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Fluorine in PDB 5avi: Crystal Structure of Lxralpha in Complex with Tert-Butyl Benzoate Analog, Compound 4

Enzymatic activity of Crystal Structure of Lxralpha in Complex with Tert-Butyl Benzoate Analog, Compound 4

All present enzymatic activity of Crystal Structure of Lxralpha in Complex with Tert-Butyl Benzoate Analog, Compound 4:
2.3.1.48;

Protein crystallography data

The structure of Crystal Structure of Lxralpha in Complex with Tert-Butyl Benzoate Analog, Compound 4, PDB code: 5avi was solved by Y.Matsui, H.Hanzawa, K.Tamaki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.70
Space group P 4 21 2
Cell size a, b, c (Å), α, β, γ (°) 124.356, 124.356, 91.916, 90.00, 90.00, 90.00
R / Rfree (%) 24.4 / 27.4

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Lxralpha in Complex with Tert-Butyl Benzoate Analog, Compound 4 (pdb code 5avi). 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 Lxralpha in Complex with Tert-Butyl Benzoate Analog, Compound 4, PDB code: 5avi:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 5avi

Go back to Fluorine Binding Sites List in 5avi
Fluorine binding site 1 out of 6 in the Crystal Structure of Lxralpha in Complex with Tert-Butyl Benzoate Analog, Compound 4


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 Lxralpha in Complex with Tert-Butyl Benzoate Analog, Compound 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:35.4
occ:1.00
 F28 A:4KM501 0.0 35.4 1.0
C27 A:4KM501 1.4 34.8 1.0
F30 A:4KM501 2.2 35.7 1.0
F29 A:4KM501 2.2 35.1 1.0
C1 A:4KM501 2.3 34.3 1.0
C2 A:4KM501 2.9 33.8 1.0
CD1 A:LEU428 3.4 49.2 1.0
CD2 A:LEU331 3.5 36.5 1.0
C6 A:4KM501 3.5 33.8 1.0
CE1 A:PHE254 4.1 46.1 1.0
C3 A:4KM501 4.2 33.7 1.0
CD1 A:LEU435 4.3 43.9 1.0
CG A:LEU428 4.5 51.2 1.0
CD2 A:LEU428 4.5 52.8 1.0
CG A:GLN424 4.6 40.6 1.0
C5 A:4KM501 4.6 33.8 1.0
CZ A:PHE254 4.6 46.5 1.0
C4 A:4KM501 4.9 33.8 1.0
CG A:LEU331 5.0 36.9 1.0

Fluorine binding site 2 out of 6 in 5avi

Go back to Fluorine Binding Sites List in 5avi
Fluorine binding site 2 out of 6 in the Crystal Structure of Lxralpha in Complex with Tert-Butyl Benzoate Analog, Compound 4


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 Lxralpha in Complex with Tert-Butyl Benzoate Analog, Compound 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:35.1
occ:1.00
 F29 A:4KM501 0.0 35.1 1.0
C27 A:4KM501 1.4 34.8 1.0
F30 A:4KM501 2.1 35.7 1.0
F28 A:4KM501 2.2 35.4 1.0
C1 A:4KM501 2.4 34.3 1.0
C2 A:4KM501 3.0 33.8 1.0
C6 A:4KM501 3.3 33.8 1.0
CZ3 A:TRP443 3.4 32.6 1.0
CE3 A:TRP443 3.7 33.0 1.0
CD1 A:LEU435 3.7 43.9 1.0
CD1 A:LEU428 3.9 49.2 1.0
CD2 A:LEU435 4.3 42.3 1.0
C3 A:4KM501 4.3 33.7 1.0
CG A:LEU435 4.3 43.3 1.0
CG2 A:VAL425 4.3 39.6 1.0
NE2 A:HIS421 4.4 31.0 1.0
C5 A:4KM501 4.5 33.8 1.0
CH2 A:TRP443 4.6 31.1 1.0
CD2 A:TRP443 4.9 31.7 1.0
C4 A:4KM501 4.9 33.8 1.0
CD2 A:HIS421 4.9 31.1 1.0

Fluorine binding site 3 out of 6 in 5avi

Go back to Fluorine Binding Sites List in 5avi
Fluorine binding site 3 out of 6 in the Crystal Structure of Lxralpha in Complex with Tert-Butyl Benzoate Analog, Compound 4


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 Lxralpha in Complex with Tert-Butyl Benzoate Analog, Compound 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:35.7
occ:1.00
 F30 A:4KM501 0.0 35.7 1.0
C27 A:4KM501 1.4 34.8 1.0
F29 A:4KM501 2.1 35.1 1.0
F28 A:4KM501 2.2 35.4 1.0
C1 A:4KM501 2.4 34.3 1.0
C6 A:4KM501 2.7 33.8 1.0
CG A:GLN424 3.4 40.6 1.0
C2 A:4KM501 3.6 33.8 1.0
CD2 A:LEU331 3.8 36.5 1.0
CD2 A:HIS421 4.0 31.1 1.0
C5 A:4KM501 4.1 33.8 1.0
CD1 A:LEU428 4.1 49.2 1.0
NE2 A:HIS421 4.2 31.0 1.0
CD A:GLN424 4.4 42.2 1.0
CE2 A:PHE335 4.4 30.7 1.0
CB A:GLN424 4.4 39.7 1.0
CG2 A:VAL425 4.5 39.6 1.0
O8 A:4KM501 4.5 34.2 1.0
C7 A:4KM501 4.7 34.0 1.0
C3 A:4KM501 4.7 33.7 1.0
CZ3 A:TRP443 4.8 32.6 1.0
CD2 A:PHE335 4.8 32.0 1.0
C4 A:4KM501 5.0 33.8 1.0
NE2 A:GLN424 5.0 44.1 1.0

