Atomistry » Fluorine » PDB 4dbu-4e28 » 4dk7
Atomistry »
  Fluorine »
    PDB 4dbu-4e28 »
      4dk7 »

Fluorine in PDB 4dk7: Crystal Structure of Lxr Ligand Binding Domain in Complex with Full Agonist 1

Enzymatic activity of Crystal Structure of Lxr Ligand Binding Domain in Complex with Full Agonist 1

All present enzymatic activity of Crystal Structure of Lxr Ligand Binding Domain in Complex with Full Agonist 1:
2.3.1.48;

Protein crystallography data

The structure of Crystal Structure of Lxr Ligand Binding Domain in Complex with Full Agonist 1, PDB code: 4dk7 was solved by D.E.Piper, H.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.45
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 87.261, 87.261, 197.709, 90.00, 90.00, 90.00
R / Rfree (%) 23 / 27

Other elements in 4dk7:

The structure of Crystal Structure of Lxr Ligand Binding Domain in Complex with Full Agonist 1 also contains other interesting chemical elements:

Calcium (Ca) 7 atoms

Fluorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Fluorine atom in the Crystal Structure of Lxr Ligand Binding Domain in Complex with Full Agonist 1 (pdb code 4dk7). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 12 binding sites of Fluorine where determined in the Crystal Structure of Lxr Ligand Binding Domain in Complex with Full Agonist 1, PDB code: 4dk7:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 12 in 4dk7

Go back to Fluorine Binding Sites List in 4dk7
Fluorine binding site 1 out of 12 in the Crystal Structure of Lxr Ligand Binding Domain in Complex with Full Agonist 1


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 Lxr Ligand Binding Domain in Complex with Full Agonist 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:59.3
occ:1.00
 F5 A:0KS501 0.0 59.3 1.0
C19 A:0KS501 1.4 55.8 1.0
F6 A:0KS501 2.2 57.0 1.0
F4 A:0KS501 2.2 56.2 1.0
C18 A:0KS501 2.4 56.4 1.0
F7 A:0KS501 2.7 57.8 1.0
O1 A:0KS501 2.8 55.4 1.0
C20 A:0KS501 3.0 55.5 1.0
CD2 A:LEU449 3.1 68.3 1.0
CG2 A:THR272 3.5 52.2 1.0
F9 A:0KS501 3.5 53.4 1.0
C1 A:0KS501 3.8 60.5 1.0
CD1 A:LEU453 3.8 57.0 1.0
F8 A:0KS501 4.3 52.8 1.0
CB A:THR272 4.4 54.5 1.0
CA A:THR272 4.4 53.7 1.0
CZ A:PHE268 4.5 58.7 1.0
CZ3 A:TRP457 4.5 53.3 1.0
CG A:LEU449 4.5 70.6 1.0
CE1 A:PHE268 4.6 57.6 1.0
C2 A:0KS501 4.6 62.0 1.0
C3 A:0KS501 4.6 62.8 1.0
CB A:ALA275 5.0 46.2 1.0
N A:THR272 5.0 54.7 1.0

Fluorine binding site 2 out of 12 in 4dk7

Go back to Fluorine Binding Sites List in 4dk7
Fluorine binding site 2 out of 12 in the Crystal Structure of Lxr Ligand Binding Domain in Complex with Full Agonist 1


