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: 187
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 RAB 0.533333 0.968254
12 XYA 0.533333 0.968254
13 ADN 0.533333 0.968254
14 6RE 0.52381 0.808219
15 NEC 0.517647 0.907692
16 VMS 0.515789 0.72619
17 54H 0.515789 0.72619
18 A4D 0.512821 0.9375
19 5CD 0.512821 0.892308
20 J7C 0.511628 0.819444
21 A5A 0.510638 0.743902
22 7D7 0.5 0.848485
23 5N5 0.5 0.9375
24 5AL 0.5 0.835616
25 5X8 0.494505 0.867647
26 A 0.494118 0.819444
27 AMP 0.494118 0.819444
28 EP4 0.493827 0.855072
29 GJV 0.488636 0.797297
30 3DH 0.488095 0.880597
31 DTA 0.487805 0.84058
32 M2T 0.487805 0.830986
33 5AD 0.486842 0.857143
34 LSS 0.484848 0.701149
35 52H 0.484536 0.717647
36 EEM 0.484211 0.8
37 SA8 0.483871 0.821918
38 3AM 0.482353 0.805556
39 MTA 0.481928 0.880597
40 TXA 0.480392 0.837838
41 53H 0.479592 0.717647
42 SFG 0.478261 0.852941
43 ABM 0.477273 0.821918
44 7D5 0.47619 0.76
45 SSA 0.474227 0.738095
46 S7M 0.474227 0.8
47 SAM 0.473684 0.8
48 0UM 0.47 0.835616
49 PAJ 0.47 0.818182
50 CA0 0.467391 0.824324
51 BA3 0.466667 0.821918
52 A3P 0.466667 0.794521
53 AMP MG 0.465909 0.797297
54 AHX 0.465347 0.805195
55 DAL AMP 0.464646 0.835616
56 5CA 0.464646 0.738095
57 SAH 0.463158 0.842857
58 SAI 0.463158 0.830986
59 Y3J 0.4625 0.80303
60 5AS 0.461538 0.717647
61 AP5 0.461538 0.821918
62 ADP 0.461538 0.821918
63 B4P 0.461538 0.821918
64 LEU LMS 0.460784 0.701149
65 A2D 0.460674 0.821918
66 ZAS 0.45977 0.816901
67 SRP 0.459184 0.813333
68 SMM 0.459184 0.769231
69 AQP 0.457447 0.821918
70 5FA 0.457447 0.821918
71 AN2 0.456522 0.810811
72 SON 0.456522 0.789474
73 S4M 0.455556 0.769231
74 DSZ 0.455446 0.717647
75 SRA 0.454545 0.776316
76 OVE 0.454545 0.786667
77 2AM 0.453488 0.819444
78 NVA 2AD 0.452632 0.897059
79 PTJ 0.451923 0.782051
80 NB8 0.451923 0.782051
81 MHZ 0.451613 0.759494
82 M33 0.451613 0.835616
83 AU1 0.451613 0.8
84 NVA LMS 0.45098 0.701149
85 A12 0.450549 0.789474
86 AP2 0.450549 0.789474
87 48N 0.45045 0.805195
88 QQX 0.448276 0.736842
89 G5A 0.447917 0.717647
90 ATP 0.446809 0.821918
91 ACP 0.446809 0.8
92 A3N 0.444444 0.895522
93 GAP 0.443299 0.824324
94 ACQ 0.443299 0.8
95 GSU 0.442308 0.697674
96 KAA 0.442308 0.693182
97 PRX 0.442105 0.8
98 APC 0.442105 0.789474
99 2A5 0.442105 0.776316
100 NSS 0.441176 0.717647
101 AMO 0.441176 0.813333
102 A7D 0.44086 0.882353
103 7D3 0.43956 0.763158
104 3AD 0.439024 0.921875
105 SXZ 0.438095 0.8
106 ME8 0.438095 0.753086
107 PAP 0.4375 0.808219
108 62X 0.436893 0.769231
109 ADX 0.43617 0.740741
110 ADP MG 0.43617 0.786667
111 YSA 0.435185 0.697674
112 XAH 0.435185 0.753086
113 A2P 0.434783 0.780822
114 MAO 0.434783 0.759494
115 DSH 0.433333 0.819444
116 AOC 0.433333 0.880597
117 K15 0.432692 0.789474
118 BEF ADP 0.431579 0.766234
119 50T 0.431579 0.810811
120 ADP BEF 0.431579 0.766234
121 LAD 0.428571 0.772152
122 ANP 0.428571 0.8
123 TAT 0.428571 0.789474
124 4AD 0.427184 0.802632
125 AR6 0.427083 0.821918
126 APR 0.427083 0.821918
127 QQY 0.426966 0.746667
128 ACK 0.426966 0.788732
129 YLP 0.424779 0.756098
130 FYA 0.424528 0.786667
131 PPS 0.424242 0.719512
