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Fluorine in PDB 5i4v: Discovery of Novel, Orally Efficacious Liver X Receptor (Lxr) Beta Agonists

Protein crystallography data

The structure of Discovery of Novel, Orally Efficacious Liver X Receptor (Lxr) Beta Agonists, PDB code: 5i4v was solved by G.Chen, B.M.Mckeever, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.72 / 2.61
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 68.637, 101.221, 143.274, 90.00, 90.00, 90.00
R / Rfree (%) 20.8 / 24.8

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Discovery of Novel, Orally Efficacious Liver X Receptor (Lxr) Beta Agonists (pdb code 5i4v). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Discovery of Novel, Orally Efficacious Liver X Receptor (Lxr) Beta Agonists, PDB code: 5i4v:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 5i4v

Go back to Fluorine Binding Sites List in 5i4v
Fluorine binding site 1 out of 6 in the Discovery of Novel, Orally Efficacious Liver X Receptor (Lxr) Beta Agonists


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Discovery of Novel, Orally Efficacious Liver X Receptor (Lxr) Beta Agonists within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:89.0
occ:1.00
 F2 A:67S501 0.0 89.0 1.0
C7 A:67S501 1.3 81.1 1.0
F3 A:67S501 2.1 83.3 1.0
F1 A:67S501 2.2 93.5 1.0
C6 A:67S501 2.3 68.3 1.0
C9 A:67S501 2.8 69.9 1.0
C8 A:67S501 2.8 66.8 1.0
CD2 A:LEU345 3.2 39.2 1.0
N2 A:67S501 3.4 54.4 1.0
CE1 A:PHE268 3.7 34.3 1.0
CD1 A:LEU442 4.0 32.0 1.0
O1 A:67S501 4.1 77.7 1.0
C10 A:67S501 4.2 63.5 1.0
CD1 A:PHE268 4.4 34.3 1.0
CZ A:PHE268 4.4 33.2 1.0
OG1 A:THR272 4.5 37.7 1.0
C5 A:67S501 4.5 51.6 1.0
CG A:LEU345 4.6 37.1 1.0
N3 A:67S501 4.8 60.5 1.0
CD2 A:LEU442 4.8 30.9 1.0

Fluorine binding site 2 out of 6 in 5i4v

Go back to Fluorine Binding Sites List in 5i4v
Fluorine binding site 2 out of 6 in the Discovery of Novel, Orally Efficacious Liver X Receptor (Lxr) Beta Agonists


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Discovery of Novel, Orally Efficacious Liver X Receptor (Lxr) Beta Agonists within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:93.5
occ:1.00
 F1 A:67S501 0.0 93.5 1.0
C7 A:67S501 1.3 81.1 1.0
F2 A:67S501 2.2 89.0 1.0
F3 A:67S501 2.2 83.3 1.0
C6 A:67S501 2.3 68.3 1.0
N2 A:67S501 2.5 54.4 1.0
OG1 A:THR272 3.5 37.7 1.0
N A:THR272 3.5 34.5 1.0
CB A:PHE271 3.5 34.5 1.0
C8 A:67S501 3.6 66.8 1.0
C A:PHE271 3.7 34.6 1.0
CA A:THR272 3.8 33.6 1.0
C5 A:67S501 3.9 51.6 1.0
O A:PHE271 4.0 34.5 1.0
CD2 A:LEU345 4.2 39.2 1.0
O A:PHE268 4.3 34.9 1.0
CA A:PHE271 4.3 34.4 1.0
C9 A:67S501 4.3 69.9 1.0
CB A:THR272 4.3 35.9 1.0
CE1 A:PHE268 4.4 34.3 1.0
CD1 A:PHE268 4.6 34.3 1.0
CG A:PHE271 4.6 34.8 1.0
C10 A:67S501 4.6 63.5 1.0
CD2 A:PHE271 4.7 36.1 1.0
N3 A:67S501 4.7 60.5 1.0
N1 A:67S501 4.7 44.0 1.0
C11 A:67S501 4.8 43.5 1.0

