Receptor
PDB id Resolution Class Description Source Keywords
1ZH6 2.5 Å EC: 6.1.1.1 CRYSTAL STRUCTURE OF P-ACETYLPHENYLALANINE-TRNA SYNTHETASE I WITH P-ACETYLPHENYLALANINE METHANOCALDOCOCCUS JANNASCHII STRUCTURAL PLASTICITY UNNATURAL AMINO ACID TRNA SYNTHETASELIGASE
Ref.: STRUCTURAL CHARACTERIZATION OF A P-ACETYLPHENYLALAN AMINOACYL-TRNA SYNTHETASE. J.AM.CHEM.SOC. V. 127 14976 2005
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
4AF A:315;
 Valid;
 none;
 submit data
207.226 C11 H13 N O3 CC(=O...
BME A:402;
A:403;
 Invalid;
Invalid;
 none;
none;
 submit data
78.133 C2 H6 O S C(CS)...
View in 3D viewer
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: 4AF; Similar ligands found: 18
No: Ligand ECFP6 Tc MDL keys Tc
1 4AF 1 1
2 0A1 0.619048 0.806452
3 TYR 0.585366 0.827586
4 DTY 0.585366 0.827586
5 4BF 0.571429 0.709677
6 PFF 0.571429 0.709677
7 PHI 0.571429 0.709677
8 PBF 0.5625 0.892857
9 7N8 0.545455 0.638889
10 4CF 0.533333 0.758621
11 PHE 0.52381 0.846154
12 DPN 0.52381 0.846154
13 TFQ 0.521739 0.6875
14 PTR 0.520833 0.609756
15 2L7 0.480769 0.609756
16 YOF 0.44 0.685714
17 DAH 0.4375 0.705882
18 IYR 0.411765 0.685714
Similar Ligands (3D)
Ligand no: 1; Ligand: 4AF; Similar ligands found: 404
No: Ligand Similarity coefficient
1 RPN 0.9568
2 PPN 0.9542
3 NAL 0.9443
4 R7T 0.9441
5 M28 0.9353
6 4FC 0.9321
7 TEF 0.9321
8 6P3 0.9319
9 ISA 0.9286
10 1EB 0.9284
11 14N 0.9283
12 ENO 0.9278
13 B41 0.9274
14 EYJ 0.9271
15 4NP 0.9264
16 PQS 0.9246
17 J1K 0.9234
18 NK5 0.9233
19 GJG 0.9228
20 LR8 0.9217
21 1A5 0.9213
22 2O8 0.9196
23 SOJ 0.9193
24 EQW 0.9189
25 4BX 0.9183
26 1Q1 0.9178
27 4MP 0.9166
28 G8V 0.9163
29 G14 0.9145
30 R9J 0.9139
31 2P3 0.9132
32 8EU 0.9131
33 4NS 0.9120
34 RQD 0.9117
35 4MB 0.9114
36 QME 0.9114
37 5O6 0.9107
38 I2E 0.9107
39 PNP 0.9103
40 FCW 0.9101
41 9VQ 0.9096
42 P4T 0.9087
43 OLU 0.9087
44 5TT 0.9084
45 B15 0.9083
46 EN1 0.9083
47 TMG 0.9080
48 KPV 0.9075
49 ODK 0.9074
50 72D 0.9070
51 TYC 0.9070
52 EYY 0.9070
53 AHC 0.9069
54 1OS 0.9065
55 6SD 0.9063
56 J4K 0.9061
57 QTD 0.9060
58 7EH 0.9058
59 TYE 0.9054
60 AWE 0.9053
61 7G0 0.9052
62 AD6 0.9047
63 2QC 0.9044
64 HWD 0.9041
65 CTE 0.9037
66 HC4 0.9036
67 JAH 0.9033
68 YI6 0.9033
69 80G 0.9032
70 72E 0.9032
71 0OK 0.9031
72 8V8 0.9031
73 4Z9 0.9028
74 657 0.9021
75 A4N 0.9011
76 MMS 0.9007
77 HXY 0.9005
78 613 0.9003
79 1AJ 0.9000
80 3IP 0.9000
81 NY4 0.8998
82 109 0.8997
83 E9P 0.8995
84 FTV 0.8995
85 4CN 0.8993
