Calcium in PDB 6p8z: Crystal Structure of Human Kras G12C Covalently Bound to An Acryloylazetidine Acetamide Inhibitor

The structure of Crystal Structure of Human Kras G12C Covalently Bound to An Acryloylazetidine Acetamide Inhibitor, PDB code: 6p8z 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 / 1.65
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.758, 65.392, 62.596, 90.00, 105.09, 90.00
R / Rfree (%)	22.9 / 26.9

The structure of Crystal Structure of Human Kras G12C Covalently Bound to An Acryloylazetidine Acetamide Inhibitor also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Calcium atom in the Crystal Structure of Human Kras G12C Covalently Bound to An Acryloylazetidine Acetamide Inhibitor (pdb code 6p8z). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Human Kras G12C Covalently Bound to An Acryloylazetidine Acetamide Inhibitor, PDB code: 6p8z:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Human Kras G12C Covalently Bound to An Acryloylazetidine Acetamide Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Human Kras G12C Covalently Bound to An Acryloylazetidine Acetamide Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:21.1 occ:1.00 O A:HOH431 2.3 22.0 1.0 O A:HOH426 2.3 23.1 1.0 OG A:SER17 2.3 19.1 1.0 O1B A:GDP303 2.3 20.4 1.0 O A:HOH451 2.3 22.0 1.0 O A:HOH418 2.3 21.0 1.0 CB A:SER17 3.4 18.6 1.0 PB A:GDP303 3.5 20.4 1.0 O3B A:GDP303 3.7 21.6 1.0 OD2 A:ASP57 4.2 22.2 1.0 N A:SER17 4.2 18.4 1.0 O1A A:GDP303 4.3 22.4 1.0 CA A:SER17 4.4 18.2 1.0 CA A:PRO34 4.4 28.1 1.0 OD1 A:ASP57 4.5 21.9 1.0 CD2 A:TYR32 4.5 26.3 1.0 O A:ASP33 4.5 27.8 1.0 O3A A:GDP303 4.5 21.1 1.0 O2B A:GDP303 4.6 20.2 1.0 O A:ILE36 4.6 25.4 1.0 O04 A:O5S304 4.6 26.9 1.0 PA A:GDP303 4.7 22.0 1.0 CG A:ASP57 4.7 21.8 1.0 O A:PRO34 4.8 28.0 1.0 O A:THR58 4.8 23.4 1.0 O2A A:GDP303 4.8 22.5 1.0 CB A:ALA59 4.9 31.7 1.0 C A:PRO34 4.9 28.3 1.0 O A:TYR32 5.0 27.1 1.0 CE A:LYS16 5.0 19.3 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Human Kras G12C Covalently Bound to An Acryloylazetidine Acetamide Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Human Kras G12C Covalently Bound to An Acryloylazetidine Acetamide Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:39.1 occ:1.00 O A:GLY138 2.3 26.6 1.0 O A:HOH443 2.3 38.4 1.0 O A:HOH530 3.2 39.7 1.0 C A:GLY138 3.5 24.5 1.0 CA A:GLY138 4.2 25.2 1.0 N A:ILE139 4.5 23.2 1.0 OE1 A:GLU162 4.5 25.3 1.0 O A:HOH411 4.6 23.9 1.0 O A:HOH523 4.7 32.5 1.0 CA A:ILE139 4.8 22.0 1.0 CG2 A:ILE139 4.8 21.7 1.0 O A:TYR137 4.9 25.4 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Human Kras G12C Covalently Bound to An Acryloylazetidine Acetamide Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Human Kras G12C Covalently Bound to An Acryloylazetidine Acetamide Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:30.0 occ:1.00 O1B B:GDP303 2.3 28.2 1.0 O B:HOH426 2.3 29.6 1.0 O B:HOH467 2.3 32.5 1.0 O B:HOH415 2.3 30.0 1.0 OG B:SER17 2.3 29.1 1.0 O B:HOH405 2.3 31.4 1.0 CB B:SER17 3.4 28.6 1.0 PB B:GDP303 3.5 27.1 1.0 O3B B:GDP303 3.6 27.7 1.0 O2A B:GDP303 4.1 29.6 1.0 N B:SER17 4.1 27.7 1.0 OD2 B:ASP57 4.2 31.1 1.0 CA B:PRO34 4.3 41.8 1.0 CA B:SER17 4.4 28.5 1.0 OD1 B:ASP57 4.4 31.1 1.0 O3A B:GDP303 4.5 28.3 1.0 O B:ASP33 4.5 41.9 1.0 O B:PRO34 4.6 40.5 1.0 PA B:GDP303 4.6 29.4 1.0 O B:ILE36 4.6 40.5 1.0 O2B B:GDP303 4.6 27.2 1.0 CD2 B:TYR32 4.6 43.9 1.0 CG B:ASP57 4.7 31.1 1.0 O B:THR58 4.7 30.0 1.0 O1A B:GDP303 4.7 29.8 1.0 C B:PRO34 4.7 41.4 1.0 O B:HOH420 4.8 31.4 1.0 O04 B:O5S304 4.9 27.9 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Human Kras G12C Covalently Bound to An Acryloylazetidine Acetamide Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Human Kras G12C Covalently Bound to An Acryloylazetidine Acetamide Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:44.2 occ:1.00 O B:GLY138 2.3 31.8 1.0 O B:HOH473 2.3 45.2 1.0 O B:HOH489 2.3 46.2 1.0 O B:HOH498 2.3 33.2 1.0 O B:HOH404 2.8 46.5 1.0 O B:HOH453 2.9 38.9 1.0 C B:GLY138 3.5 27.6 1.0 CA B:GLY138 4.2 27.4 1.0 O B:HOH456 4.4 41.3 1.0 O B:HOH414 4.4 30.3 1.0 N B:ILE139 4.5 26.9 1.0 CG2 B:ILE139 4.5 25.9 1.0 OE1 B:GLU162 4.5 30.9 1.0 O B:HOH490 4.6 36.6 1.0 CA B:ILE139 4.7 26.1 1.0 O B:TYR137 4.7 27.5 1.0 O B:HOH458 4.9 30.0 1.0 OD1 B:ASP108 4.9 45.2 1.0

Y.Shin, J.W.Jeong, R.P.Wurz, P.Achanta, T.Arvedson, M.D.Bartberger, I.D.G.Campuzano, R.Fucini, S.K.Hansen, J.Ingersoll, J.S.Iwig, J.R.Lipford, V.Ma, D.J.Kopecky, J.Mccarter, T.San Miguel, C.Mohr, S.Sabet, A.Y.Saiki, A.Sawayama, S.Sethofer, C.M.Tegley, L.P.Volak, K.Yang, B.A.Lanman, D.A.Erlanson, V.J.Cee. Discovery Ofn-(1-Acryloylazetidin-3-Yl)-2-(1H-Indol-1-Yl) Acetamides As Covalent Inhibitors of KRASG12C. Acs Med.Chem.Lett. V. 10 1302 2019.
ISSN: ISSN 1948-5875
PubMed: 31531201
DOI: 10.1021/ACSMEDCHEMLETT.9B00258