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Fluorine in PDB 7nya: Crystal Structure of Human Cytosolic Branched-Chain Aminotransferase (BCAT1) in Complex with Plp and Small Molecule Inhibitor Bay-069 (Compound 36)

Enzymatic activity of Crystal Structure of Human Cytosolic Branched-Chain Aminotransferase (BCAT1) in Complex with Plp and Small Molecule Inhibitor Bay-069 (Compound 36)

All present enzymatic activity of Crystal Structure of Human Cytosolic Branched-Chain Aminotransferase (BCAT1) in Complex with Plp and Small Molecule Inhibitor Bay-069 (Compound 36):
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 Bay-069 (Compound 36), PDB code: 7nya 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) 47.90 / 1.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 66.584, 103.294, 108.118, 90, 90, 90
R / Rfree (%) 18.3 / 22.1

Other elements in 7nya:

The structure of Crystal Structure of Human Cytosolic Branched-Chain Aminotransferase (BCAT1) in Complex with Plp and Small Molecule Inhibitor Bay-069 (Compound 36) also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Chlorine (Cl) 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 Bay-069 (Compound 36) (pdb code 7nya). 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 Bay-069 (Compound 36), PDB code: 7nya:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 7nya

Go back to Fluorine Binding Sites List in 7nya
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 Bay-069 (Compound 36)


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 Bay-069 (Compound 36) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:35.5
occ:1.00
 F30 A:UUZ401 0.0 35.5 1.0
C28 A:UUZ401 1.3 38.0 1.0
F29 A:UUZ401 2.1 44.0 1.0
F31 A:UUZ401 2.2 35.4 1.0
C27 A:UUZ401 2.3 33.8 1.0
N22 A:UUZ401 2.8 33.0 1.0
CD A:GLN234 3.2 28.3 1.0
OE1 A:GLN244 3.2 32.2 1.0
O A:HOH521 3.3 22.2 1.0
NE2 A:GLN234 3.3 28.3 1.0
OE1 A:GLN234 3.4 29.0 1.0
C26 A:UUZ401 3.5 26.0 1.0
CG A:GLN234 3.7 28.0 1.0
NE2 A:GLN244 3.7 32.1 1.0
CD A:GLN244 3.7 30.3 1.0
C21 A:UUZ401 4.1 35.0 1.0
O A:HOH776 4.1 40.9 1.0
O A:GLN243 4.3 28.1 1.0
O B:HOH554 4.4 32.9 1.0
CB A:GLN234 4.6 26.4 1.0
C24 A:UUZ401 4.6 26.4 1.0
O A:HOH715 4.7 40.4 1.0
N12 A:UUZ401 4.8 30.0 1.0
O B:VAL175 4.9 33.3 1.0
O23 A:UUZ401 4.9 40.8 1.0

Fluorine binding site 2 out of 6 in 7nya

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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 Bay-069 (Compound 36)


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 Bay-069 (Compound 36) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:35.4
occ:1.00
 F31 A:UUZ401 0.0 35.4 1.0
C28 A:UUZ401 1.3 38.0 1.0
F29 A:UUZ401 2.2 44.0 1.0
F30 A:UUZ401 2.2 35.5 1.0
C27 A:UUZ401 2.4 33.8 1.0
C26 A:UUZ401 2.8 26.0 1.0
O B:VAL175 3.2 33.3 1.0
O A:HOH715 3.3 40.4 1.0
O B:HOH554 3.3 32.9 1.0
CG A:GLN234 3.4 28.0 1.0
NE2 A:GLN234 3.5 28.3 1.0
CD A:GLN234 3.6 28.3 1.0
N22 A:UUZ401 3.6 33.0 1.0
C24 A:UUZ401 4.2 26.4 1.0
OE1 A:GLN234 4.4 29.0 1.0
C B:VAL175 4.5 30.6 1.0
CB A:GLN234 4.5 26.4 1.0
C21 A:UUZ401 4.8 35.0 1.0
O25 A:UUZ401 5.0 27.9 1.0
N12 A:UUZ401 5.0 30.0 1.0
O A:HOH722 5.0 35.5 1.0

Fluorine binding site 3 out of 6 in 7nya

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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 Bay-069 (Compound 36)


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 Bay-069 (Compound 36) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:44.0
occ:1.00
 F29 A:UUZ401 0.0 44.0 1.0
C28 A:UUZ401 1.3 38.0 1.0
F30 A:UUZ401 2.1 35.5 1.0
F31 A:UUZ401 2.2 35.4 1.0
C27 A:UUZ401 2.3 33.8 1.0
N22 A:UUZ401 2.9 33.0 1.0
NE2 A:GLN234 3.1 28.3 1.0
C26 A:UUZ401 3.5 26.0 1.0
NE2 A:GLN244 3.5 32.1 1.0
O A:HOH559 3.5 39.9 1.0
O A:GLN243 3.7 28.1 1.0
O A:HOH715 3.7 40.4 1.0
CD A:GLN234 3.8 28.3 1.0
O A:HOH760 4.0 48.0 1.0
CD A:GLN244 4.1 30.3 1.0
C21 A:UUZ401 4.2 35.0 1.0
OE1 A:GLN244 4.2 32.2 1.0
CG A:GLN234 4.4 28.0 1.0
OE1 A:GLN234 4.4 29.0 1.0
C24 A:UUZ401 4.6 26.4 1.0
N12 A:UUZ401 4.9 30.0 1.0
C A:GLN243 4.9 26.2 1.0
O A:HOH521 5.0 22.2 1.0
O23 A:UUZ401 5.0 40.8 1.0