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 Lxr Ligand Binding Domain in Complex with Full Agonist 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:56.2
occ:1.00
 F4 A:0KS501 0.0 56.2 1.0
C19 A:0KS501 1.4 55.8 1.0
F6 A:0KS501 2.2 57.0 1.0
F5 A:0KS501 2.2 59.3 1.0
C18 A:0KS501 2.4 56.4 1.0
O1 A:0KS501 2.8 55.4 1.0
C1 A:0KS501 2.9 60.5 1.0
CB A:ALA275 3.0 46.2 1.0
C3 A:0KS501 3.3 62.8 1.0
CD1 A:LEU453 3.7 57.0 1.0
CZ3 A:TRP457 3.8 53.3 1.0
C20 A:0KS501 3.8 55.5 1.0
C2 A:0KS501 3.9 62.0 1.0
CA A:THR272 4.2 53.7 1.0
F7 A:0KS501 4.2 57.8 1.0
CH2 A:TRP457 4.3 53.0 1.0
C5 A:0KS501 4.4 64.9 1.0
F9 A:0KS501 4.4 53.4 1.0
CA A:ALA275 4.5 48.0 1.0
CG2 A:THR272 4.5 52.2 1.0
O A:PHE271 4.6 55.8 1.0
N A:THR272 4.7 54.7 1.0
CB A:THR272 4.8 54.5 1.0
CG A:LEU453 4.8 57.1 1.0
CE3 A:TRP457 4.9 52.6 1.0
F8 A:0KS501 4.9 52.8 1.0
C4 A:0KS501 4.9 65.9 1.0
C A:PHE271 4.9 56.0 1.0
O A:THR272 4.9 52.4 1.0
CD2 A:LEU449 4.9 68.3 1.0
CD2 A:LEU453 4.9 54.0 1.0

Fluorine binding site 3 out of 12 in 4dk7

Go back to Fluorine Binding Sites List in 4dk7
Fluorine binding site 3 out of 12 in the Crystal Structure of Lxr Ligand Binding Domain in Complex with Full Agonist 1


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 Lxr Ligand Binding Domain in Complex with Full Agonist 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:57.0
occ:1.00
 F6 A:0KS501 0.0 57.0 1.0
C19 A:0KS501 1.4 55.8 1.0
F5 A:0KS501 2.2 59.3 1.0
F4 A:0KS501 2.2 56.2 1.0
C18 A:0KS501 2.4 56.4 1.0
C1 A:0KS501 3.0 60.5 1.0
F9 A:0KS501 3.0 53.4 1.0
C20 A:0KS501 3.1 55.5 1.0
C2 A:0KS501 3.2 62.0 1.0
F7 A:0KS501 3.6 57.8 1.0
O1 A:0KS501 3.6 55.4 1.0
CG2 A:THR272 3.8 52.2 1.0
N A:THR272 4.0 54.7 1.0
CA A:THR272 4.0 53.7 1.0
C3 A:0KS501 4.1 62.8 1.0
CB A:PHE271 4.1 57.8 1.0
C A:PHE271 4.2 56.0 1.0
C4 A:0KS501 4.4 65.9 1.0
F8 A:0KS501 4.4 52.8 1.0
O A:PHE271 4.5 55.8 1.0
CE1 A:PHE268 4.5 57.6 1.0
CB A:THR272 4.6 54.5 1.0
CB A:ALA275 4.6 46.2 1.0
CD1 A:PHE271 4.8 57.6 1.0
CA A:PHE271 4.8 56.8 1.0
CG A:PHE271 5.0 57.5 1.0

Fluorine binding site 4 out of 12 in 4dk7

Go back to Fluorine Binding Sites List in 4dk7
Fluorine binding site 4 out of 12 in the Crystal Structure of Lxr Ligand Binding Domain in Complex with Full Agonist 1


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 Lxr Ligand Binding Domain in Complex with Full Agonist 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:57.8
occ:1.00
 F7 A:0KS501 0.0 57.8 1.0
C20 A:0KS501 1.4 55.5 1.0
F9 A:0KS501 2.2 53.4 1.0
F8 A:0KS501 2.2 52.8 1.0
C18 A:0KS501 2.4 56.4 1.0
F5 A:0KS501 2.7 59.3 1.0
O1 A:0KS501 2.8 55.4 1.0
C19 A:0KS501 3.0 55.8 1.0
CD1 A:LEU442 3.0 80.9 1.0
CD2 A:LEU449 3.6 68.3 1.0
F6 A:0KS501 3.6 57.0 1.0
C1 A:0KS501 3.8 60.5 1.0
F4 A:0KS501 4.2 56.2 1.0
CG2 A:VAL439 4.3 53.5 1.0
NE2 A:HIS435 4.4 45.9 1.0
CE1 A:PHE268 4.4 57.6 1.0
C2 A:0KS501 4.4 62.0 1.0
CG A:LEU442 4.5 80.3 1.0
CZ A:PHE268 4.6 58.7 1.0
CG A:GLN438 4.6 52.0 1.0
CG A:LEU449 4.7 70.6 1.0
CA A:VAL439 4.8 55.7 1.0
C3 A:0KS501 4.9 62.8 1.0

