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Fluorine in PDB 7ny9: Crystal Structure of Human Cytosolic Branched-Chain Aminotransferase (BCAT1) in Complex with Plp and Small Molecule Inhibitor Compound 38

Enzymatic activity of Crystal Structure of Human Cytosolic Branched-Chain Aminotransferase (BCAT1) in Complex with Plp and Small Molecule Inhibitor Compound 38

All present enzymatic activity of Crystal Structure of Human Cytosolic Branched-Chain Aminotransferase (BCAT1) in Complex with Plp and Small Molecule Inhibitor Compound 38:
2.6.1.42;

Protein crystallography data

The structure of Crystal Structure of Human Cytosolic Branched-Chain Aminotransferase (BCAT1) in Complex with Plp and Small Molecule Inhibitor Compound 38, PDB code: 7ny9 was solved by R.C.Hillig, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.32 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 66.425, 103.001, 109.432, 90, 90, 90
R / Rfree (%) 17.4 / 20.5

Other elements in 7ny9:

The structure of Crystal Structure of Human Cytosolic Branched-Chain Aminotransferase (BCAT1) in Complex with Plp and Small Molecule Inhibitor Compound 38 also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Human Cytosolic Branched-Chain Aminotransferase (BCAT1) in Complex with Plp and Small Molecule Inhibitor Compound 38 (pdb code 7ny9). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of Human Cytosolic Branched-Chain Aminotransferase (BCAT1) in Complex with Plp and Small Molecule Inhibitor Compound 38, PDB code: 7ny9:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 7ny9

Go back to Fluorine Binding Sites List in 7ny9
Fluorine binding site 1 out of 6 in the Crystal Structure of Human Cytosolic Branched-Chain Aminotransferase (BCAT1) in Complex with Plp and Small Molecule Inhibitor Compound 38


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Human Cytosolic Branched-Chain Aminotransferase (BCAT1) in Complex with Plp and Small Molecule Inhibitor Compound 38 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:33.2
occ:0.85
 F26 A:UV5401 0.0 33.2 0.8
C24 A:UV5401 1.3 29.9 0.8
F27 A:UV5401 2.2 34.0 0.8
F25 A:UV5401 2.2 30.0 0.8
C19 A:UV5401 2.3 25.2 0.8
C18 A:UV5401 2.8 23.5 0.8
NH2 A:ARG163 3.0 18.2 1.0
OH A:TYR161 3.3 18.9 1.0
OH B:TYR90 3.5 18.1 1.0
N20 A:UV5401 3.5 22.9 0.8
O A:HOH542 3.9 20.2 1.0
C17 A:UV5401 4.2 25.6 0.8
CZ A:TYR161 4.2 18.9 1.0
CZ A:PHE49 4.2 23.9 1.0
O B:LEU173 4.3 19.6 1.0
CZ A:ARG163 4.3 18.0 1.0
CE2 A:PHE49 4.3 24.3 1.0
CZ B:TYR90 4.5 17.5 1.0
CE2 A:PHE95 4.5 16.9 1.0
C21 A:UV5401 4.7 26.6 0.8
CE1 B:TYR90 4.8 17.2 1.0
CE2 A:TYR161 4.8 18.9 1.0
CG2 B:VAL175 4.8 24.7 1.0
NH1 A:ARG163 4.9 17.8 1.0
N16 A:UV5401 5.0 25.8 0.8

Fluorine binding site 2 out of 6 in 7ny9

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Fluorine binding site 2 out of 6 in the Crystal Structure of Human Cytosolic Branched-Chain Aminotransferase (BCAT1) in Complex with Plp and Small Molecule Inhibitor Compound 38


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Human Cytosolic Branched-Chain Aminotransferase (BCAT1) in Complex with Plp and Small Molecule Inhibitor Compound 38 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:34.0
occ:0.85
 F27 A:UV5401 0.0 34.0 0.8
C24 A:UV5401 1.3 29.9 0.8
F26 A:UV5401 2.2 33.2 0.8
F25 A:UV5401 2.2 30.0 0.8
C19 A:UV5401 2.3 25.2 0.8
O A:HOH542 2.7 20.2 1.0
N20 A:UV5401 2.8 22.9 0.8
OH A:TYR161 3.1 18.9 1.0
O A:HOH769 3.3 37.2 1.0
C18 A:UV5401 3.4 23.5 0.8
CZ A:PHE49 3.6 23.9 1.0
CZ A:TYR161 3.7 18.9 1.0
CE1 A:TYR161 3.9 18.9 1.0
CB A:ALA334 4.0 21.3 1.0
C21 A:UV5401 4.0 26.6 0.8
CE2 A:PHE49 4.3 24.3 1.0
O A:HOH629 4.3 31.6 1.0
CE1 A:PHE49 4.4 24.7 1.0
NH2 A:ARG163 4.5 18.2 1.0
C17 A:UV5401 4.5 25.6 0.8
CE2 A:TYR161 4.7 18.9 1.0
N16 A:UV5401 4.8 25.8 0.8
O23 A:UV5401 4.8 28.0 0.8
N A:ALA334 4.9 21.0 1.0
CA A:ALA334 4.9 21.0 1.0

