0.802632
92 TAT 0.461538 0.769231
93 APR 0.460674 0.8
94 AR6 0.460674 0.8
95 PRX 0.460674 0.75641
96 7D3 0.458824 0.74359
97 0UM 0.458333 0.863014
98 54H 0.457447 0.689655
99 52H 0.457447 0.681818
100 VMS 0.457447 0.689655
101 PPS 0.456522 0.702381
102 AD9 0.455556 0.779221
103 NVA 2AD 0.455556 0.871429
104 RBY 0.455556 0.792208
105 ADP PO3 0.455556 0.797297
106 ADV 0.455556 0.792208
107 TXA 0.454545 0.792208
108 PTJ 0.454545 0.740741
109 NB8 0.454545 0.807692
110 SXZ 0.454545 0.802632
111 DLL 0.453608 0.789474
112 MAO 0.453488 0.78481
113 53H 0.452632 0.681818
114 TSB 0.452632 0.717647
115 DAL AMP 0.452632 0.789474
116 5CA 0.452632 0.761905
117 ATF 0.451613 0.769231
118 ATP MG 0.450549 0.766234
119 8QN 0.447917 0.789474
120 OOB 0.447917 0.789474
121 SMM 0.446809 0.772152
122 ANP MG 0.446809 0.7375
123 CC5 0.445946 0.907692
124 V3L 0.445652 0.776316
125 2A5 0.444444 0.779221
126 KAA 0.444444 0.735632
127 PR8 0.444444 0.810127
128 LAD 0.444444 0.820513
129 DSZ 0.443299 0.741176
130 4AD 0.443299 0.828947
131 AMO 0.443299 0.84
132 LSS 0.443299 0.704545
133 NSS 0.443299 0.741176
134 A7D 0.443182 0.884058
135 3D1 0.441558 0.910448
136 3L1 0.441558 0.910448
137 AAT 0.44086 0.849315
138 A5D 0.43956 0.816901
139 ATR 0.43956 0.773333
140 00A 0.438776 0.75
141 NVA LMS 0.438776 0.685393
142 7D4 0.438202 0.74359
143 A22 0.4375 0.789474
144 MAP 0.4375 0.759494
145 XAH 0.436893 0.8
146 ADP ALF 0.43617 0.7375
147 ALF ADP 0.43617 0.7375
148 ADP BMA 0.434343 0.802632
149 3UK 0.434343 0.779221
150 OAD 0.434343 0.802632
151 LEU LMS 0.434343 0.685393
152 25A 0.43299 0.776316
153 GEK 0.43299 0.835616
154 ADP VO4 0.431579 0.766234
155 VO4 ADP 0.431579 0.766234
156 P5A 0.43 0.727273
157 WAQ 0.43 0.772152
158 GSU 0.43 0.72093
159 SP1 0.428571 0.730769
160 RP1 0.428571 0.730769
161 0XU 0.428571 0.855072
162 A1R 0.428571 0.842105
163 ADQ 0.428571 0.802632
164 YLP 0.425926 0.780488
165 ME8 0.425743 0.756098
166 1ZZ 0.425743 0.714286
167 3OD 0.425743 0.802632
168 7MD 0.424528 0.822785
169 62X 0.424242 0.794872
170 YSA 0.423077 0.72093
171 MYR AMP 0.421569 0.714286
172 2BA 0.420455 0.77027
173 CMP 0.420455 0.780822
174 K15 0.42 0.815789
175 A A A 0.42 0.789474
176 5SV 0.418367 0.719512
177 9SN 0.417476 0.740741
178 ARG AMP 0.416667 0.790123
179 7C5 0.415094 0.8
180 3AT 0.414894 0.8
181 YLB 0.414414 0.780488
182 FA5 0.413462 0.815789
183 YAP 0.413462 0.805195
184 5F1 0.4125 0.811594
185 A2R 0.412371 0.789474
186 FYA 0.411765 0.813333
187 J7V 0.409836 0.712644
188 TYR AMP 0.409524 0.792208
189 NAX 0.409091 0.7875
190 25L 0.407767 0.789474
191 KB1 0.407767 0.837838
192 4YB 0.407407 0.704545
193 KH3 0.407407 0.828947
194 101 0.406977 0.763158
195 AV2 0.40625 0.730769
196 A6D 0.405941 0.725
197 NA7 0.405941 0.792208
198 4UV 0.40566 0.759494
199 COD 0.405172 0.77381
200 AHZ 0.40367 0.714286
201 DCA 0.403361 0.764706
202 ETB 0.403361 0.77381
203 DA 0.402299 0.763158
204 D5M 0.402299 0.763158
205 A A 0.401961 0.776316
206 YLC 0.401786 0.8
207 7MC 0.401786 0.802469
208 AFX 0.4 0.75
209 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: 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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