Receptor
PDB id Resolution Class Description Source Keywords
6UZG 1.94 Å NON-ENZYME: SIGNAL_HORMONE CRYSTAL STRUCTURE OF GLUN1/GLUN2A-4M MUTANT LIGAND-BINDING D COMPLEX WITH GLYCINE AND HOMOQUINOLINIC ACID RATTUS NORVEGICUS NMDAR LIGAND-BINDING DOMAIN AGONIST MEMBRANE PROTEIN
Ref.: STRUCTURAL BASIS OF SUBTYPE-SELECTIVE COMPETITIVE A FOR GLUN2C/2D-CONTAINING NMDA RECEPTORS. NAT COMMUN V. 11 423 2020
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GLY A:1001;
 Valid;
 none;
 submit data
75.067 C2 H5 N O2 C(C(=...
QM1 B:301;
 Valid;
 none;
 submit data
181.145 C8 H7 N O4 c1cc(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5DEX 2.4 Å NON-ENZYME: SIGNAL_HORMONE CRYSTAL STRUCTURE OF GLUN1/GLUN2A NMDA RECEPTOR AGONIST BIND DOMAINS WITH GLYCINE AND ANTAGONIST, PHENYL-ACEPC RATTUS NORVEGICUS TRANSPORT PROTEIN RECEPTOR
Ref.: STRUCTURAL BASIS OF SUBUNIT SELECTIVITY FOR COMPETI RECEPTOR ANTAGONISTS WITH PREFERENCE FOR GLUN2A OVE SUBUNITS. PROC. NATL. ACAD. SCI. 2017 U.S.A.
Members (29)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 289 families.
1 5VII Ki = 51.8 nM 5DY C16 H18 F N3 O4 c1cc(ccc1C....
2 6USU - QGM C17 H15 Cl2 N3 O3 c1ccc(cc1)....
3 5H8F - GLY C2 H5 N O2 C(C(=O)O)N
4 2A5T - GLY C2 H5 N O2 C(C(=O)O)N
5 5VIJ Ki = 24.3 nM 5DX C13 H12 Br N3 O4 c1cc(ccc1n....
6 6UZW - GLY C2 H5 N O2 C(C(=O)O)N
7 6UZG - QM1 C8 H7 N O4 c1cc(c(nc1....
8 6UZX - GLY C2 H5 N O2 C(C(=O)O)N
9 5I57 - GLY C2 H5 N O2 C(C(=O)O)N
10 5H8Q - 5YE C18 H18 F N3 O S CCN(CC1=CC....
11 5U8C Ki = 29.58 nM 84J C17 H17 Br N3 O5 P C[C@@H](c1....
12 6UZR - QM1 C8 H7 N O4 c1cc(c(nc1....
13 5KCJ - GLY C2 H5 N O2 C(C(=O)O)N
14 5DEX Ki = 22.6 nM 5E0 C13 H13 N3 O4 c1ccc(cc1)....
15 5H8N - 5YD C20 H18 F N3 O3 S c1cc(cnc1)....
16 5TPA - GLY C2 H5 N O2 C(C(=O)O)N
17 4NF8 - GLU C5 H9 N O4 C(CC(=O)O)....
18 5KDT - GLU C5 H9 N O4 C(CC(=O)O)....
19 4NF4 - GLU C5 H9 N O4 C(CC(=O)O)....
20 4NF5 - 2JJ C5 H12 N O5 P C(C[C@H](C....
21 6USV - QGP C16 H16 Cl2 N O6 P c1cc(c(cc1....
22 5TP9 - GLU C5 H9 N O4 C(CC(=O)O)....
23 6UZ6 - GLY C2 H5 N O2 C(C(=O)O)N
24 5VIH Ki = 32.2 nM 5DZ C13 H12 F N3 O4 c1cc(ccc1n....
25 5H8H - GLY C2 H5 N O2 C(C(=O)O)N
26 5I59 ic50 = 641 nM 67Q C18 H19 F2 N5 O3 S2 Cc1c(ncc(n....
