Fluorine in PDB 6sbt: Structure of GLUK1 Ligand-Binding Domain (S1S2) in Complex with N-(7- (1H-Imidazol-1-Yl)-2,3-Dioxo-6-(Trifluoromethyl)-3,4- Dihydroquinoxalin-1(2H)-Yl Benzamide at 2.3 A Resolution

The structure of Structure of GLUK1 Ligand-Binding Domain (S1S2) in Complex with N-(7- (1H-Imidazol-1-Yl)-2,3-Dioxo-6-(Trifluoromethyl)-3,4- Dihydroquinoxalin-1(2H)-Yl Benzamide at 2.3 A Resolution, PDB code: 6sbt was solved by S.Moellerud, K.Frydenvang, J.S.Kastrup, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.64 / 2.30
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	89.275, 89.275, 156.321, 90.00, 90.00, 120.00
R / Rfree (%)	20.5 / 24.9

The structure of Structure of GLUK1 Ligand-Binding Domain (S1S2) in Complex with N-(7- (1H-Imidazol-1-Yl)-2,3-Dioxo-6-(Trifluoromethyl)-3,4- Dihydroquinoxalin-1(2H)-Yl Benzamide at 2.3 A Resolution also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Fluorine atom in the Structure of GLUK1 Ligand-Binding Domain (S1S2) in Complex with N-(7- (1H-Imidazol-1-Yl)-2,3-Dioxo-6-(Trifluoromethyl)-3,4- Dihydroquinoxalin-1(2H)-Yl Benzamide at 2.3 A Resolution (pdb code 6sbt). 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 GLUK1 Ligand-Binding Domain (S1S2) in Complex with N-(7- (1H-Imidazol-1-Yl)-2,3-Dioxo-6-(Trifluoromethyl)-3,4- Dihydroquinoxalin-1(2H)-Yl Benzamide at 2.3 A Resolution, PDB code: 6sbt:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Structure of GLUK1 Ligand-Binding Domain (S1S2) in Complex with N-(7- (1H-Imidazol-1-Yl)-2,3-Dioxo-6-(Trifluoromethyl)-3,4- Dihydroquinoxalin-1(2H)-Yl Benzamide at 2.3 A Resolution


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of GLUK1 Ligand-Binding Domain (S1S2) in Complex with N-(7- (1H-Imidazol-1-Yl)-2,3-Dioxo-6-(Trifluoromethyl)-3,4- Dihydroquinoxalin-1(2H)-Yl Benzamide at 2.3 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:F303 b:31.4 occ:1.00 F1 A:L5H303 0.0 31.4 1.0 C16 A:L5H303 1.3 28.1 1.0 F3 A:L5H303 2.1 29.4 1.0 F2 A:L5H303 2.2 26.1 1.0 C6 A:L5H303 2.4 28.9 1.0 HG2 A:GLU13 2.8 31.5 1.0 CD A:GLU13 2.8 34.2 1.0 HG3 A:GLU13 2.9 31.5 1.0 N4 A:L5H303 3.0 44.1 1.0 CG A:GLU13 3.0 26.2 1.0 C5 A:L5H303 3.0 35.3 1.0 OE1 A:GLU13 3.1 33.3 1.0 C19 A:L5H303 3.2 38.4 1.0 H12 A:L5H303 3.2 46.0 1.0 OE2 A:GLU13 3.3 35.4 1.0 C1 A:L5H303 3.5 29.2 1.0 HH A:TYR61 3.5 29.8 1.0 H1 A:L5H303 3.6 35.1 1.0 O A:HOH427 3.7 32.5 1.0 C17 A:L5H303 3.7 45.3 1.0 OH A:TYR61 3.9 24.9 1.0 C18 A:L5H303 3.9 37.3 1.0 HE1 A:TYR16 4.0 25.8 1.0 H10 A:L5H303 4.2 54.3 1.0 N5 A:L5H303 4.3 41.8 1.0 C4 A:L5H303 4.4 34.8 1.0 H11 A:L5H303 4.5 44.7 1.0 HG3 A:PRO88 4.5 29.3 1.0 CB A:GLU13 4.5 23.7 1.0 HD1 A:TYR16 4.6 27.6 1.0 C2 A:L5H303 4.7 24.3 1.0 CE1 A:TYR16 4.7 21.5 1.0 HG2 A:PRO88 4.7 29.3 1.0 HB2 A:PRO88 4.8 25.2 1.0 HB2 A:GLU13 4.9 28.4 1.0 HB3 A:GLU13 4.9 28.4 1.0 OH A:TYR216 4.9 26.5 1.0 HE1 A:TYR61 4.9 23.2 1.0 H2 A:L5H303 5.0 41.8 1.0 CD1 A:TYR16 5.0 23.0 1.0 CZ A:TYR61 5.0 20.4 1.0

