Fluorine in PDB 5yg4: Plasmodium Vivax Shmt Bound with Plp-Glycine and S-GS849

All present enzymatic activity of Plasmodium Vivax Shmt Bound with Plp-Glycine and S-GS849:
2.1.2.1;

The structure of Plasmodium Vivax Shmt Bound with Plp-Glycine and S-GS849, PDB code: 5yg4 was solved by P.Chitnumsub, A.Jaruwat, U.Leartsakulpanich, G.Schwertz, F.Diederich, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	100.848, 58.207, 234.497, 90.00, 89.99, 90.00
R / Rfree (%)	21.5 / 27.8

The structure of Plasmodium Vivax Shmt Bound with Plp-Glycine and S-GS849 also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Fluorine atom in the Plasmodium Vivax Shmt Bound with Plp-Glycine and S-GS849 (pdb code 5yg4). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Plasmodium Vivax Shmt Bound with Plp-Glycine and S-GS849, PDB code: 5yg4:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and S-GS849


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Plasmodium Vivax Shmt Bound with Plp-Glycine and S-GS849 within 5.0Å range: probe atom residue distance (Å) B Occ A:F502 b:33.3 occ:1.00 F29 A:8UF502 0.0 33.3 1.0 C18 A:8UF502 1.3 34.5 1.0 C17 A:8UF502 2.3 33.0 1.0 C41 A:8UF502 2.4 36.5 1.0 C44 A:8UF502 2.9 32.9 1.0 O A:HOH704 3.1 37.2 1.0 CE A:LYS355 3.2 25.4 1.0 C16 A:8UF502 3.6 31.5 1.0 CG A:LYS355 3.7 23.6 1.0 C19 A:8UF502 3.7 34.5 1.0 CD A:LYS355 3.8 24.2 1.0 O A:LYS355 3.8 22.4 1.0 CD2 B:TYR63 4.0 50.4 1.0 C20 A:8UF502 4.1 34.5 1.0 C14 A:8UF502 4.3 31.5 1.0 CB B:TYR63 4.5 42.9 1.0 C A:LYS355 4.5 22.4 1.0 NZ A:LYS355 4.5 27.3 1.0 C4 A:8UF502 4.7 29.4 1.0 O B:TYR63 4.7 35.5 1.0 CG B:TYR63 4.8 47.3 1.0 C15 A:8UF502 4.8 31.8 1.0 CB A:LYS355 4.8 22.4 1.0 N35 A:8UF502 4.9 37.9 1.0 N9 A:8UF502 4.9 26.0 1.0 CE2 B:TYR63 5.0 53.5 1.0 C8 A:8UF502 5.0 28.6 1.0

Fluorine binding site 2 out of 3 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and S-GS849


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Plasmodium Vivax Shmt Bound with Plp-Glycine and S-GS849 within 5.0Å range: probe atom residue distance (Å) B Occ B:F502 b:35.4 occ:1.00 F29 B:8UF502 0.0 35.4 1.0 C18 B:8UF502 1.3 35.6 1.0 C17 B:8UF502 2.4 33.7 1.0 C41 B:8UF502 2.4 36.2 1.0 C44 B:8UF502 3.0 33.6 1.0 CE B:LYS355 3.2 28.3 1.0 CD B:LYS355 3.5 26.7 1.0 CG B:LYS355 3.6 26.2 1.0 C16 B:8UF502 3.6 32.8 1.0 C19 B:8UF502 3.7 35.1 1.0 O B:LYS355 3.8 22.7 1.0 CD2 A:TYR63 4.0 44.7 1.0 C20 B:8UF502 4.2 34.3 1.0 C14 B:8UF502 4.4 32.6 1.0 CB A:TYR63 4.5 40.1 1.0 C B:LYS355 4.5 22.4 1.0 NZ B:LYS355 4.6 29.8 1.0 CG A:TYR63 4.7 42.0 1.0 C4 B:8UF502 4.7 30.6 1.0 CB B:LYS355 4.8 24.2 1.0 C15 B:8UF502 4.8 32.9 1.0 O A:TYR63 4.8 37.5 1.0 N35 B:8UF502 4.8 36.7 1.0 CE2 A:TYR63 4.9 46.0 1.0

Fluorine binding site 3 out of 3 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and S-GS849


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Plasmodium Vivax Shmt Bound with Plp-Glycine and S-GS849 within 5.0Å range: probe atom residue distance (Å) B Occ C:F502 b:34.4 occ:1.00 F29 C:8UF502 0.0 34.4 1.0 C18 C:8UF502 1.4 36.0 1.0 C17 C:8UF502 2.4 34.3 1.0 C41 C:8UF502 2.4 36.5 1.0 C44 C:8UF502 3.0 33.5 1.0 CE C:LYS355 3.1 26.8 1.0 CG C:LYS355 3.5 24.3 1.0 C16 C:8UF502 3.6 33.2 1.0 O C:LYS355 3.7 21.5 1.0 CD C:LYS355 3.7 24.9 1.0 C19 C:8UF502 3.7 35.2 1.0 C20 C:8UF502 4.2 34.9 1.0 C14 C:8UF502 4.4 32.0 1.0 NZ C:LYS355 4.4 29.1 1.0 C C:LYS355 4.4 21.3 1.0 CB C:LYS355 4.6 22.3 1.0 C4 C:8UF502 4.7 31.7 1.0 C15 C:8UF502 4.8 31.6 1.0 N35 C:8UF502 4.8 35.1 1.0 CA C:LYS355 4.9 21.3 1.0

G.Schwertz, M.C.Witschel, M.Rottmann, U.Leartsakulpanich, P.Chitnumsub, A.Jaruwat, W.Amornwatcharapong, W.Ittarat, A.Schafer, R.A.Aponte, N.Trapp, P.Chaiyen, F.Diederich. Potent Inhibitors of Plasmodial Serine Hydroxymethyltransferase (Shmt) Featuring A Spirocyclic Scaffold Chemmedchem V. 13 931 2018.
ISSN: ESSN 1860-7187
PubMed: 29655285
DOI: 10.1002/CMDC.201800053