Fluorine in PDB 5ybf: Crystal Structure of the GLUA2O Lbd in Complex with Glutamate and HBT1

The structure of Crystal Structure of the GLUA2O Lbd in Complex with Glutamate and HBT1, PDB code: 5ybf was solved by S.Sogabe, S.Igaki, A.Hirokawa, Y.Zama, W.Lane, G.Snell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 1.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	113.596, 162.074, 47.103, 90.00, 89.99, 90.00
R / Rfree (%)	18.4 / 20.8

The structure of Crystal Structure of the GLUA2O Lbd in Complex with Glutamate and HBT1 also contains other interesting chemical elements:

Zinc

(Zn)

10 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Fluorine atom in the Crystal Structure of the GLUA2O Lbd in Complex with Glutamate and HBT1 (pdb code 5ybf). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 18 binding sites of Fluorine where determined in the Crystal Structure of the GLUA2O Lbd in Complex with Glutamate and HBT1, PDB code: 5ybf:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 18 in the Crystal Structure of the GLUA2O Lbd in Complex with Glutamate and HBT1


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 GLUA2O Lbd in Complex with Glutamate and HBT1 within 5.0Å range: probe atom residue distance (Å) B Occ A:F902 b:25.0 occ:0.50 F23 A:8SR902 0.0 25.0 0.5 C13 A:8SR902 1.0 17.4 0.5 C11 A:8SR902 1.0 16.4 0.5 C16 A:8SR902 1.3 21.1 0.5 C12 A:8SR902 1.6 16.9 0.5 C4 A:8SR902 1.9 16.2 0.5 F25 A:8SR902 2.1 21.4 0.5 F24 A:8SR902 2.2 21.5 0.5 C5 A:8SR902 2.3 17.6 0.5 C10 A:8SR902 2.5 16.3 0.5 C3 A:8SR902 2.5 17.0 0.5 C1 A:8SR902 2.9 17.5 0.5 CD2 B:LEU772 3.5 18.9 1.0 S26 A:8SR902 3.5 16.9 0.5 N17 A:8SR902 3.6 17.3 0.5 C2 A:8SR902 3.8 17.1 0.5 CG2 A:ILE502 4.1 14.2 1.0 C6 A:8SR902 4.2 16.3 0.5 CB B:LYS514 4.3 16.0 1.0 C7 A:8SR902 4.3 17.8 0.5 O B:PRO515 4.4 17.9 1.0 N18 A:8SR902 4.4 16.7 0.5 CA A:LYS751 4.5 14.8 1.0 CB A:LYS751 4.5 15.7 1.0 CB A:ILE502 4.5 13.9 1.0 CG B:LYS514 4.7 16.6 1.0 O A:ILE502 4.8 16.1 1.0 N A:GLY752 4.8 13.5 1.0 CD B:PRO515 4.8 15.2 1.0 CD B:LYS514 4.9 18.7 1.0 ND2 B:ASN775 4.9 32.1 1.0 CG B:LEU772 5.0 18.8 1.0 CG B:PRO515 5.0 18.5 1.0 CD1 A:ILE502 5.0 14.8 1.0 C A:LYS751 5.0 14.5 1.0 C8 A:8SR902 5.0 19.0 0.5

Fluorine binding site 2 out of 18 in the Crystal Structure of the GLUA2O Lbd in Complex with Glutamate and HBT1


