Fluorine in PDB 8txe: Crystal Structure of Kras G12D in Complex with Gdp and Compound 5

Enzymatic activity of Crystal Structure of Kras G12D in Complex with Gdp and Compound 5

All present enzymatic activity of Crystal Structure of Kras G12D in Complex with Gdp and Compound 5:
3.6.5.2;

Protein crystallography data

The structure of Crystal Structure of Kras G12D in Complex with Gdp and Compound 5, PDB code: 8txe was solved by P.Chen, A.Irimia, Z.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.77 / 1.35
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 37.815, 62.166, 71.925, 90, 91.86, 90
R / Rfree (%) 18.8 / 21.5

Other elements in 8txe:

The structure of Crystal Structure of Kras G12D in Complex with Gdp and Compound 5 also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Magnesium (Mg) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Kras G12D in Complex with Gdp and Compound 5 (pdb code 8txe). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 10 binding sites of Fluorine where determined in the Crystal Structure of Kras G12D in Complex with Gdp and Compound 5, PDB code: 8txe:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 10 in 8txe

Go back to Fluorine Binding Sites List in 8txe
Fluorine binding site 1 out of 10 in the Crystal Structure of Kras G12D in Complex with Gdp and Compound 5


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Kras G12D in Complex with Gdp and Compound 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F203

b:10.9
occ:1.00
 F22 A:VM9203 0.0 10.9 1.0
C21 A:VM9203 1.3 9.8 1.0
C20 A:VM9203 2.3 9.7 1.0
C12 A:VM9203 2.4 9.8 1.0
N19 A:VM9203 2.7 9.6 1.0
C6 A:VM9203 2.7 9.7 1.0
NE2 A:HIS95 3.2 10.0 1.0
C7 A:VM9203 3.2 9.7 1.0
F11 A:VM9203 3.3 11.3 1.0
OH A:TYR64 3.4 18.2 1.0
N5 A:VM9203 3.4 10.2 1.0
F10 A:VM9203 3.5 9.9 1.0
C8 A:VM9203 3.5 10.3 1.0
C13 A:VM9203 3.6 11.0 1.0
C15 A:VM9203 3.6 9.7 1.0
CG A:GLN99 3.8 10.2 1.0
CE1 A:HIS95 3.8 10.7 1.0
O A:HOH350 3.9 37.6 1.0
CE1 A:TYR64 3.9 16.9 1.0
CB A:GLN99 3.9 9.2 1.0
C18 A:VM9203 4.0 9.7 1.0
C14 A:VM9203 4.1 10.5 1.0
CZ A:TYR64 4.1 16.7 1.0
CD2 A:HIS95 4.1 9.7 1.0
CE1 A:TYR96 4.2 9.8 1.0
CD1 A:TYR96 4.2 8.9 1.0
C2 A:VM9203 4.2 10.6 1.0
C4 A:VM9203 4.4 11.5 1.0
C16 A:VM9203 4.7 9.8 1.0
C3 A:VM9203 4.7 11.3 1.0
O23 A:VM9203 4.8 9.7 1.0
F9 A:VM9203 4.8 10.4 1.0
N17 A:VM9203 4.9 9.7 1.0
ND1 A:HIS95 4.9 11.0 1.0
CD A:GLN99 4.9 12.0 1.0

Fluorine binding site 2 out of 10 in 8txe

Go back to Fluorine Binding Sites List in 8txe
Fluorine binding site 2 out of 10 in the Crystal Structure of Kras G12D in Complex with Gdp and Compound 5


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Kras G12D in Complex with Gdp and Compound 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F203

b:14.8
occ:1.00
 F32 A:VM9203 0.0 14.8 1.0
C31 A:VM9203 1.4 12.8 1.0
C33 A:VM9203 2.3 11.6 1.0
C30 A:VM9203 2.3 12.1 1.0
N29 A:VM9203 2.9 11.4 1.0
C25 A:VM9203 3.0 11.3 1.0
C28 A:VM9203 3.2 12.4 1.0
C26 A:VM9203 3.3 12.8 1.0
O A:HOH387 3.5 25.9 1.0
O A:HOH309 3.8 27.1 1.0
C27 A:VM9203 3.9 13.4 1.0
OD1 A:ASP92 4.0 16.8 1.0
C24 A:VM9203 4.4 10.6 1.0
NZ A:LYS88 4.5 28.3 1.0
CG A:ASP92 4.7 15.7 1.0
O23 A:VM9203 4.8 9.7 1.0
CG A:HIS95 4.8 9.7 1.0
CB A:HIS95 4.9 8.5 1.0

