Fluorine in PDB 5zg2: Crystal Structure of the GLUA2O Lbd in Complex with ZK200775 and Compound-2

The structure of Crystal Structure of the GLUA2O Lbd in Complex with ZK200775 and Compound-2, PDB code: 5zg2 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 / 1.25
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	49.384, 56.565, 90.779, 90.00, 91.74, 90.00
R / Rfree (%)	16.9 / 19

The structure of Crystal Structure of the GLUA2O Lbd in Complex with ZK200775 and Compound-2 also contains other interesting chemical elements:

Zinc

(Zn)

5 atoms

The binding sites of Fluorine atom in the Crystal Structure of the GLUA2O Lbd in Complex with ZK200775 and Compound-2 (pdb code 5zg2). 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 the GLUA2O Lbd in Complex with ZK200775 and Compound-2, PDB code: 5zg2:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in the Crystal Structure of the GLUA2O Lbd in Complex with ZK200775 and Compound-2


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 ZK200775 and Compound-2 within 5.0Å range: probe atom residue distance (Å) B Occ A:F901 b:12.3 occ:1.00 FAF A:ZK1901 0.0 12.3 1.0 CAZ A:ZK1901 1.3 11.5 1.0 FAG A:ZK1901 2.1 12.1 1.0 FAH A:ZK1901 2.1 12.3 1.0 CAS A:ZK1901 2.3 10.2 1.0 CAJ A:ZK1901 2.7 10.4 1.0 OH A:TYR753 3.1 11.5 1.0 OH A:TYR426 3.3 11.8 0.5 CZ A:TYR426 3.4 10.8 0.5 CE2 A:TYR426 3.4 9.7 0.5 CE2 A:TYR426 3.5 10.6 0.5 CB A:PRO499 3.6 9.9 1.0 CG A:PRO499 3.7 10.0 1.0 CZ A:TYR753 3.7 10.2 1.0 CAR A:ZK1901 3.7 10.7 1.0 CAV A:ZK1901 4.1 9.4 1.0 CZ A:TYR426 4.1 9.8 0.5 OH A:TYR426 4.1 12.1 0.5 OG1 A:THR728 4.1 14.4 1.0 CE1 A:TYR426 4.2 9.4 0.5 OH A:TYR471 4.2 14.3 1.0 NAX A:ZK1901 4.2 12.1 1.0 CE2 A:TYR753 4.2 10.6 1.0 CD2 A:TYR426 4.3 9.6 0.5 CD2 A:TYR426 4.3 9.7 0.5 CE1 A:TYR753 4.3 9.9 1.0 CG A:GLU423 4.4 15.9 1.0 O A:PRO499 4.6 9.0 1.0 CAI A:ZK1901 4.8 9.7 1.0 NAP A:ZK1901 4.9 9.7 1.0 CAN A:ZK1901 4.9 14.7 1.0 CD1 A:TYR426 4.9 9.4 0.5 CA A:PRO499 5.0 9.4 1.0 CAW A:ZK1901 5.0 9.1 1.0 CG A:TYR426 5.0 9.4 0.5 CZ A:TYR471 5.0 11.0 1.0

Fluorine binding site 2 out of 6 in the Crystal Structure of the GLUA2O Lbd in Complex with ZK200775 and Compound-2


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 ZK200775 and Compound-2 within 5.0Å range: probe atom residue distance (Å) B Occ A:F901 b:12.1 occ:1.00 FAG A:ZK1901 0.0 12.1 1.0 CAZ A:ZK1901 1.3 11.5 1.0 FAF A:ZK1901 2.1 12.3 1.0 FAH A:ZK1901 2.2 12.3 1.0 CAS A:ZK1901 2.3 10.2 1.0 NAX A:ZK1901 3.0 12.1 1.0 CAR A:ZK1901 3.0 10.7 1.0 OH A:TYR753 3.3 11.5 1.0 CAJ A:ZK1901 3.4 10.4 1.0 CB A:MET729 3.7 10.6 1.0 OG1 A:THR728 3.7 14.4 1.0 CB A:GLU726 3.8 12.4 1.0 OH A:TYR426 3.8 11.8 0.5 CAM A:ZK1901 3.9 15.4 1.0 CG A:GLU726 3.9 13.2 1.0 CAN A:ZK1901 4.1 14.7 1.0 N A:MET729 4.2 9.0 1.0 CAK A:ZK1901 4.3 17.8 1.0 CAI A:ZK1901 4.3 9.7 1.0 CD A:GLU726 4.4 13.6 1.0 CZ A:TYR753 4.5 10.2 1.0 CA A:MET729 4.5 9.2 1.0 CZ A:TYR426 4.5 10.8 0.5 CAV A:ZK1901 4.6 9.4 1.0 CAL A:ZK1901 4.6 17.2 1.0 CE A:MET729 4.6 16.2 1.0 CE2 A:TYR426 4.6 9.7 0.5 CG A:MET729 4.7 10.8 1.0 OE2 A:GLU726 4.7 11.9 1.0 O A:HOH1065 4.9 16.5 1.0 CAW A:ZK1901 4.9 9.1 1.0 OE1 A:GLU726 5.0 15.5 1.0 CE2 A:TYR426 5.0 10.6 0.5 OAQ A:ZK1901 5.0 18.7 1.0

