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Receptor
PDB id Resolution Class Description Source Keywords
4RRF 1.7 Å EC: 6.1.1.3 EDITING DOMAIN OF THREONYL-TRNA SYNTHETASE FROM METHANOCOCCU JANNASCHII WITH L-SER3AA 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
MG C:202;
D:202;
Invalid;
Invalid;
none;
none;
submit data
24.305 Mg [Mg+2...
A3S C:201;
D:201;
E:201;
F:201;
A:501;
B:201;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
none;
none;
Kd = 555.6 uM
353.334 C13 H19 N7 O5 c1nc(...
CL A:502;
Invalid;
none;
submit data
35.453 Cl [Cl-]
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: A3S; Similar ligands found: 200
No: Ligand ECFP6 Tc MDL keys Tc
1 A3S 1 1
2 A3T 0.763158 0.953846
3 D3Y 0.743902 0.969697
4 A3G 0.716216 0.984615
5 3NZ 0.701149 0.927536
6 VRT 0.574713 0.941176
7 2VA 0.55814 0.925373
8 SSA 0.549451 0.771084
9 RAB 0.547945 0.953125
10 XYA 0.547945 0.953125
11 ADN 0.547945 0.953125
12 SO8 0.539326 0.911765
13 AHX 0.536842 0.842105
14 6RE 0.536585 0.847222
15 NVA 2AD 0.52809 0.927536
16 A4D 0.526316 0.923077
17 5CD 0.526316 0.878788
18 5X8 0.522727 0.910448
19 SRP 0.516129 0.851351
20 7D7 0.513514 0.835821
21 5N5 0.513158 0.923077
22 EEM 0.51087 0.813333
23 0UM 0.510417 0.849315
24 AMP 0.506024 0.808219
25 A 0.506024 0.808219
26 J7C 0.505882 0.859155
27 SFG 0.505618 0.895522
28 5CA 0.505263 0.771084
29 GJV 0.5 0.835616
30 M2T 0.5 0.794521
31 DTA 0.5 0.828571
32 LSS 0.494845 0.712644
33 SA8 0.494505 0.835616
34 NEC 0.494118 0.865672
35 3AM 0.493976 0.794521
36 53H 0.489583 0.689655
37 A5A 0.489362 0.714286
38 SAI 0.48913 0.871429
39 SAH 0.48913 0.884058
40 7D5 0.487805 0.75
41 EP4 0.4875 0.816901
42 S7M 0.484211 0.813333
43 SAM 0.483871 0.813333
44 3DH 0.481928 0.84058
45 5AD 0.48 0.815385
46 DSZ 0.479592 0.75
47 VMS 0.479167 0.697674
48 54H 0.479167 0.697674
49 5AL 0.478723 0.8
50 CA0 0.477778 0.813333
51 A3P 0.477273 0.783784
52 MTA 0.47561 0.84058
53 NB8 0.475248 0.818182
54 Y3J 0.474359 0.791045
55 TSB 0.474227 0.72619
56 ADP 0.47191 0.810811
57 ABM 0.471264 0.786667
58 A2D 0.471264 0.810811
59 ZAS 0.470588 0.830986
60 LMS 0.470588 0.710843
61 QQY 0.470588 0.736842
62 SMM 0.46875 0.782051
63 SON 0.466667 0.802632
64 AN2 0.466667 0.8
65 GSU 0.465347 0.729412
66 KAA 0.465347 0.724138
67 SRA 0.465116 0.766234
68 OVE 0.465116 0.776316
69 AMO 0.464646 0.851351
70 2AM 0.464286 0.808219
71 52H 0.463918 0.689655
72 AU1 0.461538 0.789474
73 AP2 0.460674 0.802632
74 BA3 0.460674 0.810811
75 A12 0.460674 0.802632
76 QQX 0.458824 0.727273
77 G5A 0.457447 0.75
78 YSA 0.457143 0.729412
79 XAH 0.457143 0.7875
80 ACP 0.456522 0.813333
81 ATP 0.456522 0.810811
82 HEJ 0.456522 0.810811
83 AP5 0.455556 0.810811
84 B4P 0.455556 0.810811
85 5AS 0.455556 0.689655
86 9ZD 0.454545 0.759494
87 9ZA 0.454545 0.759494
88 8QN 0.454545 0.8
89 A3N 0.454545 0.882353
90 ACK 0.453488 0.777778