Fluorine binding site 3 out of 10 in 8txe

Go back to Fluorine Binding Sites List in 8txe
Fluorine binding site 3 out of 10 in the Crystal Structure of Kras G12D in Complex with Gdp and Compound 5


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Kras G12D in Complex with Gdp and Compound 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F203

b:10.4
occ:1.00
 F9 A:VM9203 0.0 10.4 1.0
C8 A:VM9203 1.4 10.3 1.0
F10 A:VM9203 2.1 9.9 1.0
F11 A:VM9203 2.2 11.3 1.0
C7 A:VM9203 2.3 9.7 1.0
C1 A:VM9203 2.8 11.1 1.0
C2 A:VM9203 2.9 10.6 1.0
CE A:MET72 3.3 20.3 1.0
C6 A:VM9203 3.5 9.7 1.0
CG1 A:ILE100 3.5 8.1 1.0
CG1 A:VAL9 3.7 9.3 1.0
CE2 A:PHE78 4.0 10.2 1.0
C12 A:VM9203 4.2 9.8 1.0
C3 A:VM9203 4.2 11.3 1.0
CD1 A:ILE100 4.2 8.9 1.0
CD2 A:PHE78 4.3 8.5 1.0
CB A:VAL9 4.5 7.9 1.0
N5 A:VM9203 4.6 10.2 1.0
CB A:MET72 4.7 12.5 1.0
CG A:MET72 4.7 14.0 1.0
CL42 A:VM9203 4.7 12.6 1.0
CG2 A:VAL9 4.8 8.2 1.0
SD A:MET72 4.8 21.0 1.0
C13 A:VM9203 4.8 11.0 1.0
F22 A:VM9203 4.8 10.9 1.0
CB A:ILE100 4.9 7.9 1.0
C21 A:VM9203 4.9 9.8 1.0
C4 A:VM9203 4.9 11.5 1.0
N A:ILE100 4.9 8.6 1.0
CA A:ILE100 5.0 8.3 1.0
O A:TYR96 5.0 9.6 1.0

Fluorine binding site 4 out of 10 in 8txe

Go back to Fluorine Binding Sites List in 8txe
Fluorine binding site 4 out of 10 in the Crystal Structure of Kras G12D in Complex with Gdp and Compound 5


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Kras G12D in Complex with Gdp and Compound 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F203

b:9.9
occ:1.00
 F10 A:VM9203 0.0 9.9 1.0
C8 A:VM9203 1.4 10.3 1.0
F9 A:VM9203 2.1 10.4 1.0
F11 A:VM9203 2.2 11.3 1.0
C7 A:VM9203 2.4 9.7 1.0
C12 A:VM9203 2.6 9.8 1.0
C6 A:VM9203 2.8 9.7 1.0
C21 A:VM9203 3.2 9.8 1.0
C13 A:VM9203 3.2 11.0 1.0
F22 A:VM9203 3.5 10.9 1.0
CG1 A:VAL9 3.5 9.3 1.0
CD1 A:TYR96 3.5 8.9 1.0
C2 A:VM9203 3.7 10.6 1.0
CL42 A:VM9203 3.7 12.6 1.0
CB A:VAL9 3.8 7.9 1.0
CE1 A:TYR96 3.9 9.8 1.0
C20 A:VM9203 4.1 9.7 1.0
C14 A:VM9203 4.1 10.5 1.0
N5 A:VM9203 4.1 10.2 1.0
CE A:MET72 4.1 20.3 1.0
C1 A:VM9203 4.3 11.1 1.0
CG2 A:VAL9 4.4 8.2 1.0
C15 A:VM9203 4.5 9.7 1.0
CG A:TYR96 4.7 7.8 1.0
O A:HOH397 4.7 9.4 1.0
C3 A:VM9203 4.8 11.3 1.0
C4 A:VM9203 4.9 11.5 1.0
N19 A:VM9203 5.0 9.6 1.0

