Fluorine in PDB 8cx5: Crystal Structure of Small Molecule Alpha,Beta-Ketoamide 4 Covalently Bound to K-Ras(G12R)

All present enzymatic activity of Crystal Structure of Small Molecule Alpha,Beta-Ketoamide 4 Covalently Bound to K-Ras(G12R):
3.6.5.2;

The structure of Crystal Structure of Small Molecule Alpha,Beta-Ketoamide 4 Covalently Bound to K-Ras(G12R), PDB code: 8cx5 was solved by Z.Zhang, J.Morstein, A.Ecker, K.Z.Guiley, K.M.Shokat, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	59.83 / 1.72
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	41.21, 65.661, 61.13, 90, 101.85, 90
R / Rfree (%)	18.9 / 22.1

The structure of Crystal Structure of Small Molecule Alpha,Beta-Ketoamide 4 Covalently Bound to K-Ras(G12R) also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Magnesium	(Mg)	2 atoms
Sodium	(Na)	1 atom

The binding sites of Fluorine atom in the Crystal Structure of Small Molecule Alpha,Beta-Ketoamide 4 Covalently Bound to K-Ras(G12R) (pdb code 8cx5). 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 Alpha,Beta-Ketoamide 4 Covalently Bound to K-Ras(G12R), PDB code: 8cx5:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Crystal Structure of Small Molecule Alpha,Beta-Ketoamide 4 Covalently Bound to K-Ras(G12R)


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 Alpha,Beta-Ketoamide 4 Covalently Bound to K-Ras(G12R) within 5.0Å range: probe atom residue distance (Å) B Occ A:F202 b:17.1 occ:1.00 F13 A:P7U202 0.0 17.1 1.0 C12 A:P7U202 1.4 15.9 1.0 C14 A:P7U202 2.4 16.6 1.0 C11 A:P7U202 2.5 19.4 1.0 N52 A:P7U202 2.7 18.2 1.0 C10 A:P7U202 2.8 18.2 1.0 C53 A:P7U202 3.2 17.9 1.0 NE2 A:HIS95 3.3 21.2 1.0 C02 A:P7U202 3.4 15.6 1.0 OH A:TYR64 3.4 22.0 1.0 CL01 A:P7U202 3.4 20.9 1.0 CE1 A:TYR64 3.5 19.2 1.0 C09 A:P7U202 3.5 18.9 1.0 CG A:GLN99 3.6 16.3 1.0 C15 A:P7U202 3.6 18.4 1.0 N17 A:P7U202 3.7 20.9 1.0 CZ A:TYR64 3.9 19.7 1.0 CB A:GLN99 4.0 17.5 1.0 C41 A:P7U202 4.1 20.3 1.0 C16 A:P7U202 4.1 20.3 1.0 C06 A:P7U202 4.1 13.5 1.0 CE1 A:HIS95 4.1 19.9 1.0 CD2 A:HIS95 4.1 19.3 1.0 CE1 A:TYR96 4.3 19.3 1.0 CD1 A:TYR96 4.4 16.8 1.0 C08 A:P7U202 4.5 18.5 1.0 C03 A:P7U202 4.5 15.1 1.0 CD1 A:TYR64 4.6 19.6 1.0 CD A:GLN99 4.7 14.4 1.0 C07 A:P7U202 4.7 21.3 1.0 C18 A:P7U202 4.7 21.4 1.0 N40 A:P7U202 4.9 23.6 1.0 O42 A:P7U202 4.9 24.5 1.0

Fluorine binding site 2 out of 2 in the Crystal Structure of Small Molecule Alpha,Beta-Ketoamide 4 Covalently Bound to K-Ras(G12R)


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 Alpha,Beta-Ketoamide 4 Covalently Bound to K-Ras(G12R) within 5.0Å range: probe atom residue distance (Å) B Occ B:F202 b:26.2 occ:1.00 F13 B:P7U202 0.0 26.2 1.0 C12 B:P7U202 1.3 22.1 1.0 C14 B:P7U202 2.4 23.0 1.0 C11 B:P7U202 2.4 20.6 1.0 C10 B:P7U202 2.7 24.0 1.0 N52 B:P7U202 2.8 23.1 1.0 OH B:TYR64 3.2 25.2 1.0 C53 B:P7U202 3.2 20.8 1.0 CG B:GLN99 3.3 20.1 1.0 NE2 B:HIS95 3.3 21.9 1.0 C09 B:P7U202 3.4 25.8 1.0 CE1 B:TYR64 3.5 21.5 1.0 CL01 B:P7U202 3.5 24.1 1.0 C15 B:P7U202 3.6 23.0 1.0 C02 B:P7U202 3.6 24.1 1.0 N17 B:P7U202 3.6 23.2 1.0 CB B:GLN99 3.7 20.3 1.0 CZ B:TYR64 3.8 23.8 1.0 CE1 B:HIS95 3.9 22.0 1.0 C16 B:P7U202 4.1 24.4 1.0 C41 B:P7U202 4.1 21.6 1.0 C06 B:P7U202 4.2 20.7 1.0 CD2 B:HIS95 4.2 19.1 1.0 C08 B:P7U202 4.3 25.9 1.0 CD B:GLN99 4.3 24.3 1.0 CD1 B:TYR96 4.4 16.7 1.0 CE1 B:TYR96 4.4 18.7 1.0 C07 B:P7U202 4.6 24.7 1.0 OE1 B:GLN99 4.6 24.2 1.0 CD1 B:TYR64 4.7 27.0 1.0 C18 B:P7U202 4.7 22.3 1.0 C03 B:P7U202 4.7 22.2 1.0 O42 B:P7U202 4.9 23.2 1.0 N40 B:P7U202 4.9 22.7 1.0 ND1 B:HIS95 5.0 21.9 1.0

Z.Zhang, J.Morstein, A.K.Ecker, K.Z.Guiley, K.M.Shokat. Chemoselective Covalent Modification of K-Ras(G12R) with A Small Molecule Electrophile. J.Am.Chem.Soc. V. 144 15916 2022.
ISSN: ESSN 1520-5126
PubMed: 36001446
DOI: 10.1021/JACS.2C05377