Fluorine in PDB 5jv0: Crystal Structure of Human Fpps in Complex with An Allosteric Inhibitor Cl-08-038

All present enzymatic activity of Crystal Structure of Human Fpps in Complex with An Allosteric Inhibitor Cl-08-038:
2.5.1.1; 2.5.1.10;

The structure of Crystal Structure of Human Fpps in Complex with An Allosteric Inhibitor Cl-08-038, PDB code: 5jv0 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)	41.70 / 2.40
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	111.540, 111.540, 75.980, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 23.5

The binding sites of Fluorine atom in the Crystal Structure of Human Fpps in Complex with An Allosteric Inhibitor Cl-08-038 (pdb code 5jv0). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of Human Fpps in Complex with An Allosteric Inhibitor Cl-08-038, PDB code: 5jv0:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Crystal Structure of Human Fpps in Complex with An Allosteric Inhibitor Cl-08-038


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-08-038 within 5.0Å range: probe atom residue distance (Å) B Occ F:F403 b:96.2 occ:1.00 FBD F:YL5403 0.0 96.2 1.0 CAZ F:YL5403 1.3 98.7 1.0 CAY F:YL5403 2.3 99.0 1.0 CBA F:YL5403 2.3 94.2 1.0 CD1 F:LEU246 3.5 55.8 1.0 CAX F:YL5403 3.5 99.9 1.0 CBB F:YL5403 3.6 95.0 1.0 CG2 F:THR255 4.0 97.7 1.0 CBC F:YL5403 4.0 99.9 1.0 CA F:THR255 4.2 0.8 1.0 N3 F:YL5403 4.3 97.2 1.0 C2 F:YL5403 4.3 0.8 1.0 CAV F:YL5403 4.7 96.7 1.0 CB F:THR255 4.7 0.9 1.0 O F:VAL254 4.7 0.9 1.0 N F:THR255 4.8 0.8 1.0 CG F:LEU246 4.9 56.3 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of Human Fpps in Complex with An Allosteric Inhibitor Cl-08-038


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-08-038 within 5.0Å range: probe atom residue distance (Å) B Occ F:F404 b:59.0 occ:1.00 FBD F:YL5404 0.0 59.0 1.0 CAZ F:YL5404 1.4 65.2 1.0 CAY F:YL5404 2.4 67.5 1.0 CBA F:YL5404 2.5 60.9 1.0 CD F:PRO337 3.3 39.4 1.0 O F:PRO335 3.4 47.2 1.0 CD2 F:LEU71 3.6 53.5 1.0 CA F:LEU336 3.7 42.6 1.0 CBB F:YL5404 3.7 61.8 1.0 CAX F:YL5404 3.7 72.4 1.0 CD2 F:LEU336 4.0 44.7 1.0 N F:PRO337 4.2 39.2 1.0 CBC F:YL5404 4.2 63.1 1.0 C F:PRO335 4.2 46.7 1.0 N F:LEU336 4.4 45.6 1.0 CG F:PRO337 4.4 39.8 1.0 C F:LEU336 4.4 41.3 1.0 O F:LEU71 4.4 61.4 1.0 CD1 F:ILE219 4.5 45.8 1.0 CB F:LEU336 4.5 43.7 1.0 CA F:LEU71 4.8 55.7 1.0 CG F:LEU336 4.9 44.8 1.0 NAB F:YL5404 4.9 97.2 1.0 CAV F:YL5404 4.9 75.7 1.0 CG F:LEU71 4.9 51.0 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of Human Fpps in Complex with An Allosteric Inhibitor Cl-08-038


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 Human Fpps in Complex with An Allosteric Inhibitor Cl-08-038 within 5.0Å range: probe atom residue distance (Å) B Occ F:F405 b:0.3 occ:1.00 FBD F:YL5405 0.0 0.3 1.0 CAZ F:YL5405 1.4 1.0 1.0 CAY F:YL5405 2.4 0.9 1.0 CBA F:YL5405 2.5 98.9 1.0 CAX F:YL5405 3.7 0.9 1.0 CB F:TYR322 3.7 59.6 1.0 CG F:TYR322 3.7 63.4 1.0 CBB F:YL5405 3.7 95.6 1.0 CD1 F:TYR322 3.8 64.3 1.0 CD2 F:TYR349 4.0 56.6 1.0 CBC F:YL5405 4.2 99.6 1.0 CB F:TYR349 4.2 62.0 1.0 CD2 F:TYR322 4.4 70.0 1.0 CG F:GLU318 4.5 64.4 1.0 CE1 F:TYR322 4.5 68.8 1.0 CG F:TYR349 4.5 57.3 1.0 O F:GLU318 4.5 53.8 1.0 O F:TYR349 4.7 70.6 1.0 CAL F:YL5405 4.8 0.7 1.0 CAV F:YL5405 4.8 0.9 1.0 OE2 F:GLU318 4.9 69.5 1.0 CAP F:YL5405 4.9 0.5 1.0 NAB F:YL5405 5.0 0.4 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