Fluorine in PDB 5yg3: Plasmodium Vivax Shmt Bound with Plp-Glycine and S-GS834

All present enzymatic activity of Plasmodium Vivax Shmt Bound with Plp-Glycine and S-GS834:
2.1.2.1;

The structure of Plasmodium Vivax Shmt Bound with Plp-Glycine and S-GS834, PDB code: 5yg3 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)	19.81 / 2.40
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	101.623, 58.727, 236.139, 90.00, 90.32, 90.00
R / Rfree (%)	22.2 / 30

The structure of Plasmodium Vivax Shmt Bound with Plp-Glycine and S-GS834 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-GS834 (pdb code 5yg3). 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-GS834, PDB code: 5yg3:
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-GS834


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-GS834 within 5.0Å range: probe atom residue distance (Å) B Occ A:F502 b:54.6 occ:1.00 F29 A:8UC502 0.0 54.6 1.0 C18 A:8UC502 1.3 52.0 1.0 C17 A:8UC502 2.3 49.4 1.0 C35 A:8UC502 2.4 51.7 1.0 C38 A:8UC502 2.9 50.1 1.0 C16 A:8UC502 3.6 48.0 1.0 CE A:LYS355 3.6 36.4 1.0 C19 A:8UC502 3.7 49.2 1.0 CD A:LYS355 3.8 36.1 1.0 CG A:LYS355 3.8 34.5 1.0 O A:LYS355 3.9 35.1 1.0 CD1 B:TYR63 4.0 40.4 1.0 C20 A:8UC502 4.1 51.7 1.0 C14 A:8UC502 4.3 49.1 1.0 NZ A:LYS355 4.6 37.2 1.0 CE1 B:TYR63 4.6 43.5 1.0 C A:LYS355 4.6 32.6 1.0 C4 A:8UC502 4.7 46.4 1.0 C30 A:8UC502 4.7 47.8 1.0 CG A:PRO367 4.8 49.9 1.0 CB A:LYS355 4.8 30.9 1.0 N9 A:8UC502 4.9 49.6 1.0 CG B:TYR63 4.9 39.4 1.0 C41 A:8UC502 5.0 48.3 1.0

Fluorine binding site 2 out of 3 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and S-GS834


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-GS834 within 5.0Å range: probe atom residue distance (Å) B Occ B:F502 b:51.7 occ:1.00 F29 B:8UC502 0.0 51.7 1.0 C18 B:8UC502 1.4 51.7 1.0 C17 B:8UC502 2.3 50.7 1.0 C35 B:8UC502 2.4 51.6 1.0 C38 B:8UC502 2.9 50.8 1.0 O B:LYS355 3.4 29.9 1.0 CE B:LYS355 3.6 33.6 1.0 C16 B:8UC502 3.6 49.9 1.0 CG B:LYS355 3.7 31.7 1.0 CD B:LYS355 3.7 32.3 1.0 C19 B:8UC502 3.7 49.5 1.0 C B:LYS355 4.1 29.7 1.0 CD1 A:TYR63 4.2 41.4 1.0 C20 B:8UC502 4.2 49.8 1.0 C14 B:8UC502 4.3 49.5 1.0 CB B:LYS355 4.5 28.7 1.0 NZ B:LYS355 4.5 33.8 1.0 C30 B:8UC502 4.7 48.2 1.0 C4 B:8UC502 4.7 47.6 1.0 CE1 A:TYR63 4.7 44.3 1.0 CG B:PRO367 4.8 46.3 1.0 CA B:LYS355 4.8 28.0 1.0 N B:ASN356 4.8 29.0 1.0 N9 B:8UC502 4.9 50.2 1.0 C8 B:8UC502 5.0 51.4 1.0

Fluorine binding site 3 out of 3 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and S-GS834


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-GS834 within 5.0Å range: probe atom residue distance (Å) B Occ C:F502 b:52.1 occ:1.00 F29 C:8UC502 0.0 52.1 1.0 C18 C:8UC502 1.4 52.3 1.0 C17 C:8UC502 2.4 51.8 1.0 C35 C:8UC502 2.4 52.6 1.0 C38 C:8UC502 3.0 52.1 1.0 O C:LYS355 3.0 29.3 1.0 CG C:LYS355 3.6 33.4 1.0 C16 C:8UC502 3.6 50.5 1.0 C19 C:8UC502 3.7 52.4 1.0 CE C:LYS355 3.8 36.7 1.0 CD C:LYS355 3.9 34.0 1.0 C C:LYS355 4.0 29.9 1.0 C20 C:8UC502 4.2 51.2 1.0 C14 C:8UC502 4.5 50.3 1.0 N C:LYS355 4.5 27.7 1.0 CB C:LYS355 4.5 30.0 1.0 CA C:LYS355 4.5 28.5 1.0 C4 C:8UC502 4.7 49.6 1.0 ND2 C:ASN354 4.9 24.9 1.0 CB C:ASN354 4.9 27.9 1.0 N C:ASN356 5.0 28.2 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