Chlorine 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:

Fluorine	(F)	2 atoms
Magnesium	(Mg)	2 atoms
Sodium	(Na)	1 atom

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

Chlorine 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 Chlorine with other atoms in the Cl 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:Cl202 b:20.9 occ:1.00 CL01 A:P7U202 0.0 20.9 1.0 C02 A:P7U202 1.8 15.6 1.0 C03 A:P7U202 2.7 15.1 1.0 C53 A:P7U202 2.8 17.9 1.0 C11 A:P7U202 3.0 19.4 1.0 C12 A:P7U202 3.2 15.9 1.0 C10 A:P7U202 3.2 18.2 1.0 F13 A:P7U202 3.4 17.1 1.0 CD1 A:TYR96 3.6 16.8 1.0 N17 A:P7U202 3.6 20.9 1.0 CE1 A:TYR96 3.7 19.3 1.0 C14 A:P7U202 3.9 16.6 1.0 C04 A:P7U202 4.0 16.2 1.0 CG1 A:VAL9 4.0 15.5 1.0 C06 A:P7U202 4.1 13.5 1.0 C16 A:P7U202 4.2 20.3 1.0 CE A:MET72 4.2 30.9 1.0 CB A:VAL9 4.3 12.9 1.0 C15 A:P7U202 4.3 18.4 1.0 N38 A:P7U202 4.5 28.9 1.0 C05 A:P7U202 4.5 15.3 1.0 C09 A:P7U202 4.6 18.9 1.0 N52 A:P7U202 4.7 18.2 1.0 SD A:MET72 4.8 24.7 1.0 CG A:TYR96 4.9 15.5 1.0

Chlorine 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 Chlorine with other atoms in the Cl 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:Cl202 b:24.1 occ:1.00 CL01 B:P7U202 0.0 24.1 1.0 C02 B:P7U202 1.8 24.1 1.0 C03 B:P7U202 2.8 22.2 1.0 C53 B:P7U202 2.8 20.8 1.0 C11 B:P7U202 2.9 20.6 1.0 C10 B:P7U202 3.1 24.0 1.0 C12 B:P7U202 3.2 22.1 1.0 N17 B:P7U202 3.4 23.2 1.0 CD1 B:TYR96 3.5 16.7 1.0 F13 B:P7U202 3.5 26.2 1.0 CE1 B:TYR96 3.7 18.7 1.0 CG1 B:VAL9 3.8 11.6 1.0 C14 B:P7U202 3.9 23.0 1.0 C16 B:P7U202 4.0 24.4 1.0 CB B:VAL9 4.0 14.0 1.0 C06 B:P7U202 4.1 20.7 1.0 C04 B:P7U202 4.1 24.8 1.0 N38 B:P7U202 4.2 21.2 1.0 C15 B:P7U202 4.3 23.0 1.0 C09 B:P7U202 4.5 25.8 1.0 C05 B:P7U202 4.6 21.2 1.0 CG2 B:THR58 4.7 17.5 0.7 CE B:MET72 4.7 26.8 1.0 CG B:TYR96 4.7 15.1 1.0 N52 B:P7U202 4.8 23.1 1.0 CG2 B:VAL9 4.8 14.6 1.0 C37 B:P7U202 4.9 26.3 1.0 SD B:MET72 5.0 30.2 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