27 4NF6 Ki = 0.82 uM 2JL C21 H18 N2 O5 c1ccc2c(c1....
28 5I56 ic50 = 1530 nM 67P C21 H17 Cl F N3 O4 S c1ccc(cc1)....
29 5I2N - GLY C2 H5 N O2 C(C(=O)O)N
70% Homology Family (29)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 214 families.
1 5VII Ki = 51.8 nM 5DY C16 H18 F N3 O4 c1cc(ccc1C....
2 6USU - QGM C17 H15 Cl2 N3 O3 c1ccc(cc1)....
3 5H8F - GLY C2 H5 N O2 C(C(=O)O)N
4 2A5T - GLY C2 H5 N O2 C(C(=O)O)N
5 5VIJ Ki = 24.3 nM 5DX C13 H12 Br N3 O4 c1cc(ccc1n....
6 6UZW - GLY C2 H5 N O2 C(C(=O)O)N
7 6UZG - QM1 C8 H7 N O4 c1cc(c(nc1....
8 6UZX - GLY C2 H5 N O2 C(C(=O)O)N
9 5I57 - GLY C2 H5 N O2 C(C(=O)O)N
10 5H8Q - 5YE C18 H18 F N3 O S CCN(CC1=CC....
11 5U8C Ki = 29.58 nM 84J C17 H17 Br N3 O5 P C[C@@H](c1....
12 6UZR - QM1 C8 H7 N O4 c1cc(c(nc1....
13 5KCJ - GLY C2 H5 N O2 C(C(=O)O)N
14 5DEX Ki = 22.6 nM 5E0 C13 H13 N3 O4 c1ccc(cc1)....
15 5H8N - 5YD C20 H18 F N3 O3 S c1cc(cnc1)....
16 5TPA - GLY C2 H5 N O2 C(C(=O)O)N
17 4NF8 - GLU C5 H9 N O4 C(CC(=O)O)....
18 5KDT - GLU C5 H9 N O4 C(CC(=O)O)....
19 4NF4 - GLU C5 H9 N O4 C(CC(=O)O)....
20 4NF5 - 2JJ C5 H12 N O5 P C(C[C@H](C....
21 6USV - QGP C16 H16 Cl2 N O6 P c1cc(c(cc1....
22 5TP9 - GLU C5 H9 N O4 C(CC(=O)O)....
23 6UZ6 - GLY C2 H5 N O2 C(C(=O)O)N
24 5VIH Ki = 32.2 nM 5DZ C13 H12 F N3 O4 c1cc(ccc1n....
25 5H8H - GLY C2 H5 N O2 C(C(=O)O)N
26 5I59 ic50 = 641 nM 67Q C18 H19 F2 N5 O3 S2 Cc1c(ncc(n....
27 4NF6 Ki = 0.82 uM 2JL C21 H18 N2 O5 c1ccc2c(c1....
28 5I56 ic50 = 1530 nM 67P C21 H17 Cl F N3 O4 S c1ccc(cc1)....
29 5I2N - GLY C2 H5 N O2 C(C(=O)O)N
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 181 families.