Fluorine binding site 4 out of 6 in 7nya

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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 Bay-069 (Compound 36)


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 Bay-069 (Compound 36) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:44.5
occ:1.00
 F30 B:UUZ401 0.0 44.5 1.0
C28 B:UUZ401 1.3 39.3 1.0
F31 B:UUZ401 2.2 35.9 1.0
F29 B:UUZ401 2.2 46.0 1.0
C27 B:UUZ401 2.3 33.1 1.0
O B:HOH590 2.9 22.9 1.0
N22 B:UUZ401 2.9 38.8 1.0
CD B:GLN234 3.3 28.5 1.0
OE1 B:GLN234 3.3 29.3 1.0
OE1 B:GLN244 3.4 39.8 1.0
C26 B:UUZ401 3.5 29.4 1.0
NE2 B:GLN234 3.6 28.4 1.0
O B:HOH735 3.7 45.8 1.0
CG B:GLN234 3.8 27.1 1.0
O B:HOH745 4.0 33.5 1.0
CD B:GLN244 4.1 34.7 1.0
C21 B:UUZ401 4.2 43.0 1.0
NE2 B:GLN244 4.2 35.9 1.0
CB B:GLN234 4.5 24.0 1.0
O A:VAL175 4.5 26.5 1.0
O B:HOH519 4.6 41.1 1.0
C24 B:UUZ401 4.6 29.7 1.0
O B:GLN243 4.6 30.0 1.0
N12 B:UUZ401 4.9 33.3 1.0

Fluorine binding site 5 out of 6 in 7nya

Go back to Fluorine Binding Sites List in 7nya
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 Bay-069 (Compound 36)


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 Bay-069 (Compound 36) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:35.9
occ:1.00
 F31 B:UUZ401 0.0 35.9 1.0
C28 B:UUZ401 1.3 39.3 1.0
F29 B:UUZ401 2.2 46.0 1.0
F30 B:UUZ401 2.2 44.5 1.0
C27 B:UUZ401 2.4 33.1 1.0
C26 B:UUZ401 2.8 29.4 1.0
O A:VAL175 3.0 26.5 1.0
NE2 B:GLN234 3.3 28.4 1.0
CG B:GLN234 3.4 27.1 1.0
CD B:GLN234 3.4 28.5 1.0
N22 B:UUZ401 3.6 38.8 1.0
O B:HOH694 3.7 34.4 1.0
OE1 B:GLN234 4.1 29.3 1.0
C24 B:UUZ401 4.2 29.7 1.0
C A:VAL175 4.2 25.4 1.0
CB B:GLN234 4.5 24.0 1.0
O B:HOH735 4.6 45.8 1.0
C21 B:UUZ401 4.8 43.0 1.0
CB A:VAL175 4.8 26.8 1.0
O B:HOH590 4.8 22.9 1.0
O B:HOH567 4.9 47.1 1.0
O25 B:UUZ401 4.9 26.1 1.0
N12 B:UUZ401 5.0 33.3 1.0

Fluorine binding site 6 out of 6 in 7nya

Go back to Fluorine Binding Sites List in 7nya
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 Bay-069 (Compound 36)


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 Bay-069 (Compound 36) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:46.0
occ:1.00
 F29 B:UUZ401 0.0 46.0 1.0
C28 B:UUZ401 1.3 39.3 1.0
F31 B:UUZ401 2.2 35.9 1.0
F30 B:UUZ401 2.2 44.5 1.0
C27 B:UUZ401 2.3 33.1 1.0
N22 B:UUZ401 2.9 38.8 1.0
NE2 B:GLN234 3.0 28.4 1.0
NE2 B:GLN244 3.3 35.9 1.0
O B:GLN243 3.4 30.0 1.0
C26 B:UUZ401 3.4 29.4 1.0
O B:HOH567 3.4 47.1 1.0
CD B:GLN234 3.6 28.5 1.0
CD B:GLN244 3.7 34.7 1.0
OE1 B:GLN244 3.8 39.8 1.0
OE1 B:GLN234 4.0 29.3 1.0
O B:HOH694 4.0 34.4 1.0
C21 B:UUZ401 4.2 43.0 1.0
O B:HOH590 4.3 22.9 1.0
CG B:GLN234 4.3 27.1 1.0
C24 B:UUZ401 4.6 29.7 1.0
C B:GLN243 4.6 27.3 1.0
CG B:GLN244 4.8 30.9 1.0
N12 B:UUZ401 4.9 33.3 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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