Magnesium in PDB 7r0m: KRASG12C in Complex with Gdp and JDQ443

The structure of KRASG12C in Complex with Gdp and JDQ443, PDB code: 7r0m was solved by N.Ostermann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	60.41 / 1.61
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	33.652, 39.496, 62.362, 77.24, 80.85, 77.15
R / Rfree (%)	19.3 / 24.9

The structure of KRASG12C in Complex with Gdp and JDQ443 also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Magnesium atom in the KRASG12C in Complex with Gdp and JDQ443 (pdb code 7r0m). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the KRASG12C in Complex with Gdp and JDQ443, PDB code: 7r0m:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the KRASG12C in Complex with Gdp and JDQ443


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of KRASG12C in Complex with Gdp and JDQ443 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1001 b:7.1 occ:1.00 O A:HOH1146 2.1 4.8 1.0 O A:HOH1136 2.2 11.7 1.0 O2B A:GDP1004 2.3 12.5 1.0 OG A:SER17 2.3 13.9 1.0 O A:HOH1108 2.3 16.9 1.0 O A:HOH1173 2.5 7.4 1.0 CB A:SER17 3.3 11.2 1.0 PB A:GDP1004 3.5 12.5 1.0 O3B A:GDP1004 3.8 12.3 1.0 N A:SER17 4.1 8.5 1.0 OD2 A:ASP57 4.1 17.1 1.0 CB A:ALA59 4.1 14.0 1.0 O1A A:GDP1004 4.3 13.9 1.0 CA A:SER17 4.3 9.7 1.0 O A:ASP33 4.4 16.1 1.0 CA A:PRO34 4.4 15.6 1.0 OD1 A:ASP57 4.5 19.3 1.0 CD2 A:TYR32 4.5 18.4 1.0 O A:THR58 4.5 13.5 1.0 O A:ILE36 4.6 15.2 1.0 O3A A:GDP1004 4.7 13.2 1.0 CG A:ASP57 4.7 17.8 1.0 O1B A:GDP1004 4.7 12.9 1.0 O36 A:H2T1003 4.8 16.6 1.0 PA A:GDP1004 4.8 13.7 1.0 O A:PRO34 5.0 16.2 1.0

Magnesium binding site 2 out of 4 in the KRASG12C in Complex with Gdp and JDQ443


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of KRASG12C in Complex with Gdp and JDQ443 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1002 b:3.9 occ:1.00 OE1 A:GLU63 2.2 25.2 1.0 OE2 A:GLU63 2.5 18.7 1.0 CD A:GLU63 2.6 22.0 1.0 CG A:GLU63 4.1 20.1 1.0 O A:HOH1205 4.7 21.6 1.0 NE2 A:GLN61 4.8 26.9 1.0 O A:HOH1210 4.9 20.4 1.0 CG A:GLN61 5.0 23.4 1.0

Magnesium binding site 3 out of 4 in the KRASG12C in Complex with Gdp and JDQ443


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of KRASG12C in Complex with Gdp and JDQ443 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1001 b:10.4 occ:1.00 O1B B:GDP1004 2.2 15.0 1.0 O B:HOH1124 2.3 20.3 1.0 O B:HOH1148 2.3 17.0 1.0 O B:HOH1130 2.4 18.7 1.0 OG B:SER17 2.4 15.5 1.0 O B:HOH1121 2.5 15.1 1.0 CB B:SER17 3.4 13.0 1.0 PB B:GDP1004 3.4 15.1 1.0 O3B B:GDP1004 3.7 16.0 1.0 N B:SER17 4.1 11.2 1.0 OD2 B:ASP57 4.2 23.2 1.0 CA B:SER17 4.3 11.4 1.0 CD2 B:TYR32 4.3 30.4 1.0 O2A B:GDP1004 4.3 16.3 1.0 O B:ASP33 4.3 25.7 1.0 CB B:ALA59 4.3 14.6 1.0 O B:PRO34 4.4 29.5 1.0 OD1 B:ASP57 4.5 20.2 1.0 CA B:PRO34 4.5 28.1 1.0 O3A B:GDP1004 4.5 16.0 1.0 O2B B:GDP1004 4.6 14.6 1.0 O B:ILE36 4.6 29.3 1.0 CE2 B:TYR32 4.7 31.7 1.0 PA B:GDP1004 4.7 16.8 1.0 CG B:ASP57 4.7 20.1 1.0 O B:THR58 4.7 15.7 1.0 C B:PRO34 4.8 29.5 1.0 O36 B:H2T1003 4.8 19.2 1.0 O B:HOH1133 4.8 20.9 1.0 CB B:LYS16 4.8 10.7 1.0 CE B:LYS16 4.8 13.2 1.0 O1A B:GDP1004 4.8 16.1 1.0

Magnesium binding site 4 out of 4 in the KRASG12C in Complex with Gdp and JDQ443


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of KRASG12C in Complex with Gdp and JDQ443 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1002 b:8.1 occ:1.00 OE2 B:GLU63 2.5 23.6 1.0 OE1 B:GLU63 2.6 28.1 1.0 CD B:GLU63 2.9 24.9 1.0 CG B:GLU63 4.4 20.0 1.0 OE1 B:GLN61 4.7 23.1 1.0 CG B:GLN61 5.0 16.2 1.0

A.Weiss, E.Lorthiois, L.Barys, K.S.Beyer, C.Bomio-Confaglia, H.Burks, X.Chen, X.Cui, R.De Kanter, L.Dharmarajan, C.Fedele, M.Gerspacher, D.A.Guthy, V.Head, A.Jaeger, E.J.Nunez, J.D.Kearns, C.Leblanc, S.M.Maira, J.Murphy, H.Oakman, N.Ostermann, J.Ottl, P.Rigollier, D.Roman, C.Schnell, R.Sedrani, T.Shimizu, R.Stringer, A.Vaupel, H.Voshol, P.Wessels, T.Widmer, R.Wilcken, K.Xu, F.Zecri, A.F.Farago, S.Cotesta, S.M.Brachmann. Discovery, Preclinical Characterization, and Early Clinical Activity of JDQ443, A Structurally Novel, Potent, and Selective Covalent Oral Inhibitor of KRASG12C. Cancer Discov V. 12 1500 2022.
ISSN: ESSN 2159-8290
PubMed: 35404998
DOI: 10.1158/2159-8290.CD-22-0158