Fluorine in PDB 7nxn: Crystal Structure of Human Cytosolic Branched-Chain Aminotransferase (BCAT1) in Complex with Plp and Small Molecule Inhibitor Compound 21(5-F)

Enzymatic activity of Crystal Structure of Human Cytosolic Branched-Chain Aminotransferase (BCAT1) in Complex with Plp and Small Molecule Inhibitor Compound 21(5-F)

All present enzymatic activity of Crystal Structure of Human Cytosolic Branched-Chain Aminotransferase (BCAT1) in Complex with Plp and Small Molecule Inhibitor Compound 21(5-F):
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 21(5-F), PDB code: 7nxn 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) 41.55 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 66.723, 106.188, 109.326, 90, 90, 90
R / Rfree (%) 19 / 22.4

Other elements in 7nxn:

The structure of Crystal Structure of Human Cytosolic Branched-Chain Aminotransferase (BCAT1) in Complex with Plp and Small Molecule Inhibitor Compound 21(5-F) also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

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 21(5-F) (pdb code 7nxn). 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 21(5-F), PDB code: 7nxn:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 7nxn

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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 21(5-F)


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 21(5-F) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:54.7
occ:1.00
 F8 A:UU2401 0.0 54.7 1.0
C3 A:UU2401 1.4 50.3 1.0
C2 A:UU2401 2.4 43.9 1.0
C4 A:UU2401 2.4 50.4 1.0
N9 A:UU2401 2.7 45.5 1.0
C17 A:UU2401 3.2 45.7 1.0
O19 A:UU2401 3.3 49.5 1.0
C22 A:UU2401 3.5 40.8 1.0
OE1 A:GLN244 3.6 36.5 1.0
C1 A:UU2401 3.6 61.6 1.0
NE2 A:GLN244 3.7 45.1 1.0
C5 A:UU2401 3.7 52.7 1.0
CG2 A:THR260 3.7 33.7 1.0
CB B:VAL175 3.7 40.9 1.0
O23 A:UU2401 3.9 53.0 1.0
CD A:GLN244 4.0 35.6 1.0
CG1 B:VAL175 4.0 45.4 1.0
C6 A:UU2401 4.1 74.4 1.0
OG1 A:THR260 4.2 29.6 1.0
O B:VAL175 4.2 43.5 1.0
N18 A:UU2401 4.2 35.2 1.0
CG2 B:VAL175 4.4 36.5 1.0
C21 A:UU2401 4.5 43.9 1.0
O A:HOH510 4.5 33.4 1.0
CB A:THR260 4.5 29.5 1.0
CD A:GLN234 4.7 41.6 1.0
CA B:VAL175 4.7 34.9 1.0
C20 A:UU2401 4.8 41.9 1.0
OE1 A:GLN234 4.8 39.8 1.0
C33 A:UU2401 4.8 43.5 1.0
NE2 A:GLN234 4.9 37.1 1.0
C B:VAL175 4.9 36.5 1.0
N B:VAL175 4.9 31.5 1.0

Fluorine binding site 2 out of 6 in 7nxn

Go back to Fluorine Binding Sites List in 7nxn
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 21(5-F)


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 21(5-F) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:39.7
occ:1.00
 F25 A:UU2401 0.0 39.7 1.0
C24 A:UU2401 1.3 43.4 1.0
C26 A:UU2401 2.3 35.7 1.0
F27 A:UU2401 2.3 34.6 1.0
C20 A:UU2401 2.4 41.9 1.0
C28 A:UU2401 2.6 31.2 1.0
N18 A:UU2401 2.8 35.2 1.0
O A:HOH546 3.2 33.2 1.0
O A:HOH713 3.3 34.6 1.0
C21 A:UU2401 3.6 43.9 1.0
C32 A:UU2401 3.6 34.4 1.0
CB A:ALA334 3.6 45.6 1.0
OH A:TYR161 3.8 27.4 1.0
CZ A:PHE49 3.9 33.7 1.0
C29 A:UU2401 4.0 30.2 1.0
O A:HOH527 4.0 50.6 1.0
C17 A:UU2401 4.2 45.7 1.0
CZ A:TYR161 4.4 27.8 1.0
CE1 A:PHE49 4.5 35.2 1.0
CE1 A:TYR161 4.5 26.5 1.0
CE2 A:PHE49 4.6 34.5 1.0
O A:HOH506 4.6 50.0 1.0
C31 A:UU2401 4.7 32.8 1.0
C22 A:UU2401 4.7 40.8 1.0
CA A:ALA334 4.8 37.9 1.0
C30 A:UU2401 4.8 30.1 1.0
NH2 A:ARG163 4.9 25.0 1.0
N A:ALA334 4.9 34.0 1.0
N9 A:UU2401 5.0 45.5 1.0
O19 A:UU2401 5.0 49.5 1.0

