Fluorine in PDB 8e9e: Rat Protein Farnesyltransferase in Complex with Fpp and Inhibitor 2F

All present enzymatic activity of Rat Protein Farnesyltransferase in Complex with Fpp and Inhibitor 2F:
2.5.1.58; 2.5.1.59;

The structure of Rat Protein Farnesyltransferase in Complex with Fpp and Inhibitor 2F, PDB code: 8e9e was solved by Y.Wang, Y.Shi, L.S.Beese, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.38 / 2.84
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	169.898, 169.898, 69.339, 90, 90, 120
R / Rfree (%)	17.6 / 19.4

The structure of Rat Protein Farnesyltransferase in Complex with Fpp and Inhibitor 2F also contains other interesting chemical elements:

Zinc	(Zn)	1 atom
Bromine	(Br)	1 atom

The binding sites of Fluorine atom in the Rat Protein Farnesyltransferase in Complex with Fpp and Inhibitor 2F (pdb code 8e9e). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Rat Protein Farnesyltransferase in Complex with Fpp and Inhibitor 2F, PDB code: 8e9e:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Rat Protein Farnesyltransferase in Complex with Fpp and Inhibitor 2F


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Rat Protein Farnesyltransferase in Complex with Fpp and Inhibitor 2F within 5.0Å range: probe atom residue distance (Å) B Occ B:F503 b:37.7 occ:1.00 F34 B:XMY503 0.0 37.7 1.0 C33 B:XMY503 1.4 39.3 1.0 F35 B:XMY503 2.2 43.4 1.0 F36 B:XMY503 2.2 43.0 1.0 O32 B:XMY503 2.2 39.1 1.0 CH2 B:TRP102 3.0 39.7 1.0 CZ3 B:TRP102 3.1 38.3 1.0 C13 B:FPP501 3.2 36.3 1.0 C12 B:FPP501 3.3 37.3 1.0 CH2 B:TRP303 3.4 31.1 1.0 CZ2 B:TRP303 3.5 29.1 1.0 OH B:TYR365 3.5 36.4 1.0 C28 B:XMY503 3.6 37.4 1.0 C15 B:FPP501 3.6 44.0 1.0 C14 B:FPP501 3.7 26.0 1.0 C11 B:FPP501 3.8 33.9 1.0 CZ2 B:TRP102 3.8 44.0 1.0 CE3 B:TRP102 4.1 40.0 1.0 C27 B:XMY503 4.2 33.8 1.0 CZ B:TYR365 4.4 34.0 1.0 CZ3 B:TRP303 4.6 31.6 1.0 C29 B:XMY503 4.6 36.6 1.0 CE2 B:TRP102 4.6 39.0 1.0 CE1 B:TYR365 4.7 33.6 1.0 CD2 B:TRP102 4.8 39.6 1.0 CE2 B:TRP303 4.8 31.4 1.0 NE1 B:TRP106 5.0 40.0 1.0 CE1 B:TYR361 5.0 32.8 1.0

Fluorine binding site 2 out of 3 in the Rat Protein Farnesyltransferase in Complex with Fpp and Inhibitor 2F


