Fluorine in PDB 8txg: Crystal Structure of Kras G12D in Complex with Gdp and Compound 8

All present enzymatic activity of Crystal Structure of Kras G12D in Complex with Gdp and Compound 8:
3.6.5.2;

The structure of Crystal Structure of Kras G12D in Complex with Gdp and Compound 8, PDB code: 8txg was solved by P.Chen, A.Irimia, Z.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.28 / 1.50
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	74.327, 74.327, 202.985, 90, 90, 120
R / Rfree (%)	19.8 / 22.3

The structure of Crystal Structure of Kras G12D in Complex with Gdp and Compound 8 also contains other interesting chemical elements:

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

The binding sites of Fluorine atom in the Crystal Structure of Kras G12D in Complex with Gdp and Compound 8 (pdb code 8txg). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of Kras G12D in Complex with Gdp and Compound 8, PDB code: 8txg:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Crystal Structure of Kras G12D in Complex with Gdp and Compound 8


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 Kras G12D in Complex with Gdp and Compound 8 within 5.0Å range: probe atom residue distance (Å) B Occ A:F203 b:18.6 occ:1.00 F11 A:VQT203 0.0 18.6 1.0 C8 A:VQT203 1.3 17.2 1.0 C9 A:VQT203 2.4 16.2 1.0 C7 A:VQT203 2.4 16.6 1.0 S10 A:VQT203 3.1 16.9 1.0 CG2 A:VAL103 3.2 19.1 1.0 O A:GLN99 3.4 16.6 1.0 CA A:ILE100 3.5 15.5 1.0 C A:GLN99 3.6 15.4 1.0 N A:ILE100 3.6 15.1 1.0 C6 A:VQT203 3.7 16.8 1.0 C4 A:VQT203 3.7 15.7 1.0 CB A:MET72 3.7 15.2 1.0 CG1 A:ILE100 3.8 16.8 1.0 C5 A:VQT203 4.2 16.2 1.0 CB A:ILE100 4.3 15.4 1.0 CB A:GLN99 4.3 15.6 1.0 CB A:VAL103 4.4 18.8 1.0 CG1 A:VAL103 4.4 19.4 1.0 CG A:MET72 4.5 16.3 1.0 CE2 A:PHE78 4.5 18.4 1.0 CE A:MET72 4.5 19.5 1.0 CA A:GLN99 4.6 15.3 1.0 C2 A:VQT203 4.6 17.2 1.0 C A:ILE100 4.6 17.3 1.0 N3 A:VQT203 4.7 16.4 1.0 O A:ILE100 4.7 18.7 1.0 CZ A:PHE78 4.8 18.1 1.0 C A:MET72 4.9 16.6 1.0 CA A:MET72 4.9 15.8 1.0 O A:MET72 5.0 17.4 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of Kras G12D in Complex with Gdp and Compound 8


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 Kras G12D in Complex with Gdp and Compound 8 within 5.0Å range: probe atom residue distance (Å) B Occ A:F203 b:16.4 occ:1.00 F22 A:VQT203 0.0 16.4 1.0 C21 A:VQT203 1.3 16.2 1.0 C20 A:VQT203 2.4 15.9 1.0 C12 A:VQT203 2.4 16.1 1.0 N19 A:VQT203 2.7 15.8 1.0 C5 A:VQT203 2.7 16.2 1.0 NE2 A:HIS95 3.1 17.0 1.0 C6 A:VQT203 3.3 16.8 1.0 C4 A:VQT203 3.5 15.7 1.0 OH A:TYR64 3.5 19.4 1.0 CG A:GLN99 3.6 17.4 1.0 C13 A:VQT203 3.6 16.6 1.0 C15 A:VQT203 3.6 15.2 1.0 CD1 A:TYR96 3.7 15.3 1.0 CE1 A:HIS95 3.7 17.5 1.0 CE1 A:TYR96 3.7 15.8 1.0 CD2 A:HIS95 3.9 16.6 1.0 CB A:GLN99 3.9 15.6 1.0 N3 A:VQT203 4.0 16.4 1.0 C18 A:VQT203 4.0 16.9 1.0 C14 A:VQT203 4.1 15.9 1.0 O A:HOH404 4.2 17.9 1.0 C7 A:VQT203 4.3 16.6 1.0 CE1 A:TYR64 4.4 18.5 1.0 CZ A:TYR64 4.4 18.9 1.0 C9 A:VQT203 4.5 16.2 1.0 CG A:TYR96 4.6 15.9 1.0 CZ A:TYR96 4.6 16.6 1.0 CA A:TYR96 4.7 15.8 1.0 ND1 A:HIS95 4.7 17.4 1.0 C16 A:VQT203 4.7 15.7 1.0 O23 A:VQT203 4.8 18.0 1.0 CG A:HIS95 4.8 15.4 1.0 C8 A:VQT203 4.8 17.2 1.0 CD A:GLN99 4.8 19.2 1.0 N17 A:VQT203 4.9 16.4 1.0 O A:HIS95 5.0 16.4 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of Kras G12D in Complex with Gdp and Compound 8


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Kras G12D in Complex with Gdp and Compound 8 within 5.0Å range: probe atom residue distance (Å) B Occ A:F203 b:21.2 occ:1.00 F32 A:VQT203 0.0 21.2 1.0 C31 A:VQT203 1.4 20.0 1.0 C30 A:VQT203 2.3 19.5 1.0 C33 A:VQT203 2.4 19.4 1.0 N29 A:VQT203 3.0 19.2 1.0 C25 A:VQT203 3.0 19.1 1.0 O A:HOH445 3.0 46.0 1.0 C28 A:VQT203 3.2 20.7 1.0 C26 A:VQT203 3.3 20.2 1.0 O A:HOH355 3.5 28.2 1.0 C27 A:VQT203 3.8 20.8 1.0 NZ A:LYS88 4.2 31.5 1.0 OD1 A:ASP92 4.2 21.4 1.0 C24 A:VQT203 4.5 18.6 1.0 O A:HOH353 4.6 34.7 1.0 O23 A:VQT203 4.8 18.0 1.0 CG A:ASP92 4.9 20.9 1.0

H.Cheng, P.Li, P.Chen, A.Irimia, J.H.Bae, A.Brooun, P.Fagan, R.Lam, B.Lin, J.Zhang, X.Zhan, X.Wu, N.Xie, G.Chiang, R.Shoemaker, J.M.Vernier. Structure-Based Design and Synthesis of Potent and Selective Kras G12D Inhibitors. Acs Med.Chem.Lett. V. 14 1351 2023.
ISSN: ISSN 1948-5875
PubMed: 37849557
DOI: 10.1021/ACSMEDCHEMLETT.3C00245