Chlorine in PDB 5n53: Crystal Structure of Human 3-Phosphoglycerate Dehydrogenase in Complex with N-(3-Chloro-4-Methoxyphenyl) Acetamide

All present enzymatic activity of Crystal Structure of Human 3-Phosphoglycerate Dehydrogenase in Complex with N-(3-Chloro-4-Methoxyphenyl) Acetamide:
1.1.1.95;

The structure of Crystal Structure of Human 3-Phosphoglycerate Dehydrogenase in Complex with N-(3-Chloro-4-Methoxyphenyl) Acetamide, PDB code: 5n53 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)	50.12 / 1.48
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	43.353, 45.323, 55.255, 97.90, 110.06, 106.35
R / Rfree (%)	18.9 / 24.4

The binding sites of Chlorine atom in the Crystal Structure of Human 3-Phosphoglycerate Dehydrogenase in Complex with N-(3-Chloro-4-Methoxyphenyl) Acetamide (pdb code 5n53). 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 N-(3-Chloro-4-Methoxyphenyl) Acetamide, PDB code: 5n53:
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 N-(3-Chloro-4-Methoxyphenyl) Acetamide


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 N-(3-Chloro-4-Methoxyphenyl) Acetamide within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl301 b:48.7 occ:1.00 CL1 B:8NB301 0.0 48.7 1.0 C5 B:8NB301 1.7 42.9 1.0 C4 B:8NB301 2.7 42.9 1.0 C6 B:8NB301 2.7 41.4 1.0 O1 B:8NB301 2.9 47.8 1.0 CG2 B:THR207 3.4 13.3 1.0 CD2 B:TYR174 3.5 24.4 1.0 N B:GLY152 3.7 11.8 1.0 O B:TYR174 3.8 18.6 1.0 CE2 B:TYR174 3.8 28.6 1.0 CD B:PRO176 3.9 24.1 1.0 C3 B:8NB301 4.0 44.0 1.0 C1 B:8NB301 4.0 41.4 1.0 C B:LEU151 4.0 11.4 1.0 CA B:GLY152 4.2 12.2 1.0 C7 B:8NB301 4.2 47.9 1.0 CA B:ASP175 4.3 18.2 1.0 CA B:LEU151 4.4 11.1 1.0 C B:TYR174 4.4 15.5 1.0 CB B:LEU151 4.4 11.6 1.0 C2 B:8NB301 4.5 37.9 1.0 O B:LEU151 4.5 12.2 1.0 CD2 B:LEU216 4.6 16.7 1.0 CB B:THR207 4.6 13.2 1.0 CG B:TYR174 4.7 21.7 1.0 N B:ASP175 4.8 16.5 1.0 OD2 B:ASP175 5.0 22.1 1.0 N B:PRO176 5.0 24.4 1.0 CG B:PRO176 5.0 22.4 1.0

Chlorine binding site 2 out of 2 in the Crystal Structure of Human 3-Phosphoglycerate Dehydrogenase in Complex with N-(3-Chloro-4-Methoxyphenyl) Acetamide


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 N-(3-Chloro-4-Methoxyphenyl) Acetamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl301 b:23.2 occ:1.00 CL1 A:8NB301 0.0 23.2 1.0 C5 A:8NB301 1.8 17.8 1.0 C6 A:8NB301 2.7 15.4 1.0 C4 A:8NB301 2.7 16.7 1.0 O1 A:8NB301 2.8 21.5 1.0 N A:GLY152 3.4 10.8 1.0 CG2 A:THR207 3.4 12.5 1.0 O A:TYR174 3.6 13.8 1.0 CD2 A:TYR174 3.6 14.5 1.0 CD A:PRO176 3.7 16.9 1.0 CA A:GLY152 3.8 10.7 1.0 C A:LEU151 3.8 9.9 1.0 CE2 A:TYR174 3.9 16.4 1.0 C1 A:8NB301 4.0 19.0 1.0 C3 A:8NB301 4.0 19.6 1.0 CA A:ASP175 4.0 14.4 1.0 C7 A:8NB301 4.3 20.6 1.0 C A:TYR174 4.3 12.2 1.0 CA A:LEU151 4.4 9.9 1.0 O A:LEU151 4.5 10.9 1.0 C2 A:8NB301 4.5 16.8 1.0 N A:ASP175 4.5 14.8 1.0 OD2 A:ASP175 4.6 18.4 1.0 CB A:LEU151 4.6 9.7 1.0 N A:PRO176 4.7 14.6 1.0 CB A:THR207 4.7 11.7 1.0 CG A:PRO176 4.8 18.1 1.0 CG A:TYR174 4.8 13.9 1.0 CG A:ASP175 4.8 17.3 1.0 CB A:ASP175 4.8 14.3 1.0 C A:ASP175 4.9 16.1 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