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 GLUA2O Lbd in Complex with Glutamate and HBT1 within 5.0Å range: probe atom residue distance (Å) B Occ A:F902 b:24.4 occ:0.50 F23 A:8SR902 0.0 24.4 0.5 C11 A:8SR902 0.9 15.4 0.5 C13 A:8SR902 1.2 15.1 0.5 C16 A:8SR902 1.3 22.6 0.5 C12 A:8SR902 1.7 15.3 0.5 C4 A:8SR902 1.8 14.8 0.5 F25 A:8SR902 2.2 23.2 0.5 F24 A:8SR902 2.2 24.6 0.5 C5 A:8SR902 2.3 18.5 0.5 C3 A:8SR902 2.4 15.0 0.5 C10 A:8SR902 2.5 14.4 0.5 C1 A:8SR902 2.9 18.0 0.5 S26 A:8SR902 3.3 15.5 0.5 N17 A:8SR902 3.6 17.9 0.5 CD2 A:LEU772 3.6 18.9 1.0 C2 A:8SR902 3.7 15.2 0.5 CG2 B:ILE502 4.1 16.3 1.0 C7 A:8SR902 4.1 15.4 0.5 C6 A:8SR902 4.2 17.2 0.5 CB A:LYS514 4.2 15.5 1.0 O A:PRO515 4.4 15.2 1.0 N18 A:8SR902 4.4 17.9 0.5 CB B:ILE502 4.4 14.5 1.0 CA B:LYS751 4.6 14.6 1.0 CB B:LYS751 4.6 16.9 1.0 CG A:LYS514 4.6 16.4 1.0 OD1 A:ASN775 4.8 34.4 1.0 O B:ILE502 4.8 16.4 1.0 CD A:PRO515 4.8 14.5 1.0 N B:GLY752 4.8 13.7 1.0 CD1 B:ILE502 4.9 15.8 1.0 CD A:LYS514 4.9 20.3 1.0 C8 A:8SR902 4.9 16.1 0.5

Fluorine binding site 3 out of 18 in the Crystal Structure of the GLUA2O Lbd in Complex with Glutamate and HBT1


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 GLUA2O Lbd in Complex with Glutamate and HBT1 within 5.0Å range: probe atom residue distance (Å) B Occ A:F902 b:21.5 occ:0.50 F24 A:8SR902 0.0 21.5 0.5 C11 A:8SR902 1.2 16.4 0.5 C16 A:8SR902 1.4 21.1 0.5 C4 A:8SR902 2.1 16.2 0.5 F25 A:8SR902 2.2 21.4 0.5 F23 A:8SR902 2.2 25.0 0.5 C5 A:8SR902 2.4 17.6 0.5 C13 A:8SR902 2.4 17.4 0.5 S26 A:8SR902 2.8 16.9 0.5 N17 A:8SR902 2.9 17.3 0.5 N A:GLY752 3.0 13.5 1.0 CB A:ILE502 3.3 13.9 1.0 C3 A:8SR902 3.3 17.0 0.5 CD1 A:ILE502 3.5 14.8 1.0 C1 A:8SR902 3.5 17.5 0.5 C A:LYS751 3.5 14.5 1.0 C12 A:8SR902 3.6 16.9 0.5 CA A:LYS751 3.6 14.8 1.0 CB A:LYS751 3.6 15.7 1.0 CG2 A:ILE502 3.7 14.2 1.0 O A:GLY752 3.7 14.4 1.0 CA A:GLY752 3.7 13.2 1.0 CG1 A:ILE502 3.9 14.7 1.0 C10 A:8SR902 4.0 16.3 0.5 C A:GLY752 4.0 13.5 1.0 N18 A:8SR902 4.1 16.7 0.5 O A:ILE502 4.1 16.1 1.0 C7 A:8SR902 4.2 17.8 0.5 C2 A:8SR902 4.4 17.1 0.5 C6 A:8SR902 4.5 16.3 0.5 CA A:ILE502 4.5 13.9 1.0 O A:LYS751 4.5 15.4 1.0 C A:ILE502 4.7 14.8 1.0 N A:ILE502 4.8 13.5 1.0 CG A:LYS751 4.9 16.3 1.0 CG A:PRO515 5.0 17.8 1.0 CD2 B:LEU772 5.0 18.9 1.0

Fluorine binding site 4 out of 18 in the Crystal Structure of the GLUA2O Lbd in Complex with Glutamate and HBT1


