Receptor
PDB id Resolution Class Description Source Keywords
2RCB 1.62 Å NON-ENZYME: SIGNAL_HORMONE CRYSTAL STRUCTURE OF THE NR3B LIGAND BINDING CORE COMPLEX WI SERINE AT 1.62 ANGSTROM RESOLUTION RATTUS NORVEGICUS MEMBRANE PROTEIN CELL JUNCTION GLYCOPROTEIN ION TRANSPORTCHANNEL MAGNESIUM POSTSYNAPTIC CELL MEMBRANE RECEPTOR STRANSMEMBRANE TRANSPORT
Ref.: MOLECULAR MECHANISM OF LIGAND RECOGNITION BY NR3 SU GLUTAMATE RECEPTORS. EMBO J. V. 27 2158 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
DSN A:901;
B:902;
 Valid;
Valid;
 none;
none;
 submit data
105.093 C3 H7 N O3 C([C@...
GOL A:902;
 Invalid;
 none;
 submit data
92.094 C3 H8 O3 C(C(C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2RCA 1.58 Å NON-ENZYME: SIGNAL_HORMONE CRYSTAL STRUCTURE OF THE NR3B LIGAND BINDING CORE COMPLEX WI AT 1.58 ANGSTROM RESOLUTION RATTUS NORVEGICUS MEMBRANE PROTEIN CELL JUNCTION GLYCOPROTEIN ION TRANSPORTCHANNEL MAGNESIUM POSTSYNAPTIC CELL MEMBRANE RECEPTOR STRANSMEMBRANE TRANSPORT
Ref.: MOLECULAR MECHANISM OF LIGAND RECOGNITION BY NR3 SU GLUTAMATE RECEPTORS. EMBO J. V. 27 2158 2008
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 289 families.
1 2RCB - DSN C3 H7 N O3 C([C@H](C(....
2 2RCA Kd = 16.4 nM GLY C2 H5 N O2 C(C(=O)O)N
70% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 214 families.
1 2RC9 - 1AC C4 H7 N O2 C1CC1(C(=O....
2 2RC8 - DSN C3 H7 N O3 C([C@H](C(....
3 2RC7 - GLY C2 H5 N O2 C(C(=O)O)N
4 2RCB - DSN C3 H7 N O3 C([C@H](C(....
5 2RCA Kd = 16.4 nM GLY C2 H5 N O2 C(C(=O)O)N
50% Homology Family (19)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 181 families.
1 3OEM - OEM C5 H9 N O4 CN[C@H](CC....
2 3OEN - GLU C5 H9 N O4 C(CC(=O)O)....
3 3OEK - ASP C4 H7 N O4 C([C@@H](C....
4 4JWY - 1N4 C8 H13 N3 O3 CCCc1cnn(c....
5 3OEL - DGL C5 H9 N O4 C(CC(=O)O)....
6 4JWX - 1N4 C8 H13 N3 O3 CCCc1cnn(c....
7 2A5S - GLU C5 H9 N O4 C(CC(=O)O)....
8 2RC9 - 1AC C4 H7 N O2 C1CC1(C(=O....
9 2RC8 - DSN C3 H7 N O3 C([C@H](C(....
10 2RC7 - GLY C2 H5 N O2 C(C(=O)O)N
11 2RCB - DSN C3 H7 N O3 C([C@H](C(....
12 2RCA Kd = 16.4 nM GLY C2 H5 N O2 C(C(=O)O)N
13 1Y20 Ki = 4.8 uM 1AC C4 H7 N O2 C1CC1(C(=O....
14 1PB7 - GLY C2 H5 N O2 C(C(=O)O)N
15 1Y1Z Ki = 0.831 mM 192 C5 H9 N O2 C1CC(C1)(C....
16 1PB8 Ki = 7.02 uM DSN C3 H7 N O3 C([C@H](C(....
17 1Y1M Ki = 15.3 mM AC5 C6 H11 N O2 C1CCC(C1)(....
18 1PBQ Ki = 0.54 uM DK1 C10 H5 Cl2 N O3 c1c(cc(c2c....
