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Fluorine in PDB 8v9m: Human Ornithine Aminotransferase Cocrystallized with Its Inhibitor, (R)-3-Amino-5,5-Difluorocyclohex-1-Ene-1-Carboxylic Acid.

Enzymatic activity of Human Ornithine Aminotransferase Cocrystallized with Its Inhibitor, (R)-3-Amino-5,5-Difluorocyclohex-1-Ene-1-Carboxylic Acid.

All present enzymatic activity of Human Ornithine Aminotransferase Cocrystallized with Its Inhibitor, (R)-3-Amino-5,5-Difluorocyclohex-1-Ene-1-Carboxylic Acid.:
2.6.1.13;

Protein crystallography data

The structure of Human Ornithine Aminotransferase Cocrystallized with Its Inhibitor, (R)-3-Amino-5,5-Difluorocyclohex-1-Ene-1-Carboxylic Acid., PDB code: 8v9m was solved by A.L.Vargas, A.Devitt, N.Kaley, R.Silverman, D.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.01 / 1.61
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 115.334, 115.334, 186.292, 90, 90, 120
R / Rfree (%) 16.4 / 19.3

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Human Ornithine Aminotransferase Cocrystallized with Its Inhibitor, (R)-3-Amino-5,5-Difluorocyclohex-1-Ene-1-Carboxylic Acid. (pdb code 8v9m). 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 Ornithine Aminotransferase Cocrystallized with Its Inhibitor, (R)-3-Amino-5,5-Difluorocyclohex-1-Ene-1-Carboxylic Acid., PDB code: 8v9m:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 8v9m

Go back to Fluorine Binding Sites List in 8v9m
Fluorine binding site 1 out of 3 in the Human Ornithine Aminotransferase Cocrystallized with Its Inhibitor, (R)-3-Amino-5,5-Difluorocyclohex-1-Ene-1-Carboxylic Acid.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Human Ornithine Aminotransferase Cocrystallized with Its Inhibitor, (R)-3-Amino-5,5-Difluorocyclohex-1-Ene-1-Carboxylic Acid. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:33.0
occ:1.00
 F11 A:YR5501 0.0 33.0 1.0
C02 A:YR5501 1.4 34.0 1.0
C01 A:YR5501 2.3 26.9 1.0
C03 A:YR5501 2.5 31.5 1.0
NZ A:LYS405 2.5 51.1 1.0
OE2 A:GLU235 2.8 40.7 1.0
CE1 A:TYR85 3.0 39.6 1.0
CD A:GLU235 3.0 37.9 1.0
CZ A:TYR85 3.2 37.6 1.0
CD1 A:TYR85 3.5 41.1 1.0
OE1 A:GLU235 3.5 33.0 1.0
OH A:TYR85 3.5 43.2 1.0
C04 A:YR5501 3.7 25.5 1.0
CG A:GLU235 3.7 35.0 1.0
C06 A:YR5501 3.7 29.1 1.0
CE2 A:TYR85 3.9 36.2 1.0
CE A:LYS405 4.0 38.0 1.0
CG A:TYR85 4.2 38.0 1.0
C05 A:YR5501 4.2 25.8 1.0
CD2 A:TYR85 4.3 32.9 1.0
CD A:LYS405 4.5 49.2 1.0
O A:HOH825 4.5 42.3 1.0
O A:HOH853 4.7 49.3 1.0
O A:HOH680 4.8 38.4 1.0
N10 A:YR5501 4.9 27.3 1.0
C07 A:YR5501 4.9 31.9 1.0

