Receptor
PDB id Resolution Class Description Source Keywords
4RRG 1.93 Å EC: 6.1.1.3 EDITING DOMAIN OF THREONYL-TRNA SYNTHETASE FROM METHANOCOCCU JANNASCHII WITH L-THR3AA METHANOCALDOCOCCUS JANNASCHII 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
A3T A:501;
B:201;
C:201;
Valid;
Valid;
Valid;
none;
none;
none;
Kd = 3875.9 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
4RRG 1.93 Å EC: 6.1.1.3 EDITING DOMAIN OF THREONYL-TRNA SYNTHETASE FROM METHANOCOCCU JANNASCHII WITH L-THR3AA METHANOCALDOCOCCUS JANNASCHII 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 (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 7 families.
1 4RRF Kd = 555.6 uM A3S C13 H19 N7 O5 c1nc(c2c(n....
2 4RRG Kd = 3875.9 uM A3T C14 H21 N7 O5 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: A3T; Similar ligands found: 196
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 VRT 0.544444 0.926471
10 8QN 0.536842 0.835616
11 NVA 2AD 0.533333 0.913043
12 XYA 0.533333 0.968254
13 RAB 0.533333 0.968254
14 ADN 0.533333 0.968254
15 6RE 0.52381 0.808219
16 NEC 0.517647 0.907692
17 54H 0.515789 0.72619
18 VMS 0.515789 0.72619
19 5CD 0.512821 0.892308
20 A4D 0.512821 0.9375
21 J7C 0.511628 0.819444
22 A5A 0.510638 0.743902
23 5AL 0.5 0.835616
24 7D7 0.5 0.848485
25 5N5 0.5 0.9375
26 5X8 0.494505 0.867647
27 A 0.494118 0.819444
28 AMP 0.494118 0.819444
29 EP4 0.493827 0.855072
30 GJV 0.488636 0.797297
31 3DH 0.488095 0.880597
32 M2T 0.487805 0.830986
33 DTA 0.487805 0.84058
34 5AD 0.486842 0.857143
35 LSS 0.484848 0.701149
36 52H 0.484536 0.717647
37 EEM 0.484211 0.8
38 SA8 0.483871 0.821918
39 3AM 0.482353 0.805556
40 MTA 0.481928 0.880597
41 TXA 0.480392 0.837838
42 53H 0.479592 0.717647
43 SFG 0.478261 0.852941
44 ABM 0.477273 0.821918
45 7D5 0.47619 0.76
46 9ZA 0.474747 0.792208
47 9ZD 0.474747 0.792208
48 SSA 0.474227 0.738095
49 S7M 0.474227 0.8
50 SAM 0.473684 0.8
51 PAJ 0.47 0.818182
52 0UM 0.47 0.835616
53 CA0 0.467391 0.824324
54 A3P 0.466667 0.794521
55 BA3 0.466667 0.821918
56 AHX 0.465347 0.805195
57 DAL AMP 0.464646 0.835616
58 5CA 0.464646 0.738095
59 SAH 0.463158 0.842857
60 SAI 0.463158 0.830986
61 Y3J 0.4625 0.80303
62 B4P 0.461538 0.821918
63 5AS 0.461538 0.717647
64 ADP 0.461538 0.821918
65 AP5 0.461538 0.821918
66 LEU LMS 0.460784 0.693182
67 A2D 0.460674 0.821918
68 LMS 0.45977 0.719512
69 ZAS 0.45977 0.816901
70 SMM 0.459184 0.769231
71 SRP 0.459184 0.813333
72 AQP 0.457447 0.821918
73 5FA 0.457447 0.821918
74 AN2 0.456522 0.810811
75 SON 0.456522 0.789474
76 S4M 0.455556 0.769231
77 DSZ 0.455446 0.717647
78 SRA 0.454545 0.776316
79 OVE 0.454545 0.786667
80 2AM 0.453488 0.819444
81 NB8 0.451923 0.782051
82 PTJ 0.451923 0.782051
83 AU1 0.451613 0.8
84 MHZ 0.451613 0.759494
85 M33 0.451613 0.835616
86 NVA LMS 0.45098 0.693182
87 AP2 0.450549 0.789474
88 A12 0.450549 0.789474
89 48N 0.45045 0.805195
90 QQX 0.448276 0.736842
91 G5A 0.447917 0.717647
92 ACP 0.446809 0.8
93 HEJ 0.446809 0.821918
94 ATP 0.446809 0.821918
95 A3N 0.444444 0.895522
96 GAP 0.443299 0.824324
97 ACQ 0.443299 0.8
