Receptor
PDB id Resolution Class Description Source Keywords
3QE4 2.3 Å EC: 6.1.1.1 AN EVOLVED AMINOACYL-TRNA SYNTHETASE WITH ATYPICAL POLYSUBST SPECIFICITY METHANOCALDOCOCCUS JANNASCHII EVOLVED TRNA SYNTHETASE TRNA SYNTHETASE EVOLVED TO BIND UNNAMINO ACIDS TRNA LIGASE
Ref.: AN EVOLVED AMINOACYL-TRNA SYNTHETASE WITH ATYPICAL POLYSUBSTRATE SPECIFICITY . BIOCHEMISTRY V. 50 1894 2011
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
4CF A:313;
B:313;
 Valid;
Valid;
 none;
none;
 submit data
190.199 C10 H10 N2 O2 c1cc(...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5N5U 1.6 Å EC: 6.1.1.1 STRUCTURE OF P-BORONOPHENYLALANYL TRNA SYNTHETASE IN COMPLEX BORONOPHENYLALANINE AND ADENOSINE MONOPHOSPHATE METHANOCALDOCOCCUS JANNASCHII (STRAIN 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) AMINOACYLATION LIGASE NON-NATURAL AMINO ACID SYNTHETIC BI
Ref.: STRUCTURAL BASIS FOR THE SPECIFIC COTRANSLATIONAL INCORPORATION OF P-BORONOPHENYLALANINE INTO BIOSYNT PROTEINS. BIOCHEMISTRY V. 57 2597 2018
Members (21)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 13 families.
1 4NX2 - 2LT C9 H9 Cl2 N O3 c1c(cc(c(c....
2 3QE4 - 4CF C10 H10 N2 O2 c1cc(ccc1C....
3 4NDA - NIY C9 H10 N2 O5 c1cc(c(cc1....
4 3D6V - TFQ C11 H12 F3 N O2 c1cc(ccc1C....
5 2AG6 - 4BF C9 H10 Br N O2 c1cc(ccc1C....
6 3D6U - T11 C11 H12 F3 N3 O2 c1cc(ccc1C....
7 4PBT - 2LQ C18 H24 N2 O3 c1cc(ccc1C....
8 5N5U - AMP C10 H14 N5 O7 P c1nc(c2c(n....
9 2HGZ - PBF C16 H15 N O3 c1ccc(cc1)....
10 4PBR - 2L7 C13 H17 Br N2 O3 CC(C)(C(=O....
11 5L7P - BUU C16 H16 N2 O6 c1ccc(c(c1....
12 2PXH - BP5 C13 H13 N3 O2 c1ccnc(c1)....
13 5NSF - 96Z C13 H15 N O2 C1C=CC2=CC....
14 3N2Y - TEF C10 H11 N5 O2 c1cc(ccc1C....
15 6WRN - NIY C9 H10 N2 O5 c1cc(c(cc1....
16 1ZH6 - 4AF C11 H13 N O3 CC(=O)c1cc....
17 4PBS - 2L7 C13 H17 Br N2 O3 CC(C)(C(=O....
18 6WRK - NIY C9 H10 N2 O5 c1cc(c(cc1....
19 1ZH0 - NAL C13 H13 N O2 c1ccc2cc(c....
20 6WRQ - NIY C9 H10 N2 O5 c1cc(c(cc1....
21 6WRT - NIY C9 H10 N2 O5 c1cc(c(cc1....
70% Homology Family (22)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 10 families.
1 2CYB - TYR C9 H11 N O3 c1cc(ccc1C....
2 4NX2 - 2LT C9 H9 Cl2 N O3 c1c(cc(c(c....
3 3QE4 - 4CF C10 H10 N2 O2 c1cc(ccc1C....
4 4NDA - NIY C9 H10 N2 O5 c1cc(c(cc1....
5 3D6V - TFQ C11 H12 F3 N O2 c1cc(ccc1C....
6 2AG6 - 4BF C9 H10 Br N O2 c1cc(ccc1C....
7 3D6U - T11 C11 H12 F3 N3 O2 c1cc(ccc1C....
8 4PBT - 2LQ C18 H24 N2 O3 c1cc(ccc1C....
9 5N5U - AMP C10 H14 N5 O7 P c1nc(c2c(n....
10 2HGZ - PBF C16 H15 N O3 c1ccc(cc1)....
11 4PBR - 2L7 C13 H17 Br N2 O3 CC(C)(C(=O....
12 5L7P - BUU C16 H16 N2 O6 c1ccc(c(c1....
