Fluorine in PDB 5ewm: Crystal Structure of Amino Terminal Domains of the Nmda Receptor Subunit GLUN1 and GLUN2B in Complex with Evt-101

The structure of Crystal Structure of Amino Terminal Domains of the Nmda Receptor Subunit GLUN1 and GLUN2B in Complex with Evt-101, PDB code: 5ewm was solved by J.Pandit, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.41 / 2.76
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	268.400, 60.610, 144.500, 90.00, 116.27, 90.00
R / Rfree (%)	17.1 / 21.1

The structure of Crystal Structure of Amino Terminal Domains of the Nmda Receptor Subunit GLUN1 and GLUN2B in Complex with Evt-101 also contains other interesting chemical elements:

Sodium

(Na)

5 atoms

The binding sites of Fluorine atom in the Crystal Structure of Amino Terminal Domains of the Nmda Receptor Subunit GLUN1 and GLUN2B in Complex with Evt-101 (pdb code 5ewm). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of Amino Terminal Domains of the Nmda Receptor Subunit GLUN1 and GLUN2B in Complex with Evt-101, PDB code: 5ewm:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in the Crystal Structure of Amino Terminal Domains of the Nmda Receptor Subunit GLUN1 and GLUN2B in Complex with Evt-101


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 Amino Terminal Domains of the Nmda Receptor Subunit GLUN1 and GLUN2B in Complex with Evt-101 within 5.0Å range: probe atom residue distance (Å) B Occ B:F503 b:48.7 occ:1.00 F1 B:5SM503 0.0 48.7 1.0 C16 B:5SM503 1.4 48.0 1.0 F2 B:5SM503 2.1 52.9 1.0 C14 B:5SM503 2.3 44.6 1.0 C13 B:5SM503 3.2 46.7 1.0 C15 B:5SM503 3.2 42.3 1.0 F3 B:5SM503 3.3 52.0 1.0 CG1 B:ILE111 3.5 44.0 1.0 CD1 B:ILE82 3.7 56.2 1.0 CD2 B:PHE114 3.8 43.4 1.0 CG2 B:ILE111 3.9 45.5 1.0 CB B:PRO78 3.9 45.8 1.0 CB B:ILE111 4.0 44.5 1.0 CA B:ILE111 4.1 41.2 1.0 CE2 B:PHE114 4.3 45.9 1.0 C12 B:5SM503 4.4 45.0 1.0 C10 B:5SM503 4.4 46.6 1.0 CG1 B:ILE82 4.4 49.9 1.0 CG B:PHE114 4.4 43.1 1.0 OG1 A:THR110 4.5 41.4 1.0 CA B:PRO78 4.6 44.6 1.0 CB B:PHE114 4.7 42.7 1.0 O B:ILE111 4.7 49.9 1.0 CD1 B:ILE111 4.7 35.6 1.0 CB A:ALA75 4.7 48.4 1.0 C11 B:5SM503 4.9 47.3 1.0 C B:ILE111 4.9 49.0 1.0

Fluorine binding site 2 out of 6 in the Crystal Structure of Amino Terminal Domains of the Nmda Receptor Subunit GLUN1 and GLUN2B in Complex with Evt-101


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 Amino Terminal Domains of the Nmda Receptor Subunit GLUN1 and GLUN2B in Complex with Evt-101 within 5.0Å range: probe atom residue distance (Å) B Occ B:F503 b:52.9 occ:1.00 F2 B:5SM503 0.0 52.9 1.0 C16 B:5SM503 1.4 48.0 1.0 F1 B:5SM503 2.1 48.7 1.0 C14 B:5SM503 2.4 44.6 1.0 C15 B:5SM503 2.7 42.3 1.0 CD2 B:PHE114 3.2 43.4 1.0 CE2 B:PHE114 3.3 45.9 1.0 CG B:PHE114 3.5 43.1 1.0 C13 B:5SM503 3.7 46.7 1.0 CZ B:PHE114 3.7 43.1 1.0 OG1 A:THR110 3.7 41.4 1.0 CD1 B:PHE114 3.9 44.4 1.0 CB A:ALA75 3.9 48.4 1.0 CE1 B:PHE114 4.0 43.8 1.0 C10 B:5SM503 4.1 46.6 1.0 F3 B:5SM503 4.2 52.0 1.0 CB B:PHE114 4.3 42.7 1.0 CB A:TYR109 4.3 39.5 1.0 O A:PRO106 4.7 46.9 1.0 CD1 B:ILE82 4.7 56.2 1.0 CD2 A:TYR109 4.7 43.7 1.0 C12 B:5SM503 4.8 45.0 1.0 N A:THR110 4.8 41.7 1.0 C11 B:5SM503 5.0 47.3 1.0 CB A:THR110 5.0 43.4 1.0 CA A:PRO106 5.0 44.4 1.0

