Receptor
PDB id Resolution Class Description Source Keywords
3OEM 1.9 Å NON-ENZYME: SIGNAL_HORMONE CRYSTAL STRUCTURE OF GLUN2D LIGAND-BINDING CORE IN COMPLEX W METHYL-D-ASPARTATE RATTUS NORVEGICUS ION CHANNEL N-METHYL-D-ASPARTATE TRANSPORT PROTEIN
Ref.: LIGAND-SPECIFIC DEACTIVATION TIME COURSE OF GLUN1/G NMDA RECEPTORS. NAT COMMUN V. 2 294 2011
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
OEM A:287;
 Valid;
 none;
 submit data
147.129 C5 H9 N O4 CN[C@...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3OEN 1.8 Å NON-ENZYME: SIGNAL_HORMONE CRYSTAL STRUCTURE OF GLUN2D LIGAND-BINDING CORE IN COMPLEX W GLUTAMATE RATTUS NORVEGICUS ION CHANNEL L-GLUTAMATE DISULFIDE BONDS TRANSPORT PROTEIN
Ref.: LIGAND-SPECIFIC DEACTIVATION TIME COURSE OF GLUN1/G NMDA RECEPTORS. NAT COMMUN V. 2 294 2011
Members (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 289 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)....
70% Homology Family (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 214 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)....
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: OEM; Similar ligands found: 6
No: Ligand ECFP6 Tc MDL keys Tc
1 OEM 1 1
2 MLE 0.592593 0.666667
3 NCD 0.5 0.621622
4 NFQ 0.46875 0.69697
5 EKN 0.441176 0.621622
6 158 0.416667 0.685714
Similar Ligands (3D)
Ligand no: 1; Ligand: OEM; Similar ligands found: 418
No: Ligand Similarity coefficient
1 SC2 0.9731
2 CIZ 0.9629
3 DAS 0.9600
4 MLT 0.9594
5 IOM 0.9569
6 P4B 0.9541
7 ASP 0.9532
8 AN0 0.9526
9 ASN 0.9521
10 OAA 0.9499
11 N8P 0.9471
12 8EZ 0.9454
13 TEO 0.9435
14 FPK 0.9432
15 NXA 0.9427
16 CMS 0.9419
17 CRN 0.9410
18 LEU 0.9404
19 SRT 0.9374
20 LMR 0.9366
21 98J 0.9364
22 7N0 0.9363
23 TLA 0.9359
24 ITN 0.9356
25 GLU 0.9339
26 2PG 0.9337
27 DOR 0.9335
28 CDV 0.9328
29 PEZ 0.9317
30 6JN 0.9296
31 COI 0.9271
32 PRZ 0.9261
33 6CS 0.9255
34 DGL 0.9252
35 2IT 0.9252
36 PEP 0.9251
37 2RH 0.9239
38 JYD 0.9235
39 ORO 0.9235
40 MEV 0.9229
41 AKG 0.9223
42 SIF 0.9221
43 PZI 0.9218
44 AUD 0.9212
45 GLY CYS 0.9206
46 IPM 0.9199
47 GLN 0.9193
48 3OC 0.9193
49 2DR 0.9193
50 GYE 0.9192
51 URQ 0.9172
52 8EW 0.9156
53 UGC 0.9141
54 RBL 0.9131
55 AHR 0.9124
56 HDA 0.9123
57 DPF 0.9120
58 HL5 0.9118
59 5HY 0.9114
60 PCA 0.9113
61 EHM 0.9107
62 40E 0.9096
63 VPR 0.9095
64 GLY PRO 0.9094
65 SPV 0.9093
66 N7P 0.9092
67 6LW 0.9089
68 4CS 0.9089
69 AC5 0.9080
70 YCP 0.9077
71 GLY ALA 0.9076
72 DPJ 0.9074
73 GZ3 0.9074
74 TRA 0.9072
75 CAM 0.9070
76 2TQ 0.9069
77 ICF 0.9067
78 23B 0.9065
79 261 0.9065
80 ZGL 0.9061
81 QFH 0.9060
82 ROR 0.9059
83 TAR 0.9058
84 BE2 0.9053
85 PEQ 0.9052
86 ORN 0.9051