86 E0O 0.8990
87 B5A 0.8988
88 VC3 0.8988
89 C82 0.8988
90 M25 0.8984
91 F4K 0.8981
92 S0D 0.8978
93 5TO 0.8977
94 6WR 0.8976
95 YIH 0.8975
96 3W3 0.8975
97 RVE 0.8975
98 5O5 0.8974
99 ESE 0.8973
100 3W6 0.8973
101 UA5 0.8972
102 397 0.8967
103 9NB 0.8965
104 0F3 0.8964
105 9JH 0.8963
106 TRP 0.8960
107 LVP 0.8960
108 8D6 0.8959
109 F90 0.8957
110 1BW 0.8957
111 Y4L 0.8951
112 TID 0.8950
113 2UB 0.8949
114 9B3 0.8949
115 ERZ 0.8948
116 6DQ 0.8946
117 D25 0.8946
118 SNV 0.8943
119 S0W 0.8942
120 90M 0.8938
121 6C5 0.8938
122 WCU 0.8936
123 4FE 0.8933
124 KLE 0.8932
125 9FH 0.8932
126 3VR 0.8931
127 A5Q 0.8931
128 A9K 0.8927
129 G2V 0.8922
130 7ZO 0.8921
131 54E 0.8921
132 CBE 0.8921
133 PV4 0.8919
134 FMQ 0.8918
135 RKN 0.8912
136 0UL 0.8909
137 CH8 0.8907
138 K4V 0.8905
139 ZTW 0.8896
140 P81 0.8895
141 MJ5 0.8893
142 N2Y 0.8892
143 HLP 0.8891
144 16Z 0.8891
145 QH3 0.8889
146 FY8 0.8887
147 FT6 0.8884
148 6C4 0.8883
149 CT0 0.8883
150 RA7 0.8882
151 EYV 0.8882
152 REG 0.8881
153 848 0.8881
154 0ON 0.8881
155 EZL 0.8879
156 FER 0.8879
157 2L1 0.8878
158 Y3L 0.8878
159 SWX 0.8877
160 RNK 0.8877
161 HPP 0.8875
162 11X 0.8875
163 BFL 0.8875
164 AAN 0.8875
165 26C 0.8874
166 A7Q 0.8872
167 PH3 0.8869
168 JCZ 0.8865
169 MKN 0.8863
170 AES 0.8859
171 NIY 0.8858
172 TFM 0.8856
173 L15 0.8854
174 68B 0.8853
175 N4E 0.8853
176 DTE 0.8852
177 ZZA 0.8851
178 4AU 0.8851
179 KLS 0.8851
180 DHC 0.8850
181 L1T 0.8850
182 H75 0.8849
183 6EL 0.8848
184 A6Z 0.8848
185 8CC 0.8846
186 833 0.8845
187 G1L 0.8845
188 A18 0.8844
189 FWD 0.8844
190 BWD 0.8841
191 PPT 0.8840
192 3G3 0.8839
193 A4T 0.8838
194 EUH 0.8838
195 BQ2 0.8838
196 5S9 0.8837
197 M29 0.8837
198 VD9 0.8837
199 EF2 0.8836
200 SYE 0.8835
201 NPX 0.8834
202 2JX 0.8834
203 S7D 0.8833
204 J27 0.8832
205 GHQ 0.8831
206 U55 0.8828
207 EPE 0.8828
208 3VS 0.8828
209 2LT 0.8825
210 NPS 0.8825
211 88L 0.8823
212 ITW 0.8820
213 5M2 0.8820
214 IWD 0.8820
215 BVS 0.8820
216 5RP 0.8819
217 FPL 0.8818
218 363 0.8818
219 L1O 0.8816
220 FZM 0.8815
221 P2L 0.8815
222 1KN 0.8815
223 TBJ 0.8814
224 D26 0.8813
225 OQC 0.8812
226 IC9 0.8812
227 CFA 0.8812
228 F02 0.8810
229 S7V 0.8810
230 TG6 0.8810
231 PTB 0.8809
232 52F 0.8806
233 YF3 0.8806
234 6ZX 0.8806
235 3VX 0.8806
236 6N4 0.8805
237 RYV 0.8804
238 531 0.8803
239 121 0.8803
240 SJR 0.8801
241 RGP 0.8800
242 KW7 0.8800
243 L4K 0.8798
244 L2K 0.8798
245 4FP 0.8797
246 N9M 0.8796
247 XCG 0.8795
248 0OO 0.8792
249 VJJ 0.8791
250 1Q2 0.8791
251 GB4 0.8788
252 DVK 0.8787
253 Z13 0.8784
254 S8G 0.8783
255 6H2 0.8783
256 E3X 0.8783
257 W1G 0.8781
258 D1G 0.8780
259 3CX 0.8780
260 S8P 0.8780
261 OSP 0.8780
262 536 0.8780
263 A7K 0.8778
264 AU8 0.8774
265 2B4 0.8774
266 GB5 0.8773
267 9JT 0.8771
268 50C 0.8770
269 7FU 0.8769
270 CC5 0.8768
271 NDD 0.8768
272 CWD 0.8767
273 OHJ 0.8762
274 GGG 0.8759
275 GJB 0.8759
276 IBP 0.8758
277 3W1 0.8757
278 HX8 0.8757
279 T1N 0.8757
280 BMZ 0.8756
281 PF1 0.8755
282 YIE 0.8755
283 H4B 0.8755
284 NAG 0.8749
285 51Y 0.8748
286 92O 0.8748
287 C53 0.8745
288 27K 0.8745
289 3VQ 0.8745
290 MP5 0.8744
291 5AD 0.8743
292 5C1 0.8741
293 4JE 0.8741
294 BL0 0.8740
295 IS2 0.8740
296 5OO 0.8737
297 5SP 0.8737
298 OJD 0.8736
299 JA5 0.8732
300 A6W 0.8732
301 RYY 0.8730
302 LR2 0.8729
303 LZ5 0.8729
304 HNT 0.8728
305 YE6 0.8728
306 RES 0.8724
307 3UF 0.8724
308 BSU 0.8724
309 0SY 0.8723
310 0QA 0.8722
311 EAT 0.8722
312 96Z 0.8720
313 M4N 0.8718
314 C4E 0.8716
315 EV2 0.8716
316 5H6 0.8713
317 JA3 0.8713
318 2D2 0.8712
319 7PJ 0.8711
320 GLY GLY GLY 0.8711
321 ADN 0.8711
322 36M 0.8708
323 BSA 0.8707
324 DTR 0.8706
325 GT4 0.8703
326 JPQ 0.8703
327 F52 0.8702
328 6C9 0.8701
329 ENG 0.8700
330 ZYX 0.8699
331 0NX 0.8695
332 6MW 0.8695
333 BX4 0.8694
334 4EU 0.8692
335 3D3 0.8691
336 FHV 0.8691
337 4UM 0.8690
338 K82 0.8689
339 KHP 0.8684
340 A7N 0.8683
341 MGB 0.8683
342 X6W 0.8682
343 KF5 0.8681
344 STZ 0.8681
345 YX1 0.8681
346 JF5 0.8680
347 AMR 0.8678
348 S0F 0.8677
349 250 0.8676
350 AOY 0.8674
351 CPZ 0.8672
352 BC5 0.8666
353 EQA 0.8663
354 AVX 0.8660
355 OJM 0.8657
356 ESJ 0.8655
357 E9S 0.8651
358 VFJ 0.8650
359 YPN 0.8649
360 LWA 0.8649
361 PLP 0.8648
362 NFM 0.8646
363 1OT 0.8645
364 F6R 0.8640
365 XYP XYS 0.8635
366 CS2 0.8633
367 8YH 0.8631
368 22T 0.8630
369 BRH 0.8630
370 Y0V 0.8629
371 LOT 0.8628
372 3XR 0.8622
373 88R 0.8622
374 22M 0.8620
375 FT2 0.8618
376 0OY 0.8617
377 5WN 0.8615
378 EEK 0.8613
379 DVQ 0.8610
380 DG6 0.8608
381 ZRK 0.8607
382 3W8 0.8605
383 X48 0.8604
384 HFA 0.8604
385 FT3 0.8603
386 D2G 0.8599
387 20N 0.8592
388 FLP 0.8591
389 R5P 0.8584
390 S0A 0.8582
391 A4Q 0.8571
392 1Z6 0.8570
393 1FE 0.8570
394 TJM 0.8570
395 SJK 0.8568
396 5F1 0.8567
397 LEG 0.8565
398 U13 0.8562
399 3N1 0.8548
400 BBY 0.8539
401 OA1 0.8538
402 M2E 0.8533
403 36Y 0.8524
404 FUD 0.8508
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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