Receptor
PDB id Resolution Class Description Source Keywords
4NF5 1.9 Å NON-ENZYME: SIGNAL_HORMONE CRYSTAL STRUCTURE OF GLUN1/GLUN2A LIGAND-BINDING DOMAIN IN C WITH GLYCINE AND D-AP5 RATTUS NORVEGICUS RECEPTOR GLYCINE AND D-AP5 TRANSPORT PROTEIN
Ref.: STRUCTURAL INSIGHTS INTO COMPETITIVE ANTAGONISM IN RECEPTORS. NEURON V. 81 366 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GOL B:303;
A:902;
B:302;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
2JJ B:301;
Valid;
none;
submit data
197.126 C5 H12 N O5 P C(C[C...
GLY A:901;
Valid;
none;
submit data
75.067 C2 H5 N O2 C(C(=...
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 4NF5 - 2JJ C5 H12 N O5 P C(C[C@H](C....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: 2JJ; Similar ligands found: 19
No: Ligand ECFP6 Tc MDL keys Tc
1 2JJ 1 1
2 5OY 1 1
3 API 0.566667 0.631579
4 PAO 0.488372 0.74
5 11C 0.485714 0.675676
6 UN1 0.485714 0.675676
7 DHH 0.472222 0.657895
8 ONH 0.459459 0.613636
9 NPI 0.459459 0.657895
10 6CL 0.447368 0.615385
11 26P 0.447368 0.666667
12 ABH 0.435897 0.853659
13 RPI 0.425532 0.72
14 6HN 0.425 0.612245
15 PSQ 0.416667 0.610169
16 RGP 0.404762 0.897436
17 GGL 0.4 0.648649
18 GLU 0.4 0.648649
19 DGL 0.4 0.648649
Ligand no: 2; 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
Similar Ligands (3D)
Ligand no: 1; Ligand: 2JJ; Similar ligands found: 233
No: Ligand Similarity coefficient
1 LUQ 0.9634
2 DER 0.9583
3 MF3 0.9513
4 3PG 0.9470
5 FOM 0.9460
6 F98 0.9429
7 DXP 0.9322
8 KPA 0.9317
9 OOG 0.9314
10 RES 0.9313
11 DHM 0.9302
12 KPC 0.9298
13 M3P 0.9295
14 DEZ 0.9292
15 PC 0.9290
16 4TP 0.9261
17 TZP 0.9261
18 5RP 0.9251
19 2FM 0.9248
20 E4P 0.9228
21 1PS 0.9223
22 AKG 0.9213
23 0L1 0.9185
24 9GB 0.9185
25 1HS 0.9183
26 ABF 0.9179
27 LX1 0.9176
28 QFJ 0.9173
29 E79 0.9164
30 HBU 0.9134
31 GVA 0.9109
32 GGB 0.9104
33 ARG 0.9078
34 DX5 0.9077
35 MES 0.9066
36 4TB 0.9064
37 R5P 0.9060
38 5DL 0.9057
39 M3L 0.9046
40 DAR 0.9045
41 650 0.9044
42 A5P 0.9042
43 JX7 0.9040
44 NSB 0.9040
45 HCI 0.9038
46 XRX 0.9037
47 ILO 0.9036
48 LVD 0.9033
49 BL0 0.9030
50 HSX 0.9022
51 SEP 0.9021
52 IAR 0.9019
53 CIR 0.9019
54 RP5 0.9016
55 1X4 0.9013
56 AHN 0.9013
57 CLT 0.9010
58 MLY 0.9003
59 AZM 0.8996
60 CCD 0.8995
61 5LD 0.8986
62 RP3 0.8982
63 MSL 0.8977
64 R52 0.8976
65 O45 0.8974
66 G3P 0.8972
67 IVL 0.8969
68 Q06 0.8968
69 PHE 0.8958
70 PML 0.8957
71 HC4 0.8948
72 JFM 0.8946
73 NFA 0.8945
74 HFA 0.8944
75 ENW 0.8941
76 PBA 0.8940
77 GPJ 0.8939