87 3SK 0.9050
88 0OC 0.9044
89 TRC 0.9039
90 HIO 0.9034
91 5AC 0.9033
92 PPR 0.9033
93 R9S 0.9032
94 HZP 0.9031
95 FOC 0.9031
96 9X7 0.9023
97 2HG 0.9017
98 QDK 0.9017
99 HSE 0.9016
100 69O 0.9011
101 CXF 0.9009
102 ALO 0.9008
103 BDR 0.9007
104 ISD 0.9006
105 2EH 0.9005
106 3PG 0.9002
107 FP1 0.9000
108 VNJ 0.8999
109 IP0 0.8996
110 FB1 0.8996
111 2AL 0.8995
112 5XB 0.8993
113 F9P 0.8992
114 HYA 0.8991
115 AOR 0.8986
116 DCL 0.8983
117 G2H 0.8982
118 RUU 0.8971
119 GAG 0.8969
120 PBE 0.8967
121 VAL 0.8964
122 0V5 0.8964
123 SAL 0.8962
124 AMC 0.8961
125 FBV 0.8958
126 CIT 0.8958
127 WTZ 0.8956
128 RIB 0.8954
129 DAB 0.8953
130 JKE 0.8951
131 NTM 0.8949
132 1AL 0.8949
133 51F 0.8944
134 AKB 0.8944
135 TFB 0.8943
136 THE 0.8943
137 FUB 0.8942
138 HPA 0.8940
139 TZE 0.8939
140 3SL 0.8938
141 URP 0.8935
142 CCB 0.8930
143 GBD 0.8930
144 3AL 0.8929
145 RMN 0.8925
146 NMJ 0.8923
147 3U4 0.8921
148 FLC 0.8920
149 MET 0.8918
150 DIG 0.8917
151 9TY 0.8915
152 DS0 0.8914
153 XLS 0.8914
154 ASC 0.8913
155 NVA 0.8910
156 XUL 0.8904
157 PAF 0.8903
158 EDG 0.8903
159 THR 0.8902
160 SJ5 0.8902
161 IFL 0.8899
162 9J3 0.8898
163 FPY 0.8895
164 FUM 0.8895
165 5FX 0.8895
166 RNS 0.8894
167 UY7 0.8894
168 RSF 0.8891
169 2AS 0.8887
170 6UA 0.8886
171 PRO 0.8883
172 ILE 0.8881
173 ES6 0.8880
174 JZ3 0.8880
175 3MV 0.8879
176 HY3 0.8874
177 TMH 0.8872
178 192 0.8869
179 R67 0.8865
180 2RA 0.8864
181 XYL 0.8863
182 DXX 0.8862
183 DHS 0.8862
184 PSV 0.8862
185 IQ0 0.8860
186 SD4 0.8859
187 2A7 0.8858
188 4PW 0.8857
189 7HP 0.8855
190 AHB 0.8855
191 2LP 0.8854
192 SIN 0.8854
193 OHP 0.8853
194 GBN 0.8853
195 XSP 0.8853
196 OXQ 0.8850
197 TCM 0.8850
198 GLY LEU 0.8848
199 PLU 0.8844
200 RB0 0.8843
201 RNT 0.8842
202 MAE 0.8841
203 ADE 0.8839
204 R2B 0.8839
205 SKG 0.8838
206 4MV 0.8838
207 HYP 0.8837
208 ATH 0.8836
209 KYD 0.8835
210 AZF 0.8834
211 1LN 0.8832
212 2XX 0.8832
213 TZZ 0.8829
214 NK 0.8829
215 LNO 0.8828
216 DGN 0.8828
217 FPI 0.8827
218 PHT 0.8822
219 1WD 0.8822
220 32O 0.8821
221 1AB 0.8820
222 LRH 0.8820
223 60P 0.8820
224 ZZ3 0.8819
225 S76 0.8819
226 GUA 0.8818
227 VAH 0.8817
228 GG6 0.8817
229 2FT 0.8814
230 FLA 0.8813
231 12M 0.8812
232 LLQ 0.8808
233 NEQ 0.8807
234 HCS 0.8807
235 ZBT 0.8806
236 SF6 0.8803
237 4HM 0.8802
238 MUC 0.8802
239 GLY ASP 0.8802
240 P22 0.8801
241 DII 0.8796
242 KPL 0.8795
243 0MK 0.8793
244 R1X 0.8792
245 LER 0.8791
246 IXW 0.8790
247 FRU 0.8790
248 23W 0.8789
249 IFM 0.8789
250 QY9 0.8789
251 RB5 0.8788
252 DMV 0.8787
253 IPZ 0.8787
254 278 0.8786
255 2CO 0.8785
256 G4D 0.8785
257 XYS 0.8784
258 BR8 0.8784
259 SF9 0.8783
260 DGJ 0.8782
261 3V4 0.8781
