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Fluorine in PDB 7t47: Kras G12D (Gppcp) with Mrtx-1133

Enzymatic activity of Kras G12D (Gppcp) with Mrtx-1133

All present enzymatic activity of Kras G12D (Gppcp) with Mrtx-1133:
3.6.5.2;

Protein crystallography data

The structure of Kras G12D (Gppcp) with Mrtx-1133, PDB code: 7t47 was solved by N.C.Thomas, R.J.Gunn, J.D.Lawson, X.Wang, M.A.Matthew, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.45 / 1.27
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 40.311, 50.579, 92.903, 90, 90, 90
R / Rfree (%) 15.2 / 17.2

Other elements in 7t47:

The structure of Kras G12D (Gppcp) with Mrtx-1133 also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Kras G12D (Gppcp) with Mrtx-1133 (pdb code 7t47). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Kras G12D (Gppcp) with Mrtx-1133, PDB code: 7t47:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 7t47

Go back to Fluorine Binding Sites List in 7t47
Fluorine binding site 1 out of 3 in the Kras G12D (Gppcp) with Mrtx-1133


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Kras G12D (Gppcp) with Mrtx-1133 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F201

b:10.5
occ:1.00
F01 A:6IC201 0.0 10.5 1.0
C07 A:6IC201 1.4 9.9 1.0
C02 A:6IC201 2.3 10.1 1.0
C06 A:6IC201 2.5 10.7 1.0
N01 A:6IC201 2.7 9.8 1.0
C08 A:6IC201 2.9 10.6 1.0
C20 A:6IC201 3.2 10.3 1.0
NE2 A:HIS95 3.3 10.6 1.0
OH A:TYR64 3.3 11.9 1.0
CE2 A:TYR64 3.3 11.6 1.0
C24 A:6IC201 3.3 9.8 1.0
C32 A:6IC201 3.3 9.6 1.0
CG A:GLN99 3.5 9.9 1.0
C01 A:6IC201 3.6 9.8 1.0
N03 A:6IC201 3.7 10.5 1.0
CZ A:TYR64 3.7 10.5 1.0
C33 A:6IC201 3.8 10.6 1.0
C16 A:6IC201 3.8 12.1 1.0
CD A:GLN99 4.0 12.6 1.0
CE1 A:HIS95 4.0 10.0 1.0
CB A:GLN99 4.0 9.6 1.0
C03 A:6IC201 4.0 9.7 1.0
CD2 A:HIS95 4.1 9.3 1.0
C05 A:6IC201 4.1 10.9 1.0
C19 A:6IC201 4.2 9.3 1.0
C23 A:6IC201 4.2 8.5 1.0
CE1 A:TYR96 4.3 9.4 1.0
OE1 A:GLN99 4.3 15.1 1.0
CD1 A:TYR96 4.3 9.3 1.0
CD2 A:TYR64 4.4 11.1 1.0
NE2 A:GLN99 4.6 12.9 1.0
C17 A:6IC201 4.7 11.4 1.0
C04 A:6IC201 4.7 10.9 1.0
C18 A:6IC201 4.8 10.0 1.0
O01 A:6IC201 4.8 10.4 1.0
N02 A:6IC201 4.9 10.1 1.0
F23 A:6IC201 4.9 10.4 1.0
C21 A:6IC201 5.0 10.0 1.0

Fluorine binding site 2 out of 3 in 7t47

Go back to Fluorine Binding Sites List in 7t47
Fluorine binding site 2 out of 3 in the Kras G12D (Gppcp) with Mrtx-1133


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Kras G12D (Gppcp) with Mrtx-1133 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F201

b:15.4
occ:1.00
F02 A:6IC201 0.0 15.4 1.0
C27 A:6IC201 1.4 11.8 1.0
C28 A:6IC201 2.3 13.9 1.0
C26 A:6IC201 2.4 12.3 1.0
N06 A:6IC201 2.9 12.3 1.0
C25 A:6IC201 3.0 11.4 1.0
C29 A:6IC201 3.2 15.9 1.0
O A:HOH512 3.2 22.8 1.0
O A:HOH398 3.2 23.6 1.0
C31 A:6IC201 3.3 14.7 1.0
OD1 A:ASP92 3.8 13.2 1.0
C30 A:6IC201 3.9 16.9 1.0
NZ A:LYS88 4.0 18.0 1.0
O A:HOH350 4.1 22.6 1.0
CG A:ASP92 4.4 13.2 1.0
C09 A:6IC201 4.5 11.8 1.0
OD2 A:ASP92 4.8 14.7 1.0
O01 A:6IC201 4.9 10.4 1.0
CG A:HIS95 4.9 8.6 1.0
CB A:HIS95 5.0 9.4 1.0

Fluorine binding site 3 out of 3 in 7t47

Go back to Fluorine Binding Sites List in 7t47
Fluorine binding site 3 out of 3 in the Kras G12D (Gppcp) with Mrtx-1133


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Kras G12D (Gppcp) with Mrtx-1133 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F201

b:10.4
occ:1.00
F23 A:6IC201 0.0 10.4 1.0
C23 A:6IC201 1.4 8.5 1.0
C22 A:6IC201 2.3 9.6 1.0
C24 A:6IC201 2.3 9.8 1.0
C32 A:6IC201 2.7 9.6 1.0
C33 A:6IC201 3.4 10.6 1.0
CG1 A:VAL9 3.4 9.1 1.0
CG1 A:ILE100 3.5 9.8 1.0
C21 A:6IC201 3.5 10.0 1.0
C20 A:6IC201 3.6 10.3 1.0
CD1 A:ILE100 4.0 10.0 1.0
CB A:VAL9 4.0 7.3 1.0
C19 A:6IC201 4.1 9.3 1.0
O A:TYR96 4.2 8.6 1.0
CG2 A:VAL9 4.2 9.3 1.0
CD1 A:TYR96 4.4 9.3 1.0
SD A:MET72 4.5 16.0 1.0
CD2 A:PHE78 4.5 9.9 1.0
CE2 A:PHE78 4.6 11.5 1.0
CB A:GLN99 4.6 9.6 1.0
N A:ILE100 4.7 9.2 1.0
CB A:TYR96 4.8 9.2 1.0
CB A:ILE100 4.8 9.6 1.0
C08 A:6IC201 4.8 10.6 1.0
CE A:MET72 4.9 18.7 1.0
CA A:TYR96 4.9 8.6 1.0
C A:TYR96 4.9 10.0 1.0
F01 A:6IC201 4.9 10.5 1.0
CA A:ILE100 5.0 9.7 1.0

Reference:

J.Christensen, J.Hallin, V.Bowcut, A.Calinsan, D.Briere, L.Hargis, L.Engstrom, J.Laguer, J.Medwid, D.Vanderpool, E.Lifset, D.Trinh, N.Hoffman, X.Wang, J.Lawson, R.Gunn, C.Smith, N.Thomas, M.Martinson, A.Bergstrom, F.Sullivan, K.Bouhana, S.Winski, L.He, F.B.Julio, A.Pavlicek, J.Hafing, L.Rahbaek, M.Marx, P.Olson. A Non-Covalent KRASG12D Allele Specific Inhibitor Demonstrates Potent Inhibition of Kras-Dependent Signaling and Regression of KRASG12D-Mutant Tumors Nature 2022.
ISSN: ESSN 1476-4687
DOI: 10.21203/RS.3.RS-1261963/V1
Page generated: Fri Aug 2 13:17:34 2024

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