Chlorine in PDB 4ymb: Structure of the Ligand-Binding Domain of GLUK1 in Complex with the Antagonist CNG10111

The structure of Structure of the Ligand-Binding Domain of GLUK1 in Complex with the Antagonist CNG10111, PDB code: 4ymb was solved by C.Moller, D.Tapken, J.S.Kastrup, K.Frydenvang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.90 / 1.93
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	71.813, 71.813, 230.126, 90.00, 90.00, 90.00
R / Rfree (%)	17.9 / 22

The binding sites of Chlorine atom in the Structure of the Ligand-Binding Domain of GLUK1 in Complex with the Antagonist CNG10111 (pdb code 4ymb). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Structure of the Ligand-Binding Domain of GLUK1 in Complex with the Antagonist CNG10111, PDB code: 4ymb:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Structure of the Ligand-Binding Domain of GLUK1 in Complex with the Antagonist CNG10111


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of the Ligand-Binding Domain of GLUK1 in Complex with the Antagonist CNG10111 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl303 b:51.6 occ:1.00 H A:GLY62 2.5 21.7 1.0 HB2 A:ALA63 2.7 19.2 1.0 HH21 A:ARG95 2.8 16.0 1.0 HB2 A:TYR61 3.0 23.4 1.0 O A:HOH566 3.1 17.9 1.0 O A:HOH548 3.2 36.6 1.0 N A:GLY62 3.3 18.1 1.0 O A:GLY62 3.3 14.8 1.0 C A:GLY62 3.4 14.8 1.0 NH2 A:ARG95 3.5 13.3 1.0 CB A:ALA63 3.5 16.0 1.0 HH22 A:ARG95 3.6 16.0 1.0 HB3 A:ALA63 3.6 19.2 1.0 H A:TYR61 3.6 15.9 1.0 N A:ALA63 3.8 15.2 1.0 CB A:TYR61 3.8 19.5 1.0 CA A:GLY62 3.9 15.3 1.0 HB3 A:TYR61 4.1 23.4 1.0 H A:ALA63 4.1 18.3 1.0 N A:TYR61 4.2 13.3 1.0 CA A:ALA63 4.2 18.3 1.0 C A:TYR61 4.2 13.0 1.0 HB1 A:ALA63 4.3 19.2 1.0 CA A:TYR61 4.3 12.7 1.0 HB3 A:LYS60 4.4 24.3 1.0 O A:HOH605 4.5 28.8 1.0 HA2 A:GLY62 4.5 18.4 1.0 HA A:ALA63 4.5 21.9 1.0 HD2 A:TYR61 4.5 28.5 1.0 HA3 A:GLY62 4.6 18.4 1.0 OXT A:4E7301 4.7 11.7 1.0 HE A:ARG95 4.7 14.8 1.0 CZ A:ARG95 4.7 28.2 1.0 O A:HOH474 4.8 26.6 1.0 OD1 A:ASN71 4.9 19.4 1.0 CG A:TYR61 5.0 26.1 1.0

Chlorine binding site 2 out of 4 in the Structure of the Ligand-Binding Domain of GLUK1 in Complex with the Antagonist CNG10111