19 1PB9 Ki = 241 uM 4AX C3 H6 N2 O2 C1[C@H](C(....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: DSN; 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: DSN; Similar ligands found: 632
No: Ligand Similarity coefficient
1 03W 1.0000
2 A3B 1.0000
3 HIU 1.0000
4 KG7 1.0000
5 3PY 0.9996
6 2KT 0.9996
7 DXX 0.9864
8 SMB 0.9827
9 LAC 0.9822
10 THR 0.9804
11 1AC 0.9792
12 HUI 0.9784
13 DAL 0.9783
14 39J 0.9761
15 ALQ 0.9729
16 2OP 0.9728
17 DE2 0.9720
18 MB3 0.9710
19 9X7 0.9708
20 PYR 0.9707
21 OXM 0.9696
22 OXL 0.9682
23 OXD 0.9635
24 HBR 0.9634
25 23W 0.9621
26 9YL 0.9620
27 IPH 0.9610
28 2HA 0.9608
29 GXV 0.9607
30 3OH 0.9601
31 MLI 0.9599
32 CAQ 0.9591
33 AKB 0.9589
34 BAL 0.9588
35 1SP 0.9584
36 SSN 0.9583
37 CEJ 0.9583
38 NIS 0.9578
39 E60 0.9572
40 TF4 0.9570
41 192 0.9570
42 BUO 0.9570
43 HBS 0.9569
44 VAL 0.9569
45 HDA 0.9567
46 MMZ 0.9563
47 BUA 0.9556
48 MEU 0.9552
49 LER 0.9551
50 LEA 0.9549
51 SAR 0.9547
52 AOA 0.9540
53 KSW 0.9535
54 BUB 0.9532
55 GOL 0.9529
56 2IM 0.9529
57 3GR 0.9527
58 GXE 0.9524
59 BU4 0.9520
60 A2Q 0.9519
61 KIV 0.9518
62 PYM 0.9517
63 BAQ 0.9517
64 ALA 0.9510
65 FW5 0.9509
66 AAE 0.9508
67 NAK 0.9503
68 HGY 0.9500
69 ALO 0.9487
70 CYH 0.9486
71 V1L 0.9483
72 MLA 0.9483
73 69O 0.9482
74 MLM 0.9477
75 PRS 0.9475
76 HSL 0.9472
77 CXL 0.9472
78 PPF 0.9471
79 PRI 0.9470
80 MBN 0.9469
81 5Y9 0.9469
82 4AX 0.9456
83 280 0.9455
84 MAE 0.9454
85 7EX 0.9453
86 C5J 0.9448
87 2AP 0.9448
88 HVK 0.9448
89 8CL 0.9447
90 TAY 0.9447
91 MRY 0.9447
92 DPR 0.9446
93 24T 0.9444
94 IVA 0.9441
95 HYN 0.9438
96 WOT 0.9438
97 MAK 0.9432
98 93B 0.9431
99 3AP 0.9429
100 D2P 0.9429
101 MMU 0.9428
102 HHN 0.9423
103 BMD 0.9422
104 25T 0.9420
105 XIX 0.9420
106 BUQ 0.9419
107 3ZQ 0.9419
108 4AP 0.9417
109 TTO 0.9416
110 DTU 0.9413
111 HRZ 0.9411
112 NVI 0.9411
113 2PC 0.9408
114 ATQ 0.9407
115 URA 0.9403
116 LGA 0.9402
117 HAI 0.9399
118 BAE 0.9398
119 1DH 0.9389
120 RCO 0.9389
121 MTG 0.9389
122 TMZ 0.9388
123 SIN 0.9382
124 P2D 0.9382
125 GBL 0.9382
126 DMG 0.9381
127 26D 0.9379
128 8GF 0.9378
129 LG5 0.9377
130 CHT 0.9376
131 BEW 0.9371
132 FP2 0.9368
133 LG3 0.9367
134 9PO 0.9366
135 IQ0 0.9364
136 DCD 0.9363
137 278 0.9362
138 L89 0.9359
139 3CH 0.9358
140 40O 0.9355
141 SGL 0.9355
142 AMT 0.9350
143 HBX 0.9349
144 6SP 0.9349
145 ABU 0.9345
146 H3M 0.9345
147 93Q 0.9344
148 PIH 0.9343
149 HPY 0.9343
150 TMT 0.9342
151 J1Z 0.9340
152 LG4 0.9339
153 HQE 0.9337
154 HVQ 0.9336
155 DA1 0.9336
156 PRO 0.9335
