Fluorine in PDB 6t5b: KRASG12C Ligand Complex

Protein crystallography data

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

Other elements in 6t5b:

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

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

Fluorine Binding Sites:

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 6t5b

Go back to Fluorine Binding Sites List in 6t5b
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 6t5b

Go back to Fluorine Binding Sites List in 6t5b
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

Reference:

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
Page generated: Sun Dec 13 13:13:56 2020

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