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Receptor
PDB id Resolution Class Description Source Keywords
4RRH 1.55 Å EC: 6.1.1.3 K116M MUTANT OF N-TERMINAL EDITING DOMAIN OF THREONYL-TRNA S FROM AEROPYRUM PERNIX WITH L-SER3AA AEROPYRUM PERNIX 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
A3S A:201;
Valid;
none;
submit data
353.334 C13 H19 N7 O5 c1nc(...
MG A:202;
Invalid;
none;
submit data
24.305 Mg [Mg+2...
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 = 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 : 4RR7; Ligand: A3S; Similar sites found with APoc: 58
This union binding pocket(no: 1) in the query (biounit: 4rr7.bio1) has 22 residues
No: Leader PDB Ligand Sequence Similarity
1 2ZX2 RAM None
2 1DCP HBI None
3 3ZQE DXC None
4 2BOS GLA GAL GLC None
5 6EMU SAM None
6 2BOS GLA GAL GLC NBU None
7 6FX2 FUC C4W NAG BMA MAN NAG GAL None
8 5A89 FMN None
9 3HCH RSM None
10 5F6U 5VK 0.735294
11 4CNE SAH 2.20588
12 1SQL GUN 2.20588
13 3SHR CMP 2.20588
14 1ELI PYC 2.20588
15 4MCC 21X 2.20588
16 4GK9 MAN BMA MAN MAN MAN 3.67647
17 1MJH ATP 3.67647
18 1YXM ADE 3.67647
19 5A7Y SAH 4.41176
20 1P9P SAH 4.41176
21 5Y4R C2E 4.41176
22 4CNG SAH 4.41176
23 1SBR VIB 4.41176
24 3K56 IS3 4.41176
25 5AHW CMP 5.14706
26 6IIL A8F 5.14706
27 4JWF SAH 5.14706
28 3ESS 18N 5.14706
29 5H4S RAM 5.88235
30 2UXR ICT 5.88235
31 3HGM ATP 5.88235
32 4R2M ANP 5.88235
33 1Q19 SSC 5.88235
34 4JWH SAH 5.88235
35 3AIA SAM 5.88235
36 2YY8 SAM 6.46766
37 6EK3 OUL 6.61765
38 5T63 ALA ALA ALA ALA 6.61765
39 1GPM AMP 6.61765
40 1B4B ARG 7.04225
41 4NBI D3Y 7.35294
42 1KOR ANP 7.35294
43 1KOR ARG 7.35294
44 1KOR SIN 7.35294
45 5E9G GLV 7.35294
46 3EF0 ALF 7.35294
47 1N07 FMN 8.08823
48 1N07 ADP 8.08823
49 6GMR F4K 8.47458
50 1OBD AMP 8.82353
51 4JWJ SAH 8.82353
52 5IFK HPA 10.2941
53 4FXQ G9L 11.0294
54 4JAL SAH 11.7647
55 2C5S AMP 12.5
56 4FK7 P34 19.1176
57 1CT9 AMP 24.2647
58 1O94 AMP 28.6765
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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