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Rat Protein Farnesyltransferase in Complex with Fpp and Inhibitor 2F within 5.0Å range: probe atom residue distance (Å) B Occ B:F503 b:43.4 occ:1.00 F35 B:XMY503 0.0 43.4 1.0 C33 B:XMY503 1.4 39.3 1.0 F34 B:XMY503 2.2 37.7 1.0 F36 B:XMY503 2.3 43.0 1.0 O32 B:XMY503 2.3 39.1 1.0 C27 B:XMY503 2.7 33.8 1.0 C28 B:XMY503 2.9 37.4 1.0 C12 B:FPP501 3.6 37.3 1.0 C24 B:XMY503 3.6 41.2 1.0 CE1 B:TYR361 3.6 32.8 1.0 CZ2 B:TRP303 3.6 29.1 1.0 BR23 B:XMY503 3.8 62.1 1.0 C11 B:FPP501 3.8 33.9 1.0 C26 B:XMY503 4.1 33.5 1.0 C22 B:XMY503 4.2 43.2 1.0 CH2 B:TRP303 4.2 31.1 1.0 C29 B:XMY503 4.2 36.6 1.0 C13 B:FPP501 4.2 36.3 1.0 C10 B:FPP501 4.3 24.8 1.0 CD1 B:TYR361 4.4 35.6 1.0 OH B:TYR361 4.4 31.8 1.0 CZ B:TYR361 4.4 34.8 1.0 CE2 B:TRP303 4.5 31.4 1.0 C9 B:FPP501 4.6 39.2 1.0 C8 B:FPP501 4.6 38.3 1.0 C25 B:XMY503 4.7 36.7 1.0 N07 B:XMY503 4.7 36.7 1.0 C15 B:FPP501 4.7 44.0 1.0 OH B:TYR365 4.8 36.4 1.0 C06 B:XMY503 4.8 35.0 1.0 NE1 B:TRP303 4.8 30.3 1.0 CH2 B:TRP102 4.9 39.7 1.0 CE1 B:TYR365 4.9 33.6 1.0 CZ3 B:TRP102 4.9 38.3 1.0

Fluorine binding site 3 out of 3 in the Rat Protein Farnesyltransferase in Complex with Fpp and Inhibitor 2F


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Rat Protein Farnesyltransferase in Complex with Fpp and Inhibitor 2F within 5.0Å range: probe atom residue distance (Å) B Occ B:F503 b:43.0 occ:1.00 F36 B:XMY503 0.0 43.0 1.0 C33 B:XMY503 1.4 39.3 1.0 F34 B:XMY503 2.2 37.7 1.0 O32 B:XMY503 2.2 39.1 1.0 F35 B:XMY503 2.3 43.4 1.0 C28 B:XMY503 2.8 37.4 1.0 C27 B:XMY503 3.2 33.8 1.0 CZ2 B:TRP106 3.3 36.5 1.0 NE1 B:TRP106 3.3 40.0 1.0 OH B:TYR365 3.4 36.4 1.0 CE1 B:TYR361 3.4 32.8 1.0 CZ3 B:TRP102 3.4 38.3 1.0 CD1 B:TYR361 3.6 35.6 1.0 CE1 B:TYR365 3.6 33.6 1.0 CE2 B:TRP106 3.6 42.5 1.0 CE3 B:TRP102 3.7 40.0 1.0 C29 B:XMY503 3.8 36.6 1.0 CZ B:TYR365 3.9 34.0 1.0 CH2 B:TRP102 4.0 39.7 1.0 CZ2 B:TRP303 4.1 29.1 1.0 CD2 B:TRP102 4.4 39.6 1.0 C26 B:XMY503 4.4 33.5 1.0 CH2 B:TRP106 4.5 36.9 1.0 CH2 B:TRP303 4.6 31.1 1.0 CD1 B:TRP106 4.6 36.8 1.0 CZ2 B:TRP102 4.6 44.0 1.0 CZ B:TYR361 4.7 34.8 1.0 CD1 B:TYR365 4.8 37.5 1.0 CE2 B:TRP102 4.8 39.0 1.0 C30 B:XMY503 4.9 40.7 1.0 CG B:TYR361 4.9 36.9 1.0

Y.Wang, F.Xu, C.B.Nichols, Y.Shi, H.W.Hellinga, J.A.Alspaugh, M.D.Distefano, L.S.Beese. Structure-Guided Discovery of Potent Antifungals That Prevent Ras Signaling By Inhibiting Protein Farnesyltransferase. J.Med.Chem. V. 65 13753 2022.
ISSN: ISSN 0022-2623
PubMed: 36218371
DOI: 10.1021/ACS.JMEDCHEM.2C00902