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Fluorine in PDB 5lp1: Crystal Structure of Human Lipoprotein-Associated Phospholipase A2 in Complex with A [1.1.1]Bicyclopentane-Containing Inhibitor at 1.91A Resolution.

Enzymatic activity of Crystal Structure of Human Lipoprotein-Associated Phospholipase A2 in Complex with A [1.1.1]Bicyclopentane-Containing Inhibitor at 1.91A Resolution.

All present enzymatic activity of Crystal Structure of Human Lipoprotein-Associated Phospholipase A2 in Complex with A [1.1.1]Bicyclopentane-Containing Inhibitor at 1.91A Resolution.:
3.1.1.47;

Protein crystallography data

The structure of Crystal Structure of Human Lipoprotein-Associated Phospholipase A2 in Complex with A [1.1.1]Bicyclopentane-Containing Inhibitor at 1.91A Resolution., PDB code: 5lp1 was solved by D.Somers, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.91
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 100.280, 91.560, 51.650, 90.00, 111.88, 90.00
R / Rfree (%) 16.2 / 19.2

Other elements in 5lp1:

The structure of Crystal Structure of Human Lipoprotein-Associated Phospholipase A2 in Complex with A [1.1.1]Bicyclopentane-Containing Inhibitor at 1.91A Resolution. also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Human Lipoprotein-Associated Phospholipase A2 in Complex with A [1.1.1]Bicyclopentane-Containing Inhibitor at 1.91A Resolution. (pdb code 5lp1). 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 Lipoprotein-Associated Phospholipase A2 in Complex with A [1.1.1]Bicyclopentane-Containing Inhibitor at 1.91A Resolution., PDB code: 5lp1:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 5lp1

Go back to Fluorine Binding Sites List in 5lp1
Fluorine binding site 1 out of 4 in the Crystal Structure of Human Lipoprotein-Associated Phospholipase A2 in Complex with A [1.1.1]Bicyclopentane-Containing Inhibitor at 1.91A Resolution.


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 Lipoprotein-Associated Phospholipase A2 in Complex with A [1.1.1]Bicyclopentane-Containing Inhibitor at 1.91A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F503

b:40.5
occ:1.00
F3 A:71H503 0.0 40.5 1.0
C32 A:71H503 1.4 39.9 1.0
C31 A:71H503 2.3 36.3 1.0
C33 A:71H503 2.4 33.9 1.0
CD2 A:PHE357 3.1 26.4 1.0
CE2 A:PHE357 3.1 26.6 1.0
CD1 A:LEU159 3.5 25.7 1.0
C30 A:71H503 3.6 32.5 1.0
C34 A:71H503 3.6 34.9 1.0
CD2 A:LEU107 3.7 33.5 1.0
C14 A:71H503 3.9 38.5 1.0
C13 A:71H503 3.9 39.5 1.0
C29 A:71H503 4.1 34.9 1.0
CG A:PHE357 4.1 25.8 1.0
CZ A:PHE357 4.2 27.7 1.0
CG A:LEU159 4.8 26.2 1.0
CB A:PHE357 4.8 25.1 1.0
CD1 A:LEU107 4.9 33.5 1.0
O A:GLY154 4.9 25.5 1.0
CG A:LEU107 4.9 32.1 1.0
CD1 A:PHE357 5.0 25.7 1.0

Fluorine binding site 2 out of 4 in 5lp1

Go back to Fluorine Binding Sites List in 5lp1
Fluorine binding site 2 out of 4 in the Crystal Structure of Human Lipoprotein-Associated Phospholipase A2 in Complex with A [1.1.1]Bicyclopentane-Containing Inhibitor at 1.91A Resolution.


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 Lipoprotein-Associated Phospholipase A2 in Complex with A [1.1.1]Bicyclopentane-Containing Inhibitor at 1.91A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F503