Fluorine binding site 3 out of 6 in 5i4v

Go back to Fluorine Binding Sites List in 5i4v
Fluorine binding site 3 out of 6 in the Discovery of Novel, Orally Efficacious Liver X Receptor (Lxr) Beta Agonists


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Discovery of Novel, Orally Efficacious Liver X Receptor (Lxr) Beta Agonists within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:83.3
occ:1.00
 F3 A:67S501 0.0 83.3 1.0
C7 A:67S501 1.3 81.1 1.0
F2 A:67S501 2.1 89.0 1.0
F1 A:67S501 2.2 93.5 1.0
C6 A:67S501 2.3 68.3 1.0
C8 A:67S501 3.0 66.8 1.0
C9 A:67S501 3.1 69.9 1.0
N2 A:67S501 3.2 54.4 1.0
OG1 A:THR272 3.3 37.7 1.0
CA A:THR272 4.0 33.6 1.0
CB A:THR272 4.2 35.9 1.0
C10 A:67S501 4.2 63.5 1.0
CD1 A:LEU453 4.2 30.0 1.0
C5 A:67S501 4.4 51.6 1.0
CE1 A:PHE268 4.4 34.3 1.0
O1 A:67S501 4.5 77.7 1.0
N A:THR272 4.5 34.5 1.0
CG2 A:THR272 4.5 38.3 1.0
CZ A:PHE268 4.6 33.2 1.0
CD2 A:LEU449 4.6 47.9 1.0
N3 A:67S501 4.7 60.5 1.0
CG A:LEU449 4.8 48.8 1.0
CB A:ALA275 4.8 30.3 1.0
CD1 A:LEU442 5.0 32.0 1.0

Fluorine binding site 4 out of 6 in 5i4v

Go back to Fluorine Binding Sites List in 5i4v
Fluorine binding site 4 out of 6 in the Discovery of Novel, Orally Efficacious Liver X Receptor (Lxr) Beta Agonists


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Discovery of Novel, Orally Efficacious Liver X Receptor (Lxr) Beta Agonists within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F501

b:0.5
occ:1.00
 F2 E:67S501 0.0 0.5 1.0
C7 E:67S501 1.3 0.1 1.0
F3 E:67S501 2.2 0.0 1.0
F1 E:67S501 2.2 0.1 1.0
C6 E:67S501 2.3 89.1 1.0
C8 E:67S501 2.9 80.6 1.0
C9 E:67S501 2.9 81.3 1.0
CD2 E:LEU345 3.1 38.5 1.0
N2 E:67S501 3.4 75.3 1.0
CE1 E:PHE268 3.6 43.8 1.0
C10 E:67S501 4.2 77.2 1.0
O1 E:67S501 4.2 84.0 1.0
CD1 E:PHE268 4.2 42.0 1.0
CD1 E:LEU442 4.3 45.5 1.0
CZ E:PHE268 4.4 44.0 1.0
OG1 E:THR272 4.4 40.6 1.0
CG E:LEU345 4.5 37.7 1.0
C5 E:67S501 4.5 68.6 1.0
N3 E:67S501 4.8 74.4 1.0
CD2 E:LEU449 4.9 68.5 1.0
CD1 E:LEU345 5.0 37.3 1.0
CD2 E:LEU442 5.0 46.5 1.0

Fluorine binding site 5 out of 6 in 5i4v

Go back to Fluorine Binding Sites List in 5i4v
Fluorine binding site 5 out of 6 in the Discovery of Novel, Orally Efficacious Liver X Receptor (Lxr) Beta Agonists


