Fluorine in PDB 5o9a: Crystal Structure of the GLUA2 Ligand-Binding Domain (S1S2J-L504Y- N775S) in Complex with Glutamate and BPAM121 at 1.78 A Resolution

The structure of Crystal Structure of the GLUA2 Ligand-Binding Domain (S1S2J-L504Y- N775S) in Complex with Glutamate and BPAM121 at 1.78 A Resolution, PDB code: 5o9a was solved by S.Laulumaa, K.Rovinskaja, K.A.Frydenvang, J.S.Kastrup, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.20 / 1.78
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	47.308, 98.408, 121.787, 90.00, 90.53, 90.00
R / Rfree (%)	15.3 / 17.9

The structure of Crystal Structure of the GLUA2 Ligand-Binding Domain (S1S2J-L504Y- N775S) in Complex with Glutamate and BPAM121 at 1.78 A Resolution also contains other interesting chemical elements:

Chlorine

(Cl)

11 atoms

The binding sites of Fluorine atom in the Crystal Structure of the GLUA2 Ligand-Binding Domain (S1S2J-L504Y- N775S) in Complex with Glutamate and BPAM121 at 1.78 A Resolution (pdb code 5o9a). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of the GLUA2 Ligand-Binding Domain (S1S2J-L504Y- N775S) in Complex with Glutamate and BPAM121 at 1.78 A Resolution, PDB code: 5o9a:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Crystal Structure of the GLUA2 Ligand-Binding Domain (S1S2J-L504Y- N775S) in Complex with Glutamate and BPAM121 at 1.78 A Resolution


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of the GLUA2 Ligand-Binding Domain (S1S2J-L504Y- N775S) in Complex with Glutamate and BPAM121 at 1.78 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:F305 b:20.3 occ:1.00 F1 A:7M6305 0.0 20.3 1.0 C9 A:7M6305 1.3 18.5 1.0 C8 A:7M6305 2.4 16.8 1.0 N1 A:7M6305 3.0 14.5 1.0 N A:MET107 3.0 10.4 1.0 C A:PHE106 3.1 10.6 1.0 C7 A:7M6305 3.2 12.2 1.0 CA A:MET107 3.2 10.3 1.0 C2 A:7M6305 3.3 13.7 1.0 O A:PHE106 3.3 11.9 1.0 C A:MET107 3.5 10.8 1.0 O A:PRO105 3.6 10.8 1.0 N A:SER108 3.7 11.8 1.0 O A:HOH592 3.8 13.9 1.0 OG A:SER108 3.8 13.2 0.3 CA A:PHE106 3.9 9.2 1.0 O A:HOH541 3.9 34.3 1.0 O B:HOH446 3.9 22.6 1.0 C A:PRO105 4.0 9.6 1.0 C3 A:7M6305 4.0 14.9 1.0 N A:PHE106 4.1 8.7 1.0 O A:MET107 4.2 10.7 1.0 C6 A:7M6305 4.3 12.7 1.0 O A:HOH462 4.3 35.2 1.0 CL1 B:7M6304 4.4 14.2 1.0 C1 A:7M6305 4.6 13.1 1.0 CB A:PRO105 4.6 10.3 1.0 N2 A:7M6305 4.7 14.7 1.0 OG B:SER217 4.7 19.5 1.0 CB A:MET107 4.7 11.2 1.0 CA A:SER108 4.7 12.3 0.7 CA A:SER108 4.7 12.2 0.3 CB A:SER108 4.8 12.9 0.7 CB A:SER108 4.8 12.8 0.3 CA A:PRO105 4.9 9.8 1.0 CG A:PRO105 5.0 10.7 1.0

Fluorine binding site 2 out of 4 in the Crystal Structure of the GLUA2 Ligand-Binding Domain (S1S2J-L504Y- N775S) in Complex with Glutamate and BPAM121 at 1.78 A Resolution


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of the GLUA2 Ligand-Binding Domain (S1S2J-L504Y- N775S) in Complex with Glutamate and BPAM121 at 1.78 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:F304 b:23.1 occ:1.00 F1 B:7M6304 0.0 23.1 1.0 C9 B:7M6304 1.3 21.2 1.0 C8 B:7M6304 2.4 18.8 1.0 N1 B:7M6304 3.0 14.7 1.0 C7 B:7M6304 3.1 11.9 1.0 N B:MET107 3.1 9.1 1.0 C B:PHE106 3.2 11.1 1.0 CA B:MET107 3.2 9.6 1.0 O B:PHE106 3.3 11.7 1.0 C2 B:7M6304 3.3 12.7 1.0 C B:MET107 3.5 9.6 1.0 N B:SER108 3.7 10.8 1.0 O B:HOH431 3.7 9.6 0.4 O B:PRO105 3.7 10.4 1.0 O B:HOH576 3.8 13.9 1.0 OG B:SER108 3.9 12.5 0.3 CA B:PHE106 3.9 11.4 1.0 O A:HOH565 4.1 28.9 1.0 C B:PRO105 4.1 10.6 1.0 C3 B:7M6304 4.1 15.7 1.0 C6 B:7M6304 4.2 12.3 1.0 N B:PHE106 4.2 10.8 1.0 O B:MET107 4.2 9.2 1.0 CL1 A:7M6305 4.3 14.9 1.0 O B:HOH428 4.3 40.7 1.0 CB B:PRO105 4.6 9.1 1.0 C1 B:7M6304 4.6 11.4 1.0 CA B:SER108 4.7 11.6 0.3 CA B:SER108 4.7 11.5 0.7 CB B:MET107 4.7 10.9 1.0 OG A:SER217 4.7 19.1 1.0 CB B:SER108 4.8 12.9 0.7 CB B:SER108 4.8 12.8 0.3 N2 B:7M6304 4.8 15.8 1.0 CG B:PRO105 5.0 9.8 1.0