Fluorine binding site 5 out of 10 in 8txe

Go back to Fluorine Binding Sites List in 8txe
Fluorine binding site 5 out of 10 in the Crystal Structure of Kras G12D in Complex with Gdp and Compound 5


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of Kras G12D in Complex with Gdp and Compound 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F203

b:11.3
occ:1.00
 F11 A:VM9203 0.0 11.3 1.0
C8 A:VM9203 1.3 10.3 1.0
F10 A:VM9203 2.2 9.9 1.0
F9 A:VM9203 2.2 10.4 1.0
C7 A:VM9203 2.4 9.7 1.0
C2 A:VM9203 3.1 10.6 1.0
C1 A:VM9203 3.3 11.1 1.0
F22 A:VM9203 3.3 10.9 1.0
C6 A:VM9203 3.3 9.7 1.0
CB A:GLN99 3.5 9.2 1.0
O A:TYR96 3.5 9.6 1.0
CG1 A:ILE100 3.7 8.1 1.0
C12 A:VM9203 3.8 9.8 1.0
C21 A:VM9203 3.9 9.8 1.0
CD1 A:TYR96 3.9 8.9 1.0
CA A:TYR96 4.0 8.0 1.0
N A:ILE100 4.0 8.6 1.0
C A:TYR96 4.2 8.7 1.0
CD1 A:ILE100 4.3 8.9 1.0
C A:GLN99 4.3 8.6 1.0
C3 A:VM9203 4.4 11.3 1.0
CB A:TYR96 4.4 7.3 1.0
CA A:GLN99 4.4 8.8 1.0
CG A:GLN99 4.5 10.2 1.0
N5 A:VM9203 4.5 10.2 1.0
CG A:TYR96 4.6 7.8 1.0
CA A:ILE100 4.7 8.3 1.0
CE1 A:TYR96 4.8 9.8 1.0
CB A:ILE100 4.8 7.9 1.0
CG1 A:VAL9 4.8 9.3 1.0
C13 A:VM9203 4.9 11.0 1.0
N A:GLN99 4.9 8.6 1.0
C4 A:VM9203 4.9 11.5 1.0
C20 A:VM9203 5.0 9.7 1.0
CG2 A:VAL9 5.0 8.2 1.0

Fluorine binding site 6 out of 10 in 8txe

Go back to Fluorine Binding Sites List in 8txe
Fluorine binding site 6 out of 10 in the Crystal Structure of Kras G12D in Complex with Gdp and Compound 5


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of Kras G12D in Complex with Gdp and Compound 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F203

b:10.7
occ:1.00
 F22 B:VM9203 0.0 10.7 1.0
C21 B:VM9203 1.4 9.7 1.0
C20 B:VM9203 2.4 9.0 1.0
C12 B:VM9203 2.4 9.4 1.0
N19 B:VM9203 2.7 9.1 1.0
C6 B:VM9203 2.8 8.9 1.0
NE2 B:HIS95 3.1 10.1 1.0
C7 B:VM9203 3.3 9.3 1.0
F11 B:VM9203 3.4 11.3 1.0
N5 B:VM9203 3.5 8.5 1.0
F10 B:VM9203 3.5 9.6 1.0
C8 B:VM9203 3.5 10.2 1.0
OH B:TYR64 3.6 15.1 1.0
C13 B:VM9203 3.6 10.1 1.0
C15 B:VM9203 3.6 8.9 1.0
CE1 B:HIS95 3.7 10.2 1.0
CG B:GLN99 3.8 10.1 1.0
O B:HOH390 3.8 33.2 1.0
CB B:GLN99 4.0 8.5 1.0
C18 B:VM9203 4.0 8.8 1.0
CD2 B:HIS95 4.1 9.3 1.0
C14 B:VM9203 4.1 9.4 1.0
CE1 B:TYR64 4.2 12.8 1.0
CE1 B:TYR96 4.3 10.2 1.0
C2 B:VM9203 4.3 9.3 1.0
CD1 B:TYR96 4.3 8.8 1.0
CZ B:TYR64 4.3 13.0 1.0
C4 B:VM9203 4.4 8.8 1.0
C16 B:VM9203 4.7 8.8 1.0
C3 B:VM9203 4.7 8.8 1.0
O23 B:VM9203 4.8 9.3 1.0
ND1 B:HIS95 4.8 10.3 1.0
CD B:GLN99 4.9 12.0 1.0
F9 B:VM9203 4.9 9.8 1.0
N17 B:VM9203 4.9 8.8 1.0

