Receptor
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.
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
5E0 B:301;
Valid;
none;
Ki = 22.6 nM
275.26 C13 H13 N3 O4 c1ccc...
GLY A:1001;
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 (22)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 263 families.
1 5VII Ki = 51.8 nM 5DY C16 H18 F N3 O4 c1cc(ccc1C....
2 5H8F - GLY C2 H5 N O2 C(C(=O)O)N
3 2A5T - GLY C2 H5 N O2 C(C(=O)O)N
4 5VIJ Ki = 24.3 nM 5DX C13 H12 Br N3 O4 c1cc(ccc1n....
5 5I57 - GLY C2 H5 N O2 C(C(=O)O)N
6 5H8Q - 5YE C18 H18 F N3 O S CCN(CC1=CC....
7 5U8C ic50 = 68.4 nM 84J C17 H17 Br N3 O5 P C[C@@H](c1....
8 5KCJ - GLY C2 H5 N O2 C(C(=O)O)N
9 5DEX Ki = 22.6 nM 5E0 C13 H13 N3 O4 c1ccc(cc1)....
10 5H8N - 5YD C20 H18 F N3 O3 S c1cc(cnc1)....
11 5TPA - GLY C2 H5 N O2 C(C(=O)O)N
12 4NF8 - GLU C5 H9 N O4 C(CC(=O)O)....
13 5KDT - GLU C5 H9 N O4 C(CC(=O)O)....
14 4NF4 - GLU C5 H9 N O4 C(CC(=O)O)....
15 4NF5 - 2JJ C5 H12 N O5 P C(C[C@H](C....
16 5TP9 - GLU C5 H9 N O4 C(CC(=O)O)....
17 5VIH Ki = 32.2 nM 5DZ C13 H12 F N3 O4 c1cc(ccc1n....
18 5H8H - GLY C2 H5 N O2 C(C(=O)O)N
19 5I59 ic50 = 641 nM 67Q C18 H19 F2 N5 O3 S2 Cc1c(ncc(n....
20 4NF6 Ki = 0.82 uM 2JL C21 H18 N2 O5 c1ccc2c(c1....
21 5I56 ic50 = 1530 nM 67P C21 H17 Cl F N3 O4 S c1ccc(cc1)....
22 5I2N - GLY C2 H5 N O2 C(C(=O)O)N
70% Homology Family (22)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 196 families.
1 5VII Ki = 51.8 nM 5DY C16 H18 F N3 O4 c1cc(ccc1C....
2 5H8F - GLY C2 H5 N O2 C(C(=O)O)N
3 2A5T - GLY C2 H5 N O2 C(C(=O)O)N
4 5VIJ Ki = 24.3 nM 5DX C13 H12 Br N3 O4 c1cc(ccc1n....
5 5I57 - GLY C2 H5 N O2 C(C(=O)O)N
6 5H8Q - 5YE C18 H18 F N3 O S CCN(CC1=CC....
7 5U8C ic50 = 68.4 nM 84J C17 H17 Br N3 O5 P C[C@@H](c1....
8 5KCJ - GLY C2 H5 N O2 C(C(=O)O)N
9 5DEX Ki = 22.6 nM 5E0 C13 H13 N3 O4 c1ccc(cc1)....
10 5H8N - 5YD C20 H18 F N3 O3 S c1cc(cnc1)....
11 5TPA - GLY C2 H5 N O2 C(C(=O)O)N
12 4NF8 - GLU C5 H9 N O4 C(CC(=O)O)....
13 5KDT - GLU C5 H9 N O4 C(CC(=O)O)....
14 4NF4 - GLU C5 H9 N O4 C(CC(=O)O)....
15 4NF5 - 2JJ C5 H12 N O5 P C(C[C@H](C....
16 5TP9 - GLU C5 H9 N O4 C(CC(=O)O)....
17 5VIH Ki = 32.2 nM 5DZ C13 H12 F N3 O4 c1cc(ccc1n....
18 5H8H - GLY C2 H5 N O2 C(C(=O)O)N
19 5I59 ic50 = 641 nM 67Q C18 H19 F2 N5 O3 S2 Cc1c(ncc(n....
20 4NF6 Ki = 0.82 uM 2JL C21 H18 N2 O5 c1ccc2c(c1....
21 5I56 ic50 = 1530 nM 67P C21 H17 Cl F N3 O4 S c1ccc(cc1)....
22 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 171 families.