Fluorine binding site 2 out of 3 in the Structure of GLUK1 Ligand-Binding Domain (S1S2) in Complex with N-(7- (1H-Imidazol-1-Yl)-2,3-Dioxo-6-(Trifluoromethyl)-3,4- Dihydroquinoxalin-1(2H)-Yl Benzamide at 2.3 A Resolution


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of GLUK1 Ligand-Binding Domain (S1S2) in Complex with N-(7- (1H-Imidazol-1-Yl)-2,3-Dioxo-6-(Trifluoromethyl)-3,4- Dihydroquinoxalin-1(2H)-Yl Benzamide at 2.3 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:F303 b:26.1 occ:1.00 F2 A:L5H303 0.0 26.1 1.0 C16 A:L5H303 1.3 28.1 1.0 F3 A:L5H303 2.1 29.4 1.0 F1 A:L5H303 2.2 31.4 1.0 C6 A:L5H303 2.3 28.9 1.0 H10 A:L5H303 3.0 54.3 1.0 C5 A:L5H303 3.0 35.3 1.0 N4 A:L5H303 3.0 44.1 1.0 C17 A:L5H303 3.0 45.3 1.0 OH A:TYR216 3.3 26.5 1.0 C1 A:L5H303 3.4 29.2 1.0 HH A:TYR216 3.4 31.8 1.0 H1 A:L5H303 3.6 35.1 1.0 HG3 A:GLU190 3.7 58.8 1.0 C19 A:L5H303 3.8 38.4 1.0 N5 A:L5H303 3.9 41.8 1.0 O A:HOH414 4.0 30.5 1.0 HG A:SER193 4.0 58.2 1.0 HE1 A:TYR16 4.0 25.8 1.0 OG A:SER193 4.1 48.5 1.0 C4 A:L5H303 4.3 34.8 1.0 C18 A:L5H303 4.3 37.3 1.0 H12 A:L5H303 4.3 46.0 1.0 CZ A:TYR216 4.4 23.4 1.0 HG1 A:THR192 4.5 45.5 1.0 HG2 A:GLU13 4.5 31.5 1.0 C2 A:L5H303 4.6 24.3 1.0 HE2 A:TYR216 4.6 27.1 1.0 CG A:GLU190 4.6 49.0 1.0 HB2 A:GLU190 4.7 54.4 1.0 HG3 A:GLU13 4.7 31.5 1.0 HB2 A:PRO88 4.8 25.2 1.0 CE1 A:TYR16 4.8 21.5 1.0 H2 A:L5H303 4.9 41.8 1.0 OG1 A:THR192 4.9 37.9 1.0 CE2 A:TYR216 4.9 22.6 1.0 C3 A:L5H303 5.0 30.1 1.0 CG A:GLU13 5.0 26.2 1.0 CD A:GLU13 5.0 34.2 1.0

Fluorine binding site 3 out of 3 in the Structure of GLUK1 Ligand-Binding Domain (S1S2) in Complex with N-(7- (1H-Imidazol-1-Yl)-2,3-Dioxo-6-(Trifluoromethyl)-3,4- Dihydroquinoxalin-1(2H)-Yl Benzamide at 2.3 A Resolution


