Fluorine in PDB 7o70: KRASG12C Ligand Complex

The structure of KRASG12C Ligand Complex, PDB code: 7o70 was solved by C.Phillips, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	17.03 / 1.18
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	33.38, 70.46, 66.15, 90, 90.26, 90
R / Rfree (%)	22.6 / 25.7

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

Calcium	(Ca)	2 atoms
Magnesium	(Mg)	2 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Fluorine atom in the KRASG12C Ligand Complex (pdb code 7o70). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the KRASG12C Ligand Complex, PDB code: 7o70:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 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:F201 b:18.2 occ:1.00 F1 A:V4T201 0.0 18.2 1.0 C10 A:V4T201 1.3 17.1 1.0 C9 A:V4T201 2.4 17.0 1.0 C11 A:V4T201 2.4 17.1 1.0 N1 A:V4T201 2.7 17.4 1.0 C13 A:V4T201 2.8 18.6 1.0 CG A:GLN99 3.2 12.0 1.0 NE2 A:HIS95 3.2 16.4 1.0 C14 A:V4T201 3.3 21.6 1.0 O2 A:V4T201 3.4 26.2 1.0 CB A:GLN99 3.6 9.6 1.0 C12 A:V4T201 3.6 17.1 1.0 C18 A:V4T201 3.6 19.9 1.0 C8 A:V4T201 3.6 15.2 1.0 CD2 A:HIS95 3.9 15.2 1.0 F A:V4T201 4.0 20.6 1.0 CE1 A:HIS95 4.0 15.0 1.0 C19 A:V4T201 4.0 18.9 1.0 C7 A:V4T201 4.1 17.3 1.0 CD1 A:TYR96 4.2 11.3 1.0 CE1 A:TYR96 4.2 12.0 1.0 CD A:GLN99 4.3 14.7 1.0 O A:HOH367 4.4 24.8 0.5 C15 A:V4T201 4.4 22.1 1.0 C17 A:V4T201 4.6 19.5 1.0 OE1 A:GLN99 4.7 15.1 1.0 O A:HOH464 4.7 35.6 1.0 C20 A:V4T201 4.7 16.8 1.0 CG A:HIS95 4.9 14.5 1.0 ND1 A:HIS95 4.9 17.9 1.0 C16 A:V4T201 4.9 20.4 1.0 N2 A:V4T201 5.0 18.4 1.0

Fluorine binding site 2 out of 4 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:F201 b:20.6 occ:1.00 F A:V4T201 0.0 20.6 1.0 C18 A:V4T201 1.3 19.9 1.0 C13 A:V4T201 2.3 18.6 1.0 C17 A:V4T201 2.4 19.5 1.0 C11 A:V4T201 2.8 17.1 1.0 C12 A:V4T201 3.3 17.1 1.0 CL A:V4T201 3.4 22.2 1.0 CG1 A:VAL9 3.5 9.9 1.0 CD1 A:TYR96 3.5 11.3 1.0 C16 A:V4T201 3.6 20.4 1.0 C14 A:V4T201 3.6 21.6 1.0 C10 A:V4T201 3.6 17.1 1.0 CB A:VAL9 3.8 9.4 1.0 F1 A:V4T201 4.0 18.2 1.0 CE1 A:TYR96 4.1 12.0 1.0 C15 A:V4T201 4.1 22.1 1.0 CG2 A:VAL9 4.2 9.1 1.0 C7 A:V4T201 4.4 17.3 1.0 CG1 A:ILE100 4.5 10.1 1.0 CG A:TYR96 4.5 11.2 1.0 O A:TYR96 4.7 9.3 1.0 O2 A:V4T201 4.7 26.2 1.0 C9 A:V4T201 4.7 17.0 1.0 CB A:TYR96 4.7 9.9 1.0 SD A:MET72 4.8 17.2 1.0 CB A:GLN99 4.8 9.6 1.0 CA A:TYR96 4.9 9.0 1.0 O A:HOH387 4.9 13.6 1.0 CG A:MET72 5.0 13.3 1.0