157 92Z 0.9335
158 DMI 0.9334
159 IHG 0.9334
160 DTL 0.9334
161 MZY 0.9333
162 25R 0.9333
163 1CB 0.9332
164 SYN 0.9331
165 BXO 0.9329
166 282 0.9329
167 2CH 0.9329
168 PLQ 0.9328
169 MZ0 0.9327
170 SLP 0.9324
171 XPO 0.9322
172 938 0.9322
173 HV2 0.9321
174 8LG 0.9321
175 ABN 0.9318
176 9TY 0.9318
177 4JU 0.9318
178 HGW 0.9316
179 L60 0.9315
180 CYT 0.9314
181 1AN 0.9314
182 OXE 0.9314
183 CRS 0.9313
184 PCR 0.9313
185 BVG 0.9312
186 PYF 0.9312
187 3MT 0.9309
188 2AF 0.9307
189 FPN 0.9305
190 JZ6 0.9305
191 76X 0.9304
192 273 0.9303
193 ITU 0.9301
194 6X8 0.9301
195 BTL 0.9300
196 BVC 0.9297
197 BVF 0.9297
198 3HR 0.9296
199 ICN 0.9294
200 HGQ 0.9292
201 PXY 0.9291
202 HTS 0.9290
203 3TR 0.9287
204 XAP 0.9285
205 4HO 0.9278
206 NMG 0.9277
207 PY7 0.9277
208 0R0 0.9275
209 DTI 0.9275
210 ETX 0.9274
211 PUT 0.9272
212 3HL 0.9271
213 4CH 0.9271
214 BYZ 0.9270
215 YAN 0.9269
216 TFB 0.9264
217 4XX 0.9263
218 4MZ 0.9261
219 NBE 0.9261
220 XYD 0.9258
221 NK 0.9257
222 265 0.9257
223 2MZ 0.9253
224 PYG 0.9252
225 1MR 0.9252
226 5KX 0.9251
227 4HS 0.9249
228 TH0 0.9249
229 4H2 0.9248
230 4HA 0.9247
231 1MZ 0.9247
232 1MC 0.9247
233 URF 0.9245
234 3ZS 0.9244
235 TDR 0.9242
236 2AI 0.9241
237 4ZE 0.9238
238 FAH 0.9235
239 IDH 0.9235
240 EGD 0.9234
241 JZ3 0.9234
242 MR3 0.9233
243 4JN 0.9233
244 ECE 0.9232
245 FJO 0.9231
246 HOW 0.9231
247 PYZ 0.9230
248 5MH 0.9227
249 3BB 0.9225
250 CIG 0.9222
251 BML 0.9222
252 2EZ 0.9221
253 HEW 0.9221
254 FUM 0.9219
255 B3R 0.9216
256 2MP 0.9216
257 WBU 0.9214
258 AC5 0.9211
259 M3T 0.9208
260 1DU 0.9207
261 AMC 0.9206
262 HLT 0.9205
263 TP5 0.9205
264 MCT 0.9205
265 C21 0.9203
266 F3V 0.9202
267 275 0.9200
268 2MH 0.9198
269 9CL 0.9196
270 GOA 0.9194
271 ES3 0.9191
272 4CL 0.9191
273 JZ0 0.9188
274 284 0.9188
275 2YU 0.9187
276 BRP 0.9186
277 2AC 0.9184
278 FOA 0.9183
279 286 0.9183
280 DCL 0.9183
281 ICP 0.9182
282 PYD 0.9182
283 JZ2 0.9182
284 8X3 0.9181
285 ODV 0.9181
286 HHQ 0.9180
287 4JJ 0.9175
288 FPI 0.9174
289 H95 0.9172
290 DUC 0.9170
291 R2B 0.9168
292 5UC 0.9168
293 A8C 0.9167
294 APY 0.9167
295 CRN 0.9167
296 GLY 0.9164
297 WTZ 0.9164
298 4DX 0.9164
299 QFH 0.9163
300 MWM 0.9162
301 ITN 0.9160
302 A1U 0.9160
303 PYC 0.9157
304 23B 0.9156
305 TSZ 0.9156
306 R8A 0.9155
307 34A 0.9153
308 3SS 0.9152
309 IOL 0.9152
310 MLT 0.9151
311 27Y 0.9149
312 RP7 0.9148
313 PYJ 0.9146
314 2HE 0.9146
315 JBN 0.9146
316 RSF 0.9145
317 XBZ 0.9145
318 1AB 0.9142
319 BR9 0.9140
320 ETM 0.9139
