Receptor
PDB id Resolution Class Description Source Keywords
1YGB 2.48 Å EC: 6.1.1.7 CRYSTAL STRUCTURE OF THE CATALYTIC FRAGMENT OF ALANYL-TRNA SYNTHETASE IN COMPLEX WITH L-SERINE AQUIFEX AEOLICUS HELIX-TURN-HELIX MOTIF ALPHA-BETA FOLD AMINO ACID BINDINGLIGASE
Ref.: BREAKING SIEVE FOR STERIC EXCLUSION OF A NONCOGNATE AMINO ACID FROM ACTIVE SITE OF A TRNA SYNTHETASE. PROC.NATL.ACAD.SCI.USA V. 102 988 2005
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SER A:501;
Valid;
none;
submit data
105.093 C3 H7 N O3 C([C@...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1YFS 2.08 Å EC: 6.1.1.7 THE CRYSTAL STRUCTURE OF ALANYL-TRNA SYNTHETASE IN COMPLEX WITH L-ALANINE AQUIFEX AEOLICUS ALPHA-BETA FOLD HELIX-LOOP-HELIX MOTIF AMINO ACID BINDINGLIGASE
Ref.: BREAKING SIEVE FOR STERIC EXCLUSION OF A NONCOGNATE AMINO ACID FROM ACTIVE SITE OF A TRNA SYNTHETASE. PROC.NATL.ACAD.SCI.USA V. 102 988 2005
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 1YFS - ALA C3 H7 N O2 C[C@@H](C(....
2 1YGB - SER C3 H7 N O3 C([C@@H](C....
3 1YFT - GLY C2 H5 N O2 C(C(=O)O)N
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 1YFS - ALA C3 H7 N O2 C[C@@H](C(....
2 1YGB - SER C3 H7 N O3 C([C@@H](C....
3 1YFT - GLY C2 H5 N O2 C(C(=O)O)N
50% Homology Family (11)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 3HXX - ACP C11 H18 N5 O12 P3 c1nc(c2c(n....
2 3HXU - A5A C13 H19 N7 O7 S C[C@@H](C(....
3 3HXW - SSA C13 H19 N7 O8 S c1nc(c2c(n....
4 3HXZ - A5A C13 H19 N7 O7 S C[C@@H](C(....
5 3HXV - G5A C12 H17 N7 O7 S c1nc(c2c(n....
6 3HXY - ACP C11 H18 N5 O12 P3 c1nc(c2c(n....
7 3HY0 - G5A C12 H17 N7 O7 S c1nc(c2c(n....
8 5V59 - 8X1 C14 H19 N7 O7 S c1nc(c2c(n....
9 1YFS - ALA C3 H7 N O2 C[C@@H](C(....
10 1YGB - SER C3 H7 N O3 C([C@@H](C....
11 1YFT - GLY C2 H5 N O2 C(C(=O)O)N
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: SER; Similar ligands found: 33
No: Ligand ECFP6 Tc MDL keys Tc
1 SER 1 1
2 DSN 1 1
3 DCY 0.65 0.84
4 CYS 0.65 0.84
5 DBB 0.6 0.692308
6 ABA 0.6 0.692308
7 2RA 0.6 0.75
8 HSE 0.590909 0.821429
9 C2N 0.571429 0.730769
10 ASN 0.545455 0.625
11 ASP 0.545455 0.714286
12 DAS 0.545455 0.714286
13 DAB 0.521739 0.724138
14 HL5 0.518519 0.814815
15 AS2 0.5 0.703704
16 NVA 0.5 0.62069
17 HCS 0.5 0.777778
18 CSO 0.5 0.636364
19 LEU 0.5 0.642857
20 API 0.5 0.633333
21 CSS 0.48 0.689655
22 DGY 0.47619 0.607143
23 DGL 0.461538 0.655172
24 GLU 0.461538 0.655172
25 GGL 0.461538 0.655172
26 ORN 0.444444 0.689655
27 SLZ 0.433333 0.625
28 DLY 0.413793 0.666667
29 11C 0.413793 0.633333
30 UN1 0.413793 0.633333
31 CME 0.40625 0.666667
32 LYS 0.4 0.645161
33 DHH 0.4 0.612903