Fluorine binding site 3 out of 6 in the Crystal Structure of Amino Terminal Domains of the Nmda Receptor Subunit GLUN1 and GLUN2B in Complex with Evt-101


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 Amino Terminal Domains of the Nmda Receptor Subunit GLUN1 and GLUN2B in Complex with Evt-101 within 5.0Å range: probe atom residue distance (Å) B Occ B:F503 b:52.0 occ:1.00 F3 B:5SM503 0.0 52.0 1.0 C13 B:5SM503 1.4 46.7 1.0 C12 B:5SM503 2.3 45.0 1.0 C14 B:5SM503 2.4 44.6 1.0 C16 B:5SM503 2.9 48.0 1.0 F1 B:5SM503 3.3 48.7 1.0 CB B:PRO78 3.3 45.8 1.0 CG B:PRO78 3.5 50.6 1.0 C11 B:5SM503 3.6 47.3 1.0 C15 B:5SM503 3.6 42.3 1.0 CG1 B:ILE111 3.7 44.0 1.0 CA A:THR110 3.7 41.2 1.0 O A:TYR109 3.8 48.7 1.0 CB A:PHE113 3.9 42.0 1.0 CD2 A:PHE113 4.0 47.3 1.0 CD1 B:ILE111 4.0 35.6 1.0 C10 B:5SM503 4.1 46.6 1.0 N A:THR110 4.1 41.7 1.0 CG A:PHE113 4.2 44.7 1.0 OG1 A:THR110 4.2 41.4 1.0 F2 B:5SM503 4.2 52.9 1.0 C A:TYR109 4.2 46.8 1.0 CD B:PRO78 4.3 46.4 1.0 CB A:THR110 4.3 43.4 1.0 CG2 A:THR110 4.4 40.8 1.0 O A:THR110 4.5 48.0 1.0 CA B:PRO78 4.5 44.6 1.0 C A:THR110 4.6 46.5 1.0 CE2 A:PHE113 4.8 50.0 1.0 N B:PRO78 5.0 45.2 1.0

Fluorine binding site 4 out of 6 in the Crystal Structure of Amino Terminal Domains of the Nmda Receptor Subunit GLUN1 and GLUN2B in Complex with Evt-101


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 Amino Terminal Domains of the Nmda Receptor Subunit GLUN1 and GLUN2B in Complex with Evt-101 within 5.0Å range: probe atom residue distance (Å) B Occ D:F503 b:72.8 occ:1.00 F1 D:5SM503 0.0 72.8 1.0 C16 D:5SM503 1.4 71.6 1.0 F2 D:5SM503 2.1 69.9 1.0 C14 D:5SM503 2.4 73.5 1.0 C13 D:5SM503 3.3 69.8 1.0 C15 D:5SM503 3.3 73.9 1.0 F3 D:5SM503 3.3 66.8 1.0 CG1 D:ILE111 3.6 59.8 1.0 CD1 D:ILE82 3.6 64.2 1.0 CB D:PRO78 3.8 66.2 1.0 CG2 D:ILE111 3.8 61.9 1.0 CD2 D:PHE114 4.0 64.9 1.0 CB D:ILE111 4.1 59.5 1.0 CA D:ILE111 4.2 55.6 1.0 CG1 D:ILE82 4.4 63.1 1.0 OG1 C:THR110 4.4 67.7 1.0 CE2 D:PHE114 4.4 69.1 1.0 CA D:PRO78 4.5 64.9 1.0 C12 D:5SM503 4.5 70.9 1.0 C10 D:5SM503 4.6 72.5 1.0 CG D:PHE114 4.6 60.6 1.0 CD1 D:ILE111 4.6 62.2 1.0 CB C:ALA75 4.7 71.0 1.0 O D:ILE111 4.8 56.7 1.0 CB D:PHE114 4.9 57.5 1.0 CG D:PRO78 5.0 71.6 1.0

