Chlorine in PDB 6plf: Crystal Structure of Human Phgdh Complexed with Compound 1

All present enzymatic activity of Crystal Structure of Human Phgdh Complexed with Compound 1:
1.1.1.37; 1.1.1.399; 1.1.1.95;

The structure of Crystal Structure of Human Phgdh Complexed with Compound 1, PDB code: 6plf was solved by A.Olland, D.Lakshminarasimhan, A.White, R.K.Suto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.37 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	43.202, 126.192, 59.504, 90.00, 99.76, 90.00
R / Rfree (%)	18.5 / 22.3

The binding sites of Chlorine atom in the Crystal Structure of Human Phgdh Complexed with Compound 1 (pdb code 6plf). 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 Phgdh Complexed with Compound 1, PDB code: 6plf:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Crystal Structure of Human Phgdh Complexed with Compound 1


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 Phgdh Complexed with Compound 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl401 b:38.9 occ:1.00 CL A:ONV401 0.0 38.9 1.0 C5 A:ONV401 1.8 26.6 1.0 C4 A:ONV401 2.7 33.7 1.0 C9 A:ONV401 2.8 27.6 1.0 O2 A:ONV401 3.0 41.5 1.0 C3 A:ONV401 3.1 58.0 1.0 CD2 A:TYR174 3.4 37.8 1.0 CD1 A:LEU216 3.7 31.1 1.0 CD2 A:LEU216 3.8 29.8 1.0 CD2 A:LEU193 3.8 29.1 1.0 CD1 A:LEU193 3.9 31.3 1.0 CE2 A:TYR174 4.0 37.8 1.0 C6 A:ONV401 4.0 27.5 1.0 C8 A:ONV401 4.0 25.0 1.0 CB A:LEU151 4.1 22.7 1.0 CG A:LEU216 4.3 29.7 1.0 CG A:LEU193 4.3 30.3 1.0 CG A:TYR174 4.5 34.6 1.0 CD2 A:LEU151 4.5 24.9 1.0 C7 A:ONV401 4.5 25.5 1.0 O A:TYR174 4.6 23.5 1.0 C1 A:ONV401 4.6 61.8 1.0 CD1 A:LEU151 4.6 27.6 1.0 CG A:LEU151 4.7 23.8 1.0 CB A:TYR174 4.7 29.0 1.0 CA A:LEU151 4.8 19.4 1.0 O1 A:ONV401 4.9 66.6 1.0

Chlorine binding site 2 out of 2 in the Crystal Structure of Human Phgdh Complexed with Compound 1


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 Phgdh Complexed with Compound 1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl401 b:35.4 occ:1.00 CL B:ONV401 0.0 35.4 1.0 C5 B:ONV401 1.8 32.2 1.0 C4 B:ONV401 2.7 37.3 1.0 C9 B:ONV401 2.7 31.8 1.0 O2 B:ONV401 2.9 36.9 1.0 CD1 B:TYR174 3.4 35.0 1.0 CD2 B:LEU193 3.8 25.9 1.0 CD1 B:LEU216 3.8 33.1 1.0 CE1 B:TYR174 3.9 39.8 1.0 CD1 B:LEU193 3.9 26.9 1.0 CD2 B:LEU216 3.9 28.6 1.0 C6 B:ONV401 4.0 33.2 1.0 C8 B:ONV401 4.0 33.9 1.0 CB B:LEU151 4.1 21.5 1.0 CG B:LEU193 4.3 27.2 1.0 C3 B:ONV401 4.3 42.1 1.0 CG B:TYR174 4.4 30.8 1.0 CD1 B:LEU151 4.4 27.4 1.0 CG B:LEU216 4.5 29.2 1.0 C7 B:ONV401 4.5 32.6 1.0 CD2 B:LEU151 4.5 24.9 1.0 CG B:LEU151 4.5 23.9 1.0 O B:TYR174 4.6 20.7 1.0 CB B:TYR174 4.7 25.4 1.0 CA B:LEU151 4.8 19.4 1.0 C2 B:ONV401 5.0 48.4 1.0

E.Mullarky, J.Xu, A.D.Robin, D.J.Huggins, A.Jennings, N.Noguchi, A.Olland, D.Lakshminarasimhan, M.Miller, D.Tomita, M.Michino, T.Su, G.Zhang, A.W.Stamford, P.T.Meinke, S.Kargman, L.C.Cantley. Inhibition of 3-Phosphoglycerate Dehydrogenase (Phgdh) By Indole Amides Abrogates De Novo Serine Synthesis in Cancer Cells. Bioorg.Med.Chem.Lett. V. 29 2503 2019.
ISSN: ESSN 1464-3405
PubMed: 31327531
DOI: 10.1016/J.BMCL.2019.07.011