Fluorine binding site 5 out of 12 in 4dk7

Go back to Fluorine Binding Sites List in 4dk7
Fluorine binding site 5 out of 12 in the Crystal Structure of Lxr Ligand Binding Domain in Complex with Full Agonist 1


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 Lxr Ligand Binding Domain in Complex with Full Agonist 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:53.4
occ:1.00
 F9 A:0KS501 0.0 53.4 1.0
C20 A:0KS501 1.4 55.5 1.0
F7 A:0KS501 2.2 57.8 1.0
F8 A:0KS501 2.2 52.8 1.0
C18 A:0KS501 2.5 56.4 1.0
C2 A:0KS501 2.9 62.0 1.0
F6 A:0KS501 3.0 57.0 1.0
C1 A:0KS501 3.0 60.5 1.0
C19 A:0KS501 3.1 55.8 1.0
CD2 A:LEU345 3.2 57.5 1.0
F5 A:0KS501 3.5 59.3 1.0
O1 A:0KS501 3.6 55.4 1.0
CD1 A:LEU442 3.8 80.9 1.0
CG A:GLN438 4.1 52.0 1.0
C4 A:0KS501 4.2 65.9 1.0
CE1 A:PHE268 4.3 57.6 1.0
CG A:LEU345 4.3 58.2 1.0
F4 A:0KS501 4.4 56.2 1.0
C3 A:0KS501 4.4 62.8 1.0
CD1 A:LEU345 4.5 56.8 1.0
CD A:GLN438 4.7 54.4 1.0
NE2 A:HIS435 4.9 45.9 1.0
CG A:LEU442 5.0 80.3 1.0
CE2 A:PHE349 5.0 48.0 1.0

Fluorine binding site 6 out of 12 in 4dk7

Go back to Fluorine Binding Sites List in 4dk7
Fluorine binding site 6 out of 12 in the Crystal Structure of Lxr Ligand Binding Domain in Complex with Full Agonist 1


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 Lxr Ligand Binding Domain in Complex with Full Agonist 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:52.8
occ:1.00
 F8 A:0KS501 0.0 52.8 1.0
C20 A:0KS501 1.4 55.5 1.0
F9 A:0KS501 2.2 53.4 1.0
F7 A:0KS501 2.2 57.8 1.0
C18 A:0KS501 2.5 56.4 1.0
O1 A:0KS501 2.8 55.4 1.0
C1 A:0KS501 3.0 60.5 1.0
NE2 A:HIS435 3.0 45.9 1.0
CD2 A:HIS435 3.2 45.7 1.0
CG A:GLN438 3.3 52.0 1.0
C2 A:0KS501 3.4 62.0 1.0
C19 A:0KS501 3.9 55.8 1.0
C3 A:0KS501 3.9 62.8 1.0
CB A:GLN438 4.0 50.5 1.0
CE2 A:PHE349 4.1 48.0 1.0
CG2 A:VAL439 4.1 53.5 1.0
CE1 A:HIS435 4.2 44.7 1.0
F5 A:0KS501 4.3 59.3 1.0
CD1 A:LEU442 4.3 80.9 1.0
CG A:HIS435 4.4 46.5 1.0
F6 A:0KS501 4.4 57.0 1.0
C4 A:0KS501 4.5 65.9 1.0
O A:HIS435 4.5 50.2 1.0
CD2 A:LEU345 4.5 57.5 1.0
N A:VAL439 4.5 53.6 1.0
CD A:GLN438 4.6 54.4 1.0
CD2 A:PHE349 4.7 49.0 1.0
C A:GLN438 4.7 53.6 1.0
ND1 A:HIS435 4.8 41.8 1.0
CA A:VAL439 4.8 55.7 1.0
C5 A:0KS501 4.9 64.9 1.0
F4 A:0KS501 4.9 56.2 1.0
CZ A:PHE349 4.9 47.2 1.0