1 6UZG - QM1 C8 H7 N O4 c1cc(c(nc1....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: GLY; Similar ligands found: 5
No: Ligand ECFP6 Tc MDL keys Tc
1 GLY 1 1
2 BAL 0.5625 0.708333
3 ABU 0.473684 0.708333
4 MCR 0.466667 0.65
5 2RA 0.421053 0.692308
Ligand no: 2; Ligand: QM1; Similar ligands found: 4
No: Ligand ECFP6 Tc MDL keys Tc
1 QM1 1 1
2 1WD 0.44186 0.606061
3 NTM 0.44186 0.821429
4 O2Y 0.44 0.787879
Similar Ligands (3D)
Ligand no: 1; Ligand: GLY; Similar ligands found: 257
No: Ligand Similarity coefficient
1 GLV 1.0257
2 HAE 1.0000
3 J3K 1.0000
4 61G 1.0000
5 2A1 1.0000
6 1BP 1.0000
7 2A3 1.0000
8 EDO 1.0000
9 BRJ 1.0000
10 NOE 1.0000
11 MGX 1.0000
12 F50 1.0000
13 BXA 1.0000
14 AGU 1.0000
15 PPI 1.0000
16 AKR 1.0000
17 NIE 1.0000
18 FAH 1.0000
19 GOA 1.0000
20 R3W 1.0000
21 NMU 1.0000
22 NHY 1.0000
23 F3V 1.0000
24 HVB 1.0000
25 ATO 0.9993
26 TSZ 0.9961
27 ALA 0.9954
28 OSM 0.9953
29 CP2 0.9916
30 AOA 0.9846
31 AXO 0.9840
32 3BR 0.9835
33 9A4 0.9822
34 PXO 0.9818
35 SAR 0.9798
36 GOL 0.9787
37 BU4 0.9767
38 OXL 0.9755
39 NIS 0.9748
40 DAL 0.9737
41 OXM 0.9733
42 GXV 0.9729
43 BUA 0.9721
44 3OH 0.9719
45 BMD 0.9714
46 BRP 0.9711
47 OXD 0.9705
48 TCV 0.9704
49 LAC 0.9682
50 2OP 0.9682
51 PYR 0.9679
52 HGY 0.9660
53 QPT 0.9660
54 DCE 0.9659
55 NAK 0.9647
56 6SP 0.9642
57 1CB 0.9640
58 HBR 0.9637
59 ALQ 0.9637
60 HBS 0.9620
61 4MZ 0.9600
62 2HA 0.9597
63 PYM 0.9596
64 BAQ 0.9588
65 MEU 0.9585
66 3GR 0.9582
67 2MZ 0.9581
68 GBL 0.9579
69 BUQ 0.9570
70 BUO 0.9557
71 3CL 0.9532
72 CRD 0.9528
73 3MT 0.9523
74 HOW 0.9521
75 MR3 0.9519
76 ABA 0.9519
77 1MZ 0.9512
78 MMU 0.9510
79 3ZS 0.9509
80 2AI 0.9505
81 BUB 0.9505
82 ATQ 0.9502
83 JZ6 0.9501
84 3TR 0.9493
85 ACT 0.9492
86 ETF 0.9490
87 AMT 0.9489
88 5Y9 0.9488
89 5KX 0.9481
90 13D 0.9474
91 MTG 0.9468
92 CYS 0.9457
93 BYZ 0.9442
94 ITU 0.9434
95 BXO 0.9429
96 CB0 0.9427
97 SO2 0.9425
98 SLP 0.9425
99 HP4 0.9410
100 XAP 0.9404
101 3BB 0.9398
102 MZY 0.9395
103 TF4 0.9390
104 PYZ 0.9377
105 N2O 0.9375
106 5MP 0.9367
107 9A7 0.9366
108 ES3 0.9364
109 78T 0.9358
110 AF3 0.9357
111 2PO 0.9353
112 ACM 0.9352
113 IPA 0.9348
114 BEF 0.9339
115 VSO 0.9338
116 D2P 0.9336
117 ALF 0.9326
118 HSW 0.9325
119 PZO 0.9319
120 SEY 0.9317
121 0CL 0.9309
122 TRI 0.9307
123 IMD 0.9296
124 BBU 0.9282
125 MSF 0.9276
126 MZ0 0.9268
127 HUH 0.9266
128 MMQ 0.9235
129 MSM 0.9230
