Fluorine in PDB 5jv1: Crystal Structure of Human Fpps in Complex with An Allosteric Inhibitor Cl-08-066

All present enzymatic activity of Crystal Structure of Human Fpps in Complex with An Allosteric Inhibitor Cl-08-066:
2.5.1.1; 2.5.1.10;

The structure of Crystal Structure of Human Fpps in Complex with An Allosteric Inhibitor Cl-08-066, PDB code: 5jv1 was solved by J.Park, C.Y.Leung, Y.S.Tsantrizos, A.M.Berghuis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.66 / 2.30
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	111.050, 111.050, 76.200, 90.00, 90.00, 90.00
R / Rfree (%)	18.1 / 23.2

The structure of Crystal Structure of Human Fpps in Complex with An Allosteric Inhibitor Cl-08-066 also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Fluorine atom in the Crystal Structure of Human Fpps in Complex with An Allosteric Inhibitor Cl-08-066 (pdb code 5jv1). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of Human Fpps in Complex with An Allosteric Inhibitor Cl-08-066, PDB code: 5jv1:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Crystal Structure of Human Fpps in Complex with An Allosteric Inhibitor Cl-08-066


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 Human Fpps in Complex with An Allosteric Inhibitor Cl-08-066 within 5.0Å range: probe atom residue distance (Å) B Occ F:F403 b:0.1 occ:1.00 FBD F:YL6403 0.0 0.1 1.0 CAZ F:YL6403 1.3 98.2 1.0 CAY F:YL6403 2.3 95.6 1.0 CBA F:YL6403 2.4 91.5 1.0 NE2 F:GLN242 2.6 65.4 1.0 CD1 F:PHE239 3.3 69.1 1.0 CA F:PHE239 3.4 56.9 1.0 CD F:GLN242 3.6 64.3 1.0 O F:PHE239 3.6 60.7 1.0 CAX F:YL6403 3.6 95.8 1.0 CBB F:YL6403 3.6 98.4 1.0 O F:ILE348 3.7 75.3 1.0 CG F:GLN242 3.7 61.6 1.0 CB F:ILE348 3.7 72.6 1.0 CB F:GLN242 3.8 60.1 1.0 CG F:PHE239 3.9 66.2 1.0 CB F:PHE239 3.9 59.1 1.0 C F:PHE239 4.0 56.5 1.0 CE1 F:PHE239 4.0 70.6 1.0 CBC F:YL6403 4.1 96.4 1.0 CA F:ILE348 4.2 74.2 1.0 C F:ILE348 4.4 75.6 1.0 CG2 F:ILE348 4.4 72.0 1.0 CE2 F:PHE238 4.5 64.2 1.0 N F:PHE239 4.5 53.6 1.0 CG1 F:ILE348 4.6 69.1 1.0 O F:PHE238 4.7 55.6 1.0 OE1 F:GLN242 4.7 70.1 1.0 CD2 F:PHE238 4.7 61.6 1.0 CAV F:YL6403 4.8 94.8 1.0 N F:ASP243 4.8 56.4 1.0 CA F:GLN242 4.9 60.8 1.0 C F:PHE238 5.0 52.6 1.0

Fluorine binding site 2 out of 2 in the Crystal Structure of Human Fpps in Complex with An Allosteric Inhibitor Cl-08-066


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 Human Fpps in Complex with An Allosteric Inhibitor Cl-08-066 within 5.0Å range: probe atom residue distance (Å) B Occ F:F404 b:0.7 occ:1.00 FBD F:YL6404 0.0 0.7 1.0 CAZ F:YL6404 1.3 0.1 1.0 CAY F:YL6404 2.4 0.8 1.0 CBA F:YL6404 2.4 0.5 1.0 CG F:TYR322 3.5 79.7 1.0 CB F:TYR322 3.6 73.6 1.0 CBB F:YL6404 3.6 0.1 1.0 CAX F:YL6404 3.7 0.8 1.0 CD1 F:TYR322 3.7 80.1 1.0 CD2 F:TYR322 4.0 90.2 1.0 CBC F:YL6404 4.1 0.2 1.0 CE1 F:TYR322 4.4 84.8 1.0 CD2 F:TYR349 4.5 71.5 1.0 O F:GLU318 4.5 68.5 1.0 CAL F:YL6404 4.6 1.0 1.0 CE2 F:TYR322 4.6 94.3 1.0 CB F:TYR349 4.6 73.1 1.0 CG F:GLU318 4.8 78.5 1.0 CZ F:TYR322 4.8 93.8 1.0 CAT F:YL6404 4.9 0.9 1.0 CAV F:YL6404 4.9 91.7 1.0 NAB F:YL6404 4.9 0.3 1.0 CG F:TYR349 4.9 73.1 1.0 C5 F:YL6404 4.9 0.0 1.0 O F:TYR349 5.0 83.0 1.0

J.Park, C.Y.Leung, A.N.Matralis, C.M.Lacbay, M.Tsakos, G.Fernandez De Troconiz, A.M.Berghuis, Y.S.Tsantrizos. Pharmacophore Mapping of Thienopyrimidine-Based Monophosphonate (Thp-Mp) Inhibitors of the Human Farnesyl Pyrophosphate Synthase. J. Med. Chem. V. 60 2119 2017.
ISSN: ISSN 1520-4804
PubMed: 28208018
DOI: 10.1021/ACS.JMEDCHEM.6B01888