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Magnesium in PDB 8un4: Kras-G13D-Gdp in Complex with CPD36 ((E)-1-((3S)-4-(7-(6-Amino-4- Methyl-3-(Trifluoromethyl)Pyridin-2-Yl)-6-Chloro-8-Fluoro-2-(((S)-2- Methylenetetrahydro-1H-Pyrrolizin-7A(5H)-Yl)Methoxy)Quinazolin-4-Yl)- 3-Methylpiperazin-1-Yl)-3-(4-((Dimethylamino)Methyl)-5-Methylpyridin- 2-Yl)Prop-2-En-1-One)

Enzymatic activity of Kras-G13D-Gdp in Complex with CPD36 ((E)-1-((3S)-4-(7-(6-Amino-4- Methyl-3-(Trifluoromethyl)Pyridin-2-Yl)-6-Chloro-8-Fluoro-2-(((S)-2- Methylenetetrahydro-1H-Pyrrolizin-7A(5H)-Yl)Methoxy)Quinazolin-4-Yl)- 3-Methylpiperazin-1-Yl)-3-(4-((Dimethylamino)Methyl)-5-Methylpyridin- 2-Yl)Prop-2-En-1-One)

All present enzymatic activity of Kras-G13D-Gdp in Complex with CPD36 ((E)-1-((3S)-4-(7-(6-Amino-4- Methyl-3-(Trifluoromethyl)Pyridin-2-Yl)-6-Chloro-8-Fluoro-2-(((S)-2- Methylenetetrahydro-1H-Pyrrolizin-7A(5H)-Yl)Methoxy)Quinazolin-4-Yl)- 3-Methylpiperazin-1-Yl)-3-(4-((Dimethylamino)Methyl)-5-Methylpyridin- 2-Yl)Prop-2-En-1-One):
3.6.5.2;

Protein crystallography data

The structure of Kras-G13D-Gdp in Complex with CPD36 ((E)-1-((3S)-4-(7-(6-Amino-4- Methyl-3-(Trifluoromethyl)Pyridin-2-Yl)-6-Chloro-8-Fluoro-2-(((S)-2- Methylenetetrahydro-1H-Pyrrolizin-7A(5H)-Yl)Methoxy)Quinazolin-4-Yl)- 3-Methylpiperazin-1-Yl)-3-(4-((Dimethylamino)Methyl)-5-Methylpyridin- 2-Yl)Prop-2-En-1-One), PDB code: 8un4 was solved by M.H.Ultsch, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.74 / 1.57
Space group P 21 2 21
Cell size a, b, c (Å), α, β, γ (°) 40.73, 55.69, 85.49, 90, 90, 90
R / Rfree (%) 19 / 21.5

Other elements in 8un4:

The structure of Kras-G13D-Gdp in Complex with CPD36 ((E)-1-((3S)-4-(7-(6-Amino-4- Methyl-3-(Trifluoromethyl)Pyridin-2-Yl)-6-Chloro-8-Fluoro-2-(((S)-2- Methylenetetrahydro-1H-Pyrrolizin-7A(5H)-Yl)Methoxy)Quinazolin-4-Yl)- 3-Methylpiperazin-1-Yl)-3-(4-((Dimethylamino)Methyl)-5-Methylpyridin- 2-Yl)Prop-2-En-1-One) also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Fluorine (F) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Kras-G13D-Gdp in Complex with CPD36 ((E)-1-((3S)-4-(7-(6-Amino-4- Methyl-3-(Trifluoromethyl)Pyridin-2-Yl)-6-Chloro-8-Fluoro-2-(((S)-2- Methylenetetrahydro-1H-Pyrrolizin-7A(5H)-Yl)Methoxy)Quinazolin-4-Yl)- 3-Methylpiperazin-1-Yl)-3-(4-((Dimethylamino)Methyl)-5-Methylpyridin- 2-Yl)Prop-2-En-1-One) (pdb code 8un4). 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-G13D-Gdp in Complex with CPD36 ((E)-1-((3S)-4-(7-(6-Amino-4- Methyl-3-(Trifluoromethyl)Pyridin-2-Yl)-6-Chloro-8-Fluoro-2-(((S)-2- Methylenetetrahydro-1H-Pyrrolizin-7A(5H)-Yl)Methoxy)Quinazolin-4-Yl)- 3-Methylpiperazin-1-Yl)-3-(4-((Dimethylamino)Methyl)-5-Methylpyridin- 2-Yl)Prop-2-En-1-One), PDB code: 8un4:

Magnesium binding site 1 out of 1 in 8un4

Go back to Magnesium Binding Sites List in 8un4
Magnesium binding site 1 out of 1 in the Kras-G13D-Gdp in Complex with CPD36 ((E)-1-((3S)-4-(7-(6-Amino-4- Methyl-3-(Trifluoromethyl)Pyridin-2-Yl)-6-Chloro-8-Fluoro-2-(((S)-2- Methylenetetrahydro-1H-Pyrrolizin-7A(5H)-Yl)Methoxy)Quinazolin-4-Yl)- 3-Methylpiperazin-1-Yl)-3-(4-((Dimethylamino)Methyl)-5-Methylpyridin- 2-Yl)Prop-2-En-1-One)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Kras-G13D-Gdp in Complex with CPD36 ((E)-1-((3S)-4-(7-(6-Amino-4- Methyl-3-(Trifluoromethyl)Pyridin-2-Yl)-6-Chloro-8-Fluoro-2-(((S)-2- Methylenetetrahydro-1H-Pyrrolizin-7A(5H)-Yl)Methoxy)Quinazolin-4-Yl)- 3-Methylpiperazin-1-Yl)-3-(4-((Dimethylamino)Methyl)-5-Methylpyridin- 2-Yl)Prop-2-En-1-One) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg201

b:19.8
occ:1.00
 OG A:SER17 2.0 15.4 1.0
O1B A:GDP202 2.0 15.1 1.0
O A:HOH311 2.1 14.7 1.0
O A:HOH365 2.2 15.5 1.0
O A:HOH306 2.2 18.6 1.0
O A:HOH320 2.2 17.2 1.0
CB A:SER17 3.1 17.6 1.0
PB A:GDP202 3.3 17.9 1.0
O3B A:GDP202 3.5 18.6 1.0
N A:SER17 3.8 15.2 1.0
O2A A:GDP202 3.9 19.3 1.0
OD2 A:ASP57 4.0 18.7 1.0
CA A:SER17 4.0 16.3 1.0
OD1 A:ASP57 4.1 19.7 1.0
O2B A:GDP202 4.3 17.1 1.0
CA A:PRO34 4.3 23.6 1.0
O3A A:GDP202 4.4 20.1 1.0
O A:ASP33 4.4 17.3 1.0
CG A:ASP57 4.5 16.5 1.0
PA A:GDP202 4.5 20.0 1.0
O A:PRO34 4.5 24.4 1.0
O1A A:GDP202 4.6 20.1 1.0
O A:THR58 4.6 18.0 1.0
CD2 A:TYR32 4.6 24.6 1.0
O A:ILE36 4.6 19.0 1.0
C A:PRO34 4.8 20.3 1.0
O A:TYR32 4.8 17.1 1.0
CB A:LYS16 4.8 14.2 1.0
O A:HOH340 4.8 22.7 1.0
O A:XV3203 4.9 21.2 1.0
C A:LYS16 4.9 16.3 1.0
CE A:LYS16 5.0 18.8 1.0
NZ A:LYS16 5.0 17.5 1.0

Reference:

M.H.Ultsch, C.Nilewski. Structure-Based Design and Evaluation of Reversible Kras G13D Inhibitors To Be Published.
Page generated: Fri Aug 15 17:01:03 2025

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