Fluorine binding site 7 out of 12 in 4dk7

Go back to Fluorine Binding Sites List in 4dk7
Fluorine binding site 7 out of 12 in the Crystal Structure of Lxr Ligand Binding Domain in Complex with Full Agonist 1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure of Lxr Ligand Binding Domain in Complex with Full Agonist 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F501

b:91.1
occ:1.00
 F5 C:0KS501 0.0 91.1 1.0
C19 C:0KS501 1.4 89.8 1.0
F6 C:0KS501 2.2 90.5 1.0
F4 C:0KS501 2.2 87.4 1.0
C18 C:0KS501 2.4 90.5 1.0
F7 C:0KS501 2.7 89.0 1.0
O1 C:0KS501 2.8 90.9 1.0
C20 C:0KS501 3.0 89.9 1.0
CG2 C:THR272 3.4 62.9 1.0
F9 C:0KS501 3.6 89.3 1.0
C1 C:0KS501 3.8 92.9 1.0
CE1 C:PHE268 3.8 91.3 1.0
CB C:THR272 4.1 63.7 1.0
CA C:THR272 4.2 65.9 1.0
F8 C:0KS501 4.3 90.8 1.0
CZ C:PHE268 4.3 91.6 1.0
CB C:LEU449 4.5 80.4 1.0
CD2 C:LEU449 4.5 80.2 1.0
CD1 C:LEU453 4.5 63.0 1.0
C3 C:0KS501 4.6 94.0 1.0
C2 C:0KS501 4.6 95.3 1.0
N C:THR272 4.6 67.7 1.0
CG C:LEU449 4.8 80.8 1.0
CD1 C:PHE268 4.8 91.8 1.0
CZ3 C:TRP457 4.9 62.9 1.0

Fluorine binding site 8 out of 12 in 4dk7

Go back to Fluorine Binding Sites List in 4dk7
Fluorine binding site 8 out of 12 in the Crystal Structure of Lxr Ligand Binding Domain in Complex with Full Agonist 1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Crystal Structure of Lxr Ligand Binding Domain in Complex with Full Agonist 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F501

b:87.4
occ:1.00
 F4 C:0KS501 0.0 87.4 1.0
C19 C:0KS501 1.4 89.8 1.0
F5 C:0KS501 2.2 91.1 1.0
F6 C:0KS501 2.2 90.5 1.0
C18 C:0KS501 2.5 90.5 1.0
O1 C:0KS501 2.8 90.9 1.0
C1 C:0KS501 3.0 92.9 1.0
CB C:ALA275 3.2 56.4 1.0
C3 C:0KS501 3.3 94.0 1.0
CA C:THR272 3.6 65.9 1.0
C20 C:0KS501 3.9 89.9 1.0
CD1 C:LEU453 4.0 63.0 1.0
C2 C:0KS501 4.0 95.3 1.0
CZ3 C:TRP457 4.0 62.9 1.0
N C:THR272 4.2 67.7 1.0
O C:PHE271 4.2 67.9 1.0
F7 C:0KS501 4.3 89.0 1.0
CG2 C:THR272 4.3 62.9 1.0
CB C:THR272 4.3 63.7 1.0
C C:PHE271 4.4 70.2 1.0
C5 C:0KS501 4.4 96.7 1.0
F9 C:0KS501 4.5 89.3 1.0
C C:THR272 4.6 66.1 1.0
CA C:ALA275 4.6 58.6 1.0
O C:THR272 4.7 65.7 1.0
CH2 C:TRP457 4.7 62.5 1.0
CE3 C:TRP457 4.8 63.0 1.0
F8 C:0KS501 4.9 90.8 1.0
N C:ALA275 5.0 59.9 1.0
C4 C:0KS501 5.0 97.5 1.0