130 THR 0.9220
131 2KT 0.9218
132 TAN 0.9214
133 1AC 0.9213
134 SER 0.9211
135 TB0 0.9211
136 CNH 0.9209
137 BBX 0.9200
138 PUT 0.9192
139 FW5 0.9192
140 KCS 0.9182
141 HYN 0.9182
142 BVG 0.9180
143 DE2 0.9178
144 DSN 0.9164
145 03W 0.9162
146 DGY 0.9162
147 MTD 0.9159
148 HIU 0.9155
149 KG7 0.9153
150 BVC 0.9152
151 FJO 0.9147
152 DXX 0.9145
153 XIX 0.9143
154 MB3 0.9134
155 DBB 0.9120
156 A3B 0.9120
157 3PY 0.9118
158 HAI 0.9113
159 NVI 0.9111
160 HUI 0.9110
161 B20 0.9108
162 CXL 0.9106
163 CYH 0.9106
164 P1R 0.9098
165 A2Q 0.9098
166 0PY 0.9081
167 BNZ 0.9081
168 CEJ 0.9080
169 CHT 0.9074
170 PRI 0.9073
171 ETX 0.9072
172 25T 0.9062
173 39J 0.9057
174 SMB 0.9057
175 HSL 0.9054
176 24T 0.9050
177 4AX 0.9031
178 7EX 0.9030
179 L60 0.9028
180 1SP 0.9026
181 8FH 0.9024
182 PHZ 0.9023
183 XPO 0.9019
184 2HP 0.9019
185 2EZ 0.9013
186 SGL 0.9004
187 FPO 0.8999
188 VN4 0.8993
189 BTL 0.8991
190 HVQ 0.8987
191 TAU 0.8986
192 2IM 0.8985
193 TMO 0.8985
194 IPH 0.8983
195 DTI 0.8978
196 EGD 0.8976
197 MCH 0.8975
198 E60 0.8974
199 03S 0.8974
200 DSS 0.8968
201 DMG 0.8966
202 MLA 0.8965
203 C5J 0.8965
204 HV2 0.8963
205 C2N 0.8963
206 8X3 0.8961
207 1DH 0.8953
208 MLI 0.8952
209 V1L 0.8947
210 93B 0.8943
211 9PO 0.8942
212 MMZ 0.8940
213 4AP 0.8936
214 GB 0.8936
215 SSN 0.8935
216 LGA 0.8933
217 2AP 0.8932
218 HVK 0.8932
219 PPF 0.8931
220 3AP 0.8930
221 TAY 0.8929
222 HRZ 0.8927
223 PO4 0.8927
224 MBN 0.8919
225 KSW 0.8918
226 TBU 0.8917
227 WOT 0.8907
228 DCY 0.8904
229 BF4 0.8901
230 3HL 0.8899
231 FUS 0.8896
232 ETM 0.8887
233 DMI 0.8881
234 2HE 0.8879
235 HLT 0.8876
236 COM 0.8875
237 3HR 0.8868
238 MLM 0.8864
239 GXE 0.8857
240 AAE 0.8850
241 HHN 0.8850
242 PIH 0.8844
243 8CL 0.8841
244 P7I 0.8841
245 2PA 0.8840
246 IVA 0.8825
247 9XN 0.8811
248 POA 0.8809
249 9SB 0.8792
250 WO6 0.8776
251 TTO 0.8755
252 HGW 0.8750
253 P2D 0.8688
254 ART 0.8686
255 EFS 0.8679
256 280 0.8605
257 PEJ 0.8598
Ligand no: 2; Ligand: QM1; Similar ligands found: 318
No: Ligand Similarity coefficient
1 AIN 0.9862
2 PRZ 0.9635
3 K2P 0.9584
4 M3S 0.9550
5 9KH 0.9516
6 NLA 0.9475
7 S3B 0.9415
8 ZZ8 0.9400
9 60Q 0.9338
10 57O 0.9315
11 FLC 0.9270
12 FXH 0.9262
13 2MN 0.9244
14 M3Q 0.9241
15 BK9 0.9231
16 PHT 0.9231
17 IAC 0.9219
18 IBM 0.9203
19 GV9 0.9193
20 BGC 0.9182
21 2CL 0.9170
22 6DP 0.9158
23 HHT 0.9155
24 KLW 0.9150
25 6XI 0.9140