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of the Ligand-Binding Domain of GLUK1 in Complex with the Antagonist CNG10111 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl304 b:27.9 occ:1.00 HZ1 B:LYS103 2.3 18.0 1.0 HZ2 A:LYS103 2.4 15.3 1.0 O B:HOH459 2.8 15.3 1.0 O A:HOH497 2.8 36.1 1.0 HG2 A:LYS103 3.1 38.6 1.0 NZ B:LYS103 3.1 15.0 1.0 HD3 B:LYS103 3.1 32.5 1.0 HZ2 B:LYS103 3.2 18.0 1.0 NZ A:LYS103 3.2 12.7 1.0 HZ1 A:LYS103 3.3 15.3 1.0 HG2 B:LYS103 3.5 38.7 1.0 HZ3 B:LYS103 3.7 18.0 1.0 HZ3 A:LYS103 3.7 15.3 1.0 HG3 A:LYS103 3.8 38.6 1.0 CD B:LYS103 3.8 27.1 1.0 CG A:LYS103 3.9 32.2 1.0 HH11 B:ARG227 3.9 28.5 1.0 HE3 A:LYS103 3.9 15.0 1.0 CE B:LYS103 3.9 18.7 1.0 HH11 A:ARG227 3.9 24.6 1.0 HD3 A:ARG227 4.0 29.0 1.0 O A:PHE101 4.0 11.9 1.0 O B:PHE101 4.0 12.0 1.0 HD3 B:ARG227 4.1 21.3 1.0 CE A:LYS103 4.1 12.5 1.0 NH1 B:ARG227 4.1 23.7 1.0 CG B:LYS103 4.1 32.2 1.0 NH1 A:ARG227 4.1 20.5 1.0 HA B:LYS103 4.2 14.1 1.0 HE3 B:LYS103 4.2 22.5 1.0 HH12 B:ARG227 4.2 28.5 1.0 HA A:LYS103 4.3 16.6 1.0 HH12 A:ARG227 4.3 24.6 1.0 N B:LYS103 4.4 11.8 1.0 N A:LYS103 4.4 11.5 1.0 H B:LYS103 4.4 14.2 1.0 H A:LYS103 4.4 13.8 1.0 C B:SER102 4.6 19.2 1.0 C A:SER102 4.6 11.3 1.0 CZ A:ARG227 4.6 17.5 1.0 CZ B:ARG227 4.6 27.0 1.0 CD A:LYS103 4.6 34.4 1.0 HD2 B:LYS103 4.7 32.5 1.0 CA B:LYS103 4.7 11.8 1.0 OG1 A:THR231 4.7 13.4 1.0 CA A:LYS103 4.7 13.8 1.0 HA A:SER102 4.7 13.9 1.0 CD A:ARG227 4.8 24.2 1.0 HA B:SER102 4.8 16.1 1.0 OG1 B:THR231 4.8 13.9 1.0 HE2 B:LYS103 4.8 22.5 1.0 O B:SER102 4.8 10.9 1.0 HG21 A:THR231 4.8 19.8 1.0 HG3 B:LYS103 4.8 38.7 1.0 O A:SER102 4.8 11.1 1.0 O B:HOH502 4.8 28.2 1.0 NE A:ARG227 4.9 24.8 1.0 CD B:ARG227 4.9 17.8 1.0 HD2 A:ARG227 4.9 29.0 1.0 HE2 A:LYS103 4.9 15.0 1.0 CB A:LYS103 5.0 26.9 1.0 HG21 B:THR231 5.0 21.7 1.0 NE B:ARG227 5.0 27.4 1.0

Chlorine binding site 3 out of 4 in the Structure of the Ligand-Binding Domain of GLUK1 in Complex with the Antagonist CNG10111


