Magnesium in PDB 7rt4: Kras G12D in Complex with Compound 5B (7-(8-Chloronaphthalen-1-Yl)-8- Fluoro-2-{[(2S)-1-Methylpyrrolidin-2-Yl]Methoxy}-4-(Piperazin-1-Yl) Pyrido[4,3-D]Pyrimidine)

Enzymatic activity of Kras G12D in Complex with Compound 5B (7-(8-Chloronaphthalen-1-Yl)-8- Fluoro-2-{[(2S)-1-Methylpyrrolidin-2-Yl]Methoxy}-4-(Piperazin-1-Yl) Pyrido[4,3-D]Pyrimidine)

All present enzymatic activity of Kras G12D in Complex with Compound 5B (7-(8-Chloronaphthalen-1-Yl)-8- Fluoro-2-{[(2S)-1-Methylpyrrolidin-2-Yl]Methoxy}-4-(Piperazin-1-Yl) Pyrido[4,3-D]Pyrimidine):
3.6.5.2;

Protein crystallography data

The structure of Kras G12D in Complex with Compound 5B (7-(8-Chloronaphthalen-1-Yl)-8- Fluoro-2-{[(2S)-1-Methylpyrrolidin-2-Yl]Methoxy}-4-(Piperazin-1-Yl) Pyrido[4,3-D]Pyrimidine), PDB code: 7rt4 was solved by R.J.Gunn, N.C.Thomas, W.Xiaolun, J.D.Lawson, M.A.Marx, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.47 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 39.842, 51.693, 88.946, 90, 90, 90
R / Rfree (%) 17.6 / 23.4

Other elements in 7rt4:

The structure of Kras G12D in Complex with Compound 5B (7-(8-Chloronaphthalen-1-Yl)-8- Fluoro-2-{[(2S)-1-Methylpyrrolidin-2-Yl]Methoxy}-4-(Piperazin-1-Yl) Pyrido[4,3-D]Pyrimidine) also contains other interesting chemical elements:

Fluorine (F) 1 atom
Chlorine (Cl) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Kras G12D in Complex with Compound 5B (7-(8-Chloronaphthalen-1-Yl)-8- Fluoro-2-{[(2S)-1-Methylpyrrolidin-2-Yl]Methoxy}-4-(Piperazin-1-Yl) Pyrido[4,3-D]Pyrimidine) (pdb code 7rt4). 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 Kras G12D in Complex with Compound 5B (7-(8-Chloronaphthalen-1-Yl)-8- Fluoro-2-{[(2S)-1-Methylpyrrolidin-2-Yl]Methoxy}-4-(Piperazin-1-Yl) Pyrido[4,3-D]Pyrimidine), PDB code: 7rt4:

Magnesium binding site 1 out of 1 in 7rt4

Go back to Magnesium Binding Sites List in 7rt4
Magnesium binding site 1 out of 1 in the Kras G12D in Complex with Compound 5B (7-(8-Chloronaphthalen-1-Yl)-8- Fluoro-2-{[(2S)-1-Methylpyrrolidin-2-Yl]Methoxy}-4-(Piperazin-1-Yl) Pyrido[4,3-D]Pyrimidine)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Kras G12D in Complex with Compound 5B (7-(8-Chloronaphthalen-1-Yl)-8- Fluoro-2-{[(2S)-1-Methylpyrrolidin-2-Yl]Methoxy}-4-(Piperazin-1-Yl) Pyrido[4,3-D]Pyrimidine) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:22.4
occ:1.00
 O A:HOH356 2.0 23.8 1.0
O A:HOH310 2.1 21.1 1.0
O A:HOH352 2.2 21.8 1.0
O3B A:GDP201 2.2 23.0 1.0
O A:HOH331 2.2 19.4 1.0
OG A:SER17 2.2 22.2 1.0
CB A:SER17 3.2 16.3 1.0
PB A:GDP201 3.4 22.2 1.0
O1B A:GDP201 3.6 25.8 1.0
OD1 A:ASP57 4.0 23.7 1.0
N A:SER17 4.0 18.9 1.0
O A:ASP33 4.1 31.5 1.0
CA A:SER17 4.1 18.5 1.0
OD2 A:ASP57 4.2 21.6 1.0
O A:PRO34 4.2 25.9 1.0
CD2 A:TYR32 4.2 26.0 1.0
O1A A:GDP201 4.2 26.8 1.0
CA A:PRO34 4.3 27.7 1.0
O3A A:GDP201 4.4 20.7 1.0
CG A:ASP57 4.5 26.4 1.0
O2B A:GDP201 4.5 20.8 1.0
CB A:ALA59 4.5 20.8 1.0
PA A:GDP201 4.5 26.6 1.0
O A:HOH354 4.5 20.0 1.0
C A:PRO34 4.5 26.6 1.0
O A:ILE36 4.5 22.0 1.0
O A:THR58 4.6 15.0 1.0
CE2 A:TYR32 4.6 33.1 1.0
O A:HOH313 4.9 30.1 1.0
O2A A:GDP201 4.9 20.6 1.0
C A:ASP33 5.0 31.7 1.0

Reference:

X.Wang, S.Allen, J.F.Blake, V.Bowcut, D.M.Briere, A.Calinisan, J.R.Dahlke, J.B.Fell, J.P.Fischer, R.J.Gunn, J.Hallin, J.Laguer, J.D.Lawson, J.Medwid, B.Newhouse, P.Nguyen, J.M.O'leary, P.Olson, S.Pajk, L.Rahbaek, M.Rodriguez, C.R.Smith, T.P.Tang, N.C.Thomas, D.Vanderpool, G.P.Vigers, J.G.Christensen, M.A.Marx. Identification of MRTX1133, A Noncovalent, Potent, and Selective Kras G12D Inhibitor. J.Med.Chem. 2021.
ISSN: ISSN 0022-2623
PubMed: 34889605
DOI: 10.1021/ACS.JMEDCHEM.1C01688
Page generated: Thu Oct 3 08:06:23 2024

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