26 JKZ 0.9132
27 GCU 0.9132
28 DOR 0.9129
29 GLC 0.9129
30 EVA 0.9109
31 TRC 0.9092
32 GLG 0.9087
33 0LH 0.9087
34 790 0.9086
35 SR4 0.9082
36 GAL 0.9080
37 GT0 0.9048
38 5WX 0.9047
39 LGC 0.9047
40 AKH 0.9046
41 LSA 0.9044
42 IPM 0.9043
43 KFH 0.9042
44 FA6 0.9035
45 GCB 0.9029
46 KBG 0.9029
47 ORO 0.9027
48 BDP 0.9026
49 YSO 0.9024
50 2AL 0.9016
51 5WY 0.9015
52 IPZ 0.9009
53 Q6T 0.9008
54 2D3 0.9008
55 KED 0.9006
56 KP6 0.9002
57 MHK 0.8991
58 HNQ 0.8990
59 8XQ 0.8989
60 CDV 0.8983
61 1FF 0.8982
62 OMD 0.8976
63 HQ9 0.8976
64 FA3 0.8976
65 LT8 0.8975
66 329 0.8967
67 61O 0.8966
68 BPS 0.8966
69 S7B 0.8965
70 MIG 0.8965
71 HLZ 0.8958
72 F12 0.8954
73 PZI 0.8954
74 CIT 0.8953
75 CCB 0.8951
76 OHP 0.8950
77 MQB 0.8948
78 GJS 0.8945
79 GM7 0.8939
80 IOS 0.8939
81 67Y 0.8939
82 XQK 0.8939
83 23J 0.8938
84 3MG 0.8938
85 TSR 0.8937
86 BMA 0.8934
87 QAT 0.8931
88 TRA 0.8926
89 NCD 0.8926
90 PRY 0.8925
91 HA7 0.8925
92 GTC 0.8921
93 5WU 0.8921
94 GCS 0.8919
95 NVU 0.8918
96 34D 0.8916
97 OA3 0.8916
98 9PY 0.8912
99 42C 0.8910
100 JZ4 0.8908
101 GOG 0.8906
102 1LN 0.8906
103 MAN 0.8901
104 8VE 0.8899
105 GZ8 0.8899
106 NBG 0.8898
107 692 0.8898
108 SHG 0.8897
109 FP1 0.8897
110 IJZ 0.8897
111 7ZE 0.8895
112 GYP 0.8891
113 3RI 0.8890
114 M0Q 0.8890
115 261 0.8886
116 Z5P 0.8877
117 PFB 0.8877
118 12B 0.8875
119 M1H 0.8873
120 FOT 0.8871
121 7VS 0.8868
122 BSX 0.8864
123 4ME 0.8863
124 DBJ 0.8861
125 MMA 0.8857
126 T6Z 0.8854
127 NOJ 0.8854
128 15L 0.8852
129 QAS 0.8851
130 AH8 0.8850
131 CIP 0.8849
132 V6F 0.8847
133 ASC 0.8845
134 N8P 0.8840
135 QPR 0.8839
136 ZWZ 0.8835
137 PXM 0.8835
138 F34 0.8831
139 EV0 0.8829
140 GLY PRO 0.8827
141 2SX 0.8827
142 MFU 0.8823
143 2LP 0.8822
144 GUN 0.8821
145 DHK 0.8814
146 YQA 0.8814
147 R9S 0.8813
148 8S0 0.8810
149 UEG 0.8809
150 6W6 0.8807
151 ENL 0.8804
152 RM1 0.8803
153 ICT 0.8802
154 9FQ 0.8799
155 D1X 0.8798
156 HMQ 0.8798
157 6CS 0.8798
158 GCV 0.8797
159 12M 0.8796
160 9DG 0.8794
161 EOL 0.8794
162 M0W 0.8793
163 GC2 0.8792
164 ZON 0.8788
165 49N 0.8785
166 KG1 0.8785
167 TVP 0.8784
168 QIC 0.8783
169 3C2 0.8781
170 M1E 0.8781
171 S24 0.8781
172 2ZQ 0.8780
173 7WR 0.8775
174 3C1 0.8774
175 GZQ 0.8773
176 NGO 0.8771
177 94B 0.8769
178 XAN 0.8763
179 5HY 0.8763
180 KIA 0.8763
181 KIB 0.8763
182 TFU 0.8759
183 GTZ 0.8753
184 4HC 0.8751
185 NTZ 0.8750
186 67X 0.8749
187 UAN 0.8749
