Fluorine in PDB 7nwa: Crystal Structure of Human Cytosolic Branched-Chain Aminotransferase (BCAT1) in Complex with Plp and Compound A

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

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

Protein crystallography data

The structure of Crystal Structure of Human Cytosolic Branched-Chain Aminotransferase (BCAT1) in Complex with Plp and Compound A, PDB code: 7nwa 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) 48.49 / 1.59
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 66.986, 106.316, 108.982, 90, 90, 90
R / Rfree (%) 16.8 / 19.9

Other elements in 7nwa:

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

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

Fluorine binding site 1 out of 4 in 7nwa

Go back to Fluorine Binding Sites List in 7nwa
Fluorine binding site 1 out of 4 in the Crystal Structure of Human Cytosolic Branched-Chain Aminotransferase (BCAT1) in Complex with Plp and Compound A


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

b:19.7
occ:1.00
 F16 A:UTT401 0.0 19.7 1.0
C9 A:UTT401 1.3 16.8 1.0
C10 A:UTT401 2.3 16.9 1.0
C8 A:UTT401 2.4 16.7 1.0
C7 A:UTT401 2.8 18.4 1.0
N A:THR260 3.2 19.0 0.7
N A:THR260 3.2 18.3 0.3
N6 A:UTT401 3.2 18.9 1.0
O A:HOH677 3.2 22.8 1.0
O A:VAL258 3.3 17.2 1.0
OE1 A:GLN244 3.4 20.6 1.0
CG A:MET261 3.4 17.8 1.0
CA A:GLY259 3.4 17.8 1.0
C11 A:UTT401 3.6 17.6 1.0
C13 A:UTT401 3.6 17.1 1.0
OG1 A:THR260 3.7 28.8 0.7
C A:GLY259 3.7 20.2 1.0
C5 A:UTT401 3.8 19.2 1.0
SD A:MET261 3.8 19.3 1.0
CD A:GLN244 3.8 19.8 1.0
C A:VAL258 4.0 17.1 1.0
N A:MET261 4.0 18.0 1.0
N A:GLY259 4.1 17.8 1.0
CB A:MET261 4.1 16.5 1.0
C12 A:UTT401 4.1 18.4 1.0
CA A:THR260 4.2 21.4 0.7
CA A:THR260 4.2 18.1 0.3
CG2 A:THR260 4.3 18.8 0.3
N4 A:UTT401 4.3 18.1 1.0
C A:THR260 4.3 18.7 0.3
C A:THR260 4.4 21.9 0.7
NE2 A:GLN244 4.4 23.2 1.0
CG A:GLN244 4.5 20.4 1.0
CB A:THR260 4.5 24.7 0.7
C1 A:UTT401 4.6 16.2 1.0
CB A:THR260 4.7 17.8 0.3
CA A:MET261 4.7 17.2 1.0
F14 A:UTT401 4.7 19.9 1.0
O A:GLY259 4.9 22.4 1.0

Fluorine binding site 2 out of 4 in 7nwa

Go back to Fluorine Binding Sites List in 7nwa
Fluorine binding site 2 out of 4 in the Crystal Structure of Human Cytosolic Branched-Chain Aminotransferase (BCAT1) in Complex with Plp and Compound A


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

b:19.9
occ:1.00
 F14 A:UTT401 0.0 19.9 1.0
C13 A:UTT401 1.4 17.1 1.0
C12 A:UTT401 2.4 18.4 1.0
C8 A:UTT401 2.4 16.7 1.0
C7 A:UTT401 2.8 18.4 1.0
CZ A:PHE194 3.2 31.3 1.0
CE2 A:PHE194 3.4 28.7 1.0
CE2 A:TYR193 3.5 27.2 1.0
SG A:CYS338 3.5 26.4 1.0
N6 A:UTT401 3.6 18.9 1.0
C11 A:UTT401 3.6 17.6 1.0
C9 A:UTT401 3.6 16.8 1.0
CD2 A:TYR193 4.0 25.7 1.0
NE2 A:GLN244 4.0 23.2 1.0
O A:HOH778 4.0 31.0 1.0
C10 A:UTT401 4.1 16.9 1.0
CG1 A:VAL202 4.3 26.4 1.0
O A:HOH700 4.3 22.5 1.0
CE1 A:PHE194 4.4 30.9 1.0
CZ A:TYR193 4.4 27.4 1.0
CB A:CYS338 4.5 22.6 1.0
CD A:GLN244 4.5 19.8 1.0
CG A:GLN244 4.5 20.4 1.0
O A:HOH678 4.6 42.3 1.0
OH A:TYR193 4.6 29.2 1.0
CD2 A:PHE194 4.6 29.4 1.0
F16 A:UTT401 4.7 19.7 1.0
C5 A:UTT401 4.8 19.2 1.0
SD A:MET261 4.9 19.3 1.0