Fluorine binding site 7 out of 10 in 8txe

Go back to Fluorine Binding Sites List in 8txe
Fluorine binding site 7 out of 10 in the Crystal Structure of Kras G12D in Complex with Gdp and Compound 5


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure of Kras G12D in Complex with Gdp and Compound 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F203

b:14.3
occ:1.00
 F32 B:VM9203 0.0 14.3 1.0
C31 B:VM9203 1.4 12.4 1.0
C30 B:VM9203 2.4 10.8 1.0
C33 B:VM9203 2.4 11.3 1.0
N29 B:VM9203 3.0 10.3 1.0
C25 B:VM9203 3.0 10.6 1.0
C28 B:VM9203 3.2 10.8 1.0
C26 B:VM9203 3.3 11.7 1.0
O B:HOH383 3.6 21.5 1.0
C27 B:VM9203 3.9 11.9 1.0
O B:HOH347 4.1 28.1 1.0
OD1 B:ASP92 4.2 16.2 1.0
NZ B:LYS88 4.5 24.9 1.0
C24 B:VM9203 4.5 10.1 1.0
CG B:HIS95 4.8 9.1 1.0
O23 B:VM9203 4.8 9.3 1.0
CG B:ASP92 4.8 15.1 1.0
CB B:HIS95 4.9 7.9 1.0

Fluorine binding site 8 out of 10 in 8txe

Go back to Fluorine Binding Sites List in 8txe
Fluorine binding site 8 out of 10 in the Crystal Structure of Kras G12D in Complex with Gdp and Compound 5


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Crystal Structure of Kras G12D in Complex with Gdp and Compound 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F203

b:9.8
occ:1.00
 F9 B:VM9203 0.0 9.8 1.0
C8 B:VM9203 1.4 10.2 1.0
F10 B:VM9203 2.1 9.6 1.0
F11 B:VM9203 2.2 11.3 1.0
C7 B:VM9203 2.3 9.3 1.0
C1 B:VM9203 2.8 9.5 1.0
C2 B:VM9203 2.9 9.3 1.0
CE B:MET72 3.4 18.3 1.0
C6 B:VM9203 3.5 8.9 1.0
CG1 B:ILE100 3.6 8.2 1.0
CG1 B:VAL9 3.7 8.8 1.0
C12 B:VM9203 4.2 9.4 1.0
CE2 B:PHE78 4.2 8.9 1.0
C3 B:VM9203 4.2 8.8 1.0
CD1 B:ILE100 4.2 9.2 1.0
CD2 B:PHE78 4.4 7.7 1.0
CB B:VAL9 4.5 7.5 1.0
CG B:MET72 4.6 12.4 1.0
CB B:MET72 4.6 12.0 1.0
N5 B:VM9203 4.6 8.5 1.0
CL42 B:VM9203 4.7 12.1 1.0
SD B:MET72 4.7 18.5 1.0
C13 B:VM9203 4.8 10.1 1.0
CG2 B:VAL9 4.8 7.8 1.0
F22 B:VM9203 4.9 10.7 1.0
C4 B:VM9203 4.9 8.8 1.0
C21 B:VM9203 4.9 9.7 1.0
CB B:ILE100 4.9 8.3 1.0
N B:ILE100 5.0 8.1 1.0

Fluorine binding site 9 out of 10 in 8txe

Go back to Fluorine Binding Sites List in 8txe
Fluorine binding site 9 out of 10 in the Crystal Structure of Kras G12D in Complex with Gdp and Compound 5


