Receptor
PDB id Resolution Class Description Source Keywords
4RRA 1.7 Å EC: 6.1.1.3 N-TERMINAL EDITING DOMAIN OF THREONYL-TRNA SYNTHETASE FROM A PERNIX WITH L-THR3AA (SNAPSHOT 1) AEROPYRUM PERNIX K1 DTD-LIKE FOLD PROOFREADING LIGASE
Ref.: SPECIFICITY AND CATALYSIS HARDWIRED AT THE RNA-PROT INTERFACE IN A TRANSLATIONAL PROOFREADING ENZYME. NAT COMMUN V. 6 7552 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MG A:202;
Invalid;
none;
submit data
24.305 Mg [Mg+2...
A3T A:201;
Valid;
none;
Kd = 13.4 uM
367.36 C14 H21 N7 O5 C[C@H...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4RR7 1.86 Å EC: 6.1.1.3 N-TERMINAL EDITING DOMAIN OF THREONYL-TRNA SYNTHETASE FROM A PERNIX WITH L-SER3AA (SNAPSHOT 2) AEROPYRUM PERNIX K1 DTD-LIKE FOLD PROOFREADING LIGASE
Ref.: SPECIFICITY AND CATALYSIS HARDWIRED AT THE RNA-PROT INTERFACE IN A TRANSLATIONAL PROOFREADING ENZYME. NAT COMMUN V. 6 7552 2015
Members (14)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 7 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@....
70% Homology Family (14)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 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@....
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: A3T; Similar ligands found: 229
No: Ligand ECFP6 Tc MDL keys Tc
1 A3T 1 1
2 A3S 0.763158 0.953846
3 A3G 0.697368 0.939394
4 D3Y 0.666667 0.925373
5 3NZ 0.648352 0.913043
6 2VA 0.619048 0.969231
7 SO8 0.597701 0.954545
8 TSB 0.576087 0.756098
9 J4G 0.5625 0.779221
10 VRT 0.544444 0.926471
11 8QN 0.536842 0.835616
12 NVA 2AD 0.533333 0.913043
13 RAB 0.533333 0.968254
14 XYA 0.533333 0.968254
15 ADN 0.533333 0.968254
16 NWW 0.532468 0.873016
17 6RE 0.52381 0.808219
18 NEC 0.517647 0.907692
19 VMS 0.515789 0.72619
20 54H 0.515789 0.72619
21 A4D 0.512821 0.9375
22 5CD 0.512821 0.892308
23 J7C 0.511628 0.819444
24 A5A 0.510638 0.743902
25 GLU GMC 0.510417 0.863014
26 NWQ 0.506024 0.875
27 N5O 0.5 0.895522
28 5AL 0.5 0.835616
29 5N5 0.5 0.9375
30 7D7 0.5 0.848485
31 QA7 0.494845 0.802632
32 5X8 0.494505 0.867647
33 A 0.494118 0.819444
34 AMP 0.494118 0.819444
35 EP4 0.493827 0.855072
36 GJV 0.488636 0.797297
37 N5A 0.488636 0.865672
38 3DH 0.488095 0.880597
39 M2T 0.487805 0.830986
40 DTA 0.487805 0.84058
41 5AD 0.486842 0.857143
42 LSS 0.484848 0.701149
43 52H 0.484536 0.717647
44 EEM 0.484211 0.8
45 SA8 0.483871 0.821918
46 3AM 0.482353 0.805556
47 MTA 0.481928 0.880597
48 TXA 0.480392 0.837838
49 8LQ 0.479592 0.813333
50 53H 0.479592 0.717647
51 SFG 0.478261 0.852941
52 45A 0.477273 0.821918
53 ABM 0.477273 0.821918
54 7D5 0.47619 0.76
55 9ZA 0.474747 0.792208
56 9ZD 0.474747 0.792208
57 8LH 0.474227 0.837838
58 SSA 0.474227 0.738095
59 S7M 0.474227 0.8
60 SAM 0.473684 0.8
61 AMP MG 0.471264 0.830986
62 PAJ 0.47 0.818182
63 0UM 0.47 0.835616
64 CA0 0.467391 0.824324
65 BA3 0.466667 0.821918
66 A3P 0.466667 0.794521
67 AHX 0.465347 0.805195
68 5CA 0.464646 0.738095
69 DAL AMP 0.464646 0.835616
70 SAI 0.463158 0.830986
71 SAH 0.463158 0.842857
72 Y3J 0.4625 0.80303
73 KG4 0.462366 0.824324
74 ADP 0.461538 0.821918
75 B4P 0.461538 0.821918
76 AP5 0.461538 0.821918
77 5AS 0.461538 0.717647
78 A2D 0.460674 0.821918
79 ZAS 0.45977 0.816901
80 LMS 0.45977 0.719512
81 SRP 0.459184 0.813333
82 SMM 0.459184 0.769231
83 AQP 0.457447 0.821918
84 5FA 0.457447 0.821918
85 SON 0.456522 0.789474
86 AN2 0.456522 0.810811
87 S4M 0.455556 0.769231
88 DSZ 0.455446 0.717647
89 OVE 0.454545 0.786667
90 SRA 0.454545 0.776316
91 8LE 0.453608 0.802632
92 V2G 0.453608 0.782051
93 2AM 0.453488 0.819444
94 PTJ 0.451923 0.782051
95 NB8 0.451923 0.782051
96 M33 0.451613 0.835616
97 MHZ 0.451613 0.759494
98 AU1 0.451613 0.8
99 NVA LMS 0.45098 0.693182
100 A12 0.450549 0.789474
101 AP2 0.450549 0.789474
