Fluorine in PDB 5tp9: Structure of the Human GLUN1/GLUN2A Lbd in Complex with Compound 2 (GNE9178)

The structure of Structure of the Human GLUN1/GLUN2A Lbd in Complex with Compound 2 (GNE9178), PDB code: 5tp9 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)	47.67 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.260, 89.780, 120.860, 90.00, 90.00, 90.00
R / Rfree (%)	19 / 23.7

The structure of Structure of the Human GLUN1/GLUN2A Lbd in Complex with Compound 2 (GNE9178) also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Calcium	(Ca)	1 atom

The binding sites of Fluorine atom in the Structure of the Human GLUN1/GLUN2A Lbd in Complex with Compound 2 (GNE9178) (pdb code 5tp9). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Structure of the Human GLUN1/GLUN2A Lbd in Complex with Compound 2 (GNE9178), PDB code: 5tp9:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Structure of the Human GLUN1/GLUN2A Lbd in Complex with Compound 2 (GNE9178)


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 Compound 2 (GNE9178) within 5.0Å range: probe atom residue distance (Å) B Occ A:F303 b:46.0 occ:1.00 F23 A:7H0303 0.0 46.0 1.0 C22 A:7H0303 1.3 45.8 1.0 F24 A:7H0303 2.1 46.4 1.0 F25 A:7H0303 2.1 49.6 1.0 C20 A:7H0303 2.3 40.4 1.0 OG1 A:THR242 2.7 34.5 1.0 N21 A:7H0303 2.9 33.6 1.0 N A:GLY243 3.4 30.1 1.0 C19 A:7H0303 3.5 40.0 1.0 CG2 A:ILE116 3.6 35.7 1.0 CA A:THR242 3.6 33.7 1.0 CB A:ILE116 3.7 34.4 1.0 CB A:THR242 3.7 36.4 1.0 CD2 B:LEU270 3.7 32.2 1.0 C A:THR242 3.8 34.3 1.0 CD1 A:ILE116 3.9 32.2 1.0 N17 A:7H0303 4.1 33.7 1.0 CA A:GLY243 4.3 29.9 1.0 C18 A:7H0303 4.4 41.9 1.0 CG1 A:ILE116 4.4 33.7 1.0 O A:GLY243 4.5 35.2 1.0 CB A:PRO129 4.6 33.4 1.0 O A:ILE116 4.7 37.3 1.0 CG A:PRO129 4.7 37.6 1.0 CD B:LYS140 4.8 37.2 1.0 O A:THR242 4.8 34.1 1.0 C A:GLY243 4.8 35.1 1.0 CA A:ILE116 4.9 31.2 1.0 C A:ILE116 5.0 35.4 1.0 N A:THR242 5.0 36.3 1.0 CG2 A:THR242 5.0 31.4 1.0

Fluorine binding site 2 out of 3 in the Structure of the Human GLUN1/GLUN2A Lbd in Complex with Compound 2 (GNE9178)


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 Compound 2 (GNE9178) within 5.0Å range: probe atom residue distance (Å) B Occ A:F303 b:46.4 occ:1.00 F24 A:7H0303 0.0 46.4 1.0 C22 A:7H0303 1.3 45.8 1.0 F23 A:7H0303 2.1 46.0 1.0 F25 A:7H0303 2.1 49.6 1.0 C20 A:7H0303 2.3 40.4 1.0 N21 A:7H0303 2.9 33.6 1.0 CG A:PRO129 3.3 37.6 1.0 CD B:PRO141 3.4 32.1 1.0 CD A:PRO129 3.4 32.9 1.0 C19 A:7H0303 3.5 40.0 1.0 CD B:LYS140 3.5 37.2 1.0 CB A:PRO129 3.7 33.4 1.0 CD1 A:ILE116 4.0 32.2 1.0 CB B:LYS140 4.0 33.7 1.0 N17 A:7H0303 4.1 33.7 1.0 CG B:PRO141 4.2 36.2 1.0 CG B:LYS140 4.3 32.7 1.0 N B:PRO141 4.3 31.0 1.0 C18 A:7H0303 4.3 41.9 1.0 CG2 A:ILE116 4.5 35.7 1.0 CE B:LYS140 4.5 35.2 1.0 N A:PRO129 4.5 32.4 1.0 CD2 B:LEU270 4.5 32.2 1.0 CA B:LYS140 4.6 30.9 1.0 C B:LYS140 4.7 35.0 1.0 CA A:PRO129 4.8 32.1 1.0 N A:GLY243 4.8 30.1 1.0 CB A:ILE116 4.8 34.4 1.0 OG1 A:THR242 4.8 34.5 1.0 O B:PRO141 4.9 36.5 1.0 CG1 A:ILE116 5.0 33.7 1.0

Fluorine binding site 3 out of 3 in the Structure of the Human GLUN1/GLUN2A Lbd in Complex with Compound 2 (GNE9178)


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 Compound 2 (GNE9178) within 5.0Å range: probe atom residue distance (Å) B Occ A:F303 b:49.6 occ:1.00 F25 A:7H0303 0.0 49.6 1.0 C22 A:7H0303 1.3 45.8 1.0 F24 A:7H0303 2.1 46.4 1.0 F23 A:7H0303 2.1 46.0 1.0 C20 A:7H0303 2.3 40.4 1.0 C19 A:7H0303 2.8 40.0 1.0 CD2 B:LEU270 3.1 32.2 1.0 N21 A:7H0303 3.5 33.6 1.0 CB B:LYS140 3.8 33.7 1.0 O B:PRO141 3.9 36.5 1.0 C18 A:7H0303 4.1 41.9 1.0 CD2 B:HIS273 4.1 40.6 1.0 CD B:PRO141 4.2 32.1 1.0 NE2 B:HIS273 4.3 40.7 1.0 CD B:LYS140 4.3 37.2 1.0 N17 A:7H0303 4.4 33.7 1.0 OG1 A:THR242 4.4 34.5 1.0 N B:PRO141 4.4 31.0 1.0 CG B:LYS140 4.4 32.7 1.0 CG B:LEU270 4.5 33.6 1.0 C B:LYS140 4.6 35.0 1.0 CG2 A:ILE116 4.7 35.7 1.0 CA B:LYS140 4.7 30.9 1.0 CA A:THR242 4.8 33.7 1.0 C B:PRO141 4.9 35.6 1.0 CG B:HIS273 5.0 39.7 1.0 CG2 B:ILE269 5.0 33.5 1.0

E.Villemure, M.Volgraf, Y.Jiang, G.Wu, C.Q.Ly, P.W.Yuen, A.Lu, X.Luo, M.Liu, S.Zhang, P.J.Lupardus, H.J.Wallweber, B.M.Liederer, G.Deshmukh, E.Plise, S.Tay, T.M.Wang, J.E.Hanson, D.H.Hackos, K.Scearce-Levie, J.B.Schwarz, B.D.Sellers. GLUN2A-Selective Pyridopyrimidinone Series of Nmdar Positive Allosteric Modulators with An Improved in Vivo Profile. Acs Med Chem Lett V. 8 84 2017.
ISSN: ISSN 1948-5875
PubMed: 28105280
DOI: 10.1021/ACSMEDCHEMLETT.6B00388