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 GLUA2O Lbd in Complex with Glutamate and HBT1 within 5.0Å range: probe atom residue distance (Å) B Occ A:F902 b:24.6 occ:0.50 F24 A:8SR902 0.0 24.6 0.5 C11 A:8SR902 1.3 15.4 0.5 C16 A:8SR902 1.4 22.6 0.5 C4 A:8SR902 2.0 14.8 0.5 F25 A:8SR902 2.2 23.2 0.5 F23 A:8SR902 2.2 24.4 0.5 C5 A:8SR902 2.3 18.5 0.5 C13 A:8SR902 2.4 15.1 0.5 S26 A:8SR902 2.6 15.5 0.5 N17 A:8SR902 2.9 17.9 0.5 N B:GLY752 2.9 13.7 1.0 C3 A:8SR902 3.3 15.0 0.5 CB B:ILE502 3.4 14.5 1.0 CD1 B:ILE502 3.5 15.8 1.0 C1 A:8SR902 3.5 18.0 0.5 C B:LYS751 3.6 14.9 1.0 CA B:GLY752 3.6 14.0 1.0 O B:GLY752 3.6 15.6 1.0 C12 A:8SR902 3.7 15.3 0.5 CA B:LYS751 3.7 14.6 1.0 CB B:LYS751 3.7 16.9 1.0 CG2 B:ILE502 3.8 16.3 1.0 C B:GLY752 3.9 14.6 1.0 CG1 B:ILE502 4.0 14.7 1.0 C10 A:8SR902 4.0 14.4 0.5 N18 A:8SR902 4.0 17.9 0.5 C7 A:8SR902 4.1 15.4 0.5 O B:ILE502 4.2 16.4 1.0 C2 A:8SR902 4.3 15.2 0.5 C6 A:8SR902 4.4 17.2 0.5 CA B:ILE502 4.5 14.5 1.0 O B:LYS751 4.5 15.0 1.0 C B:ILE502 4.7 15.7 1.0 N B:ILE502 4.7 14.2 1.0 CG B:LYS751 4.9 16.8 1.0 CB B:PRO515 4.9 16.8 1.0

Fluorine binding site 5 out of 18 in the Crystal Structure of the GLUA2O Lbd in Complex with Glutamate and HBT1


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 the GLUA2O Lbd in Complex with Glutamate and HBT1 within 5.0Å range: probe atom residue distance (Å) B Occ A:F902 b:21.4 occ:0.50 F25 A:8SR902 0.0 21.4 0.5 C16 A:8SR902 1.3 21.1 0.5 C11 A:8SR902 1.8 16.4 0.5 F23 A:8SR902 2.1 25.0 0.5 C4 A:8SR902 2.2 16.2 0.5 F24 A:8SR902 2.2 21.5 0.5 C5 A:8SR902 2.4 17.6 0.5 S26 A:8SR902 2.7 16.9 0.5 N17 A:8SR902 3.0 17.3 0.5 C13 A:8SR902 3.0 17.4 0.5 C3 A:8SR902 3.3 17.0 0.5 CD B:LYS514 3.4 18.7 1.0 CD B:PRO515 3.5 15.2 1.0 C1 A:8SR902 3.5 17.5 0.5 CD1 A:ILE502 3.5 14.8 1.0 C12 A:8SR902 3.5 16.9 0.5 CB B:LYS514 3.7 16.0 1.0 CG B:PRO515 3.8 18.5 1.0 CG B:LYS514 3.8 16.6 1.0 CG2 A:ILE502 3.9 14.2 1.0 C7 A:8SR902 4.0 17.8 0.5 C10 A:8SR902 4.0 16.3 0.5 CG A:PRO515 4.0 17.8 1.0 C2 A:8SR902 4.1 17.1 0.5 N18 A:8SR902 4.1 16.7 0.5 CB A:ILE502 4.2 13.9 1.0 CD A:PRO515 4.2 14.5 1.0 N B:PRO515 4.4 15.4 1.0 CE B:LYS514 4.4 20.7 1.0 CG1 A:ILE502 4.4 14.7 1.0 C6 A:8SR902 4.5 16.3 0.5 CD2 B:LEU772 4.5 18.9 1.0 CA B:LYS514 4.6 15.4 1.0 CB A:PRO515 4.7 15.0 1.0 O B:PRO515 4.7 17.9 1.0 N A:GLY752 4.8 13.5 1.0 C B:LYS514 4.8 14.8 1.0