98 GSU 0.442308 0.697674
99 KAA 0.442308 0.693182
100 2A5 0.442105 0.776316
101 APC 0.442105 0.789474
102 PRX 0.442105 0.8
103 AMO 0.441176 0.813333
104 NSS 0.441176 0.717647
105 AT4 0.44086 0.789474
106 A7D 0.44086 0.882353
107 7D3 0.43956 0.763158
108 3AD 0.439024 0.921875
109 SXZ 0.438095 0.8
110 ME8 0.438095 0.753086
111 PAP 0.4375 0.808219
112 62X 0.436893 0.769231
113 ADX 0.43617 0.740741
114 XAH 0.435185 0.753086
115 YSA 0.435185 0.697674
116 MAO 0.434783 0.759494
117 A2P 0.434783 0.780822
118 AOC 0.433333 0.880597
119 DSH 0.433333 0.819444
120 K15 0.432692 0.789474
121 50T 0.431579 0.810811
122 6YZ 0.43 0.8
123 LAD 0.428571 0.772152
124 T99 0.428571 0.789474
125 TAT 0.428571 0.789474
126 ANP 0.428571 0.8
127 4AD 0.427184 0.802632
128 AR6 0.427083 0.821918
129 APR 0.427083 0.821918
130 QQY 0.426966 0.746667
131 ACK 0.426966 0.788732
132 YLP 0.424779 0.756098
133 FYA 0.424528 0.786667
134 9K8 0.424528 0.693182
135 PPS 0.424242 0.719512
136 7MD 0.423423 0.775
137 DLL 0.423077 0.810811
138 SAP 0.42268 0.779221
139 ADV 0.42268 0.789474
140 RBY 0.42268 0.789474
141 AD9 0.42268 0.8
142 ADP PO3 0.42268 0.819444
143 AGS 0.42268 0.779221
144 3L1 0.421687 0.880597
145 3D1 0.421687 0.880597
146 8X1 0.421569 0.693182
147 7D4 0.421053 0.763158
148 KB1 0.420561 0.786667
149 KH3 0.419643 0.802632
150 OAD 0.419048 0.849315
151 GEK 0.417476 0.808219
152 OOB 0.417476 0.810811
153 YLC 0.413793 0.775
154 YLB 0.413793 0.756098
155 A1R 0.413462 0.792208
156 FA5 0.412844 0.789474
157 YAP 0.412844 0.779221
158 8PZ 0.412844 0.717647
159 1ZZ 0.411215 0.753086
160 JB6 0.411215 0.746835
161 3OD 0.411215 0.849315
162 ARG AMP 0.410714 0.743902
163 00A 0.409524 0.769231
164 J7V 0.409449 0.729412
165 F2R 0.408333 0.756098
166 A5D 0.408163 0.84058
167 ATR 0.408163 0.794521
168 A22 0.407767 0.810811
169 MAP 0.407767 0.779221
170 CC5 0.407407 0.90625
171 MYR AMP 0.407407 0.753086
172 ALF ADP 0.405941 0.75641
173 ATF 0.405941 0.789474
174 ADP ALF 0.405941 0.75641
175 9X8 0.40566 0.802632
176 3UK 0.40566 0.8
177 WSA 0.405172 0.705882
178 COD 0.404959 0.75
179 5SV 0.403846 0.759494
180 25A 0.403846 0.797297
181 ETB 0.403226 0.75
182 DCA 0.403226 0.741176
183 ADP VO4 0.401961 0.786667
184 VO4 ADP 0.401961 0.786667
185 PR8 0.401869 0.7625
186 WAQ 0.401869 0.769231
187 B5V 0.401869 0.789474
188 P5A 0.401869 0.685393
189 7MC 0.401709 0.777778
190 B5Y 0.4 0.802632
191 A3R 0.4 0.792208
192 V3L 0.4 0.797297
193 3AT 0.4 0.797297
194 AYB 0.4 0.746988
195 B5M 0.4 0.802632
196 ADQ 0.4 0.824324
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4RRG; Ligand: A3T; 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: 4rrg.bio2) has 41 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 4RRG; Ligand: A3T; 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: 4rrg.bio1) has 41 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 4RRG; Ligand: A3T; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 4rrg.bio1) has 36 residues
No: Leader PDB Ligand Sequence Similarity
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