Fluorine in PDB 5kdt: Structure of the Human GLUN1/GLUN2A Lbd in Complex with GNE0723

The structure of Structure of the Human GLUN1/GLUN2A Lbd in Complex with GNE0723, PDB code: 5kdt was solved by H.J.A.Wallweber, P.J.Lupardus, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	72.74 / 2.44
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	55.325, 90.127, 123.185, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 24.1

The structure of Structure of the Human GLUN1/GLUN2A Lbd in Complex with GNE0723 also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Fluorine atom in the Structure of the Human GLUN1/GLUN2A Lbd in Complex with GNE0723 (pdb code 5kdt). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Structure of the Human GLUN1/GLUN2A Lbd in Complex with GNE0723, PDB code: 5kdt:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in the Structure of the Human GLUN1/GLUN2A Lbd in Complex with GNE0723


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of the Human GLUN1/GLUN2A Lbd in Complex with GNE0723 within 5.0Å range: probe atom residue distance (Å) B Occ A:F303 b:69.1 occ:1.00 F12 A:6RV303 0.0 69.1 1.0 C11 A:6RV303 1.4 67.3 1.0 F14 A:6RV303 2.2 67.4 1.0 F13 A:6RV303 2.3 64.5 1.0 C9 A:6RV303 2.3 66.4 1.0 C16 A:6RV303 2.7 69.2 1.0 C15 A:6RV303 2.7 67.8 1.0 C8 A:6RV303 2.8 67.1 1.0 CG1 A:VAL266 3.3 52.9 1.0 CG2 A:VAL266 3.5 52.6 1.0 OH B:TYR144 3.5 56.4 1.0 O B:ARG248 3.6 67.3 1.0 C17 A:6RV303 3.7 66.8 1.0 S10 A:6RV303 3.8 61.0 1.0 CB A:VAL266 4.0 53.4 1.0 N5 A:6RV303 4.0 63.4 1.0 CZ B:TYR144 4.3 56.0 1.0 CE1 B:TYR144 4.3 51.7 1.0 C B:ARG248 4.5 66.5 1.0 C4 A:6RV303 4.6 62.5 1.0

Fluorine binding site 2 out of 6 in the Structure of the Human GLUN1/GLUN2A Lbd in Complex with GNE0723


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of the Human GLUN1/GLUN2A Lbd in Complex with GNE0723 within 5.0Å range: probe atom residue distance (Å) B Occ A:F303 b:64.5 occ:1.00 F13 A:6RV303 0.0 64.5 1.0 C11 A:6RV303 1.4 67.3 1.0 F14 A:6RV303 2.2 67.4 1.0 F12 A:6RV303 2.3 69.1 1.0 C9 A:6RV303 2.4 66.4 1.0 O A:PHE130 3.2 44.6 1.0 C16 A:6RV303 3.2 69.2 1.0 C8 A:6RV303 3.3 67.1 1.0 CG2 A:VAL266 3.3 52.6 1.0 C A:PHE130 3.5 44.1 1.0 CA A:PHE130 3.5 41.2 1.0 S10 A:6RV303 3.6 61.0 1.0 C15 A:6RV303 3.6 67.8 1.0 O A:PRO129 3.8 46.4 1.0 C17 A:6RV303 3.8 66.8 1.0 CE A:MET271 3.9 69.3 1.0 CB A:PHE130 4.3 42.5 1.0 N5 A:6RV303 4.4 63.4 1.0 CG1 A:VAL266 4.5 52.9 1.0 CB A:VAL266 4.5 53.4 1.0 SD A:MET271 4.5 72.2 1.0 CG A:MET271 4.5 67.8 1.0 N A:VAL131 4.6 39.0 1.0 N A:PHE130 4.6 41.9 1.0 C A:PRO129 4.6 45.8 1.0 C4 A:6RV303 4.7 62.5 1.0 OH B:TYR144 5.0 56.4 1.0

Fluorine binding site 3 out of 6 in the Structure of the Human GLUN1/GLUN2A Lbd in Complex with GNE0723