Fluorine binding site 3 out of 4 in 7nwa

Go back to Fluorine Binding Sites List in 7nwa
Fluorine binding site 3 out of 4 in the Crystal Structure of Human Cytosolic Branched-Chain Aminotransferase (BCAT1) in Complex with Plp and Compound A


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

b:23.3
occ:1.00
 F16 B:UTT401 0.0 23.3 1.0
C9 B:UTT401 1.3 22.1 1.0
C10 B:UTT401 2.3 20.9 1.0
C8 B:UTT401 2.4 18.9 1.0
C7 B:UTT401 2.8 20.2 1.0
CZ B:PHE194 3.2 39.5 1.0
CE2 B:PHE194 3.5 36.1 1.0
CE2 B:TYR193 3.5 45.8 1.0
SG B:CYS338 3.6 25.6 1.0
C11 B:UTT401 3.6 20.3 1.0
N6 B:UTT401 3.6 20.4 1.0
C13 B:UTT401 3.6 21.0 1.0
CD2 B:TYR193 3.7 42.7 1.0
O B:HOH772 3.8 45.3 1.0
NE2 B:GLN244 4.1 25.7 1.0
C12 B:UTT401 4.1 20.0 1.0
CG1 B:VAL202 4.1 26.8 1.0
O B:HOH676 4.3 24.9 1.0
CE1 B:PHE194 4.3 40.7 1.0
CB B:CYS338 4.4 21.2 1.0
CZ B:TYR193 4.5 50.5 1.0
CD B:GLN244 4.6 24.9 1.0
CG B:GLN244 4.6 23.5 1.0
CD2 B:PHE194 4.7 40.9 1.0
F14 B:UTT401 4.7 22.4 1.0
CG B:TYR193 4.8 43.4 1.0
SD B:MET261 4.9 17.1 1.0
C5 B:UTT401 4.9 18.6 1.0
OH B:TYR193 4.9 58.3 1.0

Fluorine binding site 4 out of 4 in 7nwa

Go back to Fluorine Binding Sites List in 7nwa
Fluorine binding site 4 out of 4 in the Crystal Structure of Human Cytosolic Branched-Chain Aminotransferase (BCAT1) in Complex with Plp and Compound A


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

b:22.4
occ:1.00
 F14 B:UTT401 0.0 22.4 1.0
C13 B:UTT401 1.3 21.0 1.0
C8 B:UTT401 2.4 18.9 1.0
C12 B:UTT401 2.4 20.0 1.0
C7 B:UTT401 2.8 20.2 1.0
N6 B:UTT401 3.2 20.4 1.0
O B:HOH736 3.2 31.0 1.0
N B:THR260 3.3 16.6 1.0
OE1 B:GLN244 3.3 25.2 1.0
O B:VAL258 3.3 17.6 1.0
CA B:GLY259 3.4 19.9 1.0
CG B:MET261 3.5 16.2 1.0
C9 B:UTT401 3.6 22.1 1.0
C11 B:UTT401 3.6 20.3 1.0
C5 B:UTT401 3.7 18.6 1.0
CD B:GLN244 3.7 24.9 1.0
OG1 B:THR260 3.8 24.6 1.0
SD B:MET261 3.8 17.1 1.0
C B:GLY259 3.8 18.4 1.0
C B:VAL258 4.0 19.4 1.0
N B:GLY259 4.1 19.1 1.0
N B:MET261 4.1 14.5 1.0
C10 B:UTT401 4.1 20.9 1.0
N4 B:UTT401 4.2 17.6 1.0
CB B:MET261 4.2 15.2 1.0
NE2 B:GLN244 4.3 25.7 1.0
CA B:THR260 4.3 19.3 1.0
CG B:GLN244 4.4 23.5 1.0
C B:THR260 4.4 18.9 1.0
C1 B:UTT401 4.5 16.6 1.0
CB B:THR260 4.6 23.5 1.0
F16 B:UTT401 4.7 23.3 1.0
CA B:MET261 4.8 14.1 1.0
CB B:GLN244 5.0 21.3 1.0
O B:GLY259 5.0 20.5 1.0
C25 B:UTT401 5.0 20.2 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: Fri Aug 2 10:16:49 2024

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