132 7MD 0.423423 0.775
133 DLL 0.423077 0.810811
134 RBY 0.42268 0.789474
135 ADV 0.42268 0.789474
136 SAP 0.42268 0.779221
137 AGS 0.42268 0.779221
138 ADP PO3 0.42268 0.819444
139 AD9 0.42268 0.8
140 3D1 0.421687 0.880597
141 3L1 0.421687 0.880597
142 7D4 0.421053 0.763158
143 KB1 0.420561 0.786667
144 KH3 0.419643 0.802632
145 OAD 0.419048 0.849315
146 ATP MG 0.418367 0.786667
147 OOB 0.417476 0.810811
148 GEK 0.417476 0.808219
149 ARG AMP 0.415929 0.743902
150 ANP MG 0.415842 0.75641
151 YLB 0.413793 0.756098
152 YLC 0.413793 0.775
153 A1R 0.413462 0.792208
154 YAP 0.412844 0.779221
155 FA5 0.412844 0.789474
156 3OD 0.411215 0.849315
157 1ZZ 0.411215 0.753086
158 JB6 0.411215 0.746835
159 00A 0.409524 0.769231
160 J7V 0.409449 0.729412
161 TYR AMP 0.409091 0.789474
162 ATR 0.408163 0.794521
163 A5D 0.408163 0.84058
164 A22 0.407767 0.810811
165 MAP 0.407767 0.779221
166 MYR AMP 0.407407 0.753086
167 CC5 0.407407 0.90625
168 ATF 0.405941 0.789474
169 ADP ALF 0.405941 0.75641
170 ALF ADP 0.405941 0.75641
171 3UK 0.40566 0.8
172 WSA 0.405172 0.705882
173 COD 0.404959 0.75
174 5SV 0.403846 0.759494
175 25A 0.403846 0.797297
176 DCA 0.403226 0.741176
177 ETB 0.403226 0.75
178 ADP VO4 0.401961 0.786667
179 VO4 ADP 0.401961 0.786667
180 PR8 0.401869 0.7625
181 WAQ 0.401869 0.769231
182 P5A 0.401869 0.685393
183 7MC 0.401709 0.777778
184 ADQ 0.4 0.824324
185 V3L 0.4 0.797297
186 3AT 0.4 0.797297
187 AYB 0.4 0.746988
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4RRG; Ligand: A3T; Similar sites found: 23
This union binding pocket(no: 1) in the query (biounit: 4rrg.bio2) has 41 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4NBI D3Y 0.00000005454 0.62872 None
2 2BOS GLA GAL GLC 0.02019 0.40634 None
3 2BOS GLA GAL GLC NBU 0.02052 0.4063 None
4 4MCC 21X 0.002148 0.43303 1.41844
5 1NB9 ADP 0.02237 0.4004 2.12766
6 1NB9 RBF 0.02237 0.4004 2.12766
7 5UDS ATP 0.01031 0.41123 2.83688
8 1GPM AMP 0.008703 0.42327 3.5461
9 4CNG SAH 0.008859 0.40711 3.5461
10 5A7Y SAH 0.001081 0.40496 3.5461
11 4D4U FUC GAL NAG 0.02044 0.40078 3.5461
12 3HGM ATP 0.002995 0.41985 4.96454
13 1P9P SAH 0.001086 0.43702 5.67376
14 1KOR SIN 0.02841 0.42275 6
15 1KOR ARG 0.02841 0.42275 6
16 1KOR ANP 0.02899 0.42275 6
17 1YXM ADE 0.0169 0.41698 6.38298
18 4JWH SAH 0.005105 0.41479 6.38298
19 5G5G MCN 0.02112 0.40057 6.38298
20 1MJH ATP 0.006114 0.40636 8.51064
21 2YY8 SAM 0.002543 0.42105 9.21986
22 2YY8 MTA 0.001897 0.40477 9.21986
23 3DLG GWE 0.01189 0.43028 9.92908
Pocket No.: 2; Query (leader) PDB : 4RRG; Ligand: A3T; Similar sites found: 5
This union binding pocket(no: 2) in the query (biounit: 4rrg.bio1) has 41 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4F8L AES 0.009931 0.4288 None
2 5A89 FMN 0.01766 0.40988 None
3 5FJJ MAN 0.004727 0.43606 4.25532
4 3Q3H UDP 0.01506 0.40324 7.0922
5 5MRH Q9Z 0.01952 0.40178 13.4752
Pocket No.: 3; Query (leader) PDB : 4RRG; Ligand: A3T; Similar sites found: 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 P-value (APoc) PS_Score (APoc) Sequence Similarity
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