Similar Ligands (3D)
Ligand no: 1; Ligand: SER; Similar ligands found: 667
No: Ligand Similarity coefficient
1 DE2 1.0000
2 3PY 1.0000
3 TAR 1.0000
4 SMB 1.0000
5 HUI 1.0000
6 DXX 1.0000
7 39J 0.9987
8 2KT 0.9984
9 KG7 0.9971
10 1AC 0.9864
11 ALA 0.9831
12 THR 0.9831
13 LAC 0.9792
14 2OP 0.9775
15 03W 0.9773
16 HIU 0.9773
17 OXL 0.9770
18 A3B 0.9766
19 PYR 0.9754
20 MB3 0.9746
21 ALQ 0.9719
22 HBS 0.9705
23 SSN 0.9680
24 NIS 0.9669
25 VAL 0.9668
26 CAQ 0.9666
27 9YL 0.9662
28 OXM 0.9658
29 CEJ 0.9658
30 23W 0.9655
31 OXD 0.9655
32 HV2 0.9653
33 MLI 0.9641
34 9X7 0.9640
35 2HA 0.9633
36 LER 0.9628
37 MLA 0.9622
38 GOL 0.9620
39 GXV 0.9620
40 192 0.9617
41 E60 0.9616
42 HGY 0.9607
43 C5J 0.9606
44 3GR 0.9606
45 NAK 0.9601
46 IPH 0.9599
47 ALO 0.9596
48 HBR 0.9594
49 AKB 0.9593
50 DTL 0.9582
51 TF4 0.9582
52 BAL 0.9573
53 IQ0 0.9573
54 PPF 0.9561
55 273 0.9559
56 MMZ 0.9554
57 MEU 0.9552
58 PYM 0.9552
59 3OH 0.9551
60 TAY 0.9550
61 AOA 0.9542
62 TFB 0.9541
63 DAL 0.9540
64 BUQ 0.9538
65 PRS 0.9537
66 BUB 0.9537
67 2PC 0.9536
68 PRO 0.9536
69 BUO 0.9536
70 MRY 0.9535
71 KIV 0.9534
72 DMG 0.9533
73 BAQ 0.9531
74 SAR 0.9530
75 FW5 0.9526
76 AAE 0.9522
77 7EX 0.9519
78 KSW 0.9515
79 2IM 0.9514
80 BU4 0.9509
81 5Y9 0.9508
82 BMD 0.9504
83 40O 0.9503
84 BUA 0.9499
85 69O 0.9495
86 MAK 0.9494
87 CYH 0.9494
88 LEA 0.9492
89 CXL 0.9492
90 BAE 0.9490
91 MLM 0.9487
92 A2Q 0.9483
93 280 0.9478
94 ICN 0.9475
95 HYN 0.9471
96 3ZQ 0.9469
97 NVI 0.9464
98 BXO 0.9462
99 CHT 0.9459
100 XIX 0.9458
101 V1L 0.9451
102 4AX 0.9449
103 HDA 0.9443
104 MZ0 0.9442
105 DTI 0.9442
106 HRZ 0.9441
107 9PO 0.9440
108 3HL 0.9435
109 1SP 0.9434
110 LGA 0.9434
111 3HR 0.9432
112 DMI 0.9428
113 2AP 0.9427
114 HVK 0.9427
115 XAP 0.9427
116 IVA 0.9426
117 DCD 0.9426
118 3AP 0.9425
119 HAI 0.9424
120 MBN 0.9423
121 HSL 0.9422
122 GXE 0.9421
123 4AP 0.9420
124 HPY 0.9414
125 MTG 0.9411
126 BEW 0.9410
127 24T 0.9409
128 ATQ 0.9406
129 P2D 0.9405
130 ABU 0.9404
131 AMT 0.9404
132 GBL 0.9402
133 URA 0.9401
134 WOT 0.9400
135 MAE 0.9399
136 MMU 0.9396
137 T2C 0.9394
138 HZP 0.9393
139 DTT 0.9391
140 3TR 0.9387
141 8CL 0.9387
142 PRI 0.9384
143 TMT 0.9384
144 93B 0.9383
145 278 0.9380
146 ODV 0.9374
147 6SP 0.9371
148 L60 0.9368
149 HVQ 0.9368
150 SIN 0.9366
151 8X3 0.9363
152 25T 0.9362
153 FUM 0.9358
154 J1Z 0.9356
155 26D 0.9352
156 BVG 0.9351
157 ITU 0.9350
158 1DU 0.9348
159 CRS 0.9346
160 1CB 0.9344
161 3BB 0.9342
162 265 0.9339
163 3MT 0.9336
164 TP5 0.9336
165 A8C 0.9333
166 SLP 0.9331
167 TTO 0.9328
168 9TY 0.9327
169 HGQ 0.9323
170 DTU 0.9321
171 XPO 0.9321
172 IHG 0.9321
173 HBX 0.9319