b:41.1
occ:1.00
F2 A:71H503 0.0 41.1 1.0
C18 A:71H503 1.3 44.6 1.0
F A:71H503 2.1 43.9 1.0
F1 A:71H503 2.1 44.0 1.0
C15 A:71H503 2.4 40.8 1.0
C16 A:71H503 3.1 40.4 1.0
C14 A:71H503 3.3 38.5 1.0
CD1 A:PHE357 3.3 25.7 1.0
CE1 A:PHE357 3.5 25.4 1.0
CD1 A:LEU371 3.6 32.1 1.0
CG A:PHE357 4.2 25.8 1.0
CE2 A:PHE125 4.4 36.3 1.0
C17 A:71H503 4.4 38.2 1.0
CD1 A:LEU369 4.4 55.2 1.0
CZ A:PHE357 4.4 27.7 1.0
CZ A:PHE125 4.5 34.7 1.0
C13 A:71H503 4.5 39.5 1.0
CD2 A:LEU371 4.5 31.1 1.0
CG A:LEU371 4.6 31.2 1.0
CB A:PHE357 4.7 25.1 1.0
CD2 A:LEU121 4.9 37.3 1.0
C12 A:71H503 5.0 37.4 1.0

Fluorine binding site 3 out of 4 in 5lp1

Go back to Fluorine Binding Sites List in 5lp1
Fluorine binding site 3 out of 4 in the Crystal Structure of Human Lipoprotein-Associated Phospholipase A2 in Complex with A [1.1.1]Bicyclopentane-Containing Inhibitor at 1.91A Resolution.


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 Lipoprotein-Associated Phospholipase A2 in Complex with A [1.1.1]Bicyclopentane-Containing Inhibitor at 1.91A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F503

b:44.0
occ:1.00
F1 A:71H503 0.0 44.0 1.0
C18 A:71H503 1.3 44.6 1.0
F A:71H503 2.1 43.9 1.0
F2 A:71H503 2.1 41.1 1.0
C15 A:71H503 2.4 40.8 1.0
C14 A:71H503 2.8 38.5 1.0
CE1 A:PHE357 3.2 25.4 1.0
CZ A:PHE357 3.5 27.7 1.0
C16 A:71H503 3.6 40.4 1.0
CD1 A:PHE357 3.7 25.7 1.0
CD2 A:LEU121 3.8 37.3 1.0
C13 A:71H503 4.1 39.5 1.0
CE2 A:PHE357 4.3 26.6 1.0
CD1 A:LEU121 4.4 37.0 1.0
CD1 A:LEU111 4.5 41.0 1.0
CG A:PHE357 4.5 25.8 1.0
CE2 A:PHE125 4.5 36.3 1.0
CD2 A:PHE357 4.7 26.4 1.0
C17 A:71H503 4.8 38.2 1.0
CG A:LEU121 4.8 34.4 1.0
C12 A:71H503 5.0 37.4 1.0

Fluorine binding site 4 out of 4 in 5lp1

Go back to Fluorine Binding Sites List in 5lp1
Fluorine binding site 4 out of 4 in the Crystal Structure of Human Lipoprotein-Associated Phospholipase A2 in Complex with A [1.1.1]Bicyclopentane-Containing Inhibitor at 1.91A Resolution.


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 Lipoprotein-Associated Phospholipase A2 in Complex with A [1.1.1]Bicyclopentane-Containing Inhibitor at 1.91A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F503

b:43.9
occ:1.00
F A:71H503 0.0 43.9 1.0
C18 A:71H503 1.3 44.6 1.0
F1 A:71H503 2.1 44.0 1.0
F2 A:71H503 2.1 41.1 1.0
C15 A:71H503 2.4 40.8 1.0
C16 A:71H503 2.8 40.4 1.0
C14 A:71H503 3.6 38.5 1.0
CD2 A:LEU121 3.7 37.3 1.0
CD1 A:LEU111 4.1 41.0 1.0
C17 A:71H503 4.2 38.2 1.0
CD1 A:LEU369 4.6 55.2 1.0
C13 A:71H503 4.7 39.5 1.0
CD1 A:LEU121 4.8 37.0 1.0
CG A:LEU121 4.9 34.4 1.0
CE2 A:PHE125 4.9 36.3 1.0
CE1 A:PHE357 4.9 25.4 1.0
C12 A:71H503 5.0 37.4 1.0

Reference:

N.D.Measom, K.D.Down, D.J.Hirst, C.Jamieson, E.S.Manas, V.K.Patel, D.O.Somers. Investigation of A Bicyclo[1.1.1]Pentane As A Phenyl Replacement Within An LPPLA2 Inhibitor. Acs Med Chem Lett V. 8 43 2017.
ISSN: ISSN 1948-5875
PubMed: 28105273
DOI: 10.1021/ACSMEDCHEMLETT.6B00281
Page generated: Sun Dec 13 12:27:17 2020

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