1 5DEX Ki = 22.6 nM 5E0 C13 H13 N3 O4 c1ccc(cc1)....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 5E0; Similar ligands found: 4
No: Ligand ECFP6 Tc MDL keys Tc
1 5E0 1 1
2 5DX 0.732143 0.921569
3 5DZ 0.724138 0.921569
4 5DY 0.636364 0.903846
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 Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5DEX; Ligand: GLY; Similar sites found: 24
This union binding pocket(no: 1) in the query (biounit: 5dex.bio1) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3HUN ZZ7 0.009703 0.4052 2.05479
2 4PPF FLC 0.008756 0.4056 3.76712
3 4C0R GDS 0.0002185 0.51594 10.0806
4 2YLN CYS 0.01072 0.40301 10.6007
5 3VV5 SLZ 0.003555 0.4063 11.1538
6 2Q89 6CS 0.001108 0.43486 12.0623
7 3N26 ARG 0.001261 0.41935 15.8537
8 1XT8 CYS 0.00006784 0.51019 18.4932
9 2YJP CYS 0.00008111 0.50601 18.8356
10 4YMX ARG 0.0004795 0.43702 23.4615
11 2VHA GLU 0.000002129 0.52468 25.0883
12 4DZ1 DAL 0.0001711 0.49409 28.9575
13 5L9O GOP 0.00005254 0.41318 32.8358
14 2Y7I ARG 0.0009124 0.42766 34.0611
15 2Q2A ARG 0.00003099 0.47246 35.2941
16 4G4P GLN 0.0000265 0.51558 37.7049
17 4POW OP1 0.000000827 0.47171 38.1132
18 4KQP GLN 0.00001547 0.54272 38.7931
19 1HSL HIS 0.00002338 0.53424 39.0756
20 1WDN GLN 0.00008205 0.4814 41.5929
21 5EHS 2JJ 0.0009421 0.40794 44.7761
22 5EHS 5OY 0.0009421 0.40794 44.7761
23 4ZV1 ARG 0.0000618 0.48574 45.4936
24 4YKI GLY 0.00000002725 0.67643 47.6562
Pocket No.: 2; Query (leader) PDB : 5DEX; Ligand: 5E0; Similar sites found: 50
This union binding pocket(no: 2) in the query (biounit: 5dex.bio1) has 26 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4W9N TCL 0.03542 0.40043 2.82686
2 2DVZ GLU 0.01094 0.4183 3.08219
3 2X0K PPV 0.03664 0.41539 3.42466
4 3WMX THR 0.02649 0.4099 3.53357
5 3BY9 SIN 0.02596 0.40689 3.84615
6 1PIG BGC 0.0004444 0.40859 3.88693
7 3TY3 GGG 0.0319 0.40686 3.88693
8 4LUS TCE 0.03275 0.40361 4.10959
9 2G2Y MLI 0.01353 0.41684 4.24028
10 5U0L 8YP 0.03345 0.40005 4.24028
11 3H9A PPY 0.02102 0.41238 4.52675
12 1BVY FMN 0.005589 0.40645 4.79452
13 4RHS SIA SIA GAL 0.02181 0.40651 4.91803
14 2QES ADE 0.01314 0.4301 4.98084
15 3ZVS MLI 0.01838 0.41304 5
16 4MBY BGC SIA GAL 0.03241 0.40247 5.03597
17 2POC BG6 0.008743 0.41504 5.13699
18 4AMV F6R 0.01253 0.40408 5.47945
19 1RVV INI 0.01312 0.4186 6.49351
20 2WGV CIT 0.01664 0.42002 7.25806
21 3HQP OXL 0.04495 0.40358 7.42049
22 1TKU 5RP 0.0387 0.4003 7.84314
23 5DA3 58V 0.01594 0.41018 7.92453
24 3B8I OXL 0.007599 0.44637 8.01394
25 2HYR BGC GLC 0.005428 0.43976 8.19672
26 2GUD MAN 0.005346 0.43239 8.19672
27 2NU5 NAG 0.006784 0.42946 8.19672
28 2GUC MAN 0.004591 0.422 8.19672
29 2GUD BMA 0.01374 0.40608 8.19672
30 1N0U SO1 0.008417 0.40517 8.48057
31 2DC1 CIT 0.02422 0.41001 8.8983
32 1PS6 4TP 0.02222 0.40298 12.6712
33 1KJ1 MAN 0.03738 0.40563 18.3486
34 5GVR LMR 0.003541 0.4105 18.3761
35 1XT8 CYS 0.001601 0.47382 18.4932
36 2YJP CYS 0.006422 0.43998 18.8356
37 4KQ6 DLZ 0.01462 0.40813 19.0813
38 2VHA GLU 0.003086 0.44084 25.0883
39 4DZ1 DAL 0.002239 0.46695 28.9575
40 5L9O GOP 0.004746 0.40946 32.8358
41 2Q2A ARG 0.006471 0.4253 35.2941
42 4G4P GLN 0.002613 0.45966 37.7049
43 4POW OP1 0.002071 0.42475 38.1132
44 4KQP GLN 0.001128 0.4834 38.7931
45 1HSL HIS 0.00513 0.44744 39.0756
46 1WDN GLN 0.0121 0.42039 41.5929
47 5EHS 2JJ 0.0002368 0.48898 44.7761
48 5EHS 5OY 0.0002368 0.48898 44.7761
49 4ZV1 ARG 0.005426 0.43811 45.4936
50 4YKI GLY 0.00003474 0.56217 47.6562
Feedback