Fluorine in PDB 5v6v: Crystal Structure of Small Molecule Aziridine 3 Covalently Bound to K- Ras G12C

The structure of Crystal Structure of Small Molecule Aziridine 3 Covalently Bound to K- Ras G12C, PDB code: 5v6v was solved by L.M.Mcgregor, M.Jenkins, C.Kerwin, J.E.Burke, K.M.Shokat, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.43 / 1.72
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	33.230, 39.170, 62.340, 77.34, 81.44, 76.86
R / Rfree (%)	16.8 / 20.2

The structure of Crystal Structure of Small Molecule Aziridine 3 Covalently Bound to K- Ras G12C also contains other interesting chemical elements:

Calcium	(Ca)	6 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Fluorine atom in the Crystal Structure of Small Molecule Aziridine 3 Covalently Bound to K- Ras G12C (pdb code 5v6v). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of Small Molecule Aziridine 3 Covalently Bound to K- Ras G12C, PDB code: 5v6v:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Crystal Structure of Small Molecule Aziridine 3 Covalently Bound to K- Ras G12C


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 Small Molecule Aziridine 3 Covalently Bound to K- Ras G12C within 5.0Å range: probe atom residue distance (Å) B Occ A:F204 b:26.8 occ:1.00 F15 A:8YA204 0.0 26.8 1.0 C14 A:8YA204 1.4 23.9 1.0 HE A:ARG68 2.3 39.4 1.0 C03 A:8YA204 2.4 22.4 1.0 C16 A:8YA204 2.4 25.1 1.0 C04 A:8YA204 2.7 22.6 1.0 N17 A:8YA204 2.8 26.9 1.0 HG3 A:MET72 3.0 26.9 1.0 NE A:ARG68 3.0 32.8 1.0 C05 A:8YA204 3.1 22.6 1.0 HH21 A:ARG68 3.1 34.4 1.0 HE3 A:MET72 3.2 35.7 1.0 HG3 A:ARG68 3.2 33.0 1.0 H061 A:8YA204 3.2 30.0 1.0 C06 A:8YA204 3.4 25.0 1.0 HG2 A:ARG68 3.5 33.0 1.0 SD A:MET72 3.5 23.7 1.0 CG A:MET72 3.5 22.4 1.0 HG2 A:MET72 3.5 26.9 1.0 C02 A:8YA204 3.6 22.2 1.0 C12 A:8YA204 3.6 29.2 1.0 C32 A:8YA204 3.6 23.1 1.0 CG A:ARG68 3.7 27.5 1.0 NH2 A:ARG68 3.7 28.7 1.0 CE A:MET72 3.8 29.7 1.0 CZ A:ARG68 3.8 27.6 1.0 CD A:ARG68 3.9 29.9 1.0 H133 A:8YA204 4.1 28.7 1.0 C18 A:8YA204 4.1 25.9 1.0 C33 A:8YA204 4.1 24.1 1.0 C09 A:8YA204 4.1 25.3 1.0 H132 A:8YA204 4.1 28.7 1.0 C13 A:8YA204 4.2 23.9 1.0 HE1 A:MET72 4.2 35.7 1.0 HD2 A:ARG68 4.4 35.9 1.0 N07 A:8YA204 4.4 30.5 1.0 HH22 A:ARG68 4.5 34.4 1.0 HE2 A:MET72 4.5 35.7 1.0 C11 A:8YA204 4.6 24.9 1.0 HG21 A:THR58 4.6 21.7 1.0 H181 A:8YA204 4.6 31.0 1.0 HD3 A:ARG68 4.7 35.9 1.0 HB A:THR58 4.7 21.3 1.0 C10 A:8YA204 4.8 24.5 1.0 N08 A:8YA204 4.8 31.7 1.0 C20 A:8YA204 4.8 28.8 1.0 N19 A:8YA204 4.9 27.4 1.0 CB A:MET72 5.0 21.6 1.0

Fluorine binding site 2 out of 2 in the Crystal Structure of Small Molecule Aziridine 3 Covalently Bound to K- Ras G12C


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 Small Molecule Aziridine 3 Covalently Bound to K- Ras G12C within 5.0Å range: probe atom residue distance (Å) B Occ B:F207 b:28.0 occ:1.00 F15 B:8YA207 0.0 28.0 1.0 C14 B:8YA207 1.3 29.2 1.0 HE B:ARG68 2.3 39.7 1.0 C03 B:8YA207 2.4 24.4 1.0 C16 B:8YA207 2.4 25.8 1.0 C04 B:8YA207 2.7 26.1 1.0 N17 B:8YA207 2.8 30.7 1.0 HH21 B:ARG68 2.8 38.6 1.0 C05 B:8YA207 3.1 27.4 1.0 NE B:ARG68 3.1 33.1 1.0 H061 B:8YA207 3.2 39.0 1.0 HG3 B:MET72 3.2 32.4 1.0 HE2 B:MET72 3.3 34.4 1.0 C06 B:8YA207 3.3 32.5 1.0 SD B:MET72 3.4 28.4 1.0 NH2 B:ARG68 3.5 32.1 1.0 C32 B:8YA207 3.6 23.9 1.0 C02 B:8YA207 3.6 30.4 1.0 C12 B:8YA207 3.7 26.2 1.0 CZ B:ARG68 3.7 30.1 1.0 HG3 B:ARG68 3.7 40.2 1.0 CG B:MET72 3.7 27.0 1.0 H131 B:8YA207 3.8 32.5 1.0 CE B:MET72 3.8 28.7 1.0 HG2 B:MET72 3.9 32.4 1.0 HE1 B:MET72 4.1 34.4 1.0 HG2 B:ARG68 4.1 40.2 1.0 C33 B:8YA207 4.1 25.7 1.0 C18 B:8YA207 4.1 32.4 1.0 C09 B:8YA207 4.1 30.3 1.0 O B:HOH368 4.1 37.5 1.0 HG21 B:THR58 4.1 23.5 1.0 CD B:ARG68 4.2 33.7 1.0 CG B:ARG68 4.2 33.5 1.0 HH22 B:ARG68 4.2 38.6 1.0 C13 B:8YA207 4.3 27.1 1.0 HB B:THR58 4.3 22.2 1.0 N07 B:8YA207 4.4 35.7 1.0 HD2 B:ARG68 4.5 40.5 1.0 C11 B:8YA207 4.6 25.8 1.0 HE3 B:MET72 4.6 34.4 1.0 H181 B:8YA207 4.6 38.8 1.0 C20 B:8YA207 4.7 27.1 1.0 N08 B:8YA207 4.8 27.2 1.0 C10 B:8YA207 4.8 24.8 1.0 CG2 B:THR58 4.8 19.6 1.0 HG22 B:THR58 4.8 23.5 1.0 H132 B:8YA207 4.9 32.5 1.0 N19 B:8YA207 4.9 30.7 1.0 H133 B:8YA207 4.9 32.5 1.0 HD3 B:ARG68 4.9 40.5 1.0 NH1 B:ARG68 5.0 34.3 1.0

L.M.Mcgregor, M.L.Jenkins, C.Kerwin, J.E.Burke, K.M.Shokat. Expanding the Scope of Electrophiles Capable of Targeting K-Ras Oncogenes. Biochemistry V. 56 3178 2017.
ISSN: ISSN 1520-4995
PubMed: 28621541
DOI: 10.1021/ACS.BIOCHEM.7B00271