321 GLV 0.9139
322 6UA 0.9138
323 B20 0.9137
324 HAE 0.9135
325 LMR 0.9134
326 TAU 0.9133
327 TZC 0.9132
328 POA 0.9130
329 EDG 0.9127
330 PCA 0.9126
331 PPI 0.9126
332 NXA 0.9124
333 NIE 0.9124
334 285 0.9118
335 UYA 0.9117
336 BNZ 0.9117
337 CP 0.9116
338 OHG 0.9116
339 HX2 0.9115
340 ETF 0.9115
341 SMV 0.9113
342 BP9 0.9113
343 HT4 0.9111
344 43M 0.9109
345 MWJ 0.9106
346 0PY 0.9106
347 THE 0.9103
348 4MV 0.9100
349 HZP 0.9099
350 P1R 0.9098
351 CMS 0.9097
352 B24 0.9096
353 UY7 0.9092
354 PHZ 0.9092
355 R1X 0.9089
356 VX 0.9088
357 QOS 0.9086
358 MSF 0.9081
359 GAG 0.9081
360 T2C 0.9080
361 CIZ 0.9080
362 FLA 0.9072
363 AGU 0.9071
364 NEQ 0.9070
365 4JO 0.9068
366 GBD 0.9067
367 DTT 0.9066
368 PAE 0.9066
369 JZ1 0.9065
370 CNH 0.9064
371 2DR 0.9059
372 IPU 0.9059
373 IUR 0.9059
374 61G 0.9058
375 5MP 0.9057
376 IOM 0.9056
377 60P 0.9053
378 UGC 0.9050
379 ICC 0.9049
380 HY3 0.9046
381 JAB 0.9045
382 98J 0.9041
383 F50 0.9039
384 5JC 0.9039
385 GG6 0.9037
386 MPD 0.9033
387 IMR 0.9033
388 0R1 0.9031
389 TM7 0.9031
390 NHY 0.9030
391 ILE 0.9026
392 HSM 0.9023
393 FMS 0.9020
394 MGX 0.9019
395 5AC 0.9018
396 OAA 0.9014
397 R3W 0.9007
398 HVB 0.9003
399 YCP 0.8996
400 JZ5 0.8995
401 Y8I 0.8995
402 2A3 0.8994
403 TB0 0.8992
404 OXQ 0.8991
405 BZF 0.8991
406 YHO 0.8989
407 BZI 0.8988
408 LZ1 0.8988
409 TEO 0.8986
410 3SY 0.8985
411 P7I 0.8979
412 TAN 0.8979
413 VAH 0.8976
414 DEN 0.8975
415 IND 0.8975
416 TLD 0.8974
417 MPI 0.8973
418 2RH 0.8972
419 GVH 0.8972
420 0CT 0.8970
421 COI 0.8968
422 FUB 0.8968
423 NMU 0.8968
424 TB6 0.8967
425 JYD 0.8963
426 MRZ 0.8962
427 PXO 0.8962
428 IDM 0.8960
429 NCM 0.8958
430 FPY 0.8955
431 LDU 0.8952
432 AKR 0.8952
433 MZW 0.8952
434 COM 0.8951
435 EFS 0.8951
436 ISU 0.8950
437 ALF 0.8946
438 9A4 0.8945
439 47J 0.8945
440 1XX 0.8941
441 8FH 0.8940
442 40E 0.8938
443 HBA 0.8935
444 4VP 0.8930
445 HTX 0.8929
446 JZ9 0.8924
447 XYS 0.8923
448 HSW 0.8922
449 ATO 0.8918
450 HYA 0.8917
451 51F 0.8915
452 GLY ALA 0.8913
453 S0H 0.8913
454 3CL 0.8911
455 3FA 0.8910
456 SAT 0.8910
457 MBD 0.8908
458 URP 0.8905
459 MZG 0.8900
460 FCN 0.8896
461 4JP 0.8894
462 2A1 0.8894
463 PGA 0.8890
464 PZA 0.8886
465 FFP 0.8881
466 HYP 0.8880
467 O7U 0.8878
468 RIB 0.8877
469 6PC 0.8877
470 BEN 0.8874
471 TFS 0.8873
472 NBZ 0.8873
473 ADE 0.8873
474 BEZ 0.8872
475 XYP 0.8870
476 4SD 0.8870
477 BAM 0.8868
478 6MH 0.8867
479 H8N 0.8866
480 KYD 0.8865
481 FLM 0.8862
482 XBT 0.8860
483 BZX 0.8860
484 1DQ 0.8860