Fluorine binding site 3 out of 6 in 7nxn

Go back to Fluorine Binding Sites List in 7nxn
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 21(5-F)


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 21(5-F) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:34.6
occ:1.00
 F27 A:UU2401 0.0 34.6 1.0
C24 A:UU2401 1.4 43.4 1.0
F25 A:UU2401 2.3 39.7 1.0
C26 A:UU2401 2.3 35.7 1.0
C20 A:UU2401 2.4 41.9 1.0
C21 A:UU2401 2.7 43.9 1.0
C32 A:UU2401 2.7 34.4 1.0
NH2 A:ARG163 3.4 25.0 1.0
CE1 A:PHE49 3.4 35.2 1.0
CZ A:PHE49 3.5 33.7 1.0
C28 A:UU2401 3.5 31.2 1.0
OH B:TYR90 3.6 25.7 1.0
N18 A:UU2401 3.7 35.2 1.0
OH A:TYR161 3.7 27.4 1.0
O B:LEU173 3.8 27.5 1.0
C31 A:UU2401 4.1 32.8 1.0
C22 A:UU2401 4.1 40.8 1.0
CZ A:TYR161 4.3 27.8 1.0
O A:HOH546 4.5 33.2 1.0
CD1 A:PHE49 4.6 35.2 1.0
CZ A:ARG163 4.6 24.6 1.0
C29 A:UU2401 4.6 30.2 1.0
CE2 A:TYR161 4.7 28.4 1.0
CE2 A:PHE49 4.7 34.5 1.0
CZ B:TYR90 4.7 24.1 1.0
O23 A:UU2401 4.8 53.0 1.0
C B:LEU173 4.8 28.5 1.0
C17 A:UU2401 4.8 45.7 1.0
C30 A:UU2401 4.9 30.1 1.0
CG2 B:VAL175 5.0 36.5 1.0

Fluorine binding site 4 out of 6 in 7nxn

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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 21(5-F)


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 21(5-F) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:41.3
occ:1.00
 F8 B:UU2401 0.0 41.3 1.0
C3 B:UU2401 1.3 37.1 1.0
C4 B:UU2401 2.3 38.0 1.0
C2 B:UU2401 2.4 34.7 1.0
N9 B:UU2401 2.8 34.5 1.0
C17 B:UU2401 3.2 39.9 1.0
O19 B:UU2401 3.3 37.1 1.0
CB A:VAL175 3.4 33.3 1.0
CG2 B:THR260 3.5 29.3 1.0
C22 B:UU2401 3.6 34.8 1.0
C5 B:UU2401 3.6 40.5 1.0
C1 B:UU2401 3.6 42.0 1.0
CG1 A:VAL175 3.6 37.6 1.0
OE1 B:GLN244 3.7 32.4 1.0
NE2 B:GLN244 3.7 31.8 1.0
O23 B:UU2401 3.9 37.6 1.0
O A:VAL175 4.0 33.8 1.0
CG2 A:VAL175 4.0 31.4 1.0
CD B:GLN244 4.1 32.1 1.0
C6 B:UU2401 4.1 44.6 1.0
N18 B:UU2401 4.3 34.2 1.0
OG1 B:THR260 4.4 31.0 1.0
O B:HOH524 4.5 29.3 1.0
CA A:VAL175 4.5 29.5 1.0
CD B:GLN234 4.5 34.1 1.0
C21 B:UU2401 4.5 32.2 1.0
CB B:THR260 4.6 27.7 1.0
NE2 B:GLN234 4.6 33.6 1.0
OE1 B:GLN234 4.6 31.8 1.0
C A:VAL175 4.7 32.8 1.0
N A:VAL175 4.8 28.0 1.0
C33 B:UU2401 4.8 38.6 1.0
C20 B:UU2401 4.8 33.2 1.0
O B:GLN243 4.9 31.1 1.0
CG B:GLN234 4.9 36.8 1.0
O A:HOH684 5.0 47.1 1.0