174 TAU 0.9318
175 PYC 0.9318
176 FOA 0.9317
177 VX 0.9316
178 BVC 0.9313
179 MR3 0.9312
180 HOW 0.9311
181 2HE 0.9309
182 POA 0.9309
183 C21 0.9308
184 282 0.9304
185 WTZ 0.9303
186 2MZ 0.9303
187 SYN 0.9303
188 PYF 0.9301
189 1MZ 0.9300
190 H3M 0.9300
191 2AI 0.9298
192 JZ6 0.9297
193 SGL 0.9296
194 D2P 0.9293
195 MZY 0.9292
196 TMZ 0.9292
197 4HA 0.9291
198 EGD 0.9291
199 NXA 0.9288
200 2EZ 0.9285
201 5MP 0.9285
202 5KX 0.9285
203 4MZ 0.9284
204 1DH 0.9278
205 ETX 0.9277
206 CYT 0.9276
207 RCO 0.9276
208 GOA 0.9270
209 PUT 0.9267
210 NBE 0.9266
211 285 0.9266
212 HHN 0.9265
213 TZC 0.9265
214 DUC 0.9264
215 PE9 0.9263
216 23B 0.9263
217 PYG 0.9262
218 SMV 0.9261
219 4JU 0.9259
220 IDH 0.9259
221 ABN 0.9258
222 LDU 0.9257
223 4CH 0.9256
224 PY7 0.9253
225 JZ3 0.9250
226 LG3 0.9250
227 QFH 0.9250
228 HLT 0.9248
229 BVF 0.9245
230 HYP 0.9245
231 4XX 0.9242
232 3CH 0.9240
233 ECE 0.9239
234 WBU 0.9237
235 BYZ 0.9235
236 NMG 0.9234
237 DPR 0.9231
238 93Q 0.9230
239 APY 0.9230
240 B20 0.9225
241 PIH 0.9223
242 MLT 0.9222
243 TEO 0.9222
244 OXE 0.9219
245 FJO 0.9219
246 2DR 0.9219
247 URF 0.9217
248 PPI 0.9216
249 LG5 0.9215
250 HQE 0.9214
251 FP2 0.9213
252 BTL 0.9212
253 YAN 0.9211
254 GLY 0.9211
255 NK 0.9210
256 FAH 0.9209
257 THE 0.9209
258 JAB 0.9208
259 92Z 0.9207
260 4MV 0.9207
261 F3V 0.9205
262 8GF 0.9204
263 AC5 0.9203
264 PLQ 0.9201
265 CIG 0.9200
266 284 0.9200
267 L89 0.9199
268 1MR 0.9198
269 EDG 0.9198
270 4DX 0.9198
271 AMC 0.9197
272 4HO 0.9197
273 TDR 0.9195
274 1AB 0.9194
275 2AF 0.9194
276 JZ0 0.9193
277 3SS 0.9191
278 DA1 0.9189
279 ICC 0.9189
280 BNZ 0.9188
281 76X 0.9187
282 ITN 0.9186
283 ILE 0.9183
284 R8A 0.9182
285 HGW 0.9182
286 PHZ 0.9182
287 2A1 0.9181
288 HX2 0.9180
289 FPN 0.9178
290 HEW 0.9178
291 HTS 0.9178
292 2CH 0.9177
293 IOM 0.9176
294 UGC 0.9176
295 0PY 0.9175
296 1AN 0.9175
297 FMS 0.9174
298 LG4 0.9174
299 PYJ 0.9173
300 TH0 0.9173
301 RP7 0.9173
302 8LG 0.9170
303 3ZS 0.9169
304 4H2 0.9167
305 TB6 0.9167
306 R2B 0.9167
307 40E 0.9166
308 FPI 0.9166
309 PCR 0.9165
310 JBN 0.9164
311 ETM 0.9161
312 MCT 0.9161
313 ES3 0.9160
314 FLA 0.9158
315 AML 0.9157
316 25R 0.9157
317 HAE 0.9155
318 6X8 0.9153
319 5MH 0.9153
320 FCN 0.9152
321 2A3 0.9152
322 938 0.9152
323 GLV 0.9152
324 B3R 0.9151
325 OAA 0.9150
326 BRP 0.9149
327 XBZ 0.9149
328 CP 0.9147
329 PXY 0.9147
330 2MH 0.9147
331 CMS 0.9146
332 275 0.9145
333 JZ2 0.9144
334 PYZ 0.9143
335 HY3 0.9142
336 LMR 0.9140
337 P1R 0.9137
338 HSW 0.9137
339 4CL 0.9136
340 2AC 0.9136
341 DCL 0.9135
342 GAG 0.9134
343 0R0 0.9132
344 B24 0.9131
345 4ZE 0.9130
346 1MC 0.9129
347 CNH 0.9129