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structure of the Ligand-Binding Domain of GLUK1 in Complex with the Antagonist CNG10111 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl305 b:47.1 occ:1.00 H A:LEU55 2.4 18.3 1.0 HG A:LEU55 2.9 33.4 1.0 HA A:LYS54 3.0 19.2 1.0 N A:LEU55 3.2 15.2 1.0 HB2 A:LEU55 3.3 18.7 1.0 HH22 A:ARG31 3.4 58.7 1.0 HZ A:PHE32 3.4 29.9 1.0 CG A:LEU55 3.7 27.9 1.0 O A:HOH430 3.7 43.0 1.0 HD12 A:LEU55 3.8 28.2 1.0 HH12 A:ARG31 3.8 78.3 1.0 CB A:LEU55 3.8 15.6 1.0 CA A:LYS54 3.9 16.0 1.0 NH2 A:ARG31 3.9 48.9 1.0 C A:LYS54 4.0 23.7 1.0 CA A:LEU55 4.1 21.3 1.0 O A:HOH423 4.1 33.8 1.0 CD1 A:LEU55 4.2 23.5 1.0 NH1 A:ARG31 4.2 65.3 1.0 CZ A:PHE32 4.3 24.9 1.0 O A:VAL53 4.3 23.3 1.0 HH21 A:ARG31 4.3 58.7 1.0 CZ A:ARG31 4.3 51.8 1.0 HE2 A:PHE32 4.4 33.5 1.0 HB3 A:LYS54 4.4 25.0 1.0 HD11 A:LEU55 4.6 28.2 1.0 HG2 A:LYS54 4.6 38.8 1.0 CB A:LYS54 4.7 20.8 1.0 O A:LEU55 4.7 18.1 1.0 HB3 A:LEU55 4.7 18.7 1.0 CE2 A:PHE32 4.8 28.0 1.0 N A:LYS54 4.8 16.4 1.0 HA A:LEU55 4.8 25.5 1.0 HH11 A:ARG31 4.8 78.3 1.0 CD2 A:LEU55 4.9 27.5 1.0 C A:VAL53 4.9 24.8 1.0 C A:LEU55 5.0 25.2 1.0 HD23 A:LEU55 5.0 33.0 1.0

Chlorine binding site 4 out of 4 in the Structure of the Ligand-Binding Domain of GLUK1 in Complex with the Antagonist CNG10111


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Structure of the Ligand-Binding Domain of GLUK1 in Complex with the Antagonist CNG10111 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl305 b:34.4 occ:1.00 H B:LEU55 2.5 25.9 1.0 HA B:LYS54 2.9 17.9 1.0 HH22 B:ARG31 2.9 42.5 1.0 HH12 B:ARG31 3.1 80.5 1.0 HG B:LEU55 3.2 32.8 1.0 N B:LEU55 3.3 21.6 1.0 HB2 B:LEU55 3.4 25.8 1.0 NH2 B:ARG31 3.6 35.4 1.0 HZ B:PHE32 3.8 48.4 1.0 CA B:LYS54 3.8 14.9 1.0 NH1 B:ARG31 3.8 67.0 1.0 CB B:LEU55 3.9 21.5 1.0 HD12 B:LEU55 3.9 30.9 1.0 CG B:LEU55 3.9 27.3 1.0 C B:LYS54 4.0 18.8 1.0 CZ B:ARG31 4.1 47.6 1.0 O B:VAL53 4.2 22.4 1.0 CA B:LEU55 4.2 13.6 1.0 HH21 B:ARG31 4.2 42.5 1.0 HB3 B:LYS54 4.2 23.9 1.0 HG2 B:LYS54 4.3 49.1 1.0 CD1 B:LEU55 4.5 25.8 1.0 HH11 B:ARG31 4.5 80.5 1.0 CB B:LYS54 4.5 19.9 1.0 O B:HOH407 4.5 26.4 1.0 HE2 B:PHE32 4.6 42.2 1.0 CZ B:PHE32 4.6 40.3 1.0 O B:LEU55 4.7 16.8 1.0 N B:LYS54 4.8 17.5 1.0 HD11 B:LEU55 4.8 30.9 1.0 HB3 B:LEU55 4.8 25.8 1.0 C B:VAL53 4.9 25.0 1.0 CG B:LYS54 4.9 40.9 1.0 HA B:LEU55 4.9 16.3 1.0 O B:HOH440 5.0 33.0 1.0

N.Krogsgaard-Larsen, M.Storgaard, C.Moller, C.S.Demmer, J.Hansen, L.Han, R.N.Monrad, B.Nielsen, D.Tapken, D.S.Pickering, J.S.Kastrup, K.Frydenvang, L.Bunch. Structure-Activity Relationship Study of Ionotropic Glutamate Receptor Antagonist (2S,3R)-3-(3-Carboxyphenyl)Pyrrolidine-2-Carboxylic Acid. J.Med.Chem. V. 58 6131 2015.
ISSN: ISSN 0022-2623
PubMed: 26200741
DOI: 10.1021/ACS.JMEDCHEM.5B00750