Fluorine in PDB 5ofw: Crystal Structure of Human 3-Phosphoglycerate Dehydrogenase in Complex with 3-Chloro-4-Fluorobenzamide

All present enzymatic activity of Crystal Structure of Human 3-Phosphoglycerate Dehydrogenase in Complex with 3-Chloro-4-Fluorobenzamide:
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 3-Chloro-4-Fluorobenzamide, PDB code: 5ofw 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)	50.50 / 1.50
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	43.386, 45.835, 55.996, 97.58, 111.01, 106.01
R / Rfree (%)	17.5 / 24.2

The structure of Crystal Structure of Human 3-Phosphoglycerate Dehydrogenase in Complex with 3-Chloro-4-Fluorobenzamide also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Fluorine atom in the Crystal Structure of Human 3-Phosphoglycerate Dehydrogenase in Complex with 3-Chloro-4-Fluorobenzamide (pdb code 5ofw). 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 3-Chloro-4-Fluorobenzamide, PDB code: 5ofw:
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 3-Chloro-4-Fluorobenzamide


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 3-Chloro-4-Fluorobenzamide within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:44.4 occ:1.00 F1 B:9TW401 0.0 44.4 1.0 C3 B:9TW401 1.4 32.4 1.0 C4 B:9TW401 2.3 28.5 1.0 C2 B:9TW401 2.3 27.7 1.0 CL1 B:9TW401 2.9 31.2 1.0 CD2 B:TYR174 3.1 23.6 1.0 CE2 B:TYR174 3.3 25.7 1.0 CD1 B:LEU216 3.6 24.0 1.0 C1 B:9TW401 3.6 23.4 1.0 C5 B:9TW401 3.6 29.8 1.0 CD2 B:LEU193 3.7 25.2 1.0 CD2 B:LEU216 3.7 17.7 1.0 CD1 B:LEU193 3.9 20.6 1.0 C6 B:9TW401 4.1 33.0 1.0 CG B:LEU193 4.1 23.2 1.0 CG B:LEU216 4.2 18.2 1.0 CG B:TYR174 4.3 23.6 1.0 CB B:LEU151 4.5 12.6 1.0 CZ B:TYR174 4.6 23.3 1.0 CB B:TYR174 4.8 17.9 1.0 CD1 B:LEU151 5.0 15.2 1.0 O B:TYR174 5.0 18.3 1.0

Fluorine binding site 2 out of 2 in the Crystal Structure of Human 3-Phosphoglycerate Dehydrogenase in Complex with 3-Chloro-4-Fluorobenzamide


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 3-Chloro-4-Fluorobenzamide within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:32.2 occ:1.00 F1 A:9TW401 0.0 32.2 1.0 C3 A:9TW401 1.4 24.5 1.0 C2 A:9TW401 2.3 22.5 1.0 C4 A:9TW401 2.4 18.7 1.0 CL1 A:9TW401 2.9 28.9 1.0 CD1 A:TYR174 3.4 19.5 1.0 CD1 A:LEU216 3.5 22.7 1.0 CD2 A:LEU216 3.5 19.1 1.0 C1 A:9TW401 3.6 21.1 1.0 C5 A:9TW401 3.6 26.2 1.0 CE1 A:TYR174 3.6 22.3 1.0 CD2 A:LEU193 3.6 21.0 1.0 CD1 A:LEU193 3.9 23.8 1.0 C6 A:9TW401 4.1 24.3 1.0 CG A:LEU193 4.1 24.6 1.0 CG A:LEU216 4.1 17.1 1.0 CG A:TYR174 4.5 19.0 1.0 CB A:LEU151 4.6 12.1 1.0 CZ A:TYR174 4.9 20.4 1.0 CD1 A:LEU151 4.9 12.0 1.0 O A:HOH506 5.0 32.9 1.0 CB A:TYR174 5.0 16.8 1.0 CG2 A:THR207 5.0 20.4 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