78 LYS 0.8939
79 13P 0.8936
80 GPF 0.8934
81 DLY 0.8930
82 CHH 0.8926
83 TEG 0.8921
84 PPY 0.8919
85 IP8 0.8919
86 9YT 0.8916
87 PMV 0.8912
88 ENO 0.8911
89 2NP 0.8907
90 XRS 0.8903
91 MP5 0.8903
92 NNH 0.8902
93 FK8 0.8898
94 4LR 0.8896
95 GLR 0.8895
96 E8U 0.8894
97 TYR 0.8887
98 DIR 0.8886
99 CXP 0.8883
100 P81 0.8881
101 KNA 0.8881
102 HG3 0.8880
103 3S5 0.8878
104 SYM 0.8878
105 7OD 0.8874
106 NMH 0.8873
107 TCA 0.8864
108 PPT 0.8852
109 PLR 0.8851
110 PLP 0.8844
111 XOG 0.8841
112 7C3 0.8838
113 J0Z 0.8834
114 MLZ 0.8833
115 KDG 0.8832
116 FB6 0.8831
117 HPV 0.8827
118 4ZD 0.8818
119 GRQ 0.8813
120 DHC 0.8811
121 ENV 0.8810
122 Z70 0.8810
123 5SP 0.8809
124 PBN 0.8808
125 HGA 0.8807
126 G3H 0.8803
127 BVA 0.8800
128 61M 0.8798
129 7BC 0.8797
130 EGV 0.8797
131 F90 0.8795
132 DPN 0.8794
133 OCA 0.8791
134 3H2 0.8785
135 DLT 0.8785
136 37E 0.8780
137 N9J 0.8780
138 PGH 0.8778
139 64Z 0.8777
140 58X 0.8772
141 HPP 0.8771
142 S0W 0.8771
143 011 0.8768
144 D5X 0.8764
145 ZZU 0.8763
146 5PV 0.8763
147 MAJ 0.8762
148 SB7 0.8761
149 LSQ 0.8760
150 AG2 0.8758
151 NMM 0.8758
152 2D8 0.8754
153 LGT 0.8753
154 SSC 0.8750
155 CYX 0.8748
156 3YP 0.8747
157 DZA 0.8744
158 DTY 0.8742
159 129 0.8738
160 Q04 0.8732
161 BCH 0.8731
162 P80 0.8729
163 DXG 0.8726
164 Q9Z 0.8725
165 PO6 0.8720
166 1L5 0.8719
167 GO2 0.8718
168 PJL 0.8717
169 5WN 0.8717
170 F06 0.8714
171 PRO GLY 0.8712
172 SG3 0.8707
173 AHC 0.8703
174 XIZ 0.8702
175 XI7 0.8701
176 HMS 0.8700
177 TZM 0.8695
178 PRA 0.8694
179 GZ2 0.8693
180 S7A 0.8690
181 ATX 0.8687
182 TX4 0.8681
183 C82 0.8681
184 PFF 0.8679
185 HF2 0.8677
186 QH3 0.8677
187 8SZ 0.8675
188 GAE 0.8673
189 HXY 0.8673
190 3QO 0.8673
191 RA7 0.8671
192 MHN 0.8668
193 GRF 0.8664
194 6C4 0.8662
195 TB8 0.8659
196 R10 0.8658
197 OJD 0.8658
198 2O6 0.8657
199 SHV 0.8653
200 DAH 0.8652
201 YIE 0.8645
202 3OL 0.8643
203 EQW 0.8641
204 ACA 0.8637
205 HRG 0.8633
206 5OO 0.8623
207 TOH 0.8622
208 P7Y 0.8618
209 TYC 0.8617
210 YPN 0.8616
211 YOF 0.8606
212 S8V 0.8605
213 BHH 0.8604
214 KYN 0.8592
215 LY0 0.8589
216 LTL 0.8586
217 SB9 0.8584
218 7UC 0.8582
219 SZ7 0.8580
220 IAC 0.8577
221 N4B 0.8571
222 IPE 0.8569
223 MVH 0.8568
224 B3U 0.8567
225 A51 0.8560
226 4XF 0.8560
227 0NX 0.8558
228 HIC 0.8552
229 GVM 0.8552
230 HAR 0.8544
231 I38 0.8540
232 SOJ 0.8538
233 PA5 0.8529
Ligand no: 2; 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
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
APoc FAQ
Feedback