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of the Human GLUN1/GLUN2A Lbd in Complex with GNE0723 within 5.0Å range: probe atom residue distance (Å) B Occ A:F303 b:67.4 occ:1.00 F14 A:6RV303 0.0 67.4 1.0 C11 A:6RV303 1.4 67.3 1.0 F12 A:6RV303 2.2 69.1 1.0 F13 A:6RV303 2.2 64.5 1.0 C9 A:6RV303 2.3 66.4 1.0 S10 A:6RV303 2.8 61.0 1.0 OH B:TYR144 3.2 56.4 1.0 C8 A:6RV303 3.5 67.1 1.0 O A:PHE130 3.6 44.6 1.0 OE1 A:GLU275 3.8 69.1 1.0 CE A:MET271 4.0 69.3 1.0 O A:HOH451 4.2 45.9 1.0 CZ B:TYR144 4.2 56.0 1.0 C A:PHE130 4.2 44.1 1.0 C15 A:6RV303 4.2 67.8 1.0 C4 A:6RV303 4.3 62.5 1.0 N5 A:6RV303 4.4 63.4 1.0 C16 A:6RV303 4.4 69.2 1.0 CG2 A:VAL266 4.7 52.6 1.0 CE1 B:TYR144 4.8 51.7 1.0 N A:VAL131 4.8 39.0 1.0 CG1 A:VAL266 4.8 52.9 1.0 CA A:PHE130 4.9 41.2 1.0 CA A:VAL131 4.9 37.8 1.0

Fluorine binding site 4 out of 6 in the Structure of the Human GLUN1/GLUN2A Lbd in Complex with GNE0723


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structure of the Human GLUN1/GLUN2A Lbd in Complex with GNE0723 within 5.0Å range: probe atom residue distance (Å) B Occ A:F303 b:63.5 occ:1.00 F27 A:6RV303 0.0 63.5 1.0 C26 A:6RV303 1.4 65.0 1.0 F29 A:6RV303 2.2 68.0 1.0 F28 A:6RV303 2.3 65.1 1.0 C24 A:6RV303 2.3 61.6 1.0 C23 A:6RV303 2.7 63.1 1.0 CD2 B:LEU270 3.3 42.4 1.0 N25 A:6RV303 3.5 59.0 1.0 CB B:LYS140 3.6 33.2 1.0 O B:PRO141 3.8 38.6 1.0 C22 A:6RV303 4.0 64.7 1.0 CD B:PRO141 4.0 34.8 1.0 CD B:LYS140 4.2 37.1 1.0 N B:PRO141 4.2 34.1 1.0 CD2 B:HIS273 4.3 42.2 1.0 N21 A:6RV303 4.3 60.4 1.0 CG B:LYS140 4.3 31.7 1.0 C B:LYS140 4.5 37.3 1.0 OG1 A:THR242 4.5 35.5 1.0 NE2 B:HIS273 4.5 41.9 1.0 CA B:LYS140 4.6 32.1 1.0 CG B:LEU270 4.7 40.5 1.0 C B:PRO141 4.7 39.1 1.0 CA A:THR242 4.8 42.2 1.0 CA B:PRO141 4.9 33.5 1.0 CG2 A:ILE116 4.9 32.9 1.0 CG B:PRO141 4.9 39.4 1.0

Fluorine binding site 5 out of 6 in the Structure of the Human GLUN1/GLUN2A Lbd in Complex with GNE0723


