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Chlorine 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:

Magnesium (Mg) 1 atom
Fluorine (F) 4 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total only one binding site of Chlorine 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:

Chlorine binding site 1 out of 1 in 8un4

Go back to Chlorine Binding Sites List in 8un4
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl203

b:21.4
occ:1.00
 CL A:XV3203 0.0 21.4 1.0
C8 A:XV3203 1.7 20.4 1.0
C9 A:XV3203 2.7 19.6 1.0
C7 A:XV3203 2.7 21.4 1.0
H5 A:XV3203 2.8 23.7 1.0
C4 A:XV3203 3.0 21.1 1.0
NH2 A:ARG68 3.4 24.2 1.0
O A:HOH390 3.4 31.0 1.0
N A:XV3203 3.5 22.6 1.0
O A:HOH350 3.5 29.3 1.0
F1 A:XV3203 3.5 21.7 1.0
CE A:MET72 3.6 21.5 1.0
C5 A:XV3203 3.7 21.3 1.0
SD A:MET72 3.8 26.4 1.0
CZ A:ARG68 4.0 26.7 1.0
C12 A:XV3203 4.0 23.5 1.0
NE A:ARG68 4.0 26.5 1.0
C10 A:XV3203 4.0 22.8 1.0
C6 A:XV3203 4.1 22.9 1.0
CB A:THR58 4.2 17.9 1.0
H14 A:XV3203 4.2 41.6 1.0
CG2 A:THR58 4.2 18.0 1.0
CG A:MET72 4.3 25.2 1.0
O A:HOH316 4.4 43.0 1.0
H A:XV3203 4.4 28.6 1.0
C3 A:XV3203 4.5 26.6 1.0
C11 A:XV3203 4.5 22.8 1.0
F2 A:XV3203 4.6 21.1 1.0
OG1 A:THR58 4.7 18.1 1.0
C1 A:XV3203 4.7 20.3 1.0
O A:HOH382 5.0 20.9 1.0
C19 A:XV3203 5.0 34.5 1.0
OE1 A:GLU37 5.0 18.3 1.0

Reference:

M.H.Ultsch, C.Nilewski. Structure-Based Design and Evaluation of Reversible Kras G13D Inhibitors To Be Published.
Page generated: Sun Jul 13 14:57:11 2025

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