348 BR9 0.9127
349 HHQ 0.9126
350 NIE 0.9126
351 MWM 0.9125
352 M3T 0.9125
353 H95 0.9123
354 XYD 0.9123
355 4HS 0.9121
356 4JJ 0.9120
357 VAH 0.9117
358 HSM 0.9116
359 6UA 0.9116
360 TSZ 0.9114
361 NEQ 0.9113
362 27Y 0.9112
363 A1U 0.9111
364 286 0.9111
365 ETF 0.9110
366 SAT 0.9109
367 2MP 0.9108
368 61G 0.9106
369 34A 0.9105
370 R1X 0.9103
371 YCP 0.9102
372 PYD 0.9102
373 ICP 0.9102
374 BML 0.9102
375 RSF 0.9101
376 4JN 0.9096
377 NCM 0.9094
378 AGU 0.9093
379 JZ5 0.9091
380 J3K 0.9087
381 IPU 0.9087
382 9CL 0.9082
383 BP9 0.9082
384 2YU 0.9081
385 13D 0.9078
386 MWJ 0.9077
387 DZZ 0.9076
388 3MC 0.9076
389 CRN 0.9074
390 98J 0.9073
391 MTD 0.9071
392 IMR 0.9070
393 PAE 0.9067
394 PCA 0.9066
395 AKR 0.9062
396 PXO 0.9060
397 5UC 0.9058
398 5AC 0.9055
399 TFS 0.9051
400 YHO 0.9051
401 43M 0.9049
402 OXQ 0.9048
403 P7I 0.9047
404 3CL 0.9046
405 F50 0.9045
406 MSF 0.9045
407 COM 0.9043
408 3FA 0.9041
409 60P 0.9040
410 MPI 0.9039
411 JZ9 0.9036
412 NBZ 0.9035
413 HT4 0.9031
414 51F 0.9031
415 2CO 0.9029
416 CRD 0.9028
417 MBD 0.9028
418 FPY 0.9027
419 5JC 0.9027
420 FFP 0.9026
421 QOS 0.9025
422 ISU 0.9020
423 JZ1 0.9020
424 OHG 0.9020
425 CP2 0.9018
426 CIZ 0.9018
427 BZI 0.9018
428 4JO 0.9018
429 R3W 0.9017
430 HVB 0.9014
431 GBD 0.9014
432 0R1 0.9014
433 2CM 0.9011
434 6NA 0.9010
435 MGX 0.9008
436 TM7 0.9008
437 AX2 0.9008
438 GVH 0.9006
439 3CE 0.9005
440 VSO 0.9004
441 47J 0.9003
442 DEN 0.9002
443 2C9 0.9001
444 FLM 0.9001
445 IOL 0.9001
446 MRZ 0.9001
447 0CT 0.9000
448 BEZ 0.8998
449 GMN 0.8997
450 IUR 0.8997
451 BZF 0.8996
452 3MH 0.8995
453 14J 0.8995
454 TAN 0.8994
455 2MY 0.8994
456 9A4 0.8993
457 IND 0.8991
458 NHY 0.8988
459 EFS 0.8984
460 GG6 0.8984
461 1XX 0.8982
462 LZ1 0.8982
463 MPD 0.8978
464 NMU 0.8974
465 TM4 0.8972
466 TZZ 0.8971
467 PZA 0.8967
468 TB0 0.8963
469 IDM 0.8963
470 JZ7 0.8963
471 6MH 0.8962
472 3SY 0.8959
473 1PT 0.8958
474 1DQ 0.8957
475 2ZX 0.8955
476 NIO 0.8954
477 BAM 0.8953
478 MET 0.8949
479 6PC 0.8948
480 3AY 0.8946
481 4SD 0.8944
482 MZW 0.8944
483 WDL 0.8943
484 IT2 0.8941
485 H76 0.8938
486 DUB 0.8935
487 COI 0.8934
488 TZL 0.8934
489 ZBT 0.8934
490 NCA 0.8934
491 Z6J 0.8932
492 5ZE 0.8925
493 XYS 0.8922
494 13X 0.8921
495 PG3 0.8915
496 OPE 0.8915
497 UY7 0.8914
498 XBT 0.8910
499 MZG 0.8910
500 ALF 0.8910
501 BEN 0.8909
502 DYA 0.8907
503 XYP 0.8906
504 ATO 0.8902
505 TCV 0.8902
506 4JP 0.8901
507 VGL 0.8900
508 Y8I 0.8899
509 FUB 0.8899
510 2RH 0.8895
511 DSS 0.8892
512 TLD 0.8889
513 ADE 0.8887
514 O7U 0.8877
515 XLS 0.8875
516 PGA 0.8874
517 9SB 0.8873
518 JYD 0.8869
519 M6W 0.8869
520 M2H 0.8866
