Magnesium in PDB 8aq7: Kras G12C in Complex with Gdp and Compound 9

The structure of Kras G12C in Complex with Gdp and Compound 9, PDB code: 8aq7 was solved by N.Ostermann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.40 / 1.65
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	43.408, 64.791, 132.621, 90, 90, 90
R / Rfree (%)	21.2 / 25.3

The binding sites of Magnesium atom in the Kras G12C in Complex with Gdp and Compound 9 (pdb code 8aq7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Kras G12C in Complex with Gdp and Compound 9, PDB code: 8aq7:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Kras G12C in Complex with Gdp and Compound 9


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Kras G12C in Complex with Gdp and Compound 9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1001 b:25.1 occ:1.00 O2B A:GDP1004 2.0 21.4 1.0 OG A:SER17 2.0 23.9 1.0 O A:HOH1155 2.1 22.1 1.0 O A:HOH1128 2.1 19.9 1.0 O A:HOH1144 2.1 22.2 1.0 O A:HOH1160 2.2 24.5 1.0 CB A:SER17 3.1 23.7 1.0 PB A:GDP1004 3.2 23.6 1.0 O3B A:GDP1004 3.5 23.8 1.0 N A:SER17 3.9 22.7 1.0 CA A:SER17 4.1 23.8 1.0 OD2 A:ASP57 4.1 29.9 1.0 OD1 A:ASP57 4.2 26.0 1.0 O2A A:GDP1004 4.2 28.0 1.0 O3A A:GDP1004 4.3 25.0 1.0 O1B A:GDP1004 4.3 22.1 1.0 O26 A:NZX1003 4.5 18.9 1.0 O A:ASP33 4.5 30.8 1.0 CB A:ALA59 4.5 22.1 1.0 PA A:GDP1004 4.5 28.1 1.0 CD2 A:TYR32 4.5 45.7 1.0 CA A:PRO34 4.6 30.2 1.0 CG A:ASP57 4.6 27.9 1.0 O1A A:GDP1004 4.6 28.8 1.0 O A:THR58 4.6 19.2 1.0 O A:ILE36 4.8 31.1 1.0 O A:TYR32 4.8 36.7 1.0 CB A:LYS16 4.9 20.0 1.0 CE A:LYS16 4.9 19.9 1.0 O A:PRO34 4.9 29.8 1.0 C A:LYS16 5.0 21.4 1.0 NZ A:LYS16 5.0 19.5 1.0

Magnesium binding site 2 out of 3 in the Kras G12C in Complex with Gdp and Compound 9


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Kras G12C in Complex with Gdp and Compound 9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1002 b:19.3 occ:1.00 O A:HOH1110 2.1 18.1 1.0 O A:HOH1264 2.1 19.6 1.0 O A:HOH1147 2.1 16.7 1.0 O A:HOH1267 2.1 20.5 1.0 O A:HOH1117 2.1 17.8 1.0 O A:HOH1129 2.2 17.8 1.0 OD2 A:ASP92 3.6 18.3 1.0 OD1 A:ASP92 4.2 17.1 1.0 O A:HOH1191 4.2 20.1 1.0 OE1 A:GLU62 4.2 18.0 1.0 O B:HOH1126 4.3 21.9 1.0 CG A:ASP92 4.3 17.6 1.0 O A:HOH1209 4.4 24.9 1.0 OE2 A:GLU62 4.4 20.2 1.0 O A:HOH1174 4.4 25.8 1.0 O B:HOH1232 4.5 20.9 1.0 CG A:LYS88 4.6 19.1 1.0 O B:HOH1235 4.6 28.6 1.0 CD A:GLU62 4.8 18.8 1.0 CG B:MET67 4.8 15.4 1.0 CB A:ALA11 4.8 16.6 1.0

Magnesium binding site 3 out of 3 in the Kras G12C in Complex with Gdp and Compound 9


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Kras G12C in Complex with Gdp and Compound 9 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1001 b:23.9 occ:1.00 O B:HOH1173 2.1 20.4 1.0 O1B B:GDP1003 2.1 19.6 1.0 OG B:SER17 2.1 21.0 1.0 O B:HOH1112 2.1 18.7 1.0 O B:HOH1133 2.2 20.6 1.0 O B:HOH1117 2.2 21.1 1.0 CB B:SER17 3.2 20.4 1.0 PB B:GDP1003 3.3 21.7 1.0 O3B B:GDP1003 3.6 22.5 1.0 N B:SER17 3.9 18.7 1.0 OD2 B:ASP57 4.1 22.3 1.0 CA B:SER17 4.1 19.7 1.0 O2A B:GDP1003 4.2 27.0 1.0 OD1 B:ASP57 4.2 22.1 1.0 O B:HOH1245 4.3 41.9 1.0 O B:HOH1148 4.3 24.9 1.0 O26 B:NZX1002 4.3 19.8 1.0 O2B B:GDP1003 4.4 20.8 1.0 O3A B:GDP1003 4.4 23.7 1.0 O B:THR58 4.5 15.8 1.0 CG B:ASP57 4.5 21.9 1.0 PA B:GDP1003 4.6 26.2 1.0 O1A B:GDP1003 4.7 26.0 1.0 O B:HOH1221 4.7 53.6 1.0 CB B:ALA59 4.8 19.1 1.0 NZ B:LYS16 4.9 18.3 1.0 CB B:LYS16 4.9 17.4 1.0 C B:LYS16 5.0 18.1 1.0

E.Lorthiois, M.Gerspacher, K.S.Beyer, A.Vaupel, C.Leblanc, R.Stringer, A.Weiss, R.Wilcken, D.A.Guthy, A.Lingel, C.Bomio-Confaglia, R.Machauer, P.Rigollier, J.Ottl, D.Arz, P.Bernet, G.Desjonqueres, S.Dussauge, M.Kazic-Legueux, M.A.Lozac'h, C.Mura, M.Sorge, M.Todorov, N.Warin, F.Zink, H.Voshol, F.J.Zecri, R.C.Sedrani, N.Ostermann, S.M.Brachmann, S.Cotesta. JDQ443, A Structurally Novel, Pyrazole-Based, Covalent Inhibitor of Kras G12C For the Treatment of Solid Tumors. J.Med.Chem. V. 65 16173 2022.
ISSN: ISSN 0022-2623
PubMed: 36399068
DOI: 10.1021/ACS.JMEDCHEM.2C01438