Fluorine in PDB 8t4v: Crystal Structure of Compound 1 Bound to K-Ras(G12D)

All present enzymatic activity of Crystal Structure of Compound 1 Bound to K-Ras(G12D):
3.6.5.2;

The structure of Crystal Structure of Compound 1 Bound to K-Ras(G12D), PDB code: 8t4v was solved by Z.Zhang, Q.Zheng, 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)	59.57 / 1.47
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	41.32, 65.84, 60.85, 90, 101.75, 90
R / Rfree (%)	19 / 21.1

The structure of Crystal Structure of Compound 1 Bound to K-Ras(G12D) also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Fluorine atom in the Crystal Structure of Compound 1 Bound to K-Ras(G12D) (pdb code 8t4v). 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 Compound 1 Bound to K-Ras(G12D), PDB code: 8t4v:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Crystal Structure of Compound 1 Bound to K-Ras(G12D)


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 Compound 1 Bound to K-Ras(G12D) within 5.0Å range: probe atom residue distance (Å) B Occ A:F203 b:19.6 occ:1.00 F13 A:Y63203 0.0 19.6 1.0 C12 A:Y63203 1.4 18.4 1.0 C14 A:Y63203 2.3 20.5 1.0 C11 A:Y63203 2.4 20.9 1.0 C10 A:Y63203 2.7 19.7 1.0 N47 A:Y63203 2.7 19.4 1.0 C48 A:Y63203 3.1 21.4 1.0 NE2 A:HIS95 3.3 22.0 1.0 OH A:TYR64 3.3 20.0 1.0 C09 A:Y63203 3.4 22.2 1.0 C01 A:Y63203 3.4 21.0 1.0 C02 A:Y63203 3.4 21.6 1.0 CG A:GLN99 3.5 21.4 1.0 CE1 A:TYR64 3.5 18.5 1.0 C15 A:Y63203 3.5 18.5 1.0 N17 A:Y63203 3.6 19.5 1.0 CE1 A:HIS95 3.8 25.4 1.0 C13 A:Y63203 3.8 19.2 1.0 CZ A:TYR64 3.8 18.9 1.0 CB A:GLN99 4.0 20.3 1.0 C16 A:Y63203 4.0 17.5 1.0 C36 A:Y63203 4.0 21.6 1.0 C06 A:Y63203 4.1 20.8 1.0 CD2 A:HIS95 4.3 20.0 1.0 C08 A:Y63203 4.3 23.4 1.0 CD A:GLN99 4.4 26.2 1.0 CE1 A:TYR96 4.4 18.9 1.0 CD1 A:TYR96 4.4 20.7 1.0 C03 A:Y63203 4.5 21.7 1.0 C07 A:Y63203 4.6 22.9 1.0 OE1 A:GLN99 4.6 27.3 1.0 CD1 A:TYR64 4.7 21.8 1.0 C18 A:Y63203 4.7 22.5 1.0 O37 A:Y63203 4.9 22.6 1.0 ND1 A:HIS95 4.9 25.2 1.0 N35 A:Y63203 4.9 20.0 1.0

Fluorine binding site 2 out of 2 in the Crystal Structure of Compound 1 Bound to K-Ras(G12D)


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 Compound 1 Bound to K-Ras(G12D) within 5.0Å range: probe atom residue distance (Å) B Occ B:F203 b:16.3 occ:1.00 F13 B:Y63203 0.0 16.3 1.0 C12 B:Y63203 1.4 15.3 1.0 C14 B:Y63203 2.3 14.3 1.0 C11 B:Y63203 2.4 15.8 1.0 N47 B:Y63203 2.7 14.7 1.0 C10 B:Y63203 2.7 15.7 1.0 C48 B:Y63203 3.1 14.9 1.0 C01 B:Y63203 3.3 18.4 1.0 NE2 B:HIS95 3.3 14.9 1.0 OH B:TYR64 3.4 17.4 1.0 C02 B:Y63203 3.4 15.2 1.0 CE1 B:TYR64 3.5 16.6 1.0 C09 B:Y63203 3.5 15.6 1.0 C15 B:Y63203 3.5 16.1 1.0 CG B:GLN99 3.6 17.5 1.0 N17 B:Y63203 3.6 16.8 1.0 C13 B:Y63203 3.7 21.1 1.0 CZ B:TYR64 3.8 18.8 1.0 CE1 B:HIS95 4.0 18.8 1.0 C36 B:Y63203 4.0 16.1 1.0 CB B:GLN99 4.0 14.3 1.0 C16 B:Y63203 4.1 18.6 1.0 C06 B:Y63203 4.1 15.3 1.0 CE1 B:TYR96 4.3 14.2 1.0 CD2 B:HIS95 4.3 17.9 1.0 CD1 B:TYR96 4.3 14.8 1.0 C08 B:Y63203 4.4 16.2 1.0 C03 B:Y63203 4.5 16.7 1.0 CD1 B:TYR64 4.6 18.3 1.0 CD B:GLN99 4.6 18.7 1.0 C07 B:Y63203 4.7 15.9 1.0 C18 B:Y63203 4.7 15.7 1.0 O37 B:Y63203 4.8 16.6 1.0 N35 B:Y63203 4.9 16.3 1.0 OE1 B:GLN99 4.9 18.3 1.0

Q.Zheng, Z.Zhang, K.Z.Guiley, K.M.Shokat. Strain-Release Alkylation of ASP12 Enables Mutant Selective Targeting of K-Ras-G12D. Nat.Chem.Biol. 2024.
ISSN: ESSN 1552-4469
PubMed: 38443470
DOI: 10.1038/S41589-024-01565-W