Calcium in PDB 6pgp: Crystal Structure of Human Kras G12C Covalently Bound to A Quinazolinone Inhibitor

The structure of Crystal Structure of Human Kras G12C Covalently Bound to A Quinazolinone Inhibitor, PDB code: 6pgp was solved by C.Mohr, D.A.Whittington, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.00 / 1.50
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	33.420, 39.606, 62.451, 76.91, 81.38, 77.30
R / Rfree (%)	19 / 21.6

The structure of Crystal Structure of Human Kras G12C Covalently Bound to A Quinazolinone Inhibitor also contains other interesting chemical elements:

Fluorine	(F)	2 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Calcium atom in the Crystal Structure of Human Kras G12C Covalently Bound to A Quinazolinone Inhibitor (pdb code 6pgp). 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 A Quinazolinone Inhibitor, PDB code: 6pgp:
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 A Quinazolinone 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 A Quinazolinone Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:10.7 occ:1.00 O A:HOH642 2.3 15.7 1.0 O2B A:GDP501 2.3 10.0 1.0 OG A:SER17 2.3 10.4 1.0 O A:HOH608 2.3 13.2 1.0 O A:HOH641 2.4 12.7 1.0 O A:HOH615 2.4 10.9 1.0 CB A:SER17 3.4 9.8 1.0 PB A:GDP501 3.5 10.0 1.0 O1B A:GDP501 3.6 10.8 1.0 N A:SER17 4.1 9.5 1.0 OD2 A:ASP57 4.3 17.8 1.0 O1A A:GDP501 4.3 12.0 1.0 CA A:SER17 4.3 9.6 1.0 OD1 A:ASP57 4.4 17.1 1.0 CA A:PRO34 4.5 20.1 1.0 O A:ASP33 4.5 19.7 1.0 O3B A:GDP501 4.5 10.2 1.0 O3A A:GDP501 4.5 10.8 1.0 O A:THR58 4.6 15.2 1.0 O A:ILE36 4.6 19.2 1.0 CD2 A:TYR32 4.6 19.1 1.0 PA A:GDP501 4.7 11.2 1.0 CG A:ASP57 4.7 16.9 1.0 O A:PRO34 4.8 21.4 1.0 O3 A:OHY504 4.9 18.0 1.0 O2A A:GDP501 4.9 11.1 1.0 C A:PRO34 4.9 20.3 1.0 CB A:LYS16 4.9 9.6 1.0 CB A:ALA59 5.0 17.8 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Human Kras G12C Covalently Bound to A Quinazolinone 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 A Quinazolinone Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:15.3 occ:1.00 OE2 A:GLU63 2.3 16.4 1.0 OE1 A:GLU63 2.3 16.1 1.0 CD A:GLU63 2.7 16.0 1.0 CG A:GLU63 4.2 16.7 1.0 OE1 A:GLN61 4.6 16.9 1.0 O A:HOH678 4.9 24.9 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Human Kras G12C Covalently Bound to A Quinazolinone 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 A Quinazolinone Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca502 b:12.2 occ:1.00 O B:HOH620 2.2 17.1 1.0 O B:HOH648 2.3 14.8 1.0 O1B B:GDP501 2.3 11.9 1.0 OG B:SER17 2.3 11.8 1.0 O B:HOH617 2.3 12.8 1.0 O B:HOH610 2.4 12.9 1.0 CB B:SER17 3.4 11.0 1.0 PB B:GDP501 3.4 11.6 1.0 O3B B:GDP501 3.6 12.2 1.0 N B:SER17 4.1 10.7 1.0 OD2 B:ASP57 4.2 18.0 1.0 O2A B:GDP501 4.3 13.8 1.0 CA B:SER17 4.3 10.9 1.0 CA B:PRO34 4.4 22.5 1.0 O B:ASP33 4.5 20.4 1.0 OD1 B:ASP57 4.5 17.5 1.0 O3A B:GDP501 4.5 12.4 1.0 O2B B:GDP501 4.5 11.4 1.0 O B:THR58 4.6 16.0 1.0 O B:PRO34 4.7 24.4 1.0 O B:ILE36 4.7 22.9 1.0 CD2 B:TYR32 4.7 22.9 1.0 O3 B:OHY504 4.7 18.8 1.0 PA B:GDP501 4.7 13.2 1.0 CG B:ASP57 4.8 17.1 1.0 C B:PRO34 4.8 22.9 1.0 CE B:LYS16 4.9 10.6 1.0 O1A B:GDP501 4.9 13.3 1.0 O B:HOH622 5.0 19.4 1.0 CB B:LYS16 5.0 10.5 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Human Kras G12C Covalently Bound to A Quinazolinone 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 A Quinazolinone Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca503 b:17.4 occ:1.00 OE2 B:GLU63 2.3 19.1 1.0 OE1 B:GLU63 2.3 19.1 1.0 CD B:GLU63 2.7 18.6 1.0 O B:HOH634 4.1 42.3 1.0 CG B:GLU63 4.2 18.5 1.0 OE1 B:GLN61 4.6 17.0 1.0 O B:HOH665 4.9 20.0 1.0

B.A.Lanman, J.R.Allen, J.G.Allen, A.K.Amegadzie, K.S.Ashton, S.K.Booker, J.J.Chen, N.Chen, M.J.Frohn, G.Goodman, D.J.Kopecky, L.Liu, P.Lopez, J.D.Low, V.Ma, A.E.Minatti, T.T.Nguyen, N.Nishimura, A.J.Pickrell, A.B.Reed, Y.Shin, A.Siegmund, N.A.Tamayo, C.M.Tegley, M.C.Walton, H.L.Wang, R.P.Wurz, M.Xue, K.C.Yang, P.Achanta, M.D.Bartberger, J.Canon, L.S.Hollis, J.D.Mccarter, C.Mohr, K.Rex, A.Y.Saiki, T.San Miguel, L.Volak, K.H.Wang, D.A.Whittington, S.G.Zech, J.R.Lipford, V.J.Cee. Discovery of A Covalent Inhibitor of KRASG12C (Amg 510) For the Treatment of Solid Tumors. J.Med.Chem. 2019.
ISSN: ISSN 0022-2623
PubMed: 31820981
DOI: 10.1021/ACS.JMEDCHEM.9B01180