Fluorine binding site 3 out of 4 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 3 of KRASG12C Ligand Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:F201 b:16.7 occ:1.00 F1 D:V4T201 0.0 16.7 1.0 C10 D:V4T201 1.3 15.1 1.0 C11 D:V4T201 2.3 15.3 1.0 C9 D:V4T201 2.4 15.3 1.0 N1 D:V4T201 2.7 15.7 1.0 C13 D:V4T201 2.8 18.2 1.0 NE2 D:HIS95 3.2 13.5 1.0 CG D:GLN99 3.2 12.4 1.0 C14 D:V4T201 3.4 20.7 1.0 CB D:GLN99 3.5 9.4 1.0 O2 D:V4T201 3.5 26.4 1.0 C12 D:V4T201 3.6 14.5 1.0 C18 D:V4T201 3.6 18.6 1.0 C8 D:V4T201 3.6 13.3 1.0 CD2 D:HIS95 3.8 12.4 1.0 F D:V4T201 4.0 21.1 1.0 CE1 D:HIS95 4.0 13.2 1.0 C19 D:V4T201 4.0 16.4 1.0 C7 D:V4T201 4.1 15.6 1.0 CD1 D:TYR96 4.1 10.6 1.0 CE1 D:TYR96 4.2 10.7 1.0 CD D:GLN99 4.4 14.3 1.0 C15 D:V4T201 4.4 20.7 1.0 O D:HOH372 4.5 31.7 1.0 C17 D:V4T201 4.7 21.0 1.0 C20 D:V4T201 4.7 13.6 1.0 OE1 D:GLN99 4.7 15.3 1.0 CG D:HIS95 4.9 11.7 1.0 CA D:TYR96 4.9 8.0 1.0 ND1 D:HIS95 4.9 15.2 1.0 N2 D:V4T201 4.9 14.7 1.0 O D:HOH466 5.0 44.0 1.0 O D:HIS95 5.0 8.7 1.0 C16 D:V4T201 5.0 19.1 1.0 CG D:TYR96 5.0 9.1 1.0

Fluorine binding site 4 out of 4 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 4 of KRASG12C Ligand Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:F201 b:21.1 occ:1.00 F D:V4T201 0.0 21.1 1.0 C18 D:V4T201 1.3 18.6 1.0 C17 D:V4T201 2.3 21.0 1.0 C13 D:V4T201 2.3 18.2 1.0 C11 D:V4T201 2.8 15.3 1.0 CG1 D:VAL9 3.3 8.9 1.0 C12 D:V4T201 3.3 14.5 1.0 CD1 D:TYR96 3.3 10.6 1.0 CL D:V4T201 3.5 20.6 1.0 CB D:VAL9 3.5 8.4 1.0 C16 D:V4T201 3.6 19.1 1.0 C14 D:V4T201 3.6 20.7 1.0 C10 D:V4T201 3.6 15.1 1.0 CE1 D:TYR96 3.9 10.7 1.0 F1 D:V4T201 4.0 16.7 1.0 CG2 D:VAL9 4.0 8.6 1.0 C15 D:V4T201 4.1 20.7 1.0 C7 D:V4T201 4.4 15.6 1.0 CG D:TYR96 4.4 9.1 1.0 CB D:TYR96 4.5 8.5 1.0 O D:HOH383 4.5 11.9 1.0 C9 D:V4T201 4.7 15.3 1.0 O2 D:V4T201 4.7 26.4 1.0 O D:TYR96 4.7 8.9 1.0 CG1 D:ILE100 4.7 9.6 1.0 CA D:TYR96 4.8 8.0 1.0 SD D:MET72 4.8 21.6 1.0 CA D:VAL9 4.9 7.7 1.0 C8 D:V4T201 5.0 13.3 1.0

J.G.Kettle, S.K.Bagal, S.Bickerton, M.S.Bodnarchuk, S.Boyd, J.Breed, R.J.Carbajo, D.J.Cassar, A.Chakraborty, S.Cosulich, I.Cumming, M.Davies, N.L.Davies, A.Eatherton, L.Evans, L.Feron, S.Fillery, E.S.Gleave, F.W.Goldberg, L.Hanson, S.Harlfinger, M.Howard, R.Howells, A.Jackson, P.Kemmitt, G.Lamont, S.Lamont, H.J.Lewis, L.Liu, M.J.Niedbala, C.Phillips, R.Polanski, P.Raubo, G.Robb, D.M.Robinson, S.Ross, M.G.Sanders, M.Tonge, R.Whiteley, S.Wilkinson, J.Yang, W.Zhang. Discovery of AZD4625, A Covalent Allosteric Inhibitor of the Mutant Gtpase Kras G12C . J.Med.Chem. V. 65 6940 2022.
ISSN: ISSN 0022-2623
PubMed: 35471939
DOI: 10.1021/ACS.JMEDCHEM.2C00369