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of GLUK1 Ligand-Binding Domain (S1S2) in Complex with N-(7- (1H-Imidazol-1-Yl)-2,3-Dioxo-6-(Trifluoromethyl)-3,4- Dihydroquinoxalin-1(2H)-Yl Benzamide at 2.3 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:F303 b:29.4 occ:1.00 F3 A:L5H303 0.0 29.4 1.0 C16 A:L5H303 1.3 28.1 1.0 F2 A:L5H303 2.1 26.1 1.0 F1 A:L5H303 2.1 31.4 1.0 C6 A:L5H303 2.4 28.9 1.0 H1 A:L5H303 2.4 35.1 1.0 C1 A:L5H303 2.7 29.2 1.0 HB2 A:PRO88 2.9 25.2 1.0 HE1 A:TYR16 3.0 25.8 1.0 HG2 A:GLU13 3.0 31.5 1.0 HG3 A:PRO88 3.2 29.3 1.0 OH A:TYR216 3.3 26.5 1.0 CE1 A:TYR16 3.4 21.5 1.0 CB A:PRO88 3.5 21.0 1.0 HG2 A:PRO88 3.6 29.3 1.0 HB3 A:PRO88 3.6 25.2 1.0 CG A:PRO88 3.6 24.4 1.0 HG3 A:GLU13 3.6 31.5 1.0 HH A:TYR216 3.6 31.8 1.0 CG A:GLU13 3.7 26.2 1.0 C5 A:L5H303 3.7 35.3 1.0 CZ A:TYR216 3.9 23.4 1.0 OH A:TYR61 3.9 24.9 1.0 HE2 A:TYR216 3.9 27.1 1.0 HH A:TYR61 3.9 29.8 1.0 HD1 A:TYR16 4.0 27.6 1.0 CD1 A:TYR16 4.0 23.0 1.0 CE2 A:TYR216 4.1 22.6 1.0 C2 A:L5H303 4.1 24.3 1.0 CZ A:TYR16 4.2 29.2 1.0 CD A:GLU13 4.2 34.2 1.0 N4 A:L5H303 4.3 44.1 1.0 OH A:TYR16 4.3 25.2 1.0 OE2 A:GLU13 4.6 35.4 1.0 O A:PRO88 4.6 18.2 1.0 CE1 A:TYR216 4.7 21.4 1.0 O A:HOH414 4.8 30.5 1.0 H3 A:L5H303 4.8 29.8 1.0 C4 A:L5H303 4.8 34.8 1.0 OE1 A:GLU13 4.9 33.3 1.0 CZ A:TYR61 4.9 20.4 1.0 C17 A:L5H303 4.9 45.3 1.0 H10 A:L5H303 4.9 54.3 1.0 CA A:PRO88 4.9 21.5 1.0 HB3 A:GLU13 4.9 28.4 1.0 C19 A:L5H303 4.9 38.4 1.0 HE1 A:TYR216 5.0 25.7 1.0 CB A:GLU13 5.0 23.7 1.0 N1 A:L5H303 5.0 24.8 1.0

S.Mollerud, R.B.Hansen, J.Pallesen, P.Temperini, D.Pasini, J.Bornholt, B.Nielsen, E.Mamedova, P.Chalupnik, A.V.Paternain, J.Lerma, M.Diaz-Delcastillo, J.T.Andreasen, K.Frydenvang, J.S.Kastrup, T.N.Johansen, D.S.Pickering. N-(7-(1H-Imidazol-1-Yl)-2,3-Dioxo-6-(Trifluoromethyl)-3, 4-Dihydroquinoxalin-1(2H)-Yl)Benzamide, A New Kainate Receptor Selective Antagonist and Analgesic: Synthesis, X-Ray Crystallography, Structure-Affinity Relationships, and in Vitro and in Vivo Pharmacology. Acs Chem Neurosci V. 10 4685 2019.
ISSN: ESSN 1948-7193
PubMed: 31622082
DOI: 10.1021/ACSCHEMNEURO.9B00479