Fluorine binding site 5 out of 6 in 7nxn

Go back to Fluorine Binding Sites List in 7nxn
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 21(5-F)


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 21(5-F) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:29.8
occ:1.00
 F25 B:UU2401 0.0 29.8 1.0
C24 B:UU2401 1.3 35.5 1.0
F27 B:UU2401 2.3 29.9 1.0
C20 B:UU2401 2.3 33.2 1.0
C26 B:UU2401 2.4 27.3 1.0
C28 B:UU2401 2.7 27.0 1.0
N18 B:UU2401 2.8 34.2 1.0
O B:HOH707 3.3 31.2 1.0
CB B:ALA334 3.4 40.6 1.0
C21 B:UU2401 3.5 32.2 1.0
O B:HOH581 3.5 32.2 1.0
O B:HOH616 3.6 36.4 1.0
C32 B:UU2401 3.6 24.5 1.0
CZ B:PHE49 3.7 36.5 1.0
OH B:TYR161 3.8 23.7 1.0
C29 B:UU2401 4.1 25.3 1.0
C17 B:UU2401 4.2 39.9 1.0
CE1 B:PHE49 4.2 36.4 1.0
CZ B:TYR161 4.3 23.8 1.0
CE2 B:PHE49 4.3 37.5 1.0
CE1 B:TYR161 4.5 22.1 1.0
C22 B:UU2401 4.6 34.8 1.0
CE1 B:PHE194 4.6 60.2 1.0
CA B:ALA334 4.7 34.4 1.0
NH2 B:ARG163 4.8 22.9 1.0
C31 B:UU2401 4.8 25.3 1.0
N9 B:UU2401 4.9 34.5 1.0
N B:ALA334 4.9 30.9 1.0
O19 B:UU2401 5.0 37.1 1.0
O B:HOH575 5.0 38.6 1.0
C30 B:UU2401 5.0 27.2 1.0

Fluorine binding site 6 out of 6 in 7nxn

Go back to Fluorine Binding Sites List in 7nxn
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 21(5-F)


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 21(5-F) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:29.9
occ:1.00
 F27 B:UU2401 0.0 29.9 1.0
C24 B:UU2401 1.4 35.5 1.0
F25 B:UU2401 2.3 29.8 1.0
C26 B:UU2401 2.4 27.3 1.0
C20 B:UU2401 2.4 33.2 1.0
C21 B:UU2401 2.7 32.2 1.0
C32 B:UU2401 2.8 24.5 1.0
NH2 B:ARG163 3.3 22.9 1.0
CE1 B:PHE49 3.4 36.4 1.0
OH A:TYR90 3.5 23.0 1.0
CZ B:PHE49 3.5 36.5 1.0
C28 B:UU2401 3.6 27.0 1.0
N18 B:UU2401 3.7 34.2 1.0
OH B:TYR161 3.7 23.7 1.0
O A:LEU173 3.9 25.5 1.0
C22 B:UU2401 4.1 34.8 1.0
C31 B:UU2401 4.2 25.3 1.0
CZ B:TYR161 4.3 23.8 1.0
CZ B:ARG163 4.5 23.1 1.0
CD1 B:PHE49 4.5 37.2 1.0
CE2 B:TYR161 4.6 22.9 1.0
CZ A:TYR90 4.6 23.0 1.0
C29 B:UU2401 4.7 25.3 1.0
O B:HOH581 4.7 32.2 1.0
CE2 B:PHE49 4.7 37.5 1.0
C17 B:UU2401 4.8 39.9 1.0
O23 B:UU2401 4.9 37.6 1.0
C A:LEU173 4.9 26.9 1.0
C30 B:UU2401 5.0 27.2 1.0
NH1 B:ARG163 5.0 23.8 1.0
CB A:LEU173 5.0 25.4 1.0
N9 B:UU2401 5.0 34.5 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: Wed Apr 5 00:22:17 2023

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