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Crystal Structure of Kras G12D in Complex with Gdp and Compound 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F203

b:9.6
occ:1.00
 F10 B:VM9203 0.0 9.6 1.0
C8 B:VM9203 1.4 10.2 1.0
F9 B:VM9203 2.1 9.8 1.0
F11 B:VM9203 2.2 11.3 1.0
C7 B:VM9203 2.4 9.3 1.0
C12 B:VM9203 2.6 9.4 1.0
C6 B:VM9203 2.8 8.9 1.0
C13 B:VM9203 3.2 10.1 1.0
C21 B:VM9203 3.2 9.7 1.0
CG1 B:VAL9 3.5 8.8 1.0
F22 B:VM9203 3.5 10.7 1.0
CD1 B:TYR96 3.6 8.8 1.0
CL42 B:VM9203 3.7 12.1 1.0
C2 B:VM9203 3.7 9.3 1.0
CB B:VAL9 3.8 7.5 1.0
CE1 B:TYR96 3.9 10.2 1.0
C14 B:VM9203 4.1 9.4 1.0
C20 B:VM9203 4.1 9.0 1.0
N5 B:VM9203 4.1 8.5 1.0
CE B:MET72 4.2 18.3 1.0
C1 B:VM9203 4.3 9.5 1.0
CG2 B:VAL9 4.4 7.8 1.0
C15 B:VM9203 4.5 8.9 1.0
O B:HOH406 4.7 9.0 1.0
CG B:TYR96 4.8 8.5 1.0
C3 B:VM9203 4.8 8.8 1.0
C4 B:VM9203 4.9 8.8 1.0

Fluorine binding site 10 out of 10 in 8txe

Go back to Fluorine Binding Sites List in 8txe
Fluorine binding site 10 out of 10 in the Crystal Structure of Kras G12D in Complex with Gdp and Compound 5


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Crystal Structure of Kras G12D in Complex with Gdp and Compound 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F203

b:11.3
occ:1.00
 F11 B:VM9203 0.0 11.3 1.0
C8 B:VM9203 1.3 10.2 1.0
F10 B:VM9203 2.2 9.6 1.0
F9 B:VM9203 2.2 9.8 1.0
C7 B:VM9203 2.4 9.3 1.0
C2 B:VM9203 3.1 9.3 1.0
C1 B:VM9203 3.2 9.5 1.0
C6 B:VM9203 3.4 8.9 1.0
F22 B:VM9203 3.4 10.7 1.0
CB B:GLN99 3.5 8.5 1.0
O B:TYR96 3.5 9.2 1.0
CG1 B:ILE100 3.7 8.2 1.0
C12 B:VM9203 3.8 9.4 1.0
CD1 B:TYR96 3.9 8.8 1.0
C21 B:VM9203 3.9 9.7 1.0
CA B:TYR96 4.0 7.4 1.0
N B:ILE100 4.0 8.1 1.0
C B:TYR96 4.2 8.1 1.0
CD1 B:ILE100 4.2 9.2 1.0
C B:GLN99 4.3 8.5 1.0
C3 B:VM9203 4.4 8.8 1.0
CB B:TYR96 4.4 7.5 1.0
CA B:GLN99 4.4 8.0 1.0
CG B:GLN99 4.5 10.1 1.0
N5 B:VM9203 4.6 8.5 1.0
CG B:TYR96 4.6 8.5 1.0
CA B:ILE100 4.7 8.6 1.0
CE1 B:TYR96 4.7 10.2 1.0
CB B:ILE100 4.8 8.3 1.0
CG1 B:VAL9 4.8 8.8 1.0
C13 B:VM9203 4.8 10.1 1.0
N B:GLN99 5.0 8.1 1.0
C4 B:VM9203 5.0 8.8 1.0
CG2 B:VAL9 5.0 7.8 1.0

Reference:

H.Cheng, P.Li, P.Chen, A.Irimia, J.H.Bae, A.Brooun, P.Fagan, R.Lam, B.Lin, J.Zhang, X.Zhan, X.Wu, N.Xie, G.Chiang, R.Shoemaker, J.M.Vernier. Structure-Based Design and Synthesis of Potent and Selective Kras G12D Inhibitors. Acs Med.Chem.Lett. V. 14 1351 2023.
ISSN: ISSN 1948-5875
PubMed: 37849557
DOI: 10.1021/ACSMEDCHEMLETT.3C00245
Page generated: Sat Aug 3 00:42:54 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy