Chlorine 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:

Magnesium (Mg) 2 atoms
Fluorine (F) 8 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 2 binding sites of Chlorine 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 Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 8un5

Go back to Chlorine Binding Sites List in 8un5
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl305

b:14.8
occ:1.00
 CL56 A:XQ6305 0.0 14.8 1.0
C13 A:XQ6305 1.7 13.9 1.0
C12 A:XQ6305 2.7 12.8 1.0
C14 A:XQ6305 2.7 13.6 1.0
H62 A:XQ6305 2.9 16.4 1.0
C6 A:XQ6305 3.0 13.1 1.0
O A:HOH474 3.4 23.8 1.0
NH1 A:ARG68 3.4 20.1 1.0
N5 A:XQ6305 3.5 13.3 1.0
F11 A:XQ6305 3.5 13.5 1.0
SD A:MET72 3.5 22.0 0.5
SD A:MET72 3.6 21.1 0.5
C7 A:XQ6305 3.7 13.6 1.0
CE A:MET72 3.8 19.1 0.5
NE A:ARG68 3.9 21.2 1.0
CZ A:ARG68 3.9 19.3 1.0
C17 A:XQ6305 4.0 12.6 1.0
C15 A:XQ6305 4.0 13.4 1.0
CG A:MET72 4.1 20.3 0.5
CG2 A:THR58 4.1 14.0 1.0
CG A:MET72 4.1 14.7 0.5
C8 A:XQ6305 4.1 14.5 1.0
O A:HOH501 4.2 25.7 1.0
CB A:THR58 4.3 12.3 1.0
C4 A:XQ6305 4.4 13.0 1.0
C16 A:XQ6305 4.5 12.3 1.0
F10 A:XQ6305 4.6 15.0 1.0
H70 A:XQ6305 4.6 19.9 1.0
C2 A:XQ6305 4.6 13.7 1.0
H29 A:XQ6305 4.7 18.7 1.0
OG1 A:THR58 4.7 10.1 1.0
O A:HOH485 4.8 12.7 1.0
H69 A:XQ6305 4.8 19.9 1.0
CE A:MET72 4.8 33.3 0.5
C3 A:XQ6305 4.9 13.1 1.0

Chlorine binding site 2 out of 2 in 8un5

Go back to Chlorine Binding Sites List in 8un5
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl203

b:15.0
occ:1.00
 CL56 B:XQ6203 0.0 15.0 1.0
C13 B:XQ6203 1.7 14.1 1.0
C14 B:XQ6203 2.7 13.6 1.0
C12 B:XQ6203 2.7 12.8 1.0
H62 B:XQ6203 2.8 16.3 1.0
C6 B:XQ6203 3.1 13.5 1.0
O B:HOH352 3.4 24.9 1.0
NH1 B:ARG68 3.4 15.9 1.0
F11 B:XQ6203 3.5 15.1 1.0
N5 B:XQ6203 3.5 13.6 1.0
SD B:MET72 3.6 21.1 1.0
C7 B:XQ6203 3.8 13.8 1.0
NE B:ARG68 3.9 18.9 1.0
CZ B:ARG68 4.0 17.3 1.0
C17 B:XQ6203 4.0 14.6 1.0
C15 B:XQ6203 4.0 13.4 1.0
CG B:MET72 4.0 16.6 1.0
O B:HOH405 4.1 26.2 1.0
CG2 B:THR58 4.2 16.0 1.0
C8 B:XQ6203 4.2 15.5 1.0
CB B:THR58 4.2 11.1 1.0
CE B:MET72 4.4 27.3 1.0
C4 B:XQ6203 4.5 13.9 1.0
C16 B:XQ6203 4.5 13.8 1.0
F10 B:XQ6203 4.6 17.4 1.0
H29 B:XQ6203 4.6 21.7 1.0
H70 B:XQ6203 4.6 23.3 1.0
O B:HOH383 4.7 14.5 1.0
OG1 B:THR58 4.7 10.1 1.0
C2 B:XQ6203 4.7 13.1 1.0
H69 B:XQ6203 4.8 23.3 1.0
C3 B:XQ6203 5.0 13.4 1.0

Reference:

C.Nilewski, M.H.Ultsch. N/A N/A.
Page generated: Tue Jul 30 13:15:56 2024

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