Fluorine binding site 3 out of 4 in the Crystal Structure of the GLUA2 Ligand-Binding Domain (S1S2J-L504Y- N775S) in Complex with Glutamate and BPAM121 at 1.78 A Resolution


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of the GLUA2 Ligand-Binding Domain (S1S2J-L504Y- N775S) in Complex with Glutamate and BPAM121 at 1.78 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ C:F307 b:22.5 occ:1.00 F1 C:7M6307 0.0 22.5 1.0 C9 C:7M6307 1.3 20.4 1.0 C8 C:7M6307 2.4 18.2 1.0 N1 C:7M6307 3.0 15.1 1.0 C7 C:7M6307 3.1 13.5 1.0 N C:MET107 3.2 10.1 1.0 O4 C:SO4306 3.3 26.9 0.8 C2 C:7M6307 3.3 14.2 1.0 CA C:MET107 3.3 10.5 1.0 C C:PHE106 3.3 10.1 1.0 C C:MET107 3.5 10.8 1.0 O C:PHE106 3.6 10.3 1.0 O C:PRO105 3.6 9.9 1.0 N C:SER108 3.7 11.1 1.0 OG C:SER108 3.7 13.6 0.3 O1 C:SO4306 3.8 19.2 0.8 S C:SO4306 3.8 28.1 0.8 O2 C:SO4306 3.9 32.3 0.8 C C:PRO105 4.0 9.7 1.0 O C:HOH477 4.0 53.8 1.0 CL1 D:7M6305 4.0 13.3 1.0 CA C:PHE106 4.0 10.4 1.0 C3 C:7M6307 4.0 15.7 1.0 C6 C:7M6307 4.2 13.1 1.0 O C:MET107 4.2 10.1 1.0 N C:PHE106 4.2 9.8 1.0 CB C:PRO105 4.4 10.1 1.0 C1 C:7M6307 4.5 12.4 1.0 CA C:SER108 4.6 11.3 0.7 CA C:SER108 4.6 11.5 0.3 N2 C:7M6307 4.6 16.1 1.0 CB C:SER108 4.6 12.8 0.7 CB C:SER108 4.7 12.8 0.3 CG C:PRO105 4.8 11.9 1.0 CB C:MET107 4.8 12.3 1.0 CA C:PRO105 4.9 9.4 1.0

Fluorine binding site 4 out of 4 in the Crystal Structure of the GLUA2 Ligand-Binding Domain (S1S2J-L504Y- N775S) in Complex with Glutamate and BPAM121 at 1.78 A Resolution


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of the GLUA2 Ligand-Binding Domain (S1S2J-L504Y- N775S) in Complex with Glutamate and BPAM121 at 1.78 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ D:F305 b:20.9 occ:1.00 F1 D:7M6305 0.0 20.9 1.0 C9 D:7M6305 1.3 19.1 1.0 C8 D:7M6305 2.3 17.5 1.0 N1 D:7M6305 3.0 14.2 1.0 C7 D:7M6305 3.0 10.8 1.0 N D:MET107 3.1 10.5 1.0 C2 D:7M6305 3.3 11.7 1.0 CA D:MET107 3.3 10.5 1.0 C D:PHE106 3.3 10.9 1.0 C D:MET107 3.5 10.2 1.0 O D:PHE106 3.6 11.2 1.0 N D:SER108 3.6 10.5 1.0 O D:PRO105 3.7 10.5 1.0 OG D:SER108 3.8 11.3 0.3 O C:HOH526 3.8 26.6 1.0 O D:HOH578 3.8 11.6 1.0 O D:HOH611 3.8 12.6 0.5 C D:PRO105 4.0 10.6 1.0 CA D:PHE106 4.0 10.1 1.0 C6 D:7M6305 4.1 11.2 1.0 CL1 C:7M6307 4.1 14.3 1.0 C3 D:7M6305 4.1 15.0 1.0 O D:MET107 4.1 10.1 1.0 N D:PHE106 4.2 9.8 1.0 CB D:PRO105 4.4 11.7 1.0 C1 D:7M6305 4.5 10.7 1.0 CA D:SER108 4.6 10.9 0.7 CA D:SER108 4.6 11.4 0.3 O D:HOH414 4.7 38.1 1.0 CB D:SER108 4.7 11.7 0.7 CB D:SER108 4.7 11.7 0.3 CB D:MET107 4.8 10.4 1.0 N2 D:7M6305 4.8 15.5 1.0 CG D:PRO105 4.8 11.7 1.0 OG C:SER217 4.8 19.8 1.0 CA D:PRO105 4.9 10.2 1.0 OG D:SER108 5.0 11.8 0.7

E.Goffin, T.Drapier, A.P.Larsen, P.Geubelle, C.P.Ptak, S.Laulumaa, K.Rovinskaja, J.Gilissen, P.Tullio, L.Olsen, K.Frydenvang, B.Pirotte, J.Hanson, R.E.Oswald, J.S.Kastrup, P.Francotte. 7-Phenoxy-Substituted 3,4-Dihydro-2H-1,2,4-Benzothiadiazine 1,1-Dioxides As Positive Allosteric Modulators of Alpha-Amino-3-Hydroxy-5-Methyl-4-Isoxazolepropionic Acid (Ampa) Receptors with Nanomolar Potency. J. Med. Chem. V. 61 251 2018.
ISSN: ISSN 1520-4804
PubMed: 29256599
DOI: 10.1021/ACS.JMEDCHEM.7B01323