102 48N 0.45045 0.805195
103 QQX 0.448276 0.736842
104 G5A 0.447917 0.717647
105 ATP 0.446809 0.821918
106 ACP 0.446809 0.8
107 HEJ 0.446809 0.821918
108 LEU LMS 0.446602 0.709302
109 A3N 0.444444 0.895522
110 GAP 0.443299 0.824324
111 ACQ 0.443299 0.8
112 GSU 0.442308 0.697674
113 KAA 0.442308 0.693182
114 NWZ 0.442105 0.819444
115 2A5 0.442105 0.776316
116 APC 0.442105 0.789474
117 PRX 0.442105 0.8
118 HZ2 0.441441 0.849315
119 AMO 0.441176 0.813333
120 NSS 0.441176 0.717647
121 A7D 0.44086 0.882353
122 AT4 0.44086 0.789474
123 ADP BEF 0.44086 0.819444
124 ADP MG 0.44086 0.819444
125 7D3 0.43956 0.763158
126 3AD 0.439024 0.921875
127 SXZ 0.438095 0.8
128 ME8 0.438095 0.753086
129 PAP 0.4375 0.808219
130 62X 0.436893 0.769231
131 ADX 0.43617 0.740741
132 YSA 0.435185 0.697674
133 XAH 0.435185 0.753086
134 KYE 0.435185 0.779221
135 A2P 0.434783 0.780822
136 MAO 0.434783 0.759494
137 HY8 0.433628 0.849315
138 DSH 0.433333 0.819444
139 AOC 0.433333 0.880597
140 K15 0.432692 0.789474
141 50T 0.431579 0.810811
142 QXP 0.431373 0.743902
143 KL2 0.430233 0.767123
144 6YZ 0.43 0.8
145 V47 0.43 0.865672
146 T99 0.428571 0.789474
147 R2V 0.428571 0.743902
148 NX8 0.428571 0.833333
149 TAT 0.428571 0.789474
150 LAD 0.428571 0.772152
151 ANP 0.428571 0.8
152 4AD 0.427184 0.802632
153 AR6 0.427083 0.821918
154 APR 0.427083 0.821918
155 QQY 0.426966 0.746667
156 ACK 0.426966 0.788732
157 YLP 0.424779 0.756098
158 9K8 0.424528 0.693182
159 FYA 0.424528 0.786667
160 PPS 0.424242 0.719512
161 7MD 0.423423 0.775
162 DLL 0.423077 0.810811
163 JNT 0.423077 0.824324
164 AD9 0.42268 0.8
165 AGS 0.42268 0.779221
166 RBY 0.42268 0.789474
167 ADP PO3 0.42268 0.819444
168 ADV 0.42268 0.789474
169 ATP MG 0.42268 0.819444
170 APC MG 0.42268 0.797297
171 3D1 0.421687 0.880597
172 3L1 0.421687 0.880597
173 8X1 0.421569 0.693182
174 7D4 0.421053 0.763158
175 KB1 0.420561 0.786667
176 ANP MG 0.42 0.786667
177 KH3 0.419643 0.802632
178 OAD 0.419048 0.849315
179 QXG 0.419048 0.73494
180 BEF ADP 0.418367 0.797297
181 OOB 0.417476 0.810811
182 GEK 0.417476 0.808219
183 H1Q 0.416667 0.808219
184 CUU 0.416667 0.797297
185 YLC 0.413793 0.775
186 YLB 0.413793 0.756098
187 A1R 0.413462 0.792208
188 KYB 0.413462 0.776316
189 FA5 0.412844 0.789474
190 8PZ 0.412844 0.717647
191 HQG 0.411765 0.810811
192 1ZZ 0.411215 0.753086
193 3OD 0.411215 0.849315
194 JB6 0.411215 0.746835
195 ARG AMP 0.410714 0.743902
196 00A 0.409524 0.769231
197 J7V 0.409449 0.729412
198 F2R 0.408333 0.756098
199 A5D 0.408163 0.84058
200 ATR 0.408163 0.794521
201 MAP 0.407767 0.779221
202 KY2 0.407767 0.776316
203 A22 0.407767 0.810811
204 CC5 0.407407 0.90625
205 MYR AMP 0.407407 0.753086
206 KXW 0.40708 0.821918
207 VO4 ADP 0.405941 0.776316
208 ATF 0.405941 0.789474
209 ALF ADP 0.405941 0.75641
210 3UK 0.40566 0.8
211 9X8 0.40566 0.802632
212 WSA 0.405172 0.705882
213 COD 0.404959 0.75
214 25A 0.403846 0.797297
215 5SV 0.403846 0.759494
216 ETB 0.403226 0.75
217 DCA 0.403226 0.741176
218 P5A 0.401869 0.685393
219 WAQ 0.401869 0.769231
220 B5V 0.401869 0.789474
221 PR8 0.401869 0.7625
222 7MC 0.401709 0.777778
223 V3L 0.4 0.797297
224 3AT 0.4 0.797297
225 AYB 0.4 0.746988
226 B5Y 0.4 0.802632
227 B5M 0.4 0.802632
228 ADQ 0.4 0.824324
229 A3R 0.4 0.792208
Similar Ligands (3D)
Ligand no: 1; Ligand: A3T; Similar ligands found: 1
No: Ligand Similarity coefficient
1 EV7 0.8552
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4RR7; 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: 4rr7.bio1) has 22 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 4RR7; 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: 4rr7.bio1) has 22 residues
No: Leader PDB Ligand Sequence Similarity
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