521 HBA 0.8866
522 XUL 0.8864
523 8FH 0.8863
524 S0H 0.8861
525 FQI 0.8860
526 PAV 0.8858
527 ROR 0.8857
528 UYA 0.8857
529 32O 0.8856
530 PCT 0.8854
531 AHR 0.8854
532 BR8 0.8853
533 BXA 0.8849
534 TZE 0.8849
535 7VD 0.8845
536 ERH 0.8844
537 BDR 0.8840
538 54D 0.8838
539 9X6 0.8838
540 MMQ 0.8835
541 1BP 0.8835
542 3XX 0.8831
543 UNU 0.8831
544 2XX 0.8827
545 NTN 0.8819
546 5AN 0.8819
547 KYD 0.8817
548 AC0 0.8816
549 7HP 0.8811
550 TMH 0.8809
551 SS1 0.8809
552 34V 0.8808
553 MSE 0.8806
554 4JL 0.8804
555 BZX 0.8804
556 6AI 0.8795
557 C2A 0.8792
558 RIB 0.8792
559 2K4 0.8789
560 7CZ 0.8787
561 M58 0.8787
562 OXZ 0.8786
563 4VP 0.8786
564 SAL 0.8783
565 TLA 0.8783
566 11S 0.8780
567 0TR 0.8779
568 T6C 0.8779
569 5H1 0.8778
570 7MH 0.8775
571 0MK 0.8774
572 14O 0.8772
573 RUU 0.8771
574 QSC 0.8770
575 ES9 0.8770
576 5MB 0.8770
577 5MI 0.8769
578 KMT 0.8767
579 PAF 0.8764
580 DMV 0.8763
581 FBA 0.8763
582 94N 0.8762
583 RIP 0.8762
584 FYU 0.8761
585 6HQ 0.8761
586 SEJ 0.8757
587 PBC 0.8756
588 HPA 0.8755
589 JIF 0.8753
590 PEP 0.8751
591 PBE 0.8750
592 OEM 0.8746
593 KPL 0.8743
594 4XR 0.8740
595 F60 0.8737
596 FK1 0.8736
597 BTE 0.8730
598 KOJ 0.8721
599 BE2 0.8720
600 IP0 0.8717
601 HY1 0.8716
602 RSO 0.8715
603 VNJ 0.8711
604 4SV 0.8710
605 SS2 0.8709
606 IFM 0.8706
607 DFB 0.8706
608 AZF 0.8703
609 SRT 0.8700
610 URP 0.8700
611 2AS 0.8694
612 7WG 0.8689
613 FAN 0.8687
614 3U4 0.8686
615 9A7 0.8685
616 64K 0.8684
617 ABE 0.8684
618 1LN 0.8683
619 ES6 0.8683
620 H8N 0.8681
621 YTB 0.8680
622 271 0.8678
623 HIO 0.8677
624 ARA 0.8675
625 HMH 0.8674
626 BNS 0.8674
627 3SK 0.8673
628 FP1 0.8672
629 9EW 0.8669
630 SNE 0.8667
631 FUC 0.8658
632 ZZT 0.8656
633 TH7 0.8652
634 8EZ 0.8651
635 C2B 0.8651
636 ICF 0.8645
637 F05 0.8641
638 1DV 0.8633
639 L3Q 0.8632
640 1WD 0.8630
641 FUL 0.8628
642 261 0.8626
643 FPK 0.8625
644 MED 0.8623
645 HX3 0.8621
646 PHB 0.8620
647 OK7 0.8620
648 JKE 0.8619
649 XRG 0.8617
650 3Z7 0.8610
651 DFU 0.8609
652 PPV 0.8609
653 ARB 0.8606
654 2TQ 0.8595
655 PEL 0.8589
656 I2M 0.8587
657 F81 0.8585
658 HMU 0.8583
659 SKG 0.8580
660 24B 0.8578
661 260 0.8577
662 JZ4 0.8574
663 PEA 0.8570
664 3NT 0.8551
665 CEE 0.8546
666 FUF 0.8537
667 MXN 0.8527
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1YFS; Ligand: ALA; 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: 1yfs.bio2) has 10 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 1YFS; Ligand: ALA; 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: 1yfs.bio1) has 10 residues
No: Leader PDB Ligand Sequence Similarity
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