Fluorine binding site 5 out of 6 in the Crystal Structure of Amino Terminal Domains of the Nmda Receptor Subunit GLUN1 and GLUN2B in Complex with Evt-101


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of Amino Terminal Domains of the Nmda Receptor Subunit GLUN1 and GLUN2B in Complex with Evt-101 within 5.0Å range: probe atom residue distance (Å) B Occ D:F503 b:69.9 occ:1.00 F2 D:5SM503 0.0 69.9 1.0 C16 D:5SM503 1.4 71.6 1.0 F1 D:5SM503 2.1 72.8 1.0 C14 D:5SM503 2.4 73.5 1.0 C15 D:5SM503 2.7 73.9 1.0 CD2 D:PHE114 3.2 64.9 1.0 CE2 D:PHE114 3.4 69.1 1.0 CG D:PHE114 3.5 60.6 1.0 C13 D:5SM503 3.7 69.8 1.0 CZ D:PHE114 3.8 67.8 1.0 OG1 C:THR110 3.8 67.7 1.0 CD1 D:PHE114 3.9 64.0 1.0 CE1 D:PHE114 4.0 66.4 1.0 C10 D:5SM503 4.1 72.5 1.0 CB C:ALA75 4.1 71.0 1.0 CB D:PHE114 4.2 57.5 1.0 F3 D:5SM503 4.2 66.8 1.0 CB C:TYR109 4.2 60.9 1.0 CD2 C:TYR109 4.7 61.3 1.0 CD1 D:ILE82 4.7 64.2 1.0 O C:PRO106 4.7 72.2 1.0 C12 D:5SM503 4.8 70.9 1.0 N C:THR110 4.8 67.5 1.0 C11 D:5SM503 4.9 71.3 1.0 C8 D:5SM503 4.9 71.2 1.0 CG C:TYR109 5.0 61.0 1.0

Fluorine binding site 6 out of 6 in the Crystal Structure of Amino Terminal Domains of the Nmda Receptor Subunit GLUN1 and GLUN2B in Complex with Evt-101


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of Amino Terminal Domains of the Nmda Receptor Subunit GLUN1 and GLUN2B in Complex with Evt-101 within 5.0Å range: probe atom residue distance (Å) B Occ D:F503 b:66.8 occ:1.00 F3 D:5SM503 0.0 66.8 1.0 C13 D:5SM503 1.4 69.8 1.0 C12 D:5SM503 2.3 70.9 1.0 C14 D:5SM503 2.4 73.5 1.0 C16 D:5SM503 2.9 71.6 1.0 F1 D:5SM503 3.3 72.8 1.0 CB D:PRO78 3.4 66.2 1.0 CG D:PRO78 3.6 71.6 1.0 C11 D:5SM503 3.6 71.3 1.0 C15 D:5SM503 3.6 73.9 1.0 CG1 D:ILE111 3.7 59.8 1.0 CB C:PHE113 3.7 59.7 1.0 O C:TYR109 3.7 72.6 1.0 CA C:THR110 3.7 68.7 1.0 CD2 C:PHE113 3.8 60.5 1.0 CG C:PHE113 4.0 60.6 1.0 CD1 D:ILE111 4.0 62.2 1.0 C10 D:5SM503 4.1 72.5 1.0 C C:TYR109 4.1 69.8 1.0 N C:THR110 4.2 67.5 1.0 F2 D:5SM503 4.2 69.9 1.0 CD D:PRO78 4.3 67.7 1.0 OG1 C:THR110 4.3 67.7 1.0 O C:THR110 4.4 73.4 1.0 CB C:THR110 4.5 74.8 1.0 C C:THR110 4.6 71.7 1.0 CA D:PRO78 4.6 64.9 1.0 CG2 C:THR110 4.6 73.2 1.0 CE2 C:PHE113 4.8 64.2 1.0 CA C:PHE113 4.9 59.2 1.0

D.Stroebel, D.L.Buhl, J.D.Knafels, P.K.Chanda, M.Green, S.Sciabola, L.Mony, P.Paoletti, J.Pandit. A Novel Binding Mode Reveals Two Distinct Classes of Nmda Receptor GLUN2B-Selective Antagonists. Mol.Pharmacol. V. 89 541 2016.
ISSN: ESSN 1521-0111
PubMed: 26912815
DOI: 10.1124/MOL.115.103036