Chlorine in PDB 6f28: Crystal Structure of the Kainate Receptor GLUK3 Ligand Binding Domain in Complex with (S)-1-[2'-Amino-2'-Carboxyethyl]-6-Methyl-5,7- Dihydropyrrolo[3,4-D]Pyrimidin-2,4(1H,3H)-Dione at Resolution 2.4A

The structure of Crystal Structure of the Kainate Receptor GLUK3 Ligand Binding Domain in Complex with (S)-1-[2'-Amino-2'-Carboxyethyl]-6-Methyl-5,7- Dihydropyrrolo[3,4-D]Pyrimidin-2,4(1H,3H)-Dione at Resolution 2.4A, PDB code: 6f28 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)	28.37 / 2.40
Space group	P 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	131.039, 56.214, 87.189, 90.00, 90.00, 90.00
R / Rfree (%)	19.5 / 22.2

The structure of Crystal Structure of the Kainate Receptor GLUK3 Ligand Binding Domain in Complex with (S)-1-[2'-Amino-2'-Carboxyethyl]-6-Methyl-5,7- Dihydropyrrolo[3,4-D]Pyrimidin-2,4(1H,3H)-Dione at Resolution 2.4A also contains other interesting chemical elements:

Zinc

(Zn)

5 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]-6-Methyl-5,7- Dihydropyrrolo[3,4-D]Pyrimidin-2,4(1H,3H)-Dione at Resolution 2.4A (pdb code 6f28). 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]-6-Methyl-5,7- Dihydropyrrolo[3,4-D]Pyrimidin-2,4(1H,3H)-Dione at Resolution 2.4A, PDB code: 6f28:
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]-6-Methyl-5,7- Dihydropyrrolo[3,4-D]Pyrimidin-2,4(1H,3H)-Dione at Resolution 2.4A


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]-6-Methyl-5,7- Dihydropyrrolo[3,4-D]Pyrimidin-2,4(1H,3H)-Dione at Resolution 2.4A within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl303 b:71.0 occ:1.00 N A:HIS95 3.4 43.1 1.0 CB A:THR94 3.7 48.3 1.0 CB A:HIS95 3.9 48.5 1.0 CD2 A:HIS95 4.0 54.8 1.0 CA A:THR94 4.1 44.1 1.0 C A:THR94 4.2 46.1 1.0 CA A:HIS95 4.2 43.5 1.0 CG A:HIS95 4.2 53.3 1.0 N A:VAL96 4.3 55.4 1.0 CG2 A:VAL96 4.4 70.0 1.0 OG1 A:THR94 4.6 52.3 1.0 CG2 A:THR94 4.6 48.2 1.0 C A:HIS95 4.8 44.0 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]-6-Methyl-5,7- Dihydropyrrolo[3,4-D]Pyrimidin-2,4(1H,3H)-Dione at Resolution 2.4A


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]-6-Methyl-5,7- Dihydropyrrolo[3,4-D]Pyrimidin-2,4(1H,3H)-Dione at Resolution 2.4A within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl304 b:92.7 occ:1.00 CG A:ARG201 3.3 64.8 1.0 CD A:ARG201 3.5 68.0 1.0 NH1 A:ARG201 3.6 81.7 1.0 OE1 A:GLN200 3.6 99.0 1.0 CD1 A:TYR197 3.7 46.4 1.0 N A:ARG253 3.7 78.8 1.0 CE1 A:TYR197 3.7 50.2 1.0 O A:TYR197 3.8 46.0 1.0 CB A:GLN200 3.9 80.7 1.0 CB A:ARG253 4.0 0.8 1.0 N A:GLY254 4.1 95.5 1.0 O A:GLY254 4.3 0.4 1.0 CG A:ARG253 4.3 1.0 1.0 CA A:ARG253 4.3 94.8 1.0 NE A:ARG201 4.4 77.3 1.0 C A:TRP252 4.4 60.0 1.0 CZ A:ARG201 4.4 83.2 1.0 CG A:TYR197 4.5 43.3 1.0 CZ A:TYR197 4.5 50.4 1.0 CA A:TRP252 4.6 52.5 1.0 CD A:GLN200 4.6 97.4 1.0 CA A:TYR197 4.7 43.6 1.0 C A:TYR197 4.7 46.5 1.0 C A:ARG253 4.7 98.8 1.0 O A:TRP251 4.8 55.1 1.0 CG A:GLN200 4.8 90.6 1.0 CB A:ARG201 4.8 62.1 1.0 C A:GLN200 4.8 63.6 1.0 C A:GLY254 4.9 0.8 1.0 N A:ARG201 4.9 57.4 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]-6-Methyl-5,7- Dihydropyrrolo[3,4-D]Pyrimidin-2,4(1H,3H)-Dione at Resolution 2.4A


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]-6-Methyl-5,7- Dihydropyrrolo[3,4-D]Pyrimidin-2,4(1H,3H)-Dione at Resolution 2.4A within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl307 b:69.3 occ:0.86 N B:TYR63 3.5 71.2 1.0 CD1 B:TYR63 3.8 62.8 1.0 CD B:LYS62 3.8 85.1 1.0 O B:ASP141 4.0 94.5 1.0 CA B:LYS62 4.0 68.3 1.0 CB B:LYS62 4.1 76.4 1.0 O B:LYS140 4.1 86.9 1.0 CB B:TYR63 4.2 68.7 1.0 C B:LYS62 4.3 63.4 1.0 CA B:TYR63 4.4 72.9 1.0 CG B:TYR63 4.5 62.8 1.0 C B:ASP141 4.5 87.6 1.0 CG B:LYS62 4.6 83.6 1.0 N B:GLY64 4.7 73.9 1.0 CE1 B:TYR63 4.8 59.3 1.0 CB B:ASP141 4.9 97.7 1.0 N B:GLY142 5.0 69.2 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