Fluorine in PDB 8jjs: Human K-Ras G12D (Gdp-Bound) in Complex with Cyclic Peptide Inhibitor AP10343

The structure of Human K-Ras G12D (Gdp-Bound) in Complex with Cyclic Peptide Inhibitor AP10343, PDB code: 8jjs was solved by M.Irie, T.A.Fukami, M.Tanada, A.Ohta, T.Torizawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	57.67 / 1.53
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	66.596, 66.596, 86.613, 90, 90, 120
R / Rfree (%)	22.1 / 24.2

The structure of Human K-Ras G12D (Gdp-Bound) in Complex with Cyclic Peptide Inhibitor AP10343 also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Chlorine	(Cl)	1 atom

The binding sites of Fluorine atom in the Human K-Ras G12D (Gdp-Bound) in Complex with Cyclic Peptide Inhibitor AP10343 (pdb code 8jjs). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Human K-Ras G12D (Gdp-Bound) in Complex with Cyclic Peptide Inhibitor AP10343, PDB code: 8jjs:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Human K-Ras G12D (Gdp-Bound) in Complex with Cyclic Peptide Inhibitor AP10343


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Human K-Ras G12D (Gdp-Bound) in Complex with Cyclic Peptide Inhibitor AP10343 within 5.0Å range: probe atom residue distance (Å) B Occ I:F7 b:23.1 occ:1.00 FI1 I:IAE7 0.0 23.1 1.0 CI I:IAE7 1.3 21.9 1.0 FI2 I:IAE7 2.1 23.4 1.0 FI3 I:IAE7 2.1 22.7 1.0 CH I:IAE7 2.4 18.8 1.0 CZ2 I:IAE7 2.8 17.9 1.0 CE2 A:PHE78 3.5 17.8 1.0 CZ1 I:IAE7 3.6 17.6 1.0 O A:TYR71 3.8 17.2 1.0 CZ A:PHE78 3.9 17.2 1.0 CG2 A:VAL7 4.0 13.7 1.0 CG1 A:VAL7 4.0 13.6 1.0 CA A:MET72 4.0 19.3 1.0 C A:TYR71 4.0 17.3 1.0 N A:MET72 4.1 17.8 1.0 CE2 I:IAE7 4.1 17.3 1.0 CB A:VAL7 4.4 13.3 1.0 CB A:TYR71 4.5 15.4 1.0 CD2 A:PHE78 4.6 17.1 1.0 CB A:MET72 4.7 20.9 1.0 CE1 I:IAE7 4.7 17.5 1.0 CG A:MET72 4.8 25.9 1.0 CA A:TYR71 4.9 16.1 1.0 CG1 A:VAL103 5.0 28.9 1.0 CD I:IAE7 5.0 17.6 1.0

Fluorine binding site 2 out of 3 in the Human K-Ras G12D (Gdp-Bound) in Complex with Cyclic Peptide Inhibitor AP10343


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Human K-Ras G12D (Gdp-Bound) in Complex with Cyclic Peptide Inhibitor AP10343 within 5.0Å range: probe atom residue distance (Å) B Occ I:F7 b:23.4 occ:1.00 FI2 I:IAE7 0.0 23.4 1.0 CI I:IAE7 1.3 21.9 1.0 FI1 I:IAE7 2.1 23.1 1.0 FI3 I:IAE7 2.1 22.7 1.0 CH I:IAE7 2.3 18.8 1.0 CZ1 I:IAE7 3.1 17.6 1.0 CZ2 I:IAE7 3.2 17.9 1.0 CA A:MET72 3.5 19.3 1.0 CB A:MET72 3.5 20.9 1.0 N A:MET72 3.5 17.8 1.0 O A:ARG68 3.6 16.1 1.0 CG A:MET72 3.8 25.9 1.0 CD2 I:MLE10 3.8 20.4 1.0 CG A:ARG68 3.8 22.4 1.0 C A:TYR71 4.1 17.3 1.0 CE A:MET72 4.3 26.8 1.0 CE1 I:IAE7 4.3 17.5 1.0 CE2 I:IAE7 4.4 17.3 1.0 O A:TYR71 4.5 17.2 1.0 C A:ARG68 4.5 16.2 1.0 CB A:TYR71 4.5 15.4 1.0 CD A:ARG68 4.6 28.0 1.0 CG I:MLE10 4.8 21.1 1.0 CD1 I:MLE10 4.8 21.2 1.0 SD A:MET72 4.8 33.0 1.0 CA A:TYR71 4.9 16.1 1.0 CD I:IAE7 4.9 17.6 1.0 CA A:ARG68 5.0 16.4 1.0 CD2 A:LEU56 5.0 14.2 1.0 C A:MET72 5.0 20.3 1.0

Fluorine binding site 3 out of 3 in the Human K-Ras G12D (Gdp-Bound) in Complex with Cyclic Peptide Inhibitor AP10343


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Human K-Ras G12D (Gdp-Bound) in Complex with Cyclic Peptide Inhibitor AP10343 within 5.0Å range: probe atom residue distance (Å) B Occ I:F7 b:22.7 occ:1.00 FI3 I:IAE7 0.0 22.7 1.0 CI I:IAE7 1.3 21.9 1.0 FI2 I:IAE7 2.1 23.4 1.0 FI1 I:IAE7 2.1 23.1 1.0 CH I:IAE7 2.4 18.8 1.0 CZ1 I:IAE7 2.8 17.6 1.0 CD2 A:LEU56 3.2 14.2 1.0 CB A:TYR71 3.6 15.4 1.0 CZ2 I:IAE7 3.6 17.9 1.0 CG1 A:VAL7 3.6 13.6 1.0 CG2 A:VAL7 3.9 13.7 1.0 O A:ARG68 4.1 16.1 1.0 CE1 I:IAE7 4.2 17.5 1.0 CG A:ARG68 4.2 22.4 1.0 C A:TYR71 4.2 17.3 1.0 N A:MET72 4.3 17.8 1.0 CB A:VAL7 4.4 13.3 1.0 CG2 A:THR58 4.5 13.5 1.0 CA A:TYR71 4.5 16.1 1.0 O A:TYR71 4.5 17.2 1.0 CG A:LEU56 4.6 13.3 1.0 CG A:TYR71 4.6 15.6 1.0 CE2 I:IAE7 4.7 17.3 1.0 CA A:MET72 4.8 19.3 1.0 C A:ARG68 4.9 16.2 1.0 CA A:ARG68 4.9 16.4 1.0 CD I:IAE7 4.9 17.6 1.0 CB A:LEU56 5.0 12.6 1.0

M.Tanada, M.Tamiya, A.Matsuo, A.Chiyoda, K.Takano, T.Ito, M.Irie, T.Kotake, R.Takeyama, H.Kawada, R.Hayashi, S.Ishikawa, K.Nomura, N.Furuichi, Y.Morita, M.Kage, S.Hashimoto, K.Nii, H.Sase, K.Ohara, A.Ohta, S.Kuramoto, Y.Nishimura, H.Iikura, T.Shiraishi. Development of Orally Bioavailable Peptides Targeting An Intracellular Protein: From A Hit to A Clinical Kras Inhibitor J.Am.Chem.Soc. 2023.
ISSN: ESSN 1520-5126
DOI: 10.1021/JACS.3C03886