Fluorine binding site 3 out of 6 in the Crystal Structure of the GLUA2O Lbd in Complex with ZK200775 and Compound-2


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 ZK200775 and Compound-2 within 5.0Å range: probe atom residue distance (Å) B Occ A:F901 b:12.3 occ:1.00 FAH A:ZK1901 0.0 12.3 1.0 CAZ A:ZK1901 1.3 11.5 1.0 FAF A:ZK1901 2.1 12.3 1.0 FAG A:ZK1901 2.2 12.1 1.0 CAS A:ZK1901 2.3 10.2 1.0 NAX A:ZK1901 2.9 12.1 1.0 CAR A:ZK1901 3.0 10.7 1.0 CAN A:ZK1901 3.1 14.7 1.0 CG A:GLU423 3.2 15.9 1.0 CD A:GLU423 3.4 17.8 1.0 CAJ A:ZK1901 3.5 10.4 1.0 CE A:MET729 3.6 16.2 1.0 CAL A:ZK1901 3.7 17.2 1.0 OE2 A:GLU423 3.7 18.6 1.0 CE2 A:TYR426 3.7 9.7 0.5 OH A:TYR471 3.9 14.3 1.0 OE1 A:GLU423 4.0 17.4 1.0 OH A:TYR426 4.2 11.8 0.5 CAM A:ZK1901 4.3 15.4 1.0 CZ A:TYR426 4.3 10.8 0.5 CAI A:ZK1901 4.3 9.7 1.0 CB A:MET729 4.5 10.6 1.0 CE2 A:TYR426 4.5 10.6 0.5 CAK A:ZK1901 4.6 17.8 1.0 CD2 A:TYR426 4.6 9.7 0.5 CB A:GLU423 4.6 13.3 1.0 CAV A:ZK1901 4.6 9.4 1.0 O A:HOH1065 4.7 16.5 1.0 OAQ A:ZK1901 4.7 18.7 1.0 CG A:MET729 4.8 10.8 1.0 CZ A:TYR471 4.9 11.0 1.0 OH A:TYR753 4.9 11.5 1.0 SD A:MET729 4.9 13.3 1.0 CD2 A:TYR426 5.0 9.6 0.5 CG A:PRO499 5.0 10.0 1.0

Fluorine binding site 4 out of 6 in the Crystal Structure of the GLUA2O Lbd in Complex with ZK200775 and Compound-2


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 ZK200775 and Compound-2 within 5.0Å range: probe atom residue distance (Å) B Occ B:F901 b:13.0 occ:1.00 FAF B:ZK1901 0.0 13.0 1.0 CAZ B:ZK1901 1.3 10.9 1.0 FAH B:ZK1901 2.1 13.0 1.0 FAG B:ZK1901 2.1 12.8 1.0 CAS B:ZK1901 2.3 10.1 1.0 CAJ B:ZK1901 2.7 9.5 1.0 O B:HOH1110 3.2 18.7 1.0 OH B:TYR753 3.3 12.7 1.0 CB B:PRO499 3.6 9.7 1.0 CE2 B:TYR426 3.6 13.0 1.0 CG B:PRO499 3.7 10.0 1.0 CAR B:ZK1901 3.7 10.6 1.0 CZ B:TYR753 3.9 10.8 1.0 OH B:TYR471 4.0 12.9 1.0 CAV B:ZK1901 4.1 9.1 1.0 OH B:TYR426 4.1 15.1 1.0 CG B:GLU423 4.1 13.4 1.0 CZ B:TYR426 4.1 11.7 1.0 NAX B:ZK1901 4.2 11.6 1.0 CD2 B:TYR426 4.4 11.4 1.0 CE2 B:TYR753 4.4 11.1 1.0 CE1 B:TYR753 4.5 10.3 1.0 O B:PRO499 4.5 9.1 1.0 OG1 B:THR728 4.5 14.6 1.0 CD B:GLU423 4.7 15.0 1.0 OE2 B:GLU423 4.7 15.1 1.0 CAI B:ZK1901 4.8 9.4 1.0 CZ B:TYR471 4.8 11.4 1.0 NAP B:ZK1901 4.9 9.2 1.0 CAN B:ZK1901 4.9 13.9 1.0 CAW B:ZK1901 5.0 9.3 1.0 CA B:PRO499 5.0 8.9 1.0