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Discovery of Novel, Orally Efficacious Liver X Receptor (Lxr) Beta Agonists within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F501

b:0.1
occ:1.00
 F1 E:67S501 0.0 0.1 1.0
C7 E:67S501 1.3 0.1 1.0
F3 E:67S501 2.2 0.0 1.0
F2 E:67S501 2.2 0.5 1.0
C6 E:67S501 2.3 89.1 1.0
N2 E:67S501 2.6 75.3 1.0
OG1 E:THR272 3.3 40.6 1.0
N E:THR272 3.3 38.1 1.0
CB E:PHE271 3.5 38.4 1.0
CA E:THR272 3.6 39.3 1.0
C E:PHE271 3.6 39.6 1.0
C8 E:67S501 3.6 80.6 1.0
C5 E:67S501 3.9 68.6 1.0
O E:PHE271 4.0 39.1 1.0
CB E:THR272 4.0 40.7 1.0
O E:PHE268 4.1 39.9 1.0
CA E:PHE271 4.2 38.8 1.0
C9 E:67S501 4.3 81.3 1.0
CE1 E:PHE268 4.5 43.8 1.0
CD2 E:LEU345 4.5 38.5 1.0
CD1 E:PHE268 4.6 42.0 1.0
CG E:PHE271 4.6 37.9 1.0
C10 E:67S501 4.7 77.2 1.0
N3 E:67S501 4.8 74.4 1.0
CD2 E:PHE271 4.8 37.4 1.0
C11 E:67S501 4.8 51.0 1.0
N1 E:67S501 4.8 55.9 1.0
C E:THR272 4.9 39.8 1.0

Fluorine binding site 6 out of 6 in 5i4v

Go back to Fluorine Binding Sites List in 5i4v
Fluorine binding site 6 out of 6 in the Discovery of Novel, Orally Efficacious Liver X Receptor (Lxr) Beta Agonists


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Discovery of Novel, Orally Efficacious Liver X Receptor (Lxr) Beta Agonists within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F501

b:0.0
occ:1.00
 F3 E:67S501 0.0 0.0 1.0
C7 E:67S501 1.3 0.1 1.0
F2 E:67S501 2.2 0.5 1.0
F1 E:67S501 2.2 0.1 1.0
C6 E:67S501 2.3 89.1 1.0
C8 E:67S501 2.9 80.6 1.0
C9 E:67S501 3.0 81.3 1.0
N2 E:67S501 3.3 75.3 1.0
OG1 E:THR272 3.4 40.6 1.0
CD2 E:LEU449 3.7 68.5 1.0
C10 E:67S501 4.2 77.2 1.0
CA E:THR272 4.2 39.3 1.0
CD2 E:LEU453 4.2 48.0 1.0
CB E:THR272 4.2 40.7 1.0
O1 E:67S501 4.3 84.0 1.0
CE1 E:PHE268 4.4 43.8 1.0
C5 E:67S501 4.5 68.6 1.0
CZ E:PHE268 4.6 44.0 1.0
CG2 E:THR272 4.6 42.2 1.0
N E:THR272 4.6 38.1 1.0
N3 E:67S501 4.8 74.4 1.0

Reference:

Y.Zheng, L.Zhuang, K.Y.Fan, C.M.Tice, W.Zhao, C.Dong, S.D.Lotesta, K.Leftheris, P.R.Lindblom, Z.Liu, J.Shimada, P.B.Noto, S.Meng, A.Hardy, L.Howard, P.Krosky, J.Guo, K.Lipinski, G.Kandpal, Y.Bukhtiyarov, Y.Zhao, D.Lala, R.Van Orden, J.Zhou, G.Chen, Z.Wu, B.M.Mckeever, G.M.Mcgeehan, R.E.Gregg, D.A.Claremon, S.B.Singh. Discovery of A Novel, Orally Efficacious Liver X Receptor (Lxr) Beta Agonist. J.Med.Chem. V. 59 3264 2016.
ISSN: ISSN 0022-2623
PubMed: 26990539
DOI: 10.1021/ACS.JMEDCHEM.5B02029
Page generated: Thu Aug 1 10:05:59 2024

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