13 2PXH - BP5 C13 H13 N3 O2 c1ccnc(c1)....
14 5NSF - 96Z C13 H15 N O2 C1C=CC2=CC....
15 3N2Y - TEF C10 H11 N5 O2 c1cc(ccc1C....
16 6WRN - NIY C9 H10 N2 O5 c1cc(c(cc1....
17 1ZH6 - 4AF C11 H13 N O3 CC(=O)c1cc....
18 4PBS - 2L7 C13 H17 Br N2 O3 CC(C)(C(=O....
19 6WRK - NIY C9 H10 N2 O5 c1cc(c(cc1....
20 1ZH0 - NAL C13 H13 N O2 c1ccc2cc(c....
21 6WRQ - NIY C9 H10 N2 O5 c1cc(c(cc1....
22 6WRT - NIY C9 H10 N2 O5 c1cc(c(cc1....
50% Homology Family (27)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 2CYB - TYR C9 H11 N O3 c1cc(ccc1C....
2 4NX2 - 2LT C9 H9 Cl2 N O3 c1c(cc(c(c....
3 3QE4 - 4CF C10 H10 N2 O2 c1cc(ccc1C....
4 4NDA - NIY C9 H10 N2 O5 c1cc(c(cc1....
5 3D6V - TFQ C11 H12 F3 N O2 c1cc(ccc1C....
6 2AG6 - 4BF C9 H10 Br N O2 c1cc(ccc1C....
7 3D6U - T11 C11 H12 F3 N3 O2 c1cc(ccc1C....
8 4PBT - 2LQ C18 H24 N2 O3 c1cc(ccc1C....
9 5N5U - AMP C10 H14 N5 O7 P c1nc(c2c(n....
10 2HGZ - PBF C16 H15 N O3 c1ccc(cc1)....
11 4PBR - 2L7 C13 H17 Br N2 O3 CC(C)(C(=O....
12 5L7P - BUU C16 H16 N2 O6 c1ccc(c(c1....
13 2PXH - BP5 C13 H13 N3 O2 c1ccnc(c1)....
14 5NSF - 96Z C13 H15 N O2 C1C=CC2=CC....
15 3N2Y - TEF C10 H11 N5 O2 c1cc(ccc1C....
16 6WRN - NIY C9 H10 N2 O5 c1cc(c(cc1....
17 1ZH6 - 4AF C11 H13 N O3 CC(=O)c1cc....
18 4PBS - 2L7 C13 H17 Br N2 O3 CC(C)(C(=O....
19 6WRK - NIY C9 H10 N2 O5 c1cc(c(cc1....
20 1ZH0 - NAL C13 H13 N O2 c1ccc2cc(c....
21 6WRQ - NIY C9 H10 N2 O5 c1cc(c(cc1....
22 6WRT - NIY C9 H10 N2 O5 c1cc(c(cc1....
23 2CYC - TYR C9 H11 N O3 c1cc(ccc1C....
24 1Q11 - TYE C9 H13 N O2 c1cc(ccc1C....
25 5THH - TYR C9 H11 N O3 c1cc(ccc1C....
26 3VGJ - TYR AMP n/a n/a
27 2J5B - TYE C9 H13 N O2 c1cc(ccc1C....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: 4CF; Similar ligands found: 16
No: Ligand ECFP6 Tc MDL keys Tc
1 4CF 1 1
2 TYR 0.571429 0.733333
3 DTY 0.571429 0.733333
4 PFF 0.55814 0.733333
5 PHI 0.55814 0.733333
6 4BF 0.55814 0.733333
7 0A1 0.533333 0.666667
8 4AF 0.533333 0.758621
9 7N8 0.533333 0.611111
10 PHE 0.511628 0.88
11 DPN 0.511628 0.88
12 TFQ 0.510638 0.709677
13 PBF 0.461538 0.733333
14 DAH 0.458333 0.628571
15 IYR 0.403846 0.611111
16 YOF 0.403846 0.611111
Similar Ligands (3D)
Ligand no: 1; Ligand: 4CF; Similar ligands found: 334
No: Ligand Similarity coefficient
1 ISA 0.9644
2 ENO 0.9556
3 EQW 0.9522
4 TYC 0.9455
5 2UB 0.9407
6 AHC 0.9379
7 SOJ 0.9367
8 TYE 0.9345
9 E0O 0.9329
10 HXY 0.9298
11 HWD 0.9290
12 S0W 0.9273
13 YI6 0.9269
14 HC4 0.9263
15 PPN 0.9260
16 BVS 0.9225
17 PH3 0.9221
18 C82 0.9211
19 HPP 0.9198
20 FTV 0.9190
21 5TT 0.9187
22 9VQ 0.9186
23 R9J 0.9184
24 SNV 0.9153
25 1KN 0.9144
26 N2Y 0.9141
27 RQD 0.9140
28 J4K 0.9139