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Structure of the Human GLUN1/GLUN2A Lbd in Complex with GNE0723 within 5.0Å range: probe atom residue distance (Å) B Occ A:F303 b:65.1 occ:1.00 F28 A:6RV303 0.0 65.1 1.0 C26 A:6RV303 1.4 65.0 1.0 F29 A:6RV303 2.2 68.0 1.0 F27 A:6RV303 2.3 63.5 1.0 C24 A:6RV303 2.3 61.6 1.0 OG1 A:THR242 2.4 35.5 1.0 N25 A:6RV303 3.0 59.0 1.0 CA A:THR242 3.1 42.2 1.0 CB A:THR242 3.2 39.4 1.0 N A:GLY243 3.2 36.7 1.0 C23 A:6RV303 3.4 63.1 1.0 C A:THR242 3.5 42.6 1.0 CB A:ILE116 3.9 33.5 1.0 CD2 B:LEU270 3.9 42.4 1.0 CG2 A:ILE116 4.1 32.9 1.0 O A:ILE116 4.2 40.8 1.0 N21 A:6RV303 4.2 60.4 1.0 CA A:GLY243 4.3 35.8 1.0 C22 A:6RV303 4.3 64.7 1.0 CD1 A:ILE116 4.5 28.1 1.0 N A:THR242 4.5 44.7 1.0 O A:GLY243 4.5 35.8 1.0 O A:THR242 4.5 43.4 1.0 CG2 A:THR242 4.6 33.5 1.0 O A:THR241 4.7 52.9 1.0 CG1 A:ILE116 4.7 33.9 1.0 C A:ILE116 4.8 37.7 1.0 CA A:ILE116 4.9 31.5 1.0 C A:GLY243 4.9 38.0 1.0

Fluorine binding site 6 out of 6 in the Structure of the Human GLUN1/GLUN2A Lbd in Complex with GNE0723


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Structure of the Human GLUN1/GLUN2A Lbd in Complex with GNE0723 within 5.0Å range: probe atom residue distance (Å) B Occ A:F303 b:68.0 occ:1.00 F29 A:6RV303 0.0 68.0 1.0 C26 A:6RV303 1.4 65.0 1.0 F28 A:6RV303 2.2 65.1 1.0 F27 A:6RV303 2.2 63.5 1.0 C24 A:6RV303 2.3 61.6 1.0 N25 A:6RV303 2.8 59.0 1.0 CG A:PRO129 3.4 44.0 1.0 C23 A:6RV303 3.5 63.1 1.0 CB A:PRO129 3.6 40.0 1.0 CD1 A:ILE116 3.6 28.1 1.0 CD B:LYS140 3.6 37.1 1.0 CD A:PRO129 3.7 39.5 1.0 CD B:PRO141 3.8 34.8 1.0 N21 A:6RV303 4.0 60.4 1.0 N A:GLY243 4.2 36.7 1.0 CB A:ILE116 4.4 33.5 1.0 CG2 A:ILE116 4.4 32.9 1.0 OG1 A:THR242 4.4 35.5 1.0 C22 A:6RV303 4.4 64.7 1.0 CB B:LYS140 4.4 33.2 1.0 CG B:LYS140 4.5 31.7 1.0 N A:PRO129 4.5 39.0 1.0 CG1 A:ILE116 4.6 33.9 1.0 CA A:PRO129 4.6 38.6 1.0 CE B:LYS140 4.6 36.1 1.0 CG B:PRO141 4.6 39.4 1.0 CD2 B:LEU270 4.6 42.4 1.0 C A:THR242 4.7 42.6 1.0 CA A:GLY243 4.7 35.8 1.0 N B:PRO141 4.7 34.1 1.0 CA A:THR242 4.8 42.2 1.0

M.Volgraf, B.D.Sellers, Y.Jiang, G.Wu, C.Q.Ly, E.Villemure, R.M.Pastor, P.W.Yuen, A.Lu, X.Luo, M.Liu, S.Zhang, L.Sun, Y.Fu, P.J.Lupardus, H.J.Wallweber, B.M.Liederer, G.Deshmukh, E.Plise, S.Tay, P.Reynen, J.Herrington, A.Gustafson, Y.Liu, A.Dirksen, M.G.Dietz, Y.Liu, T.M.Wang, J.E.Hanson, D.Hackos, K.Scearce-Levie, J.B.Schwarz. Discovery of GLUN2A-Selective Nmda Receptor Positive Allosteric Modulators (Pams): Tuning Deactivation Kinetics Via Structure-Based Design. J. Med. Chem. V. 59 2760 2016.
ISSN: ISSN 1520-4804
PubMed: 26919761
DOI: 10.1021/ACS.JMEDCHEM.5B02010