Fluorine in PDB 6gqy: Kras-169 Q61H Gppnhp + Ch-3

The structure of Kras-169 Q61H Gppnhp + Ch-3, PDB code: 6gqy was solved by A.Cruz-Migoni, C.E.Quevedo, S.B.Carr, S.V.E.Phillips, T.H.Rabbitts, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	94.67 / 2.75
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	63.531, 118.678, 156.996, 90.00, 90.00, 90.00
R / Rfree (%)	20.5 / 24.7

The structure of Kras-169 Q61H Gppnhp + Ch-3 also contains other interesting chemical elements:

Magnesium

(Mg)

6 atoms

The binding sites of Fluorine atom in the Kras-169 Q61H Gppnhp + Ch-3 (pdb code 6gqy). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Kras-169 Q61H Gppnhp + Ch-3, PDB code: 6gqy:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Kras-169 Q61H Gppnhp + Ch-3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Kras-169 Q61H Gppnhp + Ch-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:F203 b:45.3 occ:1.00 F17 A:F8Q203 0.0 45.3 1.0 C12 A:F8Q203 1.3 33.6 1.0 C11 A:F8Q203 2.3 31.4 1.0 C7 A:F8Q203 2.3 31.7 1.0 O15 A:F8Q203 2.7 33.2 1.0 C16 A:F8Q203 2.7 32.4 1.0 C6 A:F8Q203 2.8 30.2 1.0 C5 A:F8Q203 3.1 31.0 1.0 CE A:LYS5 3.3 43.0 1.0 C8 A:F8Q203 3.6 30.7 1.0 C10 A:F8Q203 3.6 29.8 1.0 CD A:LYS5 3.8 39.6 1.0 C1 A:F8Q203 3.9 31.1 1.0 C9 A:F8Q203 4.0 30.6 1.0 OD2 A:ASP54 4.2 37.5 1.0 C4 A:F8Q203 4.3 32.1 1.0 CB A:ASP54 4.5 30.3 1.0 NZ A:LYS5 4.5 46.7 1.0 CG A:LYS5 4.6 33.6 1.0 CG A:ASP54 4.6 33.0 1.0 N18 A:F8Q203 4.6 30.3 1.0 C2 A:F8Q203 4.9 29.3 1.0

Fluorine binding site 2 out of 4 in the Kras-169 Q61H Gppnhp + Ch-3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Kras-169 Q61H Gppnhp + Ch-3 within 5.0Å range: probe atom residue distance (Å) B Occ B:F203 b:59.8 occ:1.00 F17 B:F8Q203 0.0 59.8 1.0 C12 B:F8Q203 1.3 55.6 1.0 C11 B:F8Q203 2.4 60.4 1.0 C7 B:F8Q203 2.4 47.6 1.0 O15 B:F8Q203 2.7 62.2 1.0 C6 B:F8Q203 2.8 43.2 1.0 C5 B:F8Q203 2.9 38.7 1.0 NZ B:LYS5 3.2 53.8 1.0 C16 B:F8Q203 3.3 63.4 1.0 C8 B:F8Q203 3.6 52.3 1.0 C10 B:F8Q203 3.7 57.5 1.0 C1 B:F8Q203 3.8 38.3 1.0 CD B:LYS5 4.0 46.3 1.0 C4 B:F8Q203 4.1 35.0 1.0 C9 B:F8Q203 4.1 54.9 1.0 CE B:LYS5 4.2 49.6 1.0 N18 B:F8Q203 4.7 56.8 1.0 C2 B:F8Q203 4.7 33.4 1.0 CB B:ASP54 4.8 37.9 1.0 C3 B:F8Q203 4.8 34.1 1.0 OD2 B:ASP54 4.9 54.9 1.0 O13 B:F8Q203 4.9 35.9 1.0 C14 B:F8Q203 5.0 38.0 1.0

Fluorine binding site 3 out of 4 in the Kras-169 Q61H Gppnhp + Ch-3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Kras-169 Q61H Gppnhp + Ch-3 within 5.0Å range: probe atom residue distance (Å) B Occ C:F203 b:47.8 occ:1.00 F17 C:F8Q203 0.0 47.8 1.0 C12 C:F8Q203 1.3 41.6 1.0 C11 C:F8Q203 2.3 42.4 1.0 C7 C:F8Q203 2.4 39.5 1.0 O15 C:F8Q203 2.7 43.2 1.0 C6 C:F8Q203 2.8 36.5 1.0 C5 C:F8Q203 2.9 34.5 1.0 C16 C:F8Q203 3.1 40.9 1.0 C8 C:F8Q203 3.6 39.0 1.0 C10 C:F8Q203 3.6 40.3 1.0 CD C:LYS5 3.8 41.4 1.0 C1 C:F8Q203 3.9 35.4 1.0 C4 C:F8Q203 4.0 33.4 1.0 CE C:LYS5 4.0 44.2 1.0 C9 C:F8Q203 4.1 37.9 1.0 O13 C:F8Q203 4.6 32.1 1.0 N18 C:F8Q203 4.7 40.8 1.0 OD2 C:ASP54 4.7 47.0 1.0 C2 C:F8Q203 4.8 33.8 1.0 C3 C:F8Q203 4.8 33.1 1.0 CB C:ASP54 4.9 39.6 1.0 CG C:LYS5 5.0 37.5 1.0

Fluorine binding site 4 out of 4 in the Kras-169 Q61H Gppnhp + Ch-3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Kras-169 Q61H Gppnhp + Ch-3 within 5.0Å range: probe atom residue distance (Å) B Occ D:F203 b:91.0 occ:1.00 F17 D:F8Q203 0.0 91.0 1.0 C12 D:F8Q203 1.4 0.7 1.0 C7 D:F8Q203 2.4 0.6 1.0 C11 D:F8Q203 2.4 0.7 1.0 O15 D:F8Q203 2.8 96.9 1.0 C6 D:F8Q203 2.8 0.9 1.0 C5 D:F8Q203 3.0 99.2 1.0 C16 D:F8Q203 3.1 91.7 1.0 NZ D:LYS5 3.2 81.4 1.0 C8 D:F8Q203 3.6 0.7 1.0 C10 D:F8Q203 3.7 99.4 1.0 C1 D:F8Q203 3.9 96.2 1.0 CE D:LYS5 3.9 72.3 1.0 CD D:LYS5 4.1 65.6 1.0 C9 D:F8Q203 4.2 96.2 1.0 C4 D:F8Q203 4.2 95.7 1.0 OD2 D:ASP54 4.7 85.7 1.0 N18 D:F8Q203 4.8 97.2 1.0 C2 D:F8Q203 4.8 92.7 1.0 C14 D:F8Q203 4.9 93.2 1.0 C3 D:F8Q203 5.0 92.8 1.0 CB D:ASP54 5.0 54.1 1.0

A.Cruz-Migoni, P.Canning, C.E.Quevedo, C.J.R.Bataille, N.Bery, A.Miller, A.J.Russell, S.E.V.Phillips, S.B.Carr, T.H.Rabbitts. Structure-Based Development of New Ras-Effector Inhibitors From A Combination of Active and Inactive Ras-Binding Compounds. Proc. Natl. Acad. Sci. V. 116 2545 2019U.S.A..
ISSN: ESSN 1091-6490
PubMed: 30683716
DOI: 10.1073/PNAS.1811360116