Magnesium in PDB 9ib5: Structure of 18 (Bi-2493) in Complex with Gdp-Kras

All present enzymatic activity of Structure of 18 (Bi-2493) in Complex with Gdp-Kras:
3.6.5.2;

The structure of Structure of 18 (Bi-2493) in Complex with Gdp-Kras, PDB code: 9ib5 was solved by J.Boettcher, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	14.77 / 1.01
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	85.639, 40.784, 56.002, 90, 90, 90
R / Rfree (%)	17.2 / 19.1

The binding sites of Magnesium atom in the Structure of 18 (Bi-2493) in Complex with Gdp-Kras (pdb code 9ib5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Structure of 18 (Bi-2493) in Complex with Gdp-Kras, PDB code: 9ib5:

Magnesium binding site 1 out of 1 in the Structure of 18 (Bi-2493) in Complex with Gdp-Kras


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of 18 (Bi-2493) in Complex with Gdp-Kras within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:7.4 occ:1.00 O A:HOH333 2.0 7.8 1.0 O2B A:GDP201 2.0 7.7 1.0 O A:HOH390 2.1 8.2 1.0 OG A:SER17 2.1 7.3 1.0 O A:HOH343 2.1 8.1 1.0 O A:HOH344 2.1 8.4 1.0 HB2 A:SER17 3.2 6.7 1.0 CB A:SER17 3.2 6.8 1.0 PB A:GDP201 3.3 7.7 1.0 H A:SER17 3.3 7.1 1.0 HA A:PRO34 3.4 9.8 0.4 HA A:PRO34 3.5 9.9 0.6 O1B A:GDP201 3.5 8.8 1.0 HB3 A:SER17 3.8 6.8 1.0 HD2 A:TYR32 3.9 10.7 1.0 N A:SER17 3.9 7.2 1.0 HB2 A:LYS16 4.0 7.3 1.0 OD2 A:ASP57 4.1 9.3 1.0 CA A:SER17 4.1 7.1 1.0 O2A A:GDP201 4.1 9.0 1.0 HB2 A:ALA59 4.2 10.3 1.0 OD1 A:ASP57 4.2 9.6 1.0 O A:PRO34 4.2 9.5 0.6 HE2 A:LYS16 4.2 9.6 1.0 O A:PRO34 4.3 10.0 0.4 O3A A:GDP201 4.3 8.0 1.0 CA A:PRO34 4.3 9.8 0.4 O A:ASP33 4.4 8.9 1.0 HA A:SER17 4.4 7.2 1.0 O3B A:GDP201 4.4 7.7 1.0 CA A:PRO34 4.4 9.9 0.6 O A:ILE36 4.4 9.0 1.0 CG A:ASP57 4.5 8.9 1.0 PA A:GDP201 4.5 8.1 1.0 O A:THR58 4.6 8.6 1.0 HB3 A:TYR32 4.6 9.2 1.0 C A:PRO34 4.6 9.5 0.4 C A:PRO34 4.6 9.1 0.6 O1A A:GDP201 4.7 10.0 1.0 HB1 A:ALA59 4.8 10.3 1.0 HZ3 A:LYS16 4.8 8.1 1.0 CD2 A:TYR32 4.8 10.7 1.0 O A:TYR32 4.8 9.6 1.0 CB A:ALA59 4.9 10.3 1.0 CB A:LYS16 4.9 7.5 1.0 HB3 A:PRO34 4.9 11.3 0.4 HZ1 A:LYS16 5.0 8.1 1.0

J.Broker, A.G.Waterson, T.R.Hodges, J.R.Abbott, A.Arnold, J.Bottcher, N.Braun, J.Cui, J.E.Fuchs, T.Gerstberger, S.Gogg, S.Hanner, L.Herdeis, L.W.Howell, A.Mantoulidis, M.Mayer, J.Phan, F.Rocchetti, K.Sankar, D.Sarkar, O.Schaaf, J.L.Sensintaffar, Q.Sun, T.Wunberg, S.W.Fesik. Discovery of Bi-2493, A Pan-Kras Inhibitor Showing in Vivo Efficacy. J.Med.Chem. 2025.
ISSN: ISSN 0022-2623
PubMed: 40709733
DOI: 10.1021/ACS.JMEDCHEM.5C00576