Fluorine binding site 6 out of 18 in the Crystal Structure of the GLUA2O Lbd in Complex with Glutamate and HBT1


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 the GLUA2O Lbd in Complex with Glutamate and HBT1 within 5.0Å range: probe atom residue distance (Å) B Occ A:F902 b:23.2 occ:0.50 F25 A:8SR902 0.0 23.2 0.5 C16 A:8SR902 1.4 22.6 0.5 C11 A:8SR902 1.8 15.4 0.5 C4 A:8SR902 2.1 14.8 0.5 F23 A:8SR902 2.2 24.4 0.5 F24 A:8SR902 2.2 24.6 0.5 C5 A:8SR902 2.4 18.5 0.5 S26 A:8SR902 2.4 15.5 0.5 N17 A:8SR902 2.9 17.9 0.5 C13 A:8SR902 3.2 15.1 0.5 C3 A:8SR902 3.3 15.0 0.5 CD1 B:ILE502 3.5 15.8 1.0 CD A:PRO515 3.5 14.5 1.0 C1 A:8SR902 3.5 18.0 0.5 CD A:LYS514 3.6 20.3 1.0 C12 A:8SR902 3.7 15.3 0.5 C7 A:8SR902 3.8 15.4 0.5 CB A:LYS514 3.8 15.5 1.0 CG A:PRO515 3.9 17.8 1.0 CG A:LYS514 3.9 16.4 1.0 CG B:PRO515 4.0 18.5 1.0 CG2 B:ILE502 4.0 16.3 1.0 C2 A:8SR902 4.0 15.2 0.5 C10 A:8SR902 4.1 14.4 0.5 N18 A:8SR902 4.1 17.9 0.5 CD B:PRO515 4.1 15.2 1.0 CB B:ILE502 4.2 14.5 1.0 N A:PRO515 4.3 12.8 1.0 CG1 B:ILE502 4.4 14.7 1.0 C6 A:8SR902 4.4 17.2 0.5 CB B:PRO515 4.4 16.8 1.0 CE A:LYS514 4.5 20.2 1.0 CA A:LYS514 4.6 14.1 1.0 N B:GLY752 4.7 13.7 1.0 O A:PRO515 4.8 15.2 1.0 CD2 A:LEU772 4.8 18.9 1.0 O22 A:8SR902 4.8 17.7 0.5 C A:LYS514 4.9 13.0 1.0 N20 A:8SR902 4.9 16.4 0.5 CA B:GLY752 5.0 14.0 1.0

Fluorine binding site 7 out of 18 in the Crystal Structure of the GLUA2O Lbd in Complex with Glutamate and HBT1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure of the GLUA2O Lbd in Complex with Glutamate and HBT1 within 5.0Å range: probe atom residue distance (Å) B Occ C:F805 b:22.1 occ:0.50 F23 C:8SR805 0.0 22.1 0.5 C13 C:8SR805 1.0 12.9 0.5 C11 C:8SR805 1.0 12.4 0.5 C16 C:8SR805 1.3 18.6 0.5 C12 C:8SR805 1.6 12.7 0.5 C4 C:8SR805 1.8 11.7 0.5 F25 C:8SR805 2.2 17.5 0.5 F24 C:8SR805 2.2 18.8 0.5 C5 C:8SR805 2.3 14.7 0.5 C3 C:8SR805 2.4 12.4 0.5 C10 C:8SR805 2.4 11.6 0.5 C1 C:8SR805 2.8 14.5 0.5 S26 C:8SR805 3.4 12.2 0.5 N17 C:8SR805 3.6 14.4 0.5 CD2 C:LEU772 3.6 15.2 1.0 C2 C:8SR805 3.7 12.5 0.5 CG2 D:ILE502 4.1 12.0 1.0 C6 C:8SR805 4.2 14.7 0.5 C7 C:8SR805 4.2 12.3 0.5 O C:PRO515 4.4 12.8 1.0 CB D:LYS751 4.4 12.9 1.0 N18 C:8SR805 4.4 14.8 0.5 CA D:LYS751 4.4 11.9 1.0 CB D:ILE502 4.5 10.8 1.0 CB C:LYS514 4.5 12.6 1.0 O D:ILE502 4.6 12.2 1.0 N D:GLY752 4.7 11.1 1.0 C8 C:8SR805 4.9 14.3 0.5 C D:LYS751 4.9 10.6 1.0 CD C:PRO515 5.0 12.5 1.0

Fluorine binding site 8 out of 18 in the Crystal Structure of the GLUA2O Lbd in Complex with Glutamate and HBT1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Crystal Structure of the GLUA2O Lbd in Complex with Glutamate and HBT1 within 5.0Å range: probe atom residue distance (Å) B Occ C:F805 b:22.8 occ:0.50 F23 C:8SR805 0.0 22.8 0.5 C13 C:8SR805 0.9 12.9 0.5 C11 C:8SR805 0.9 12.6 0.5 C16 C:8SR805 1.4 18.1 0.5 C12 C:8SR805 1.6 12.4 0.5 C4 C:8SR805 1.8 11.9 0.5 F24 C:8SR805 2.2 18.6 0.5 F25 C:8SR805 2.2 18.5 0.5 C5 C:8SR805 2.3 14.2 0.5 C3 C:8SR805 2.4 12.3 0.5 C10 C:8SR805 2.4 11.5 0.5 C1 C:8SR805 2.9 13.8 0.5 S26 C:8SR805 3.4 12.9 0.5 CD2 D:LEU772 3.6 15.0 1.0 N17 C:8SR805 3.6 14.2 0.5 C2 C:8SR805 3.7 12.7 0.5 CG2 C:ILE502 4.1 11.5 1.0 C6 C:8SR805 4.2 13.9 0.5 C7 C:8SR805 4.2 12.9 0.5 CB C:LYS751 4.4 13.2 1.0 CA C:LYS751 4.4 11.5 1.0 N18 C:8SR805 4.4 14.1 0.5 O D:PRO515 4.4 12.8 1.0 CB C:ILE502 4.5 10.2 1.0 O C:ILE502 4.5 12.0 1.0 CB D:LYS514 4.6 13.1 1.0 N C:GLY752 4.7 10.8 1.0 C8 C:8SR805 4.9 15.1 0.5 C C:LYS751 4.9 10.7 1.0

