Chlorine in PDB 8txe: Crystal Structure of Kras G12D in Complex with Gdp and Compound 5

All present enzymatic activity of Crystal Structure of Kras G12D in Complex with Gdp and Compound 5:
3.6.5.2;

The structure of Crystal Structure of Kras G12D in Complex with Gdp and Compound 5, PDB code: 8txe 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)	29.77 / 1.35
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	37.815, 62.166, 71.925, 90, 91.86, 90
R / Rfree (%)	18.8 / 21.5

The structure of Crystal Structure of Kras G12D in Complex with Gdp and Compound 5 also contains other interesting chemical elements:

Fluorine	(F)	10 atoms
Magnesium	(Mg)	2 atoms

The binding sites of Chlorine atom in the Crystal Structure of Kras G12D in Complex with Gdp and Compound 5 (pdb code 8txe). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Crystal Structure of Kras G12D in Complex with Gdp and Compound 5, PDB code: 8txe:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Crystal Structure of Kras G12D in Complex with Gdp and Compound 5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Kras G12D in Complex with Gdp and Compound 5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl203 b:12.6 occ:1.00 CL42 A:VM9203 0.0 12.6 1.0 C13 A:VM9203 1.7 11.0 1.0 C12 A:VM9203 2.7 9.8 1.0 C14 A:VM9203 2.7 10.5 1.0 C6 A:VM9203 3.0 9.7 1.0 NH2 A:ARG68 3.3 14.4 1.0 N5 A:VM9203 3.3 10.2 1.0 O A:HOH424 3.6 24.8 1.0 CE A:MET72 3.7 20.3 1.0 F10 A:VM9203 3.7 9.9 1.0 O A:HOH370 3.7 15.5 1.0 NE A:ARG68 3.8 13.3 1.0 SD A:MET72 3.8 21.0 1.0 C7 A:VM9203 3.8 9.7 1.0 CZ A:ARG68 3.9 14.6 1.0 C21 A:VM9203 3.9 9.8 1.0 C15 A:VM9203 4.0 9.7 1.0 C8 A:VM9203 4.3 10.3 1.0 CG2 A:THR58 4.3 9.3 1.0 C4 A:VM9203 4.3 11.5 1.0 CG A:MET72 4.3 14.0 1.0 O A:HOH350 4.4 37.6 1.0 C20 A:VM9203 4.5 9.7 1.0 CB A:THR58 4.6 8.9 1.0 F9 A:VM9203 4.7 10.4 1.0 C2 A:VM9203 4.8 10.6 1.0 CD A:ARG68 5.0 14.0 1.0 NH1 A:ARG68 5.0 13.7 1.0 C3 A:VM9203 5.0 11.3 1.0

Chlorine binding site 2 out of 2 in the Crystal Structure of Kras G12D in Complex with Gdp and Compound 5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Kras G12D in Complex with Gdp and Compound 5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl203 b:12.1 occ:1.00 CL42 B:VM9203 0.0 12.1 1.0 C13 B:VM9203 1.7 10.1 1.0 C12 B:VM9203 2.7 9.4 1.0 C14 B:VM9203 2.7 9.4 1.0 C6 B:VM9203 3.0 8.9 1.0 NH2 B:ARG68 3.3 11.6 1.0 O B:HOH450 3.4 26.9 1.0 N5 B:VM9203 3.4 8.5 1.0 F10 B:VM9203 3.7 9.6 1.0 CE B:MET72 3.7 18.3 1.0 NE B:ARG68 3.7 11.5 1.0 O B:HOH396 3.8 14.4 1.0 SD B:MET72 3.8 18.5 1.0 C7 B:VM9203 3.8 9.3 1.0 CZ B:ARG68 3.8 12.8 1.0 C21 B:VM9203 4.0 9.7 1.0 C15 B:VM9203 4.0 8.9 1.0 C8 B:VM9203 4.3 10.2 1.0 CG B:MET72 4.3 12.4 1.0 CG2 B:THR58 4.3 9.2 1.0 C4 B:VM9203 4.4 8.8 1.0 C20 B:VM9203 4.5 9.0 1.0 CB B:THR58 4.6 8.3 1.0 O B:HOH390 4.7 33.2 1.0 F9 B:VM9203 4.7 9.8 1.0 C2 B:VM9203 4.8 9.3 1.0 CD B:ARG68 4.9 11.5 1.0 NH1 B:ARG68 5.0 11.9 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