29 14N 0.9133
30 CFA 0.9129
31 PPT 0.9129
32 1EB 0.9126
33 6P3 0.9123
34 F90 0.9114
35 P9E 0.9111
36 MMS 0.9105
37 EN1 0.9103
38 6SD 0.9103
39 AWE 0.9098
40 TEF 0.9096
41 FCW 0.9091
42 LO1 0.9087
43 GJG 0.9084
44 EUE 0.9083
45 NY4 0.9073
46 0UL 0.9069
47 ERZ 0.9063
48 4NP 0.9061
49 AJG 0.9059
50 Y4L 0.9058
51 JAH 0.9058
52 DHC 0.9055
53 80G 0.9052
54 EZL 0.9045
55 P81 0.9044
56 F4K 0.9035
57 FWD 0.9029
58 RKN 0.9026
59 OLU 0.9020
60 JBZ 0.9018
61 4FC 0.9014
62 109 0.9013
63 DVK 0.9013
64 CWD 0.9013
65 BWD 0.9012
66 K80 0.9012
67 RPN 0.9008
68 SWX 0.9007
69 657 0.9006
70 J1K 0.9002
71 54E 0.9002
72 A7Q 0.9001
73 PQS 0.9001
74 A6W 0.9001
75 UA5 0.8991
76 RVE 0.8983
77 6ZX 0.8983
78 RA7 0.8982
79 S0F 0.8977
80 F52 0.8977
81 IWD 0.8970
82 36M 0.8969
83 2B4 0.8968
84 4Z9 0.8965
85 5OO 0.8963
86 5S9 0.8963
87 IC9 0.8958
88 TPM 0.8956
89 5NR 0.8955
90 EPE 0.8955
91 1FD 0.8952
92 HFA 0.8951
93 E3X 0.8950
94 16Z 0.8949
95 YPN 0.8946
96 HNK 0.8944
97 C53 0.8941
98 CPZ 0.8940
99 D1Y 0.8938
100 GB5 0.8938
101 B15 0.8937
102 VFG 0.8934
103 KLS 0.8930
104 GB4 0.8929
105 YIE 0.8927
106 EUH 0.8923
107 2O8 0.8923
108 7EH 0.8919
109 S0D 0.8917
110 A7H 0.8917
111 M28 0.8915
112 OHJ 0.8915
113 9B3 0.8915
114 BRH 0.8915
115 YF3 0.8914
116 4FP 0.8912
117 Y3L 0.8910
118 0NX 0.8909
119 5O6 0.8905
120 KLE 0.8901
121 ZZA 0.8900
122 VC3 0.8895
123 51Y 0.8893
124 CTE 0.8893
125 50C 0.8891
126 OQC 0.8890
127 NK5 0.8890
128 7EL 0.8890
129 1A5 0.8889
130 NAL 0.8889
131 363 0.8886
132 N9M 0.8885
133 B41 0.8882
134 FMQ 0.8881
135 ENG 0.8880
136 MP5 0.8880
137 PF1 0.8878
138 92G 0.8875
139 E9P 0.8873
140 IS2 0.8870
141 M25 0.8867
142 3VR 0.8866
143 PQM 0.8865
144 5SP 0.8865
145 DVQ 0.8864
146 AU8 0.8864
147 GLY GLY GLY 0.8863
148 AJ1 0.8862
149 NFA 0.8859
150 SJR 0.8858
151 88L 0.8854
152 AEG 0.8854
153 PTR 0.8853
154 S0E 0.8850
155 LR8 0.8849
156 2QC 0.8849
157 THU 0.8849
158 H4B 0.8846
159 XK0 0.8845
160 GT4 0.8841
161 A18 0.8838
162 0OO 0.8837
163 HIC 0.8836
164 YIH 0.8832
165 QH3 0.8832
166 JA5 0.8830
167 4FE 0.8829
168 NFM 0.8827
169 A4N 0.8827
170 NPS 0.8827
171 HX8 0.8818
172 K82 0.8817
173 STZ 0.8810
174 YX1 0.8810
175 A6Z 0.8810
176 5O5 0.8809
177 D25 0.8808
178 5TO 0.8808
179 4I8 0.8803
180 XCG 0.8803
181 HNL 0.8801
182 NPX 0.8799
183 A7K 0.8799
184 I2E 0.8799
185 36Y 0.8798
186 1Z6 0.8797
187 EAT 0.8794
188 27K 0.8794
189 5RP 0.8793
190 72D 0.8792
191 JCZ 0.8792
192 250 0.8792
193 B3U 0.8791
194 QTD 0.8790
195 C1M 0.8785
196 5VU 0.8783
197 ZEC 0.8782
198 7O4 0.8781
199 J27 0.8780
200 3EB 0.8778
201 HBI 0.8778
202 QME 0.8777
203 PV4 0.8777
204 OJD 0.8776
205 G14 0.8774
206 EYJ 0.8771
