Fluorine in PDB 5ofv: Crystal Structure of Human 3-Phosphoglycerate Dehydrogenase in Complex with 5-Fluoro-2-Methylbenzoic Acid

All present enzymatic activity of Crystal Structure of Human 3-Phosphoglycerate Dehydrogenase in Complex with 5-Fluoro-2-Methylbenzoic Acid:
1.1.1.37; 1.1.1.399; 1.1.1.95;

The structure of Crystal Structure of Human 3-Phosphoglycerate Dehydrogenase in Complex with 5-Fluoro-2-Methylbenzoic Acid, PDB code: 5ofv was solved by J.E.Unterlass, A.Basle, T.J.Blackburn, J.Tucker, C.Cano, M.E.M.Noble, N.J.Curtin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.60 / 1.50
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	43.342, 45.608, 56.269, 98.02, 111.14, 105.85
R / Rfree (%)	22.4 / 27.3

The binding sites of Fluorine atom in the Crystal Structure of Human 3-Phosphoglycerate Dehydrogenase in Complex with 5-Fluoro-2-Methylbenzoic Acid (pdb code 5ofv). 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 3-Phosphoglycerate Dehydrogenase in Complex with 5-Fluoro-2-Methylbenzoic Acid, PDB code: 5ofv:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Crystal Structure of Human 3-Phosphoglycerate Dehydrogenase in Complex with 5-Fluoro-2-Methylbenzoic Acid


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 3-Phosphoglycerate Dehydrogenase in Complex with 5-Fluoro-2-Methylbenzoic Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:29.3 occ:1.00 F1 B:9TZ401 0.0 29.3 1.0 C2 B:9TZ401 1.4 32.4 1.0 C1 B:9TZ401 2.3 31.5 1.0 C3 B:9TZ401 2.4 33.8 1.0 CD1 B:TYR174 3.2 21.6 1.0 C4 B:9TZ401 3.6 35.4 1.0 C6 B:9TZ401 3.6 29.6 1.0 CE1 B:TYR174 3.6 23.2 1.0 CD2 B:LEU216 3.7 20.4 1.0 CD2 B:LEU193 3.9 24.0 1.0 CB B:LEU151 4.0 12.1 1.0 C5 B:9TZ401 4.1 33.1 1.0 CD1 B:LEU216 4.2 22.7 1.0 O B:TYR174 4.3 20.9 1.0 CG B:TYR174 4.3 23.4 1.0 CD1 B:LEU193 4.5 19.8 1.0 CG B:LEU193 4.6 20.4 1.0 CG2 B:THR207 4.6 13.7 1.0 CG B:LEU216 4.6 18.2 1.0 CA B:LEU151 4.6 12.6 1.0 CG B:LEU151 4.6 13.6 1.0 CB B:TYR174 4.6 19.4 1.0 CD2 B:LEU151 4.7 13.2 1.0 C B:LEU151 4.7 11.8 1.0 CD1 B:LEU151 4.8 15.4 1.0 N B:GLY152 4.8 13.2 1.0 C8 B:9TZ401 4.8 34.2 1.0 C B:TYR174 4.9 19.7 1.0 CZ B:TYR174 5.0 21.1 1.0

Fluorine binding site 2 out of 2 in the Crystal Structure of Human 3-Phosphoglycerate Dehydrogenase in Complex with 5-Fluoro-2-Methylbenzoic Acid


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 3-Phosphoglycerate Dehydrogenase in Complex with 5-Fluoro-2-Methylbenzoic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:24.5 occ:1.00 F1 A:9TZ401 0.0 24.5 1.0 C2 A:9TZ401 1.4 20.6 1.0 C3 A:9TZ401 2.3 20.4 1.0 C1 A:9TZ401 2.4 19.9 1.0 CD1 A:TYR174 3.2 20.3 1.0 C4 A:9TZ401 3.6 20.6 1.0 CD2 A:LEU216 3.6 16.1 1.0 C6 A:9TZ401 3.6 20.2 1.0 CE1 A:TYR174 3.7 21.7 1.0 CB A:LEU151 3.9 10.3 1.0 CD2 A:LEU193 3.9 17.9 1.0 C5 A:9TZ401 4.1 20.6 1.0 CD1 A:LEU216 4.2 18.7 1.0 O A:TYR174 4.2 13.1 1.0 CG A:TYR174 4.3 19.3 1.0 CG A:LEU151 4.4 10.3 1.0 CA A:LEU151 4.5 10.3 1.0 CD2 A:LEU151 4.5 11.4 1.0 CG A:LEU216 4.5 16.4 1.0 CD1 A:LEU193 4.6 16.3 1.0 CG2 A:THR207 4.6 10.6 1.0 CB A:TYR174 4.6 15.5 1.0 C A:LEU151 4.6 9.9 1.0 CG A:LEU193 4.6 19.7 1.0 CD1 A:LEU151 4.6 11.5 1.0 N A:GLY152 4.7 9.7 1.0 C8 A:9TZ401 4.8 27.6 1.0 C A:TYR174 5.0 13.5 1.0

J.E.Unterlass, A.Basle, T.J.Blackburn, J.Tucker, C.Cano, M.E.M.Noble, N.J.Curtin. Validating and Enabling Phosphoglycerate Dehydrogenase (Phgdh) As A Target For Fragment-Based Drug Discovery in Phgdh-Amplified Breast Cancer. Oncotarget V. 9 13139 2018.
ISSN: ESSN 1949-2553
PubMed: 29568346
DOI: 10.18632/ONCOTARGET.11487