Fluorine binding site 3 out of 6 in 7ny9

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Fluorine binding site 3 out of 6 in the Crystal Structure of Human Cytosolic Branched-Chain Aminotransferase (BCAT1) in Complex with Plp and Small Molecule Inhibitor Compound 38


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Human Cytosolic Branched-Chain Aminotransferase (BCAT1) in Complex with Plp and Small Molecule Inhibitor Compound 38 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:30.0
occ:0.85
 F25 A:UV5401 0.0 30.0 0.8
C24 A:UV5401 1.3 29.9 0.8
F26 A:UV5401 2.2 33.2 0.8
F27 A:UV5401 2.2 34.0 0.8
C19 A:UV5401 2.3 25.2 0.8
N20 A:UV5401 2.8 22.9 0.8
O A:HOH542 3.4 20.2 1.0
C18 A:UV5401 3.5 23.5 0.8
CG2 A:THR260 3.5 22.2 0.5
O A:HOH769 3.7 37.2 1.0
OG1 A:THR260 3.8 21.7 0.5
O A:HOH629 3.8 31.6 1.0
C21 A:UV5401 4.1 26.6 0.8
OH A:TYR161 4.2 18.9 1.0
CB A:THR260 4.2 22.1 0.5
CB A:THR260 4.2 20.9 0.5
C17 A:UV5401 4.6 25.6 0.8
C4A A:PLP402 4.6 20.8 1.0
NZ A:LYS222 4.6 19.7 1.0
NH2 A:ARG163 4.7 18.2 1.0
CE2 A:PHE95 4.7 16.9 1.0
CG2 A:THR260 4.8 21.6 0.5
N16 A:UV5401 4.8 25.8 0.8
O23 A:UV5401 4.8 28.0 0.8
O A:THR260 4.8 21.2 1.0
CE A:LYS222 4.9 20.8 1.0
OG1 A:THR260 4.9 25.2 0.5

Fluorine binding site 4 out of 6 in 7ny9

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Fluorine binding site 4 out of 6 in the Crystal Structure of Human Cytosolic Branched-Chain Aminotransferase (BCAT1) in Complex with Plp and Small Molecule Inhibitor Compound 38


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Human Cytosolic Branched-Chain Aminotransferase (BCAT1) in Complex with Plp and Small Molecule Inhibitor Compound 38 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:29.2
occ:0.90
 F26 B:UV5401 0.0 29.2 0.9
C24 B:UV5401 1.3 26.5 0.9
F25 B:UV5401 2.2 25.7 0.9
F27 B:UV5401 2.2 25.9 0.9
C19 B:UV5401 2.3 23.0 0.9
C18 B:UV5401 2.7 21.4 0.9
NH2 B:ARG163 3.1 16.0 1.0
OH B:TYR161 3.5 15.7 1.0
OH A:TYR90 3.5 14.5 1.0
N20 B:UV5401 3.5 23.3 0.9
O B:HOH515 4.0 20.6 1.0
C17 B:UV5401 4.1 22.9 0.9
O A:LEU173 4.2 17.4 1.0
CZ B:PHE49 4.3 22.2 1.0
CE2 B:PHE49 4.3 21.9 1.0
CZ B:TYR161 4.3 16.3 1.0
CZ B:ARG163 4.4 15.4 1.0
CZ A:TYR90 4.5 14.5 1.0
CE2 B:PHE95 4.6 15.2 1.0
C21 B:UV5401 4.7 25.3 0.9
CG2 A:VAL175 4.8 19.6 1.0
CE1 A:TYR90 4.8 14.3 1.0
O22 B:UV5401 4.9 21.8 0.9
N16 B:UV5401 4.9 22.5 0.9
CE2 B:TYR161 4.9 16.1 1.0
O B:HOH817 4.9 29.1 1.0

