Fluorine in PDB 7lk1: Ornithine Aminotransferase (Oat) with Its Potent Inhibitor - (S)-3- Amino-4,4-Difluorocyclopent-1-Enecarboxylic Acid (Ss-1-148) - 1 Hour Soaking

Enzymatic activity of Ornithine Aminotransferase (Oat) with Its Potent Inhibitor - (S)-3- Amino-4,4-Difluorocyclopent-1-Enecarboxylic Acid (Ss-1-148) - 1 Hour Soaking

All present enzymatic activity of Ornithine Aminotransferase (Oat) with Its Potent Inhibitor - (S)-3- Amino-4,4-Difluorocyclopent-1-Enecarboxylic Acid (Ss-1-148) - 1 Hour Soaking:
2.6.1.13;

Protein crystallography data

The structure of Ornithine Aminotransferase (Oat) with Its Potent Inhibitor - (S)-3- Amino-4,4-Difluorocyclopent-1-Enecarboxylic Acid (Ss-1-148) - 1 Hour Soaking, PDB code: 7lk1 was solved by A.Butrin, S.Shen, D.Liu, R.Silverman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.32 / 1.79
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 115.65, 115.65, 186.69, 90, 90, 120
R / Rfree (%) 21.6 / 24.1

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Ornithine Aminotransferase (Oat) with Its Potent Inhibitor - (S)-3- Amino-4,4-Difluorocyclopent-1-Enecarboxylic Acid (Ss-1-148) - 1 Hour Soaking (pdb code 7lk1). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 5 binding sites of Fluorine where determined in the Ornithine Aminotransferase (Oat) with Its Potent Inhibitor - (S)-3- Amino-4,4-Difluorocyclopent-1-Enecarboxylic Acid (Ss-1-148) - 1 Hour Soaking, PDB code: 7lk1:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5;

Fluorine binding site 1 out of 5 in 7lk1

Go back to Fluorine Binding Sites List in 7lk1
Fluorine binding site 1 out of 5 in the Ornithine Aminotransferase (Oat) with Its Potent Inhibitor - (S)-3- Amino-4,4-Difluorocyclopent-1-Enecarboxylic Acid (Ss-1-148) - 1 Hour Soaking


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Ornithine Aminotransferase (Oat) with Its Potent Inhibitor - (S)-3- Amino-4,4-Difluorocyclopent-1-Enecarboxylic Acid (Ss-1-148) - 1 Hour Soaking within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:66.2
occ:0.47
 F22 A:Y37501 0.0 66.2 0.5
C19 A:Y37501 0.7 55.7 0.5
C21 A:Y37501 1.0 58.0 0.5
C18 A:Y37501 1.4 59.8 0.5
C17 A:Y37501 2.0 57.7 0.5
C33 A:Y37501 2.1 46.1 0.5
C20 A:Y37501 2.3 65.5 0.5
C17 A:Y37501 2.5 54.4 0.5
C20 A:Y37501 2.5 65.7 0.5
C18 A:Y37501 2.7 68.4 0.5
O35 A:Y37501 2.7 34.8 0.5
N11 A:Y37501 3.0 48.0 0.5
N11 A:Y37501 3.1 51.8 0.5
O34 A:Y37501 3.2 52.6 0.5
O A:HOH767 3.3 48.2 1.0
C19 A:Y37501 3.6 52.3 0.5
C21 A:Y37501 3.6 57.5 0.5
C01 A:Y37501 3.7 42.8 0.5
C01 A:Y37501 3.9 41.5 0.5
F22 A:Y37501 3.9 78.2 0.5
O16 A:Y37501 4.0 31.9 0.5
O16 A:Y37501 4.0 32.2 0.5
O A:HOH698 4.0 36.1 1.0
NZ A:LYS292 4.2 46.4 0.5
CD2 A:TYR85 4.3 55.5 1.0
NZ A:LYS292 4.3 48.5 0.5
CE A:LYS292 4.4 40.8 0.5
CE1 A:PHE177 4.5 37.7 1.0
CE A:LYS292 4.6 47.8 0.5
CE2 A:TYR85 4.6 54.9 1.0
O A:HOH697 4.6 42.2 1.0
CG A:TYR85 4.7 54.6 1.0
CZ A:PHE177 4.9 39.0 1.0

Fluorine binding site 2 out of 5 in 7lk1

Go back to Fluorine Binding Sites List in 7lk1
Fluorine binding site 2 out of 5 in the Ornithine Aminotransferase (Oat) with Its Potent Inhibitor - (S)-3- Amino-4,4-Difluorocyclopent-1-Enecarboxylic Acid (Ss-1-148) - 1 Hour Soaking