262 CNL 0.8781
263 MAN 0.8780
264 RIP 0.8780
265 1P3 0.8779
266 IT9 0.8779
267 GGL 0.8777
268 13X 0.8776
269 O7U 0.8775
270 WDL 0.8774
271 TZL 0.8773
272 GAL 0.8771
273 DCD 0.8770
274 210 0.8769
275 FUF 0.8769
276 R9M 0.8768
277 PRS 0.8768
278 DHI 0.8762
279 Z6J 0.8760
280 ALA ALA 0.8759
281 FW5 0.8757
282 XBT 0.8757
283 DFB 0.8753
284 ENL 0.8750
285 FSG 0.8749
286 7WV 0.8749
287 ICN 0.8747
288 SER 0.8746
289 9X6 0.8746
290 AGK 0.8744
291 5ZE 0.8743
292 GLA 0.8743
293 JZ4 0.8742
294 FUL 0.8741
295 5AN 0.8741
296 CRS 0.8740
297 PRY 0.8738
298 SNE 0.8737
299 T2C 0.8737
300 3AY 0.8736
301 ERH 0.8734
302 FUC 0.8733
303 286 0.8733
304 4WK 0.8733
305 2CL 0.8732
306 DFU 0.8732
307 HBU 0.8730
308 BGC 0.8730
309 GIF 0.8730
310 2PC 0.8728
311 KMT 0.8725
312 285 0.8724
313 GAF 0.8724
314 41K 0.8724
315 2ZX 0.8723
316 AX2 0.8720
317 KIV 0.8720
318 PSJ 0.8720
319 DTL 0.8719
320 TAG 0.8716
321 9YL 0.8712
322 SWA 0.8711
323 IMR 0.8710
324 V6F 0.8710
325 40O 0.8710
326 DSN 0.8709
327 SDD 0.8709
328 OXZ 0.8708
329 MRY 0.8708
330 4SD 0.8707
331 DMJ 0.8706
332 MRZ 0.8705
333 4NG 0.8703
334 MED 0.8702
335 GLC 0.8700
336 ICT 0.8698
337 ONL 0.8698
338 BSX 0.8696
339 AL0 0.8693
340 YHO 0.8690
341 SPA 0.8687
342 KLW 0.8685
343 IDH 0.8685
344 ARA 0.8683
345 7MH 0.8683
346 NLE 0.8682
347 5NU 0.8682
348 AOS 0.8681
349 BFM 0.8679
350 II6 0.8677
351 149 0.8676
352 284 0.8667
353 8GL 0.8666
354 LDU 0.8665
355 7A8 0.8661
356 BMA 0.8660
357 DGY 0.8657
358 F81 0.8656
359 DZX 0.8656
360 A3B 0.8654
361 HIU 0.8653
362 H3M 0.8652
363 JZ1 0.8650
364 13P 0.8650
365 CAH 0.8647
366 H76 0.8644
367 3LR 0.8644
368 RAT 0.8643
369 7A2 0.8640
370 ACH 0.8639
371 4SV 0.8638
372 10L 0.8637
373 GIV 0.8635
374 AS3 0.8633
375 GLY MET 0.8632
376 03W 0.8624
377 IF7 0.8621
378 3BU 0.8621
379 ARW 0.8621
380 23A 0.8616
381 UYA 0.8616
382 G8M 0.8616
383 NMG 0.8615
384 RAM 0.8614
385 2MN 0.8610
386 2FG 0.8608
387 R8S 0.8608
388 DCY 0.8607
389 2KT 0.8607
390 OAF 0.8606
391 ES4 0.8605
392 9SE 0.8604
393 FCB 0.8603
394 GLL 0.8600
395 PM6 0.8599
396 DYT 0.8595
397 DUC 0.8588
398 6MP 0.8588
399 7WA 0.8586
400 1SA 0.8583
401 MFB 0.8582
402 GRO 0.8582
403 I2M 0.8580
404 64K 0.8578
405 FAC 0.8577
406 9DA 0.8577
407 KDF 0.8577
408 9HX 0.8574
409 3PY 0.8574
410 E4P 0.8568
411 G2F 0.8558
412 GIO 0.8555
413 RM4 0.8555
414 1SP 0.8552
415 BP1 0.8551
416 3DO 0.8546
417 4VY 0.8522
418 PAV 0.8508
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3OEN; Ligand: GLU; 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: 3oen.bio1) has 16 residues
No: Leader PDB Ligand Sequence Similarity
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