Fluorine in PDB 5yfz: Plasmodium Vivax Shmt Bound with Plp-Glycine and S-GS626

All present enzymatic activity of Plasmodium Vivax Shmt Bound with Plp-Glycine and S-GS626:
2.1.2.1;

The structure of Plasmodium Vivax Shmt Bound with Plp-Glycine and S-GS626, PDB code: 5yfz 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 / 2.16
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	101.875, 58.796, 235.728, 90.00, 89.99, 90.00
R / Rfree (%)	26.3 / 33.3

The structure of Plasmodium Vivax Shmt Bound with Plp-Glycine and S-GS626 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-GS626 (pdb code 5yfz). 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-GS626, PDB code: 5yfz:
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-GS626


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-GS626 within 5.0Å range: probe atom residue distance (Å) B Occ A:F502 b:36.2 occ:1.00 F21 A:8UO502 0.0 36.2 1.0 C18 A:8UO502 1.3 36.0 1.0 C17 A:8UO502 2.3 36.0 1.0 C30 A:8UO502 2.4 36.5 1.0 CE A:LYS355 3.2 27.5 1.0 NZ A:LYS355 3.4 28.5 1.0 CG A:LYS355 3.5 26.7 1.0 C16 A:8UO502 3.6 35.2 1.0 C19 A:8UO502 3.6 36.2 1.0 O A:LYS355 3.8 29.4 1.0 CD A:LYS355 3.9 27.8 1.0 C20 A:8UO502 4.1 36.5 1.0 CG A:PRO367 4.1 39.1 1.0 C A:LYS355 4.3 26.6 1.0 CB A:LYS355 4.6 25.3 1.0 CD2 B:TYR63 4.7 38.7 1.0 N9 A:8UO502 4.8 35.1 1.0 N A:ASN356 4.8 26.2 1.0 N23 A:8UO502 4.8 39.3 1.0 CB A:PRO367 4.8 38.5 1.0 C4 A:8UO502 4.8 34.9 1.0 C15 A:8UO502 4.9 33.5 1.0 SG A:CYS364 4.9 70.5 1.0 CD A:PRO367 4.9 38.9 1.0 CA A:ASN356 4.9 24.9 1.0 C8 A:8UO502 5.0 36.9 1.0 C24 A:8UO502 5.0 42.4 1.0 O A:CYS364 5.0 62.9 1.0

Fluorine binding site 2 out of 3 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and S-GS626


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-GS626 within 5.0Å range: probe atom residue distance (Å) B Occ B:F502 b:46.4 occ:1.00 F21 B:8UO502 0.0 46.4 1.0 C18 B:8UO502 1.3 40.5 1.0 C30 B:8UO502 2.4 40.5 1.0 C17 B:8UO502 2.4 39.3 1.0 NZ B:LYS355 3.2 31.2 1.0 CD B:LYS355 3.3 27.5 1.0 CE B:LYS355 3.5 29.4 1.0 C19 B:8UO502 3.6 38.8 1.0 C16 B:8UO502 3.7 38.6 1.0 CG B:LYS355 3.7 25.3 1.0 CG B:PRO367 3.9 36.9 1.0 O B:LYS355 4.0 26.2 1.0 C20 B:8UO502 4.1 38.5 1.0 C B:LYS355 4.3 24.6 1.0 CB B:LYS355 4.5 23.5 1.0 CD B:PRO367 4.7 38.3 1.0 CB B:PRO367 4.7 36.4 1.0 N B:ASN356 4.8 24.9 1.0 N23 B:8UO502 4.8 38.7 1.0 O B:CYS364 4.9 51.2 1.0 CD2 A:TYR63 4.9 30.8 1.0 N9 B:8UO502 4.9 36.2 1.0 C4 B:8UO502 4.9 36.7 1.0 CA B:ASN356 5.0 24.2 1.0 C24 B:8UO502 5.0 41.8 1.0 C15 B:8UO502 5.0 34.5 1.0 CA B:LYS355 5.0 23.5 1.0

Fluorine binding site 3 out of 3 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and S-GS626


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-GS626 within 5.0Å range: probe atom residue distance (Å) B Occ C:F502 b:41.2 occ:1.00 F21 C:8UO502 0.0 41.2 1.0 C18 C:8UO502 1.3 39.4 1.0 C30 C:8UO502 2.4 39.1 1.0 C17 C:8UO502 2.4 37.2 1.0 CD C:LYS355 3.4 27.6 1.0 CE C:LYS355 3.5 29.7 1.0 CG C:LYS355 3.5 25.1 1.0 C19 C:8UO502 3.6 37.6 1.0 C16 C:8UO502 3.7 35.0 1.0 O C:LYS355 3.9 23.8 1.0 CG C:PRO367 3.9 37.3 1.0 NZ C:LYS355 4.0 32.8 1.0 C20 C:8UO502 4.1 36.0 1.0 C C:LYS355 4.3 23.5 1.0 O C:CYS364 4.4 54.2 1.0 CB C:LYS355 4.4 22.6 1.0 CD C:PRO367 4.7 38.8 1.0 CB C:PRO367 4.7 37.3 1.0 N23 C:8UO502 4.8 40.2 1.0 N9 C:8UO502 4.8 30.7 1.0 N C:ASN356 4.8 24.5 1.0 C4 C:8UO502 4.9 33.7 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