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Ornithine Aminotransferase (Oat) with Its Potent Inhibitor - (S)-3- Amino-4,4-Difluorocyclopent-1-Enecarboxylic Acid (Ss-1-148) - 1 Hour Soaking within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:78.2
occ:0.53
 F22 A:Y37501 0.0 78.2 0.5
C21 A:Y37501 0.7 57.5 0.5
C19 A:Y37501 1.2 52.3 0.5
C18 A:Y37501 1.4 68.4 0.5
C33 A:Y37501 1.4 43.5 0.5
C20 A:Y37501 2.0 65.7 0.5
O34 A:Y37501 2.1 42.4 0.5
C17 A:Y37501 2.3 54.4 0.5
O35 A:Y37501 2.4 45.7 0.5
C17 A:Y37501 2.5 57.7 0.5
C20 A:Y37501 2.5 65.5 0.5
C18 A:Y37501 2.6 59.8 0.5
N11 A:Y37501 2.8 51.8 0.5
N11 A:Y37501 3.6 48.0 0.5
C19 A:Y37501 3.7 55.7 0.5
C21 A:Y37501 3.7 58.0 0.5
CG A:GLU235 3.7 58.8 0.8
NE2 A:GLN266 3.8 43.7 1.0
CD1 A:TYR85 3.8 53.4 1.0
F22 A:Y37501 3.9 66.2 0.5
O10 A:Y37501 3.9 40.1 0.5
CB A:GLU235 4.0 42.0 1.0
NZ A:LYS292 4.1 46.4 0.5
O10 A:Y37501 4.1 43.3 0.5
CG A:TYR85 4.2 54.6 1.0
C01 A:Y37501 4.3 42.8 0.5
CE1 A:TYR85 4.3 52.9 1.0
C01 A:Y37501 4.4 41.5 0.5
CD1 A:PHE177 4.4 36.9 1.0
CB A:TYR85 4.4 54.9 1.0
CE1 A:PHE177 4.4 37.7 1.0
O A:HOH726 4.5 45.0 1.0
CA A:GLU235 4.5 36.2 1.0
NH2 A:ARG413 4.6 49.6 1.0
NH1 A:ARG413 4.6 49.1 1.0
CE A:LYS292 4.6 40.8 0.5
N A:GLU235 4.7 41.4 1.0
CD A:GLN266 4.7 50.6 1.0
C09 A:Y37501 4.7 37.3 0.5
CD2 A:TYR85 4.9 55.5 1.0
C09 A:Y37501 4.9 39.2 0.5
C02 A:Y37501 4.9 37.9 0.5
OE1 A:GLN266 5.0 56.7 1.0
C33 A:Y37501 5.0 46.1 0.5

Fluorine binding site 3 out of 5 in 7lk1

Go back to Fluorine Binding Sites List in 7lk1
Fluorine binding site 3 out of 5 in the Ornithine Aminotransferase (Oat) with Its Potent Inhibitor - (S)-3- Amino-4,4-Difluorocyclopent-1-Enecarboxylic Acid (Ss-1-148) - 1 Hour Soaking


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Ornithine Aminotransferase (Oat) with Its Potent Inhibitor - (S)-3- Amino-4,4-Difluorocyclopent-1-Enecarboxylic Acid (Ss-1-148) - 1 Hour Soaking within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F501

b:79.5
occ:1.00
 F22 B:Y37501 0.0 79.5 1.0
C18 B:Y37501 1.4 80.7 1.0
C17 B:Y37501 2.5 80.6 1.0
C20 B:Y37501 2.5 80.9 1.0
N11 B:Y37501 3.0 73.0 1.0
O B:HOH658 3.2 28.2 1.0
C01 B:Y37501 3.5 67.4 1.0
O15 B:Y37501 3.6 30.9 1.0
C19 B:Y37501 3.7 83.6 1.0
C21 B:Y37501 3.7 81.5 1.0
O B:HOH704 3.7 37.6 1.0
CE1 B:PHE177 4.1 57.1 1.0
NZ B:LYS292 4.3 70.2 1.0
CZ B:PHE177 4.5 48.4 1.0
CD2 B:TYR85 4.6 52.4 1.0
C02 B:Y37501 4.7 49.1 1.0
O B:HOH603 4.9 45.0 1.0
CE B:LYS292 4.9 57.1 1.0
CE2 B:TYR85 4.9 55.7 1.0
P12 B:Y37501 4.9 33.9 1.0

Fluorine binding site 4 out of 5 in 7lk1

Go back to Fluorine Binding Sites List in 7lk1
Fluorine binding site 4 out of 5 in the Ornithine Aminotransferase (Oat) with Its Potent Inhibitor - (S)-3- Amino-4,4-Difluorocyclopent-1-Enecarboxylic Acid (Ss-1-148) - 1 Hour Soaking