91 GAP 0.452632 0.813333
92 ACQ 0.452632 0.813333
93 5FA 0.451613 0.810811
94 AQP 0.451613 0.810811
95 APC 0.451613 0.802632
96 LAD 0.45098 0.807692
97 AT4 0.450549 0.779221
98 A7D 0.450549 0.897059
99 NSS 0.45 0.75
100 3AD 0.45 0.9375
101 PAJ 0.45 0.78481
102 7D3 0.449438 0.753247
103 S4M 0.449438 0.782051
104 PAP 0.446809 0.797297
105 ME8 0.446602 0.765432
106 ADX 0.445652 0.731707
107 MHZ 0.445652 0.772152
108 M33 0.445652 0.8
109 62X 0.445545 0.782051
110 DLL 0.445545 0.8
111 NVA LMS 0.445545 0.704545
112 A2P 0.444444 0.77027
113 DAL AMP 0.444444 0.8
114 ARG AMP 0.444444 0.777778
115 7MD 0.444444 0.810127
116 ATF 0.443299 0.779221
117 AOC 0.443182 0.867647
118 DSH 0.443182 0.859155
119 LEU LMS 0.441176 0.704545
120 K15 0.441176 0.802632
121 50T 0.44086 0.8
122 6YZ 0.438776 0.813333
123 TAT 0.4375 0.779221
124 ANP 0.4375 0.789474
125 T99 0.4375 0.779221
126 2A5 0.43617 0.789474
127 PRX 0.43617 0.766234
128 APR 0.43617 0.810811
129 AR6 0.43617 0.810811
130 4AD 0.435644 0.84
131 YAP 0.433962 0.815789
132 FA5 0.433962 0.826667
133 PPS 0.43299 0.710843
134 TXA 0.432692 0.802632
135 PTJ 0.432692 0.75
136 FYA 0.432692 0.824324
137 YLP 0.432432 0.768293
138 3D1 0.432099 0.924242
139 3L1 0.432099 0.924242
140 AGS 0.431579 0.769231
141 ADP PO3 0.431579 0.808219
142 SAP 0.431579 0.769231
143 AD9 0.431579 0.789474
144 ADV 0.431579 0.802632
145 RBY 0.431579 0.802632
146 7D4 0.430108 0.753247
147 8X1 0.43 0.724138
148 MAO 0.428571 0.772152
149 KB1 0.428571 0.824324
150 KH3 0.427273 0.815789
151 GEK 0.425743 0.847222
152 OOB 0.425743 0.8
153 WSA 0.424779 0.738095
154 WAQ 0.423077 0.782051
155 V3L 0.42268 0.786667
156 ADQ 0.421569 0.813333
157 A1R 0.421569 0.828947
158 YLB 0.421053 0.768293
159 0XU 0.421053 0.867647
160 YLC 0.421053 0.7875
161 8PZ 0.420561 0.75
162 48N 0.419643 0.794872
163 SXZ 0.419048 0.813333
164 CC5 0.417722 0.921875
165 00A 0.417476 0.759494
166 A5D 0.416667 0.828571
167 ATR 0.416667 0.783784
168 A22 0.415842 0.8
169 MAP 0.415842 0.769231
170 F2R 0.415254 0.790123
171 ALF ADP 0.414141 0.746835
172 ADP ALF 0.414141 0.746835
173 ADP BMA 0.413462 0.813333
174 3UK 0.413462 0.789474
175 OAD 0.413462 0.813333
176 25A 0.411765 0.786667
177 YLA 0.410256 0.768293
178 VO4 ADP 0.41 0.776316
179 ADP VO4 0.41 0.776316
180 PR8 0.409524 0.797468
181 B5V 0.409524 0.779221
182 P5A 0.409524 0.715909
183 SFB 0.408696 0.744186
184 B5M 0.407407 0.769231
185 AYB 0.40678 0.759036
186 1ZZ 0.40566 0.722892
187 3OD 0.40566 0.813333
188 9K8 0.40566 0.666667
189 5F1 0.404762 0.823529
190 RP1 0.404494 0.74026
191 SP1 0.404494 0.74026
192 AAT 0.40404 0.835616
193 MYR AMP 0.401869 0.722892
194 DQV 0.401786 0.824324
195 9X8 0.4 0.769231
196 TYM 0.4 0.826667
197 TYR AMP 0.4 0.815789
198 A6D 0.4 0.734177
199 A A A 0.4 0.8
200 AV2 0.4 0.74026
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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