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Magnesium in PDB 7rt2: Crystal Structure of Kras G12D with Compound 25 (4-(4-[(1R,5S)-3,8- Diazabicyclo[3.2.1]Octan-3-Yl]-8-Fluoro-2-{[(2R,4R,7AS)-2- Fluorotetrahydro-1H-Pyrrolizin-7A(5H)-Yl]Methoxy}Pyrido[4,3- D]Pyrimidin-7-Yl)Naphthalen-2-Ol) Bound

Enzymatic activity of Crystal Structure of Kras G12D with Compound 25 (4-(4-[(1R,5S)-3,8- Diazabicyclo[3.2.1]Octan-3-Yl]-8-Fluoro-2-{[(2R,4R,7AS)-2- Fluorotetrahydro-1H-Pyrrolizin-7A(5H)-Yl]Methoxy}Pyrido[4,3- D]Pyrimidin-7-Yl)Naphthalen-2-Ol) Bound

All present enzymatic activity of Crystal Structure of Kras G12D with Compound 25 (4-(4-[(1R,5S)-3,8- Diazabicyclo[3.2.1]Octan-3-Yl]-8-Fluoro-2-{[(2R,4R,7AS)-2- Fluorotetrahydro-1H-Pyrrolizin-7A(5H)-Yl]Methoxy}Pyrido[4,3- D]Pyrimidin-7-Yl)Naphthalen-2-Ol) Bound:
3.6.5.2;

Protein crystallography data

The structure of Crystal Structure of Kras G12D with Compound 25 (4-(4-[(1R,5S)-3,8- Diazabicyclo[3.2.1]Octan-3-Yl]-8-Fluoro-2-{[(2R,4R,7AS)-2- Fluorotetrahydro-1H-Pyrrolizin-7A(5H)-Yl]Methoxy}Pyrido[4,3- D]Pyrimidin-7-Yl)Naphthalen-2-Ol) Bound, PDB code: 7rt2 was solved by R.G.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) 45.74 / 1.59
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 40.96, 52.972, 90.708, 90, 90, 90
R / Rfree (%) 15.7 / 18

Other elements in 7rt2:

The structure of Crystal Structure of Kras G12D with Compound 25 (4-(4-[(1R,5S)-3,8- Diazabicyclo[3.2.1]Octan-3-Yl]-8-Fluoro-2-{[(2R,4R,7AS)-2- Fluorotetrahydro-1H-Pyrrolizin-7A(5H)-Yl]Methoxy}Pyrido[4,3- D]Pyrimidin-7-Yl)Naphthalen-2-Ol) Bound also contains other interesting chemical elements:

Fluorine (F) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Kras G12D with Compound 25 (4-(4-[(1R,5S)-3,8- Diazabicyclo[3.2.1]Octan-3-Yl]-8-Fluoro-2-{[(2R,4R,7AS)-2- Fluorotetrahydro-1H-Pyrrolizin-7A(5H)-Yl]Methoxy}Pyrido[4,3- D]Pyrimidin-7-Yl)Naphthalen-2-Ol) Bound (pdb code 7rt2). 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 Crystal Structure of Kras G12D with Compound 25 (4-(4-[(1R,5S)-3,8- Diazabicyclo[3.2.1]Octan-3-Yl]-8-Fluoro-2-{[(2R,4R,7AS)-2- Fluorotetrahydro-1H-Pyrrolizin-7A(5H)-Yl]Methoxy}Pyrido[4,3- D]Pyrimidin-7-Yl)Naphthalen-2-Ol) Bound, PDB code: 7rt2:

Magnesium binding site 1 out of 1 in 7rt2

Go back to Magnesium Binding Sites List in 7rt2
Magnesium binding site 1 out of 1 in the Crystal Structure of Kras G12D with Compound 25 (4-(4-[(1R,5S)-3,8- Diazabicyclo[3.2.1]Octan-3-Yl]-8-Fluoro-2-{[(2R,4R,7AS)-2- Fluorotetrahydro-1H-Pyrrolizin-7A(5H)-Yl]Methoxy}Pyrido[4,3- D]Pyrimidin-7-Yl)Naphthalen-2-Ol) Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Kras G12D with Compound 25 (4-(4-[(1R,5S)-3,8- Diazabicyclo[3.2.1]Octan-3-Yl]-8-Fluoro-2-{[(2R,4R,7AS)-2- Fluorotetrahydro-1H-Pyrrolizin-7A(5H)-Yl]Methoxy}Pyrido[4,3- D]Pyrimidin-7-Yl)Naphthalen-2-Ol) Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:13.1
occ:1.00
 O3B A:GDP201 2.0 13.4 1.0
O A:HOH328 2.0 13.2 1.0
OG A:SER17 2.1 13.9 1.0
O A:HOH346 2.1 14.0 1.0
O A:HOH323 2.2 14.8 1.0
O A:HOH326 2.2 14.0 1.0
CB A:SER17 3.2 14.0 1.0
PB A:GDP201 3.3 13.5 1.0
O1B A:GDP201 3.5 14.3 1.0
N A:SER17 3.9 13.1 1.0
OD2 A:ASP57 4.1 13.9 1.0
CA A:SER17 4.1 11.9 1.0
O1A A:GDP201 4.2 15.7 1.0
OD1 A:ASP57 4.2 14.8 1.0
O A:PRO34 4.3 17.3 1.0
O A:ASP33 4.3 19.4 1.0
O3A A:GDP201 4.3 13.4 1.0
O2B A:GDP201 4.3 12.7 1.0
CD1 A:TYR32 4.3 23.5 1.0
O A:ILE36 4.5 16.3 1.0
O A:THR58 4.5 14.3 1.0
PA A:GDP201 4.5 14.5 1.0
CA A:PRO34 4.5 20.6 1.0
CG A:ASP57 4.5 13.0 1.0
O2A A:GDP201 4.6 15.1 1.0
O A:HOH331 4.7 15.9 1.0
CE1 A:TYR32 4.7 30.2 1.0
C A:PRO34 4.7 17.0 1.0
CB A:ALA59 4.8 15.0 1.0
CB A:LYS16 4.9 11.0 1.0
O A:TYR32 4.9 26.4 1.0
C A:LYS16 5.0 12.3 1.0
NZ A:LYS16 5.0 12.7 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 08:05:59 2024

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