Fluorine in PDB 6t5b: KRASG12C Ligand Complex

The structure of KRASG12C Ligand Complex, PDB code: 6t5b was solved by C.Phillips, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.51 / 1.37
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	32.973, 36.569, 37.129, 65.49, 74.17, 77.61
R / Rfree (%)	18.4 / 23.1

The structure of KRASG12C Ligand Complex also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Chlorine	(Cl)	1 atom

The binding sites of Fluorine atom in the KRASG12C Ligand Complex (pdb code 6t5b). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the KRASG12C Ligand Complex, PDB code: 6t5b:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the KRASG12C Ligand Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of KRASG12C Ligand Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:F203 b:9.8 occ:1.00 F1 A:O7K203 0.0 9.8 1.0 C23 A:O7K203 1.3 8.7 1.0 C22 A:O7K203 2.3 8.4 1.0 C18 A:O7K203 2.3 7.2 1.0 C16 A:O7K203 2.8 6.6 1.0 C15 A:O7K203 3.2 6.4 1.0 CL A:O7K203 3.3 7.0 1.0 CD1 A:TYR96 3.6 5.6 1.0 C21 A:O7K203 3.6 8.2 1.0 C19 A:O7K203 3.6 7.8 1.0 CG1 A:VAL9 3.7 6.7 1.0 C17 A:O7K203 3.8 7.1 1.0 CB A:VAL9 3.8 5.3 1.0 CG2 A:VAL9 3.9 5.6 1.0 C20 A:O7K203 4.1 8.8 1.0 F A:O7K203 4.2 8.3 1.0 C14 A:O7K203 4.3 6.2 1.0 CE1 A:TYR96 4.3 6.6 1.0 CG1 A:ILE100 4.3 5.9 1.0 O A:TYR96 4.4 6.1 1.0 CB A:TYR96 4.5 5.1 1.0 CG A:TYR96 4.5 5.3 1.0 CA A:TYR96 4.6 4.9 1.0 SD A:MET72 4.7 5.6 1.0 CB A:GLN99 4.7 7.1 1.0 O2 A:O7K203 4.7 8.4 1.0 C8 A:O7K203 4.8 6.6 1.0 CG A:MET72 4.8 5.0 1.0 CD1 A:ILE100 4.9 5.6 1.0 C A:TYR96 4.9 5.2 1.0

Fluorine binding site 2 out of 2 in the KRASG12C Ligand Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of KRASG12C Ligand Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:F203 b:8.3 occ:1.00 F A:O7K203 0.0 8.3 1.0 C17 A:O7K203 1.3 7.1 1.0 C8 A:O7K203 2.3 6.6 1.0 C16 A:O7K203 2.4 6.6 1.0 N2 A:O7K203 2.7 7.2 1.0 C18 A:O7K203 2.9 7.2 1.0 NE2 A:HIS95 3.1 7.9 1.0 O2 A:O7K203 3.2 8.4 1.0 C19 A:O7K203 3.2 7.8 1.0 CG A:GLN99 3.2 8.2 1.0 CD1 A:TYR64 3.4 8.8 1.0 C9 A:O7K203 3.6 6.2 1.0 C15 A:O7K203 3.6 6.4 1.0 CB A:GLN99 3.7 7.1 1.0 C23 A:O7K203 3.8 8.7 1.0 CD2 A:HIS95 3.9 7.4 1.0 CE1 A:HIS95 3.9 7.6 1.0 CE1 A:TYR64 3.9 9.1 1.0 C7 A:O7K203 4.0 7.1 1.0 O A:HOH377 4.1 6.6 1.0 C14 A:O7K203 4.1 6.2 1.0 F1 A:O7K203 4.2 9.8 1.0 CD A:GLN99 4.2 11.3 1.0 C20 A:O7K203 4.3 8.8 1.0 OE1 A:GLN99 4.5 14.3 1.0 CG A:TYR64 4.5 8.3 1.0 CE1 A:TYR96 4.6 6.6 1.0 CD1 A:TYR96 4.6 5.6 1.0 C10 A:O7K203 4.8 6.5 1.0 CB A:TYR64 4.8 8.5 1.0 ND1 A:HIS95 4.8 7.7 1.0 C22 A:O7K203 4.8 8.4 1.0 CG A:HIS95 4.9 6.7 1.0 C6 A:O7K203 4.9 6.6 1.0 C21 A:O7K203 5.0 8.2 1.0

J.G.Kettle, S.K.Bagal, S.Bickerton, M.S.Bodnarchuk, J.Breed, R.J.Carbajo, D.J.Cassar, A.Chakraborty, S.Cosulich, I.Cumming, M.Davies, A.Eatherton, L.Evans, L.Feron, S.Fillery, E.S.Gleave, F.W.Goldberg, S.Harlfinger, L.Hanson, M.Howard, R.Howells, A.Jackson, P.Kemmitt, J.K.Kingston, S.Lamont, H.J.Lewis, S.Li, L.Liu, D.Ogg, C.Phillips, R.Polanski, G.Robb, D.Robinson, S.Ross, J.M.Smith, M.Tonge, R.Whiteley, J.Yang, L.Zhang, X.Zhao. Structure-Based Design and Pharmacokinetic Optimization of Covalent Allosteric Inhibitors of the Mutant Gtpase KRASG12C. J.Med.Chem. 2020.
ISSN: ISSN 0022-2623
PubMed: 32023060
DOI: 10.1021/ACS.JMEDCHEM.9B01720