485 AHR 0.8859
486 14J 0.8859
487 SS2 0.8859
488 13D 0.8859
489 MMQ 0.8857
490 NIO 0.8856
491 NCA 0.8856
492 OPE 0.8853
493 2CM 0.8852
494 VGL 0.8851
495 DUB 0.8850
496 3MC 0.8850
497 2MY 0.8848
498 1PT 0.8848
499 3XX 0.8847
500 FBA 0.8846
501 3CE 0.8846
502 TCV 0.8841
503 VSO 0.8840
504 MED 0.8839
505 TZE 0.8837
506 9SB 0.8835
507 CRD 0.8831
508 TAR 0.8830
509 4JL 0.8829
510 6AI 0.8826
511 AC0 0.8823
512 HMH 0.8821
513 2C9 0.8821
514 5MB 0.8820
515 BDR 0.8820
516 NTN 0.8817
517 SAL 0.8817
518 SS1 0.8814
519 3MH 0.8811
520 6HQ 0.8810
521 TZZ 0.8808
522 5H1 0.8805
523 C2B 0.8800
524 Z6J 0.8800
525 2K4 0.8799
526 7HP 0.8799
527 4JM 0.8796
528 BXA 0.8794
529 GMN 0.8793
530 EHM 0.8793
531 XLS 0.8792
532 7MH 0.8791
533 UNU 0.8791
534 TM4 0.8791
535 7VD 0.8789
536 ES9 0.8788
537 NSP 0.8786
538 MET 0.8784
539 HPA 0.8784
540 MTD 0.8784
541 RBL 0.8783
542 TZL 0.8782
543 FYU 0.8782
544 ARB 0.8781
545 QSC 0.8781
546 F60 0.8780
547 TH7 0.8778
548 VNJ 0.8778
549 IP0 0.8776
550 5MI 0.8776
551 7CZ 0.8772
552 14O 0.8772
553 IFM 0.8771
554 YTB 0.8769
555 T6C 0.8767
556 DPF 0.8760
557 PBC 0.8760
558 0TR 0.8759
559 CP2 0.8754
560 PAV 0.8753
561 TMH 0.8752
562 FQI 0.8751
563 4SV 0.8751
564 BE2 0.8747
565 8EZ 0.8746
566 3SK 0.8742
567 AX2 0.8742
568 ROR 0.8741
569 DSS 0.8740
570 BNS 0.8739
571 DZZ 0.8731
572 5AN 0.8731
573 3Z7 0.8721
574 94N 0.8720
575 PEP 0.8719
576 3U4 0.8719
577 ZZT 0.8719
578 FAN 0.8719
579 PAF 0.8716
580 RUU 0.8714
581 ABE 0.8713
582 WDL 0.8710
583 OEM 0.8709
584 M58 0.8706
585 HMU 0.8702
586 ES6 0.8700
587 F05 0.8699
588 BTE 0.8699
589 J3K 0.8696
590 7WG 0.8696
591 1WD 0.8692
592 TLA 0.8687
593 F81 0.8687
594 0MK 0.8682
595 FP1 0.8678
596 4XR 0.8674
597 JKE 0.8671
598 DFB 0.8671
599 PHB 0.8670
600 13X 0.8669
601 AZF 0.8668
602 RSO 0.8668
603 BR8 0.8668
604 KOJ 0.8667
605 2CO 0.8667
606 3AY 0.8666
607 ICF 0.8663
608 PPV 0.8662
609 FSG 0.8659
610 KMT 0.8650
611 5ZE 0.8644
612 JIF 0.8643
613 1BP 0.8641
614 SRT 0.8638
615 261 0.8631
616 SNE 0.8628
617 2ZX 0.8621
618 HX3 0.8616
619 1LN 0.8612
620 OXZ 0.8603
621 2AS 0.8594
622 1DV 0.8592
623 9X6 0.8588
624 PBE 0.8587
625 MSE 0.8564
626 PEA 0.8561
627 HY1 0.8555
628 8H8 0.8554
629 PAH 0.8552
630 KPL 0.8552
631 I2M 0.8550
632 271 0.8540
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2RCA; Ligand: GLY; 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: 2rca.bio1) has 11 residues
No: Leader PDB Ligand Sequence Similarity
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