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Ornithine Aminotransferase (Oat) with Its Potent Inhibitor - (S)-3- Amino-4,4-Difluorocyclopent-1-Enecarboxylic Acid (Ss-1-148) - 1 Hour Soaking within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F501

b:67.5
occ:0.56
 F22 C:Y37501 0.0 67.5 0.6
C33 C:Y37501 0.8 47.7 0.4
C21 C:Y37501 0.9 58.9 0.4
C18 C:Y37501 1.4 61.8 0.6
O35 C:Y37501 1.5 36.3 0.4
O34 C:Y37501 1.9 47.2 0.4
C19 C:Y37501 2.0 62.1 0.4
C20 C:Y37501 2.3 61.5 0.4
C17 C:Y37501 2.5 52.2 0.6
C20 C:Y37501 2.5 54.5 0.6
C17 C:Y37501 3.1 55.2 0.4
N11 C:Y37501 3.2 44.8 0.6
C18 C:Y37501 3.3 60.1 0.4
CD1 C:TYR85 3.5 47.5 1.0
C21 C:Y37501 3.6 55.0 0.6
C19 C:Y37501 3.7 51.3 0.6
NH1 C:ARG413 3.7 57.8 1.0
CB C:GLU235 3.7 46.5 1.0
N11 C:Y37501 3.8 50.8 0.4
NH2 C:ARG413 3.8 59.2 1.0
CG C:GLU235 3.8 47.4 0.8
NE2 C:GLN266 3.9 35.9 1.0
CE1 C:TYR85 3.9 48.3 1.0
CG C:TYR85 4.0 47.2 1.0
CZ C:ARG413 4.2 57.7 1.0
CA C:GLU235 4.3 40.1 1.0
F22 C:Y37501 4.4 65.0 0.4
CB C:TYR85 4.4 46.5 1.0
C01 C:Y37501 4.5 44.6 0.6
NZ C:LYS292 4.5 56.5 0.6
O10 C:Y37501 4.5 39.0 0.6
O10 C:Y37501 4.6 38.6 0.4
NZ C:LYS292 4.6 56.8 0.4
N C:GLU235 4.6 39.4 1.0
CZ C:TYR85 4.7 48.8 1.0
CD2 C:TYR85 4.8 47.9 1.0
C01 C:Y37501 4.8 48.8 0.4
CE1 C:PHE177 4.8 33.0 1.0
CD1 C:PHE177 4.8 32.5 1.0
O C:HOH737 4.8 38.5 1.0
CD C:GLN266 4.8 36.6 1.0
OE1 C:GLN266 5.0 37.4 1.0

Fluorine binding site 5 out of 5 in 7lk1

Go back to Fluorine Binding Sites List in 7lk1
Fluorine binding site 5 out of 5 in the Ornithine Aminotransferase (Oat) with Its Potent Inhibitor - (S)-3- Amino-4,4-Difluorocyclopent-1-Enecarboxylic Acid (Ss-1-148) - 1 Hour Soaking


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Ornithine Aminotransferase (Oat) with Its Potent Inhibitor - (S)-3- Amino-4,4-Difluorocyclopent-1-Enecarboxylic Acid (Ss-1-148) - 1 Hour Soaking within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F501

b:65.0
occ:0.44
 F22 C:Y37501 0.0 65.0 0.4
C21 C:Y37501 0.9 55.0 0.6
C33 C:Y37501 1.2 45.3 0.6
C18 C:Y37501 1.4 60.1 0.4
C19 C:Y37501 1.5 51.3 0.6
O34 C:Y37501 1.8 45.9 0.6
O35 C:Y37501 2.2 53.5 0.6
C20 C:Y37501 2.3 54.5 0.6
C17 C:Y37501 2.5 55.2 0.4
C20 C:Y37501 2.5 61.5 0.4
C17 C:Y37501 2.8 52.2 0.6
O C:HOH792 3.0 41.5 1.0
C18 C:Y37501 3.1 61.8 0.6
C19 C:Y37501 3.4 62.1 0.4
N11 C:Y37501 3.6 50.8 0.4
C21 C:Y37501 3.6 58.9 0.4
CE2 C:TYR85 3.9 48.6 1.0
CD2 C:TYR85 3.9 47.9 1.0
N11 C:Y37501 3.9 44.8 0.6
OH C:TYR55 4.1 37.0 1.0
O C:HOH690 4.2 31.7 1.0
F22 C:Y37501 4.4 67.5 0.6
CZ C:TYR85 4.4 48.8 1.0
O C:HOH663 4.5 38.2 1.0
O C:HOH602 4.5 45.4 1.0
C01 C:Y37501 4.6 44.6 0.6
CG C:TYR85 4.6 47.2 1.0
O16 C:Y37501 4.6 29.9 0.4
O16 C:Y37501 4.6 29.4 0.6
C01 C:Y37501 4.6 48.8 0.4
C33 C:Y37501 4.9 47.7 0.4
CZ C:PHE177 5.0 33.1 1.0
OH C:TYR85 5.0 49.6 1.0

Reference:

S.Shen, A.Butrin, P.F.Doubleday, R.D.Melani, B.A.Beaupre, M.T.Tavares, G.M.Ferreira, N.L.Kelleher, G.R.Moran, D.Liu, R.B.Silverman. Turnover and Inactivation Mechanisms For ( S )-3-Amino-4,4-Difluorocyclopent-1-Enecarboxylic Acid, A Selective Mechanism-Based Inactivator of Human Ornithine Aminotransferase. J.Am.Chem.Soc. V. 143 8689 2021.
ISSN: ESSN 1520-5126
PubMed: 34097381
DOI: 10.1021/JACS.1C02456
Page generated: Wed Apr 5 00:12:04 2023

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