Chlorine 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:

Fluorine

(F)

2 atoms

The binding sites of Chlorine 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 Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Crystal Structure of Human 3-Phosphoglycerate Dehydrogenase in Complex with 3-Chloro-4-Fluorobenzamide, PDB code: 5ofw:
Jump to Chlorine binding site number: 1; 2;

Chlorine 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 Chlorine with other atoms in the Cl 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:Cl401 b:31.2 occ:1.00 CL1 B:9TW401 0.0 31.2 1.0 C2 B:9TW401 1.7 27.7 1.0 C1 B:9TW401 2.7 23.4 1.0 C3 B:9TW401 2.7 32.4 1.0 F1 B:9TW401 2.9 44.4 1.0 N B:GLY152 3.2 14.4 1.0 O B:TYR174 3.3 18.3 1.0 CG2 B:THR207 3.4 18.6 1.0 C B:LEU151 3.6 12.2 1.0 CA B:GLY152 3.8 13.7 1.0 CD2 B:TYR174 3.9 23.6 1.0 C4 B:9TW401 4.0 28.5 1.0 C6 B:9TW401 4.0 33.0 1.0 O B:LEU151 4.0 14.5 1.0 CA B:LEU151 4.1 12.1 1.0 CD B:PRO176 4.2 29.1 1.0 C B:TYR174 4.2 15.6 1.0 CA B:ASP175 4.2 21.6 1.0 CB B:LEU151 4.2 12.6 1.0 CE2 B:TYR174 4.4 25.7 1.0 C5 B:9TW401 4.5 29.8 1.0 N B:ASP175 4.6 18.5 1.0 CB B:THR207 4.7 17.7 1.0 CG B:TYR174 4.9 23.6 1.0 OD2 B:ASP175 4.9 28.4 1.0 CB B:ASP175 4.9 22.1 1.0 CD2 B:LEU216 4.9 17.7 1.0

Chlorine 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 Chlorine with other atoms in the Cl 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:Cl401 b:28.9 occ:1.00 CL1 A:9TW401 0.0 28.9 1.0 C2 A:9TW401 1.7 22.5 1.0 C3 A:9TW401 2.7 24.5 1.0 C1 A:9TW401 2.7 21.1 1.0 F1 A:9TW401 2.9 32.2 1.0 N A:GLY152 3.2 11.8 1.0 CG2 A:THR207 3.4 20.4 1.0 O A:TYR174 3.4 17.0 1.0 C A:LEU151 3.5 10.7 1.0 CD1 A:TYR174 3.8 19.5 1.0 CA A:GLY152 3.8 11.6 1.0 C6 A:9TW401 3.9 24.3 1.0 C4 A:9TW401 3.9 18.7 1.0 CA A:LEU151 4.0 11.4 1.0 O A:LEU151 4.1 11.2 1.0 CB A:LEU151 4.1 12.1 1.0 C A:TYR174 4.2 14.8 1.0 CD A:PRO176 4.3 27.7 1.0 CE1 A:TYR174 4.3 22.3 1.0 CA A:ASP175 4.4 16.6 1.0 C5 A:9TW401 4.4 26.2 1.0 N A:ASP175 4.6 13.1 1.0 CB A:THR207 4.7 15.6 1.0 CD2 A:LEU216 4.8 19.1 1.0 CG A:TYR174 4.8 19.0 1.0 CB A:TYR174 5.0 16.8 1.0 N A:PRO176 5.0 21.2 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