207 ARG 0.8771
208 4MB 0.8770
209 9JH 0.8769
210 A4T 0.8768
211 XRX 0.8766
212 S7S 0.8764
213 0A9 0.8761
214 TRP 0.8761
215 NAG 0.8761
216 WCU 0.8759
217 2LT 0.8758
218 613 0.8758
219 H2B 0.8757
220 CBE 0.8757
221 PNP 0.8753
222 VFM 0.8751
223 RSV 0.8750
224 MLZ 0.8747
225 HNH 0.8744
226 3W1 0.8744
227 BPW 0.8742
228 W1G 0.8740
229 2JX 0.8738
230 PLP 0.8738
231 9NB 0.8737
232 0K7 0.8735
233 2P3 0.8735
234 8D6 0.8731
235 0OK 0.8731
236 72E 0.8728
237 OJM 0.8724
238 ODK 0.8724
239 EF0 0.8719
240 7FU 0.8717
241 L1T 0.8715
242 TMG 0.8714
243 JPQ 0.8714
244 DAR 0.8712
245 X48 0.8711
246 IAR 0.8711
247 3R4 0.8711
248 6C5 0.8708
249 R52 0.8705
250 R5P 0.8704
251 FZM 0.8704
252 11X 0.8703
253 3IP 0.8703
254 833 0.8702
255 6C8 0.8701
256 HLP 0.8698
257 VIB 0.8697
258 9JT 0.8696
259 A9K 0.8695
260 HL6 0.8691
261 4CN 0.8691
262 2PV 0.8691
263 Q04 0.8688
264 LZ5 0.8685
265 KPV 0.8683
266 LR2 0.8683
267 9FH 0.8682
268 KP2 0.8679
269 NGA 0.8678
270 M1T 0.8675
271 5H6 0.8674
272 0DF 0.8672
273 API 0.8671
274 VJJ 0.8670
275 GNW 0.8669
276 A5P 0.8668
277 22F 0.8666
278 1Q2 0.8663
279 8CC 0.8663
280 TOH 0.8663
281 F02 0.8662
282 B1J 0.8661
283 URI 0.8659
284 8OB 0.8657
285 2PK 0.8657
286 SBK 0.8656
287 LTN 0.8656
288 A5E 0.8655
289 Q9Z 0.8654
290 K4V 0.8651
291 RES 0.8647
292 28A 0.8645
293 H75 0.8645
294 EV2 0.8644
295 7MW 0.8643
296 RYV 0.8643
297 DTR 0.8641
298 IBP 0.8631
299 PQV 0.8631
300 M74 0.8628
301 FCD 0.8627
302 6WR 0.8627
303 4LW 0.8626
304 4BX 0.8623
305 6H2 0.8620
306 4LV 0.8618
307 121 0.8615
308 N9J 0.8613
309 0F3 0.8612
310 CIR 0.8611
311 U13 0.8610
312 9BF 0.8605
313 S7V 0.8600
314 GVY 0.8590
315 42R 0.8587
316 848 0.8583
317 TB8 0.8582
318 4UM 0.8580
319 D26 0.8580
320 26P 0.8579
321 EXY 0.8577
322 AZY 0.8571
323 VM1 0.8565
324 2C0 0.8565
325 6C9 0.8564
326 1PS 0.8559
327 CLT 0.8554
328 KYN 0.8552
329 EYY 0.8547
330 3CX 0.8539
331 A6H 0.8526
332 6N4 0.8525
333 OA1 0.8522
334 6FG 0.8518
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5N5U; Ligand: AMP; 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: 5n5u.bio1) has 50 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5N5U; Ligand: AMP; 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: 5n5u.bio1) has 50 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 5N5U; Ligand: 7N8; 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: 5n5u.bio1) has 39 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 5N5U; Ligand: 7N8; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 5n5u.bio1) has 39 residues
No: Leader PDB Ligand Sequence Similarity
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