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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: 61
This union binding pocket(no: 1) in the query (biounit: 4rrg.bio2) has 41 residues
No: Leader PDB Ligand Sequence Similarity
1 4NBI D3Y None
2 4F8L AES None
3 4R2M ANP None
4 1T57 FMN None
5 2VSU V55 None
6 2BOS GLA GAL GLC None
7 2BOS GLA GAL GLC NBU None
8 2VSS V55 None
9 3COW 52H None
10 1SBR VIB None
11 4MCC 21X 1.41844
12 4RUS NDG 1.41844
13 4RUS NAG 1.41844
14 4CNE SAH 2.12766
15 3W9F I3P 2.12766
16 4JAL SAH 2.12766
17 1NB9 RBF 2.12766
18 1NB9 ADP 2.12766
19 5H4S RAM 2.83688
20 3G5N PB2 2.83688
21 4JWJ SAH 2.83688
22 5A7Y SAH 3.5461
23 1GPM AMP 3.5461
24 4CNG SAH 3.5461
25 4GYS MLI 3.5461
26 1ZX5 LFR 3.5461
27 4D4U FUC GAL NAG 3.5461
28 2C3H GLC GLC 4.08163
29 5AHW CMP 4.25532
30 5ULP KB1 4.25532
31 6CGN DA 4.25532
32 1CT9 AMP 4.96454
33 3HGM ATP 4.96454
34 4RPM HXC 4.96454
35 4JWF SAH 4.96454
36 4OUE IPT 4.96454
37 1P9P SAH 5.67376
38 1Q19 SSC 5.67376
39 1FDJ 13P 5.67376
40 1KOR ARG 6
41 1KOR ANP 6
42 1KOR SIN 6
43 1YXM ADE 6.38298
44 4JWH SAH 6.38298
45 5G5G MCN 6.38298
46 1L0I PSR 6.41026
47 4C2C ALA ALA ALA 7.0922
48 3IWD M2T 8.06452
49 1MJH ATP 8.51064
50 2C5S AMP 8.51064
51 2YY8 MTA 9.21986
52 2YY8 SAM 9.21986
53 1OBD AMP 9.92908
54 6EMU SAM 9.92908
55 2ZX2 RAM 11.3475
56 2X2M X2M 12.766
57 5VN0 NAI 12.766
58 3RK1 ATP 18.4397
59 4IGH ORO 19.1489
60 4IGH FMN 19.1489
61 4IGH 1EA 19.1489
Pocket No.: 2; Query (leader) PDB : 4RRG; Ligand: A3T; Similar sites found with APoc: 16
This union binding pocket(no: 2) in the query (biounit: 4rrg.bio1) has 41 residues
No: Leader PDB Ligand Sequence Similarity
1 5A89 FMN None
2 5UI2 SUC 1.41844
3 2DXU BT5 2.12766
4 5ZI9 FLC 2.83688
5 5FJJ MAN 4.25532
6 2OG2 MLI 4.96454
7 3B9Q MLI 4.96454
8 6AR9 3L4 5.67376
9 5TDF ADE 7.0922
10 3Q3H UDP 7.0922
11 5CIC 51R 8.33333
12 3G5S GSH 9.21986
13 1Y7P RIP 9.92908
14 5O2N FLC 11.3475
15 5MRH Q9Z 13.4752
16 3C3D FO1 14.1844
Pocket No.: 3; Query (leader) PDB : 4RRG; Ligand: A3T; Similar sites found with APoc: 19
This union binding pocket(no: 3) in the query (biounit: 4rrg.bio1) has 36 residues
No: Leader PDB Ligand Sequence Similarity
1 4YG0 GAL NAG GAL BGC None
2 1L5Y BEF None
3 1XUJ BOZ 3.5461
4 5L2Z 70C 4.25532
5 1EFV AMP 4.25532
6 1EFV FAD 4.25532
7 4GKV NAD 4.25532
8 3TKI S25 4.96454
9 4CLI 5P8 4.96454
10 2VAP GDP 6.38298
11 2VVM PRO 8.51064
12 5X20 AOT 8.51064
13 3AIA SAM 8.51064
14 1O94 AMP 8.51064
15 3G5S FAD 9.21986
16 5H5F SAM 12.0567
17 1FEC FAD 14.1844
18 3OII SAH 14.8936
19 2X3F APC 21.2766
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