Fluorine in PDB 8fju: Human Mitochondrial Serine Hydroxymethyltransferase (SHMT2) in Complex with Plp, Glycine and AGF347 Inhibitor

Enzymatic activity of Human Mitochondrial Serine Hydroxymethyltransferase (SHMT2) in Complex with Plp, Glycine and AGF347 Inhibitor

All present enzymatic activity of Human Mitochondrial Serine Hydroxymethyltransferase (SHMT2) in Complex with Plp, Glycine and AGF347 Inhibitor:
2.1.2.1;

Protein crystallography data

The structure of Human Mitochondrial Serine Hydroxymethyltransferase (SHMT2) in Complex with Plp, Glycine and AGF347 Inhibitor, PDB code: 8fju 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) 48.55 / 2.51
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 157.338, 157.338, 207.552, 90, 90, 120
R / Rfree (%) 23.2 / 27.3

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Human Mitochondrial Serine Hydroxymethyltransferase (SHMT2) in Complex with Plp, Glycine and AGF347 Inhibitor (pdb code 8fju). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Human Mitochondrial Serine Hydroxymethyltransferase (SHMT2) in Complex with Plp, Glycine and AGF347 Inhibitor, PDB code: 8fju:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 8fju

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Fluorine binding site 1 out of 3 in the Human Mitochondrial Serine Hydroxymethyltransferase (SHMT2) in Complex with Plp, Glycine and AGF347 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 AGF347 Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F602

b:77.9
occ:0.91
 F34 A:Y79602 0.0 77.9 0.9
C13 A:Y79602 1.4 71.6 0.9
C15 A:Y79602 2.4 68.9 0.9
C12 A:Y79602 2.4 66.6 0.9
O18 A:Y79602 2.5 75.7 0.9
C17 A:Y79602 2.8 73.0 0.9
CD2 A:LEU166 3.2 51.5 1.0
C33 A:Y79602 3.6 65.7 0.9
C14 A:Y79602 3.6 64.0 0.9
N19 A:Y79602 4.1 73.6 0.9
C16 A:Y79602 4.1 60.3 0.9
CE2 A:TYR176 4.3 50.2 1.0
O A:HOH754 4.6 58.5 1.0
OH A:TYR176 4.7 55.7 1.0
CG A:LEU166 4.7 45.5 1.0
C32 A:Y79602 4.9 61.5 0.9
CZ A:TYR176 4.9 50.6 1.0
C26 A:Y79602 4.9 82.2 0.9
O27 A:Y79602 5.0 90.2 0.9

Fluorine binding site 2 out of 3 in 8fju

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Fluorine binding site 2 out of 3 in the Human Mitochondrial Serine Hydroxymethyltransferase (SHMT2) in Complex with Plp, Glycine and AGF347 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 AGF347 Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F602

b:50.8
occ:0.45
 F34 B:Y79602 0.0 50.8 0.5
C13 B:Y79602 1.4 50.3 0.5
C14 B:Y79602 2.2 47.2 0.6
C15 B:Y79602 2.4 49.4 0.5
C12 B:Y79602 2.4 48.7 0.5
C16 B:Y79602 2.7 47.4 0.6
O18 B:Y79602 2.8 51.8 0.5
C17 B:Y79602 2.8 50.1 0.5
C12 B:Y79602 3.0 48.8 0.6
C17 B:Y79602 3.6 50.8 0.6
O18 B:Y79602 3.6 52.0 0.6
C33 B:Y79602 3.6 48.2 0.5
C14 B:Y79602 3.7 47.8 0.5
C33 B:Y79602 3.8 48.5 0.6
CD2 B:LEU166 3.8 38.2 1.0
C13 B:Y79602 4.0 48.1 0.6
N19 B:Y79602 4.1 52.0 0.5
C16 B:Y79602 4.1 47.5 0.5
C15 B:Y79602 4.3 49.2 0.6
CE1 A:TYR105 4.5 59.9 1.0
N19 B:Y79602 4.7 51.8 0.6
C32 B:Y79602 4.8 45.3 0.6
C32 B:Y79602 4.9 44.6 0.5
CD1 A:TYR105 4.9 64.9 1.0
C21 B:Y79602 4.9 54.6 0.5
CG B:LEU166 5.0 40.6 1.0
CD1 B:LEU166 5.0 38.5 1.0

Fluorine binding site 3 out of 3 in 8fju

Go back to Fluorine Binding Sites List in 8fju
Fluorine binding site 3 out of 3 in the Human Mitochondrial Serine Hydroxymethyltransferase (SHMT2) in Complex with Plp, Glycine and AGF347 Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Human Mitochondrial Serine Hydroxymethyltransferase (SHMT2) in Complex with Plp, Glycine and AGF347 Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F602

b:46.3
occ:0.55
 F34 B:Y79602 0.0 46.3 0.6
C13 B:Y79602 1.4 48.1 0.6
C14 B:Y79602 2.3 47.8 0.5
C12 B:Y79602 2.4 48.8 0.6
C15 B:Y79602 2.4 49.2 0.6
N19 B:Y79602 2.5 51.8 0.6
N19 B:Y79602 2.6 52.0 0.5
C17 B:Y79602 2.8 50.8 0.6
C12 B:Y79602 3.0 48.7 0.5
C16 B:Y79602 3.1 47.5 0.5
OH A:TYR105 3.2 56.6 1.0
C17 B:Y79602 3.2 50.1 0.5
O28 B:Y79602 3.3 52.1 0.5
O27 B:Y79602 3.5 51.2 0.6
C33 B:Y79602 3.6 48.5 0.6
C14 B:Y79602 3.6 47.2 0.6
CG A:PRO321 3.7 32.5 1.0
C20 B:Y79602 3.8 53.9 0.6
C20 B:Y79602 3.9 53.3 0.5
O18 B:Y79602 4.0 52.0 0.6
C26 B:Y79602 4.0 53.6 0.5
C13 B:Y79602 4.1 50.3 0.5
C26 B:Y79602 4.1 52.8 0.6
C16 B:Y79602 4.1 47.4 0.6
CZ A:TYR105 4.1 59.9 1.0
C33 B:Y79602 4.2 48.2 0.5
CG2 B:ILE183 4.3 29.6 1.0
O18 B:Y79602 4.4 51.8 0.5
CD A:PRO321 4.4 30.4 1.0
CE1 A:TYR105 4.4 59.9 1.0
CE1 A:PHE317 4.5 37.9 1.0
C15 B:Y79602 4.6 49.4 0.5
CB A:PRO321 4.6 35.5 1.0
C22 B:Y79602 4.6 55.6 0.6
C21 B:Y79602 4.8 54.6 0.6
C22 B:Y79602 4.8 55.5 0.5
C21 B:Y79602 4.9 54.6 0.5
C32 B:Y79602 4.9 45.3 0.6
CZ A:PHE317 4.9 36.3 1.0

Reference:

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
Page generated: Fri Aug 2 19:10:23 2024

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