Fluorine in PDB 8fjt: Human Mitochondrial Serine Hydroxymethyltransferase (SHMT2) in Complex with Plp, Glycine and AGF362 Inhibitor

All present enzymatic activity of Human Mitochondrial Serine Hydroxymethyltransferase (SHMT2) in Complex with Plp, Glycine and AGF362 Inhibitor:
2.1.2.1;

The structure of Human Mitochondrial Serine Hydroxymethyltransferase (SHMT2) in Complex with Plp, Glycine and AGF362 Inhibitor, PDB code: 8fjt was solved by J.M.Katinas, C.E.Dann Iii, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.85 / 2.47
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	160.389, 160.389, 208.748, 90, 90, 120
R / Rfree (%)	24.1 / 28.5

The binding sites of Fluorine atom in the Human Mitochondrial Serine Hydroxymethyltransferase (SHMT2) in Complex with Plp, Glycine and AGF362 Inhibitor (pdb code 8fjt). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Human Mitochondrial Serine Hydroxymethyltransferase (SHMT2) in Complex with Plp, Glycine and AGF362 Inhibitor, PDB code: 8fjt:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Human Mitochondrial Serine Hydroxymethyltransferase (SHMT2) in Complex with Plp, Glycine and AGF362 Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Human Mitochondrial Serine Hydroxymethyltransferase (SHMT2) in Complex with Plp, Glycine and AGF362 Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F602 b:65.1 occ:0.87 F33 A:Y72602 0.0 65.1 0.9 C12 A:Y72602 1.4 67.6 0.9 C13 A:Y72602 2.4 57.9 0.9 C16 A:Y72602 2.5 64.5 0.9 N19 A:Y72602 2.8 69.4 0.9 C32 A:Y72602 3.0 56.4 0.9 C17 A:Y72602 3.0 64.0 0.9 C15 A:Y72602 3.7 64.0 0.9 CE1 A:TYR105 3.7 70.9 1.0 CG A:PRO321 3.8 43.9 1.0 CD1 A:TYR105 3.8 75.3 1.0 S14 A:Y72602 3.8 70.0 0.9 CE2 A:PHE320 3.9 46.2 1.0 CB A:PRO321 4.1 47.0 1.0 C20 A:Y72602 4.1 70.9 0.9 O18 A:Y72602 4.2 64.9 0.9 CZ A:PHE320 4.2 44.5 1.0 C31 A:Y72602 4.5 61.5 0.9 CZ A:TYR105 4.6 71.8 1.0 O25 A:Y72602 4.7 55.0 0.9 CG A:TYR105 4.7 67.5 1.0 CD2 A:PHE320 4.8 42.0 1.0 C21 A:Y72602 4.9 62.4 0.9

Fluorine binding site 2 out of 2 in the Human Mitochondrial Serine Hydroxymethyltransferase (SHMT2) in Complex with Plp, Glycine and AGF362 Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Human Mitochondrial Serine Hydroxymethyltransferase (SHMT2) in Complex with Plp, Glycine and AGF362 Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:F801 b:54.1 occ:1.00 F33 B:Y72801 0.0 54.1 1.0 C12 B:Y72801 1.4 49.3 1.0 C13 B:Y72801 2.4 43.7 1.0 C16 B:Y72801 2.5 47.5 1.0 C32 B:Y72801 3.0 49.1 1.0 C17 B:Y72801 3.1 51.3 1.0 N19 B:Y72801 3.1 60.1 1.0 CG B:PRO321 3.6 33.1 1.0 CE2 B:PHE320 3.6 36.6 1.0 CB B:PRO321 3.7 33.1 1.0 C15 B:Y72801 3.7 41.9 1.0 O25 B:Y72801 3.8 62.0 1.0 S14 B:Y72801 3.8 52.0 1.0 CZ B:PHE320 3.8 37.1 1.0 O18 B:Y72801 4.1 58.8 1.0 CE1 B:TYR105 4.2 52.1 1.0 CD1 B:TYR105 4.3 42.6 1.0 CD B:PRO321 4.3 33.8 1.0 C20 B:Y72801 4.4 68.3 1.0 CD2 B:PHE320 4.5 31.7 1.0 C31 B:Y72801 4.5 50.1 1.0 C21 B:Y72801 4.8 71.1 1.0 CE1 B:PHE320 4.9 32.1 1.0 CA B:PRO321 4.9 32.1 1.0 CZ B:TYR105 5.0 56.9 1.0 N B:PRO321 5.0 33.2 1.0

M.J.Nayeen, J.M.Katinas, T.Magdum, K.Shah, J.E.Wong, C.E.O'connor, A.N.Fifer, A.Wallace-Povirk, Z.Hou, L.H.Matherly, C.E.Dann 3Rd, A.Gangjee. Structure-Based Design of Transport-Specific Multitargeted One-Carbon Metabolism Inhibitors in Cytosol and Mitochondria. J.Med.Chem. V. 66 11294 2023.
ISSN: ISSN 0022-2623
PubMed: 37582241
DOI: 10.1021/ACS.JMEDCHEM.3C00763