Fluorine binding site 4 out of 6 in 5avi

Go back to Fluorine Binding Sites List in 5avi
Fluorine binding site 4 out of 6 in the Crystal Structure of Lxralpha in Complex with Tert-Butyl Benzoate Analog, Compound 4


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 Lxralpha in Complex with Tert-Butyl Benzoate Analog, Compound 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F501

b:37.1
occ:1.00
 F28 C:4KM501 0.0 37.1 1.0
C27 C:4KM501 1.4 36.4 1.0
F30 C:4KM501 2.2 36.5 1.0
F29 C:4KM501 2.2 37.7 1.0
C1 C:4KM501 2.4 35.2 1.0
C2 C:4KM501 3.0 34.3 1.0
CD2 C:LEU331 3.4 46.3 1.0
CD1 C:LEU428 3.4 58.6 1.0
C6 C:4KM501 3.4 34.6 1.0
CE1 C:PHE254 4.1 57.3 1.0
CG C:GLN424 4.2 49.6 1.0
C3 C:4KM501 4.3 34.2 1.0
CG C:LEU428 4.4 61.2 1.0
C5 C:4KM501 4.6 34.5 1.0
CD2 C:LEU428 4.6 63.7 1.0
NE2 C:GLN424 4.6 54.6 1.0
CD C:GLN424 4.7 52.4 1.0
CG C:LEU331 4.8 47.7 1.0
CZ C:PHE254 4.8 57.6 1.0
CD1 C:LEU435 4.8 49.5 1.0
C4 C:4KM501 5.0 34.1 1.0
CD1 C:PHE254 5.0 59.6 1.0

Fluorine binding site 5 out of 6 in 5avi

Go back to Fluorine Binding Sites List in 5avi
Fluorine binding site 5 out of 6 in the Crystal Structure of Lxralpha in Complex with Tert-Butyl Benzoate Analog, Compound 4


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 Lxralpha in Complex with Tert-Butyl Benzoate Analog, Compound 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F501

b:37.7
occ:1.00
 F29 C:4KM501 0.0 37.7 1.0
C27 C:4KM501 1.4 36.4 1.0
F30 C:4KM501 2.2 36.5 1.0
F28 C:4KM501 2.2 37.1 1.0
C1 C:4KM501 2.4 35.2 1.0
C2 C:4KM501 2.9 34.3 1.0
C6 C:4KM501 3.5 34.6 1.0
CD1 C:LEU435 3.6 49.5 1.0
CZ3 C:TRP443 3.6 39.3 1.0
CD1 C:LEU428 3.7 58.6 1.0
CE3 C:TRP443 3.8 39.2 1.0
C3 C:4KM501 4.2 34.2 1.0
CG2 C:VAL425 4.3 45.1 1.0
CG C:LEU435 4.4 48.1 1.0
CD2 C:LEU435 4.4 46.4 1.0
NE2 C:HIS421 4.5 40.2 1.0
C5 C:4KM501 4.6 34.5 1.0
CH2 C:TRP443 4.8 37.6 1.0
C4 C:4KM501 5.0 34.1 1.0

Fluorine binding site 6 out of 6 in 5avi

Go back to Fluorine Binding Sites List in 5avi
Fluorine binding site 6 out of 6 in the Crystal Structure of Lxralpha in Complex with Tert-Butyl Benzoate Analog, Compound 4


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 Lxralpha in Complex with Tert-Butyl Benzoate Analog, Compound 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F501

b:36.5
occ:1.00
 F30 C:4KM501 0.0 36.5 1.0
C27 C:4KM501 1.4 36.4 1.0
F29 C:4KM501 2.2 37.7 1.0
F28 C:4KM501 2.2 37.1 1.0
C1 C:4KM501 2.4 35.2 1.0
C6 C:4KM501 2.8 34.6 1.0
CG C:GLN424 3.4 49.6 1.0
CD2 C:HIS421 3.6 40.7 1.0
NE2 C:HIS421 3.6 40.2 1.0
C2 C:4KM501 3.7 34.3 1.0
CD2 C:LEU331 4.0 46.3 1.0
CG2 C:VAL425 4.1 45.1 1.0
C5 C:4KM501 4.2 34.5 1.0
CB C:GLN424 4.3 48.4 1.0
CD1 C:LEU428 4.3 58.6 1.0
CE2 C:PHE335 4.4 38.9 1.0
CD C:GLN424 4.6 52.4 1.0
O8 C:4KM501 4.6 35.6 1.0
CZ3 C:TRP443 4.7 39.3 1.0
N C:VAL425 4.7 48.8 1.0
C3 C:4KM501 4.8 34.2 1.0
CE1 C:HIS421 4.9 38.7 1.0
C7 C:4KM501 4.9 34.8 1.0
CG C:HIS421 4.9 39.4 1.0
C C:GLN424 4.9 50.6 1.0
CE3 C:TRP443 4.9 39.2 1.0
O C:HIS421 4.9 43.7 1.0
NE2 C:GLN424 5.0 54.6 1.0
CD2 C:PHE335 5.0 40.5 1.0

Reference:

Y.Matsui, T.Yamaguchi, T.Yamazaki, M.Yoshida, M.Arai, N.Terasaka, S.Honzumi, K.Wakabayashi, S.Hayashi, D.Nakai, H.Hanzawa, K.Tamaki. Discovery and Structure-Guided Optimization of Tert-Butyl 6-(Phenoxymethyl)-3-(Trifluoromethyl)Benzoates As Liver X Receptor Agonists Bioorg.Med.Chem.Lett. V. 25 3914 2015.
ISSN: ESSN 1464-3405
PubMed: 26238323
DOI: 10.1016/J.BMCL.2015.07.047
Page generated: Tue Jul 15 02:21:19 2025

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