Chlorine in PDB 6f29: Crystal Structure of the Kainate Receptor GLUK3 Ligand Binding Domain in Complex with (S)-1-[2-Amino-2-Carboxyethyl]-5,7-Dihydrothieno[3,4- D]Pyrimidin-2,4(1H,3H)-Dione at Resolution 2.6A

The structure of Crystal Structure of the Kainate Receptor GLUK3 Ligand Binding Domain in Complex with (S)-1-[2-Amino-2-Carboxyethyl]-5,7-Dihydrothieno[3,4- D]Pyrimidin-2,4(1H,3H)-Dione at Resolution 2.6A, PDB code: 6f29 was solved by R.Venskutonyte, K.Frydenvang, J.S.Kastrup, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.92 / 2.60
Space group	P 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	68.040, 68.040, 126.860, 90.00, 90.00, 90.00
R / Rfree (%)	19.2 / 24.8

The structure of Crystal Structure of the Kainate Receptor GLUK3 Ligand Binding Domain in Complex with (S)-1-[2-Amino-2-Carboxyethyl]-5,7-Dihydrothieno[3,4- D]Pyrimidin-2,4(1H,3H)-Dione at Resolution 2.6A also contains other interesting chemical elements:

Potassium

(K)

2 atoms

The binding sites of Chlorine atom in the Crystal Structure of the Kainate Receptor GLUK3 Ligand Binding Domain in Complex with (S)-1-[2-Amino-2-Carboxyethyl]-5,7-Dihydrothieno[3,4- D]Pyrimidin-2,4(1H,3H)-Dione at Resolution 2.6A (pdb code 6f29). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Crystal Structure of the Kainate Receptor GLUK3 Ligand Binding Domain in Complex with (S)-1-[2-Amino-2-Carboxyethyl]-5,7-Dihydrothieno[3,4- D]Pyrimidin-2,4(1H,3H)-Dione at Resolution 2.6A, PDB code: 6f29:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Crystal Structure of the Kainate Receptor GLUK3 Ligand Binding Domain in Complex with (S)-1-[2-Amino-2-Carboxyethyl]-5,7-Dihydrothieno[3,4- D]Pyrimidin-2,4(1H,3H)-Dione at Resolution 2.6A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of the Kainate Receptor GLUK3 Ligand Binding Domain in Complex with (S)-1-[2-Amino-2-Carboxyethyl]-5,7-Dihydrothieno[3,4- D]Pyrimidin-2,4(1H,3H)-Dione at Resolution 2.6A within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl304 b:43.7 occ:1.00 N A:LEU57 3.1 28.3 1.0 NH1 A:ARG33 3.5 31.9 1.0 NH2 A:ARG33 3.7 32.5 1.0 CA A:ARG56 3.8 27.8 1.0 CB A:LEU57 3.8 30.1 1.0 C A:ARG56 3.9 29.4 1.0 CG A:LEU57 4.0 29.3 1.0 CD1 A:LEU57 4.0 31.6 1.0 CZ A:ARG33 4.0 32.0 1.0 CA A:LEU57 4.0 29.9 1.0 O A:ILE55 4.3 27.9 1.0 CZ A:PHE34 4.4 26.5 1.0 CB A:ARG56 4.5 30.3 1.0 O A:LEU57 4.7 36.0 1.0 N A:ARG56 4.8 25.5 1.0 CG A:ARG56 4.9 33.9 1.0 C A:LEU57 4.9 34.1 1.0 C A:ILE55 5.0 24.1 1.0

Chlorine binding site 2 out of 3 in the Crystal Structure of the Kainate Receptor GLUK3 Ligand Binding Domain in Complex with (S)-1-[2-Amino-2-Carboxyethyl]-5,7-Dihydrothieno[3,4- D]Pyrimidin-2,4(1H,3H)-Dione at Resolution 2.6A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of the Kainate Receptor GLUK3 Ligand Binding Domain in Complex with (S)-1-[2-Amino-2-Carboxyethyl]-5,7-Dihydrothieno[3,4- D]Pyrimidin-2,4(1H,3H)-Dione at Resolution 2.6A within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl305 b:62.0 occ:1.00 N A:ASN31 3.2 19.5 1.0 ND2 A:ASN31 3.5 17.4 1.0 CG A:ASN31 3.5 17.8 1.0 CA A:GLY30 3.8 19.5 1.0 OD1 A:ASN31 3.9 21.6 1.0 CB A:ASN31 4.0 16.6 1.0 C A:GLY30 4.0 17.4 1.0 O A:HOH422 4.0 21.7 1.0 CA A:ASN31 4.2 19.2 1.0 O A:HOH405 4.8 24.0 1.0 O A:TYR53 4.9 21.6 1.0 CG A:GLU54 5.0 45.6 1.0

Chlorine binding site 3 out of 3 in the Crystal Structure of the Kainate Receptor GLUK3 Ligand Binding Domain in Complex with (S)-1-[2-Amino-2-Carboxyethyl]-5,7-Dihydrothieno[3,4- D]Pyrimidin-2,4(1H,3H)-Dione at Resolution 2.6A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of the Kainate Receptor GLUK3 Ligand Binding Domain in Complex with (S)-1-[2-Amino-2-Carboxyethyl]-5,7-Dihydrothieno[3,4- D]Pyrimidin-2,4(1H,3H)-Dione at Resolution 2.6A within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl306 b:56.7 occ:1.00 N A:HIS245 3.2 41.1 1.0 CA A:ASP242 3.4 53.9 1.0 CB A:LEU244 3.5 28.5 1.0 N A:LEU244 3.6 32.0 1.0 CA A:GLN239 3.6 45.7 1.0 O A:GLN239 3.7 48.4 1.0 C A:ASP242 3.7 46.8 1.0 CA A:LEU244 3.8 31.3 1.0 C A:LEU244 3.8 36.6 1.0 CB A:HIS245 3.9 54.5 1.0 CB A:GLN239 4.0 51.1 1.0 O A:HOH444 4.0 30.7 1.0 CA A:HIS245 4.1 46.0 1.0 O A:ASP242 4.1 45.6 1.0 C A:GLN239 4.1 46.5 1.0 N A:LYS243 4.2 40.6 1.0 OD2 A:ASP242 4.2 83.9 1.0 N A:ASP242 4.3 50.9 1.0 CG A:LEU244 4.3 28.2 1.0 O A:LEU238 4.4 40.9 1.0 CB A:ASP242 4.4 66.7 1.0 C A:LYS243 4.6 32.0 1.0 CD1 A:LEU244 4.7 28.1 1.0 N A:GLN239 4.7 43.1 1.0 CG A:GLN239 4.8 56.5 1.0 CG A:ASP242 4.8 78.8 1.0 O A:LEU244 4.9 37.3 1.0 C A:LEU238 4.9 39.9 1.0

S.Brogi, M.Brindisi, S.Butini, G.U.Kshirsagar, S.Maramai, G.Chemi, S.Gemma, G.Campiani, E.Novellino, P.Fiorenzani, J.Pinassi, A.M.Aloisi, M.Gynther, R.Venskutonyte, L.Han, K.Frydenvang, J.S.Kastrup, D.S.Pickering. ( S)-2-Amino-3-(5-Methyl-3-Hydroxyisoxazol-4-Yl)Propanoic Acid (Ampa) and Kainate Receptor Ligands: Further Exploration of Bioisosteric Replacements and Structural and Biological Investigation. J. Med. Chem. V. 61 2124 2018.
ISSN: ISSN 1520-4804
PubMed: 29451794
DOI: 10.1021/ACS.JMEDCHEM.8B00099