Fluorine binding site 5 out of 6 in 7ny9

Go back to Fluorine Binding Sites List in 7ny9
Fluorine binding site 5 out of 6 in the Crystal Structure of Human Cytosolic Branched-Chain Aminotransferase (BCAT1) in Complex with Plp and Small Molecule Inhibitor Compound 38


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of Human Cytosolic Branched-Chain Aminotransferase (BCAT1) in Complex with Plp and Small Molecule Inhibitor Compound 38 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:25.9
occ:0.90
 F27 B:UV5401 0.0 25.9 0.9
C24 B:UV5401 1.3 26.5 0.9
F26 B:UV5401 2.2 29.2 0.9
F25 B:UV5401 2.2 25.7 0.9
C19 B:UV5401 2.3 23.0 0.9
N20 B:UV5401 2.8 23.3 0.9
O B:HOH515 2.9 20.6 1.0
O B:HOH817 3.2 29.1 1.0
OH B:TYR161 3.3 15.7 1.0
C18 B:UV5401 3.4 21.4 0.9
CZ B:PHE49 3.6 22.2 1.0
CB B:ALA334 3.7 19.8 1.0
CZ B:TYR161 3.9 16.3 1.0
CE1 B:TYR161 4.1 16.9 1.0
C21 B:UV5401 4.1 25.3 0.9
O B:HOH629 4.1 28.9 1.0
CE2 B:PHE49 4.2 21.9 1.0
CE1 B:PHE49 4.4 21.8 1.0
C17 B:UV5401 4.5 22.9 0.9
NH2 B:ARG163 4.6 16.0 1.0
N B:ALA334 4.7 17.5 1.0
CA B:ALA334 4.7 19.5 1.0
N16 B:UV5401 4.8 22.5 0.9
CE2 B:TYR161 4.8 16.1 1.0
O23 B:UV5401 4.9 26.6 0.9
OG1 B:THR260 5.0 22.1 0.5

Fluorine binding site 6 out of 6 in 7ny9

Go back to Fluorine Binding Sites List in 7ny9
Fluorine binding site 6 out of 6 in the Crystal Structure of Human Cytosolic Branched-Chain Aminotransferase (BCAT1) in Complex with Plp and Small Molecule Inhibitor Compound 38


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of Human Cytosolic Branched-Chain Aminotransferase (BCAT1) in Complex with Plp and Small Molecule Inhibitor Compound 38 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:25.7
occ:0.90
 F25 B:UV5401 0.0 25.7 0.9
C24 B:UV5401 1.3 26.5 0.9
F26 B:UV5401 2.2 29.2 0.9
F27 B:UV5401 2.2 25.9 0.9
C19 B:UV5401 2.3 23.0 0.9
N20 B:UV5401 2.8 23.3 0.9
O B:HOH515 3.4 20.6 1.0
O B:HOH817 3.4 29.1 1.0
C18 B:UV5401 3.4 21.4 0.9
OG1 B:THR260 3.5 23.7 0.5
O B:HOH629 3.6 28.9 1.0
OG1 B:THR260 3.7 22.1 0.5
CG2 B:THR260 3.8 24.5 0.5
C21 B:UV5401 4.1 25.3 0.9
CB B:THR260 4.2 19.6 0.5
OH B:TYR161 4.3 15.7 1.0
CB B:THR260 4.3 22.2 0.5
C4A B:PLP402 4.5 18.3 1.0
NZ B:LYS222 4.6 17.7 1.0
C17 B:UV5401 4.6 22.9 0.9
O B:THR260 4.7 18.1 1.0
NH2 B:ARG163 4.7 16.0 1.0
CG2 B:THR260 4.8 19.6 0.5
CE2 B:PHE95 4.8 15.2 1.0
N16 B:UV5401 4.8 22.5 0.9
O23 B:UV5401 4.9 26.6 0.9
CE B:LYS222 4.9 18.7 1.0

Reference:

J.Gunther, R.C.Hillig, K.Zimmermann, S.Kaulfuss, C.Lemos, D.Nguyen, H.Rehwinkel, M.Habgood, C.Lechner, R.Neuhaus, U.Ganzer, M.Drewes, J.Chai, L.Bouche. Bay-069, A Novel (Trifluoromethyl)Pyrimidinedione-Based BCAT1/2 Inhibitor and Chemical Probe. J.Med.Chem. V. 65 14366 2022.
ISSN: ISSN 0022-2623
PubMed: 36261130
DOI: 10.1021/ACS.JMEDCHEM.2C00441
Page generated: Tue Jul 15 22:25:30 2025

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