Fluorine binding site 2 out of 3 in 8v9m

Go back to Fluorine Binding Sites List in 8v9m
Fluorine binding site 2 out of 3 in the Human Ornithine Aminotransferase Cocrystallized with Its Inhibitor, (R)-3-Amino-5,5-Difluorocyclohex-1-Ene-1-Carboxylic Acid.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Human Ornithine Aminotransferase Cocrystallized with Its Inhibitor, (R)-3-Amino-5,5-Difluorocyclohex-1-Ene-1-Carboxylic Acid. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F501

b:31.5
occ:1.00
 F11 B:YR5501 0.0 31.5 1.0
C02 B:YR5501 1.4 32.5 1.0
C01 B:YR5501 2.3 28.3 1.0
C03 B:YR5501 2.5 28.2 1.0
OE1 B:GLU235 2.9 36.0 1.0
CE1 B:TYR85 3.0 46.3 1.0
CZ B:TYR85 3.1 38.7 1.0
CD B:GLU235 3.3 34.6 1.0
CD1 B:TYR85 3.3 45.5 1.0
CE2 B:TYR85 3.5 36.5 1.0
OH B:TYR85 3.6 46.1 1.0
OE2 B:GLU235 3.6 38.0 1.0
C04 B:YR5501 3.6 24.7 1.0
C06 B:YR5501 3.7 27.3 1.0
CG B:TYR85 3.8 34.7 1.0
CD2 B:TYR85 3.9 33.3 1.0
NH2 B:ARG413 3.9 39.8 1.0
CG B:GLU235 4.0 28.4 1.0
C05 B:YR5501 4.2 25.8 1.0
O B:HOH696 4.2 43.8 1.0
O B:HOH748 4.6 39.6 1.0
CB B:TYR85 4.8 33.3 1.0
C07 B:YR5501 4.9 31.3 1.0
N10 B:YR5501 4.9 25.3 1.0

Fluorine binding site 3 out of 3 in 8v9m

Go back to Fluorine Binding Sites List in 8v9m
Fluorine binding site 3 out of 3 in the Human Ornithine Aminotransferase Cocrystallized with Its Inhibitor, (R)-3-Amino-5,5-Difluorocyclohex-1-Ene-1-Carboxylic Acid.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Human Ornithine Aminotransferase Cocrystallized with Its Inhibitor, (R)-3-Amino-5,5-Difluorocyclohex-1-Ene-1-Carboxylic Acid. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F501

b:29.5
occ:1.00
 F11 C:YR5501 0.0 29.5 1.0
C02 C:YR5501 1.3 23.2 1.0
C01 C:YR5501 2.3 24.6 1.0
C03 C:YR5501 2.5 23.2 1.0
OE1 C:GLU235 2.8 34.2 1.0
CD C:GLU235 3.1 33.5 1.0
CE1 C:TYR85 3.1 34.4 1.0
CD1 C:TYR85 3.2 29.5 1.0
OE2 C:GLU235 3.5 33.6 1.0
C04 C:YR5501 3.7 23.3 1.0
C06 C:YR5501 3.7 22.4 1.0
O C:HOH636 3.7 39.0 1.0
CZ C:TYR85 3.7 33.7 1.0
CG C:TYR85 3.8 31.3 1.0
CG C:GLU235 3.9 28.3 1.0
O C:HOH880 4.0 43.6 1.0
CE2 C:TYR85 4.2 36.3 1.0
C05 C:YR5501 4.2 23.6 1.0
CD2 C:TYR85 4.2 33.0 1.0
OH C:TYR85 4.4 41.6 1.0
CB C:TYR85 4.6 30.4 1.0
O C:HOH711 4.8 46.3 1.0
N10 C:YR5501 4.8 22.3 1.0
C07 C:YR5501 4.9 31.7 1.0

Reference:

A.N.Devitt, A.L.Vargas, W.Zhu, B.J.Des Soye, F.A.Butun, T.Alt, N.Kaley, G.M.Ferreira, G.R.Moran, N.L.Kelleher, D.Liu, R.B.Silverman. Design, Synthesis, and Mechanistic Studies of ( R )-3-Amino-5,5-Difluorocyclohex-1-Ene-1-Carboxylic Acid As An Inactivator of Human Ornithine Aminotransferase. Acs Chem.Biol. 2024.
ISSN: ESSN 1554-8937
PubMed: 38630468
DOI: 10.1021/ACSCHEMBIO.4C00022
Page generated: Wed Jul 16 09:42:17 2025

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