188 5NS 0.8749
189 GTQ 0.8748
190 PXL 0.8748
191 O2A 0.8747
192 C2U 0.8747
193 9BF 0.8742
194 2FG 0.8740
195 1AL 0.8737
196 T9G 0.8735
197 8GK 0.8733
198 D07 0.8732
199 948 0.8731
200 GLF 0.8731
201 MBG 0.8730
202 0GY 0.8727
203 TSS 0.8727
204 TZE 0.8725
205 PSV 0.8724
206 9MG 0.8723
207 AMG 0.8723
208 AEZ 0.8720
209 OTD 0.8719
210 M5N 0.8717
211 2H5 0.8714
212 URC 0.8714
213 1GN 0.8707
214 G3F 0.8707
215 GTR 0.8706
216 6VD 0.8704
217 II6 0.8703
218 091 0.8702
219 ATH 0.8699
220 J9W 0.8699
221 P84 0.8697
222 DCO 0.8690
223 JR2 0.8690
224 G4D 0.8690
225 L7T 0.8689
226 SRO 0.8688
227 DFB 0.8687
228 7NI 0.8687
229 6LW 0.8687
230 PA1 0.8685
231 NTC 0.8681
232 GLA 0.8680
233 AX3 0.8680
234 2A7 0.8677
235 DNC 0.8676
236 ALL 0.8674
237 5RG 0.8674
238 JTH 0.8671
239 7FF 0.8671
240 A9O 0.8671
241 OXC 0.8670
242 SFU 0.8668
243 LZ2 0.8667
244 2CG 0.8667
245 LCN 0.8664
246 GYE 0.8663
247 149 0.8663
248 SJ5 0.8662
249 ASO 0.8661
250 JXZ 0.8658
251 3AL 0.8657
252 B2Y 0.8657
253 BY5 0.8656
254 OBP 0.8655
255 1U1 0.8654
256 GDE 0.8651
257 9TZ 0.8651
258 ICO 0.8650
259 AW5 0.8650
260 IFM 0.8650
261 GOX 0.8648
262 CFA 0.8648
263 B2J 0.8646
264 7M6 0.8646
265 LFR 0.8645
266 2TQ 0.8643
267 GLT 0.8641
268 YIO 0.8640
269 A13 0.8632
270 SBK 0.8632
271 M1Q 0.8631
272 1X7 0.8631
273 SR1 0.8630
274 EJZ 0.8630
275 KDO 0.8630
276 SXS 0.8628
277 CLU 0.8628
278 MVL 0.8627
279 GIM 0.8627
280 LIP 0.8619
281 G2F 0.8617
282 54G 0.8617
283 NFQ 0.8615
284 DBH 0.8609
285 AZF 0.8608
286 ADA 0.8605
287 TNX 0.8602
288 VOH 0.8601
289 CKX 0.8600
290 GIV 0.8599
291 N2Z 0.8596
292 KYA 0.8595
293 TEP 0.8593
294 Q24 0.8591
295 NAG 0.8588
296 FBU 0.8587
297 SOE 0.8583
298 8TX 0.8583
299 KGK 0.8582
300 7Q1 0.8573
301 VNL 0.8573
302 EPR 0.8567
303 AFR 0.8562
304 5PX 0.8560
305 3DO 0.8557
306 51F 0.8557
307 X09 0.8553
308 G1P 0.8551
309 DBX 0.8551
310 V55 0.8551
311 LAO 0.8548
312 2J9 0.8545
313 3HP 0.8543
314 NZ9 0.8543
315 FRU 0.8539
316 X6X 0.8537
317 OXZ 0.8535
318 5M0 0.8535
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5DEX; 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: 5dex.bio1) has 13 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5DEX; Ligand: 5E0; 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: 5dex.bio1) has 26 residues
No: Leader PDB Ligand Sequence Similarity
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