Receptor
PDB id Resolution Class Description Source Keywords
4YKK 1.38 Å NON-ENZYME: BINDING MNEMIOPSIS LEIDYI ML032222A IGLUR LBD D-SERINE COMPLEX MNEMIOPSIS LEIDYI MEMBRANE PROTEIN GLUTAMATE RECEPTOR ION CHANNEL
Ref.: GLYCINE ACTIVATED ION CHANNEL SUBUNITS ENCODED BY C GLUTAMATE RECEPTOR GENES. PROC.NATL.ACAD.SCI.USA V. 112 E6048 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GLY B:302;
A:303;
Valid;
Valid;
none;
none;
submit data
75.067 C2 H5 N O2 C(C(=...
DSN B:301;
A:302;
Valid;
Valid;
none;
none;
Ki = 1.7 mM
105.093 C3 H7 N O3 C([C@...
MG A:301;
Part of Protein;
none;
submit data
24.305 Mg [Mg+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4YKI 1.21 Å NON-ENZYME: BINDING MNEMIOPSIS LEIDYI ML032222A IGLUR LBD GLYCINE COMPLEX MNEMIOPSIS LEIDYI MEMBRANE PROTEIN GLUTAMATE RECEPTOR ION CHANNEL
Ref.: GLYCINE ACTIVATED ION CHANNEL SUBUNITS ENCODED BY C GLUTAMATE RECEPTOR GENES. PROC.NATL.ACAD.SCI.USA V. 112 E6048 2015
Members (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 510 families.
1 4YKK Ki = 1.7 mM DSN C3 H7 N O3 C([C@H](C(....
2 5CMC Kd = 2.48 uM GLY C2 H5 N O2 C(C(=O)O)N
3 5CMB Kd = 28.3 nM GLY C2 H5 N O2 C(C(=O)O)N
4 4YKJ Ki = 37 uM ALA C3 H7 N O2 C[C@@H](C(....
5 4YKI Kd = 2.7 nM GLY C2 H5 N O2 C(C(=O)O)N
6 4YKP - GLY C2 H5 N O2 C(C(=O)O)N
70% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 391 families.
1 4YKK Ki = 1.7 mM DSN C3 H7 N O3 C([C@H](C(....
2 5CMC Kd = 2.48 uM GLY C2 H5 N O2 C(C(=O)O)N
3 5CMB Kd = 28.3 nM GLY C2 H5 N O2 C(C(=O)O)N
4 4YKJ Ki = 37 uM ALA C3 H7 N O2 C[C@@H](C(....
5 4YKI Kd = 2.7 nM GLY C2 H5 N O2 C(C(=O)O)N
6 4YKP - GLY C2 H5 N O2 C(C(=O)O)N
50% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 298 families.
1 4YKK Ki = 1.7 mM DSN C3 H7 N O3 C([C@H](C(....
2 5CMC Kd = 2.48 uM GLY C2 H5 N O2 C(C(=O)O)N
3 4ZDM Kd = 31 nM GLY C2 H5 N O2 C(C(=O)O)N
Polypharmacology
Similar Ligands
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: DSN; Similar ligands found: 33
No: Ligand ECFP6 Tc MDL keys Tc
1 DSN 1 1
2 SER 1 1
3 CYS 0.65 0.84
4 DCY 0.65 0.84
5 ABA 0.6 0.692308
6 2RA 0.6 0.75
7 DBB 0.6 0.692308
8 HSE 0.590909 0.821429
9 C2N 0.571429 0.730769
10 ASP 0.545455 0.714286
11 ASN 0.545455 0.625
12 DAS 0.545455 0.714286
13 DAB 0.521739 0.724138
14 HL5 0.518519 0.814815
15 CSO 0.5 0.636364
16 LEU 0.5 0.642857
17 API 0.5 0.633333
18 HCS 0.5 0.777778
19 NVA 0.5 0.62069
20 AS2 0.5 0.703704
21 CSS 0.48 0.689655
22 DGY 0.47619 0.607143
23 GGL 0.461538 0.655172
24 DGL 0.461538 0.655172
25 GLU 0.461538 0.655172
26 ORN 0.444444 0.689655
27 SLZ 0.433333 0.625
28 11C 0.413793 0.633333
29 UN1 0.413793 0.633333
30 DLY 0.413793 0.666667
31 CME 0.40625 0.666667
32 LYS 0.4 0.645161
33 DHH 0.4 0.612903
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4YKI; Ligand: GLY; Similar sites found with APoc: 1
This union binding pocket(no: 1) in the query (biounit: 4yki.bio1) has 15 residues
No: Leader PDB Ligand Sequence Similarity
1 2RC8 DSN 40.2344
Pocket No.: 2; Query (leader) PDB : 4YKI; 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: 2) in the query (biounit: 4yki.bio1) has 15 residues
No: Leader PDB Ligand Sequence Similarity
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