Fluorine binding site 5 out of 6 in the Crystal Structure of the GLUA2O Lbd in Complex with ZK200775 and Compound-2


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 ZK200775 and Compound-2 within 5.0Å range: probe atom residue distance (Å) B Occ B:F901 b:12.8 occ:1.00 FAG B:ZK1901 0.0 12.8 1.0 CAZ B:ZK1901 1.3 10.9 1.0 FAF B:ZK1901 2.1 13.0 1.0 FAH B:ZK1901 2.1 13.0 1.0 CAS B:ZK1901 2.3 10.1 1.0 NAX B:ZK1901 3.0 11.6 1.0 CAR B:ZK1901 3.0 10.6 1.0 O B:HOH1110 3.0 18.7 1.0 OH B:TYR753 3.4 12.7 1.0 CAJ B:ZK1901 3.4 9.5 1.0 CB B:MET729 3.8 10.4 1.0 CB B:GLU726 3.8 12.7 1.0 CAM B:ZK1901 3.9 14.4 1.0 CG B:GLU726 3.9 13.9 1.0 OG1 B:THR728 4.0 14.6 1.0 CAN B:ZK1901 4.1 13.9 1.0 CAI B:ZK1901 4.3 9.4 1.0 CAK B:ZK1901 4.3 15.1 1.0 CD B:GLU726 4.3 13.7 1.0 CAL B:ZK1901 4.5 15.8 1.0 N B:MET729 4.5 10.4 1.0 CE B:MET729 4.5 13.4 1.0 CZ B:TYR753 4.5 10.8 1.0 CAV B:ZK1901 4.6 9.1 1.0 CG B:MET729 4.7 10.9 1.0 CA B:MET729 4.7 9.8 1.0 OE1 B:GLU726 4.7 12.5 1.0 OE2 B:GLU726 4.8 15.1 1.0 CAW B:ZK1901 4.9 9.3 1.0 OAQ B:ZK1901 5.0 16.3 1.0

Fluorine binding site 6 out of 6 in the Crystal Structure of the GLUA2O Lbd in Complex with ZK200775 and Compound-2


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 ZK200775 and Compound-2 within 5.0Å range: probe atom residue distance (Å) B Occ B:F901 b:13.0 occ:1.00 FAH B:ZK1901 0.0 13.0 1.0 CAZ B:ZK1901 1.3 10.9 1.0 FAF B:ZK1901 2.1 13.0 1.0 FAG B:ZK1901 2.1 12.8 1.0 CAS B:ZK1901 2.4 10.1 1.0 NAX B:ZK1901 2.9 11.6 1.0 CAR B:ZK1901 3.0 10.6 1.0 CAN B:ZK1901 3.1 13.9 1.0 CD B:GLU423 3.2 15.0 1.0 CG B:GLU423 3.2 13.4 1.0 OE2 B:GLU423 3.4 15.1 1.0 CAJ B:ZK1901 3.5 9.5 1.0 CE B:MET729 3.5 13.4 1.0 CAL B:ZK1901 3.6 15.8 1.0 OE1 B:GLU423 3.7 16.2 1.0 O B:HOH1110 3.8 18.7 1.0 OH B:TYR471 3.9 12.9 1.0 CAM B:ZK1901 4.2 14.4 1.0 CAI B:ZK1901 4.3 9.4 1.0 CB B:MET729 4.6 10.4 1.0 CAK B:ZK1901 4.6 15.1 1.0 CE2 B:TYR426 4.6 13.0 1.0 CB B:GLU423 4.7 12.7 1.0 OAQ B:ZK1901 4.7 16.3 1.0 CAV B:ZK1901 4.7 9.1 1.0 CG B:MET729 4.8 10.9 1.0 O B:HOH1118 4.9 15.0 1.0 CZ B:TYR471 4.9 11.4 1.0 SD B:MET729 4.9 12.3 1.0 OH B:TYR753 5.0 12.7 1.0

A.Kunugi, M.Tanaka, A.Suzuki, Y.Tajima, N.Suzuki, M.Suzuki, S.Nakamura, H.Kuno, A.Yokota, S.Sogabe, Y.Kosugi, Y.Awasaki, T.Kaku, H.Kimura. Tak-137, An Ampa-R Potentiator with Little Agonistic Effect, Has A Wide Therapeutic Window. Neuropsychopharmacology V. 44 961 2019.
ISSN: ISSN 1740-634X
PubMed: 30209408
DOI: 10.1038/S41386-018-0213-7