Chlorine in PDB 8dnk: Crystal Structure of Human Kras G12C Covalently Bound with Taiho WO2020/085493A1 Compound 6

All present enzymatic activity of Crystal Structure of Human Kras G12C Covalently Bound with Taiho WO2020/085493A1 Compound 6:
3.6.5.2;

The structure of Crystal Structure of Human Kras G12C Covalently Bound with Taiho WO2020/085493A1 Compound 6, PDB code: 8dnk was solved by C.Mohr, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.23
Space group	P 2 3
Cell size a, b, c (Å), α, β, γ (°)	91.181, 91.181, 91.181, 90, 90, 90
R / Rfree (%)	18.1 / 23.5

The structure of Crystal Structure of Human Kras G12C Covalently Bound with Taiho WO2020/085493A1 Compound 6 also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Chlorine atom in the Crystal Structure of Human Kras G12C Covalently Bound with Taiho WO2020/085493A1 Compound 6 (pdb code 8dnk). 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 Human Kras G12C Covalently Bound with Taiho WO2020/085493A1 Compound 6, PDB code: 8dnk:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Crystal Structure of Human Kras G12C Covalently Bound with Taiho WO2020/085493A1 Compound 6


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 Human Kras G12C Covalently Bound with Taiho WO2020/085493A1 Compound 6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl303 b:119.8 occ:1.00 CL2 A:U50303 0.0 119.8 1.0 C15 A:U50303 1.7 60.7 1.0 N5 A:U50303 2.7 50.5 1.0 C14 A:U50303 2.7 64.7 1.0 O A:ALA59 3.1 59.6 1.0 NH1 A:ARG68 3.2 51.5 1.0 N6 A:U50303 3.2 57.9 1.0 O A:GLY60 3.3 66.3 1.0 C17 A:U50303 3.3 61.4 1.0 OE1 A:GLU37 3.6 39.0 1.0 C A:ALA59 3.6 50.5 1.0 N A:ALA59 3.8 38.3 1.0 N4 A:U50303 3.8 54.3 1.0 C13 A:U50303 3.8 53.5 1.0 CB A:THR58 4.1 34.5 1.0 CA A:ALA59 4.2 44.8 1.0 C A:GLY60 4.2 74.6 1.0 N A:GLY60 4.3 62.3 1.0 CZ A:ARG68 4.4 53.2 1.0 O1 A:U50303 4.4 58.5 1.0 C18 A:U50303 4.5 63.2 1.0 C A:THR58 4.5 37.0 1.0 O A:HOH411 4.5 26.8 1.0 C20 A:U50303 4.5 61.2 1.0 CA A:THR58 4.7 32.3 1.0 OG1 A:THR58 4.7 36.6 1.0 CD A:GLU37 4.8 50.9 1.0 CG2 A:THR58 4.9 33.7 1.0 CA A:GLY60 4.9 76.0 1.0 NE A:ARG68 4.9 51.3 1.0

Chlorine binding site 2 out of 2 in the Crystal Structure of Human Kras G12C Covalently Bound with Taiho WO2020/085493A1 Compound 6


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 Human Kras G12C Covalently Bound with Taiho WO2020/085493A1 Compound 6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl303 b:54.5 occ:1.00 CL1 A:U50303 0.0 54.5 1.0 C3 A:U50303 1.7 37.8 1.0 C2 A:U50303 2.6 37.3 1.0 C4 A:U50303 2.7 39.1 1.0 C11 A:U50303 3.1 37.4 1.0 C8 A:U50303 3.1 39.7 1.0 C10 A:U50303 3.2 38.6 1.0 C1 A:U50303 3.8 36.1 1.0 CB A:MET72 3.9 32.0 1.0 C5 A:U50303 3.9 40.3 1.0 CG1 A:ILE100 3.9 36.4 1.0 CG2 A:VAL103 4.0 51.7 1.0 C A:GLN99 4.0 43.0 1.0 CG A:MET72 4.0 36.0 1.0 O A:GLN99 4.0 43.3 1.0 N A:ILE100 4.1 38.9 1.0 CA A:ILE100 4.1 38.2 1.0 CB A:GLN99 4.2 40.6 1.0 CG1 A:VAL103 4.2 53.8 1.0 C6 A:U50303 4.4 42.9 1.0 CB A:ILE100 4.7 33.9 1.0 C9 A:U50303 4.7 40.0 1.0 CA A:GLN99 4.8 42.0 1.0 CB A:VAL103 4.8 52.3 1.0 CE1 A:TYR64 5.0 56.8 1.0 N2 A:U50303 5.0 38.3 1.0

K.Zhu, C.Li, K.Y.Wu, C.Mohr, X.Li, B.Lanman. Modeling Receptor Flexibility in the Structure-Based Design of Kras G12C Inhibitors. J.Comput.Aided Mol.Des. V. 36 591 2022.
ISSN: ESSN 1573-4951
PubMed: 35930206
DOI: 10.1007/S10822-022-00467-0