Fluorine binding site 9 out of 18 in the Crystal Structure of the GLUA2O Lbd in Complex with Glutamate and HBT1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Crystal Structure of the GLUA2O Lbd in Complex with Glutamate and HBT1 within 5.0Å range: probe atom residue distance (Å) B Occ C:F805 b:18.8 occ:0.50 F24 C:8SR805 0.0 18.8 0.5 C11 C:8SR805 1.2 12.4 0.5 C16 C:8SR805 1.4 18.6 0.5 C4 C:8SR805 2.0 11.7 0.5 F25 C:8SR805 2.2 17.5 0.5 F23 C:8SR805 2.2 22.1 0.5 C5 C:8SR805 2.3 14.7 0.5 C13 C:8SR805 2.5 12.9 0.5 S26 C:8SR805 2.6 12.2 0.5 N17 C:8SR805 2.8 14.4 0.5 N D:GLY752 3.0 11.1 1.0 C3 C:8SR805 3.3 12.4 0.5 CB D:ILE502 3.3 10.8 1.0 CD1 D:ILE502 3.5 12.4 1.0 C1 C:8SR805 3.6 14.5 0.5 O D:GLY752 3.6 11.4 1.0 CG2 D:ILE502 3.6 12.0 1.0 CA D:GLY752 3.7 10.1 1.0 C12 C:8SR805 3.7 12.7 0.5 C D:LYS751 3.7 10.6 1.0 CA D:LYS751 3.8 11.9 1.0 CB D:LYS751 3.9 12.9 1.0 CG1 D:ILE502 3.9 11.1 1.0 C D:GLY752 4.0 10.8 1.0 C10 C:8SR805 4.0 11.6 0.5 N18 C:8SR805 4.0 14.8 0.5 C7 C:8SR805 4.1 12.3 0.5 O D:ILE502 4.1 12.2 1.0 C2 C:8SR805 4.2 12.5 0.5 CA D:ILE502 4.4 10.8 1.0 C6 C:8SR805 4.5 14.7 0.5 C D:ILE502 4.6 11.1 1.0 O D:LYS751 4.6 11.9 1.0 N D:ILE502 4.6 10.5 1.0 CG D:PRO515 4.8 15.6 1.0 CB D:PRO515 4.9 13.1 1.0 CG D:LYS751 5.0 12.3 1.0

Fluorine binding site 10 out of 18 in the Crystal Structure of the GLUA2O Lbd in Complex with Glutamate and HBT1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Crystal Structure of the GLUA2O Lbd in Complex with Glutamate and HBT1 within 5.0Å range: probe atom residue distance (Å) B Occ C:F805 b:18.6 occ:0.50 F24 C:8SR805 0.0 18.6 0.5 C11 C:8SR805 1.2 12.6 0.5 C16 C:8SR805 1.4 18.1 0.5 C4 C:8SR805 2.0 11.9 0.5 F25 C:8SR805 2.1 18.5 0.5 F23 C:8SR805 2.2 22.8 0.5 C5 C:8SR805 2.3 14.2 0.5 C13 C:8SR805 2.6 12.9 0.5 S26 C:8SR805 2.6 12.9 0.5 N17 C:8SR805 2.8 14.2 0.5 N C:GLY752 3.0 10.8 1.0 CB C:ILE502 3.3 10.2 1.0 C3 C:8SR805 3.3 12.3 0.5 CD1 C:ILE502 3.5 12.0 1.0 C1 C:8SR805 3.6 13.8 0.5 O C:GLY752 3.6 11.3 1.0 CA C:GLY752 3.6 10.5 1.0 CG2 C:ILE502 3.6 11.5 1.0 C C:LYS751 3.7 10.7 1.0 C12 C:8SR805 3.7 12.4 0.5 CA C:LYS751 3.8 11.5 1.0 CB C:LYS751 3.9 13.2 1.0 CG1 C:ILE502 3.9 11.1 1.0 C C:GLY752 3.9 11.0 1.0 N18 C:8SR805 4.0 14.1 0.5 C7 C:8SR805 4.0 12.9 0.5 C10 C:8SR805 4.1 11.5 0.5 O C:ILE502 4.1 12.0 1.0 C2 C:8SR805 4.2 12.7 0.5 CA C:ILE502 4.4 11.0 1.0 C6 C:8SR805 4.4 13.9 0.5 O C:LYS751 4.6 11.9 1.0 C C:ILE502 4.6 10.9 1.0 N C:ILE502 4.7 10.4 1.0 CG C:PRO515 4.7 15.8 1.0 CB C:PRO515 4.9 12.9 1.0 CG C:LYS751 5.0 12.7 1.0

A.Kunugi, Y.Tajima, H.Kuno, S.Sogabe, H.Kimura. HBT1, A Novel Ampa Receptor Potentiator with Lower Agonistic Effect, Avoided Bell-Shaped Response in in Vitro Bdnf Production. J. Pharmacol. Exp. Ther. V. 364 377 2018.
ISSN: ESSN 1521-0103
PubMed: 29298820
DOI: 10.1124/JPET.117.245050