Fluorine binding site 9 out of 12 in 4dk7

Go back to Fluorine Binding Sites List in 4dk7
Fluorine binding site 9 out of 12 in the Crystal Structure of Lxr Ligand Binding Domain in Complex with Full Agonist 1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Crystal Structure of Lxr Ligand Binding Domain in Complex with Full Agonist 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F501

b:90.5
occ:1.00
 F6 C:0KS501 0.0 90.5 1.0
C19 C:0KS501 1.4 89.8 1.0
F5 C:0KS501 2.2 91.1 1.0
F4 C:0KS501 2.2 87.4 1.0
C18 C:0KS501 2.5 90.5 1.0
C1 C:0KS501 3.0 92.9 1.0
F9 C:0KS501 3.1 89.3 1.0
C20 C:0KS501 3.2 89.9 1.0
C2 C:0KS501 3.3 95.3 1.0
O1 C:0KS501 3.6 90.9 1.0
F7 C:0KS501 3.6 89.0 1.0
CB C:PHE271 3.7 73.8 1.0
N C:THR272 3.8 67.7 1.0
CG2 C:THR272 3.8 62.9 1.0
CA C:THR272 3.9 65.9 1.0
C C:PHE271 4.0 70.2 1.0
C3 C:0KS501 4.0 94.0 1.0
CE1 C:PHE268 4.1 91.3 1.0
O C:PHE271 4.4 67.9 1.0
C4 C:0KS501 4.5 97.5 1.0
CB C:THR272 4.5 63.7 1.0
F8 C:0KS501 4.5 90.8 1.0
CD1 C:PHE268 4.5 91.8 1.0
CA C:PHE271 4.5 72.3 1.0
O C:PHE268 4.7 90.4 1.0
CG C:PHE271 4.8 76.4 1.0
CD1 C:PHE271 4.9 77.1 1.0

Fluorine binding site 10 out of 12 in 4dk7

Go back to Fluorine Binding Sites List in 4dk7
Fluorine binding site 10 out of 12 in the Crystal Structure of Lxr Ligand Binding Domain in Complex with Full Agonist 1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Crystal Structure of Lxr Ligand Binding Domain in Complex with Full Agonist 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F501

b:89.0
occ:1.00
 F7 C:0KS501 0.0 89.0 1.0
C20 C:0KS501 1.4 89.9 1.0
F9 C:0KS501 2.2 89.3 1.0
F8 C:0KS501 2.2 90.8 1.0
C18 C:0KS501 2.5 90.5 1.0
F5 C:0KS501 2.7 91.1 1.0
O1 C:0KS501 2.8 90.9 1.0
C19 C:0KS501 3.0 89.8 1.0
CD1 C:LEU442 3.4 91.6 1.0
F6 C:0KS501 3.6 90.5 1.0
C1 C:0KS501 3.8 92.9 1.0
CG2 C:VAL439 3.9 74.2 1.0
CE1 C:PHE268 4.2 91.3 1.0
F4 C:0KS501 4.3 87.4 1.0
C2 C:0KS501 4.4 95.3 1.0
CG C:GLN438 4.5 73.2 1.0
CG C:LEU442 4.5 92.8 1.0
CA C:VAL439 4.5 77.0 1.0
NE2 C:HIS435 4.6 61.6 1.0
CZ C:PHE268 4.7 91.6 1.0
CB C:VAL439 4.8 75.5 1.0
CD2 C:LEU449 4.8 80.2 1.0
C3 C:0KS501 4.9 94.0 1.0
N C:VAL439 4.9 75.7 1.0

Reference:

D.J.Kopecky, X.Y.Jiao, B.Fisher, S.Mckendry, M.Labelle, D.E.Piper, P.Coward, A.K.Shiau, P.Escaron, J.Danao, A.Chai, J.Jaen, F.Kayser. Discovery of A New Binding Mode For A Series of Liver X Receptor Agonists. Bioorg.Med.Chem.Lett. V. 22 2407 2012.
ISSN: ISSN 0960-894X
PubMed: 22406115
DOI: 10.1016/J.BMCL.2012.02.028
Page generated: Mon Jul 14 21:11:16 2025

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy