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Magnesium in PDB 8un5: Kras-G13D-Gdp in Complex with CPD38 ((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-(1,2,3,4-Tetrahydroisoquinolin-8-Yl)Prop-2- En-1-One)

Enzymatic activity of Kras-G13D-Gdp in Complex with CPD38 ((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-(1,2,3,4-Tetrahydroisoquinolin-8-Yl)Prop-2- En-1-One)

All present enzymatic activity of Kras-G13D-Gdp in Complex with CPD38 ((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-(1,2,3,4-Tetrahydroisoquinolin-8-Yl)Prop-2- En-1-One):
3.6.5.2;

Protein crystallography data

The structure of Kras-G13D-Gdp in Complex with CPD38 ((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-(1,2,3,4-Tetrahydroisoquinolin-8-Yl)Prop-2- En-1-One), PDB code: 8un5 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) 31.19 / 1.31
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 38.96, 41.62, 55.55, 90.17, 91.35, 116.28
R / Rfree (%) 17.8 / 21.2

Other elements in 8un5:

The structure of Kras-G13D-Gdp in Complex with CPD38 ((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-(1,2,3,4-Tetrahydroisoquinolin-8-Yl)Prop-2- En-1-One) also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Fluorine (F) 8 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Kras-G13D-Gdp in Complex with CPD38 ((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-(1,2,3,4-Tetrahydroisoquinolin-8-Yl)Prop-2- En-1-One) (pdb code 8un5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Kras-G13D-Gdp in Complex with CPD38 ((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-(1,2,3,4-Tetrahydroisoquinolin-8-Yl)Prop-2- En-1-One), PDB code: 8un5:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 8un5

Go back to Magnesium Binding Sites List in 8un5
Magnesium binding site 1 out of 2 in the Kras-G13D-Gdp in Complex with CPD38 ((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-(1,2,3,4-Tetrahydroisoquinolin-8-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 CPD38 ((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-(1,2,3,4-Tetrahydroisoquinolin-8-Yl)Prop-2- En-1-One) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg304

b:11.3
occ:1.00
 O1B A:GDP303 2.0 9.9 1.0
O A:HOH419 2.1 12.4 1.0
O A:HOH422 2.1 11.8 1.0
O A:HOH461 2.2 13.9 1.0
OG A:SER17 2.2 10.3 1.0
O A:HOH435 2.2 12.9 1.0
CB A:SER17 3.2 10.3 1.0
PB A:GDP303 3.3 10.7 1.0
O3B A:GDP303 3.6 11.3 1.0
N A:SER17 3.9 12.5 1.0
O2A A:GDP303 4.0 11.9 1.0
CA A:SER17 4.1 9.9 1.0
OD2 A:ASP57 4.1 13.4 1.0
CA A:PRO34 4.1 13.3 1.0
OD1 A:ASP57 4.3 13.1 1.0
O2B A:GDP303 4.3 10.2 1.0
O A:ASP33 4.3 12.9 1.0
CB A:ALA59 4.4 14.0 1.0
O3A A:GDP303 4.4 11.5 1.0
O A:PRO34 4.4 14.7 1.0
O A:THR58 4.5 11.8 1.0
PA A:GDP303 4.6 11.0 1.0
C A:PRO34 4.6 15.6 1.0
CG A:ASP57 4.6 12.0 1.0
O1A A:GDP303 4.7 11.7 1.0
O A:ILE36 4.7 14.1 1.0
O A:TYR32 4.8 14.0 1.0
CE A:LYS16 4.9 10.4 1.0
CD2 A:TYR32 4.9 14.7 1.0
CB A:LYS16 4.9 10.2 1.0
CB A:PRO34 4.9 13.7 1.0
C A:LYS16 5.0 10.3 1.0

Magnesium binding site 2 out of 2 in 8un5

Go back to Magnesium Binding Sites List in 8un5
Magnesium binding site 2 out of 2 in the Kras-G13D-Gdp in Complex with CPD38 ((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-(1,2,3,4-Tetrahydroisoquinolin-8-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 2 of Kras-G13D-Gdp in Complex with CPD38 ((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-(1,2,3,4-Tetrahydroisoquinolin-8-Yl)Prop-2- En-1-One) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg202

b:12.8
occ:1.00
 O B:HOH323 2.1 9.1 1.0
O2B B:GDP201 2.1 10.6 1.0
OG B:SER17 2.1 11.4 1.0
O B:HOH326 2.1 10.2 1.0
O B:HOH354 2.2 15.9 1.0
O B:HOH336 2.2 12.6 1.0
CB B:SER17 3.1 9.4 1.0
PB B:GDP201 3.4 11.5 1.0
O3B B:GDP201 3.7 10.5 1.0
N B:SER17 3.9 8.2 1.0
O1A B:GDP201 4.1 10.4 1.0
CA B:SER17 4.1 8.1 1.0
OD2 B:ASP57 4.1 12.7 1.0
CA B:PRO34 4.1 12.9 1.0
OD1 B:ASP57 4.2 14.1 1.0
O B:ASP33 4.3 12.4 1.0
CB B:ALA59 4.4 13.0 1.0
O1B B:GDP201 4.4 10.3 1.0
O3A B:GDP201 4.4 9.9 1.0
O B:PRO34 4.5 11.3 1.0
PA B:GDP201 4.6 10.6 1.0
CG B:ASP57 4.6 12.7 1.0
O2A B:GDP201 4.6 11.1 1.0
C B:PRO34 4.6 14.0 1.0
O B:THR58 4.6 11.1 1.0
O B:ILE36 4.7 13.1 1.0
CD2 B:TYR32 4.8 14.2 1.0
O B:TYR32 4.9 12.5 1.0
CB B:LYS16 4.9 11.1 1.0
CB B:PRO34 4.9 10.6 1.0
CE B:LYS16 4.9 8.8 1.0
C B:LYS16 5.0 7.7 1.0

Reference:

C.Nilewski, M.H.Ultsch. N/A N/A.
Page generated: Thu Dec 28 10:36:13 2023

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