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 (22)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 301 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 221 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 181 families.
1 4NF5 - 2JJ C5 H12 N O5 P C(C[C@H](C....
Polypharmacology
Similar Ligands
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 UN1 0.485714 0.675676
6 11C 0.485714 0.675676
7 DHH 0.472222 0.657895
8 NPI 0.459459 0.657895
9 ONH 0.459459 0.613636
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 DGL 0.4 0.648649
19 GLU 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 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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