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Fluorine in PDB 3vg1: Crystal Structure of Human Beta Secretase in Complex with Nvp-BUR436, Derived From A Soaking Experiment

Enzymatic activity of Crystal Structure of Human Beta Secretase in Complex with Nvp-BUR436, Derived From A Soaking Experiment

All present enzymatic activity of Crystal Structure of Human Beta Secretase in Complex with Nvp-BUR436, Derived From A Soaking Experiment:
3.4.23.46;

Protein crystallography data

The structure of Crystal Structure of Human Beta Secretase in Complex with Nvp-BUR436, Derived From A Soaking Experiment, PDB code: 3vg1 was solved by J.M.Rondeau, E.Bourgier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 59.44 / 1.77
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 48.702, 72.239, 104.585, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Human Beta Secretase in Complex with Nvp-BUR436, Derived From A Soaking Experiment (pdb code 3vg1). 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 Beta Secretase in Complex with Nvp-BUR436, Derived From A Soaking Experiment, PDB code: 3vg1:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 3vg1

Go back to Fluorine Binding Sites List in 3vg1
Fluorine binding site 1 out of 4 in the Crystal Structure of Human Beta Secretase in Complex with Nvp-BUR436, Derived From A Soaking Experiment


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 Beta Secretase in Complex with Nvp-BUR436, Derived From A Soaking Experiment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:29.0
occ:0.50
 F1 A:0GT401 0.0 29.0 0.5
F4 A:0GT401 0.7 24.7 0.5
C2 A:0GT401 1.4 27.0 0.5
C2 A:0GT401 1.5 25.0 0.5
C5 A:0GT401 2.2 24.5 0.5
F4 A:0GT401 2.2 28.1 0.5
C5 A:0GT401 2.4 26.1 0.5
F1 A:0GT401 2.7 26.2 0.5
OG1 A:THR220 3.1 18.4 1.0
O A:GLY218 3.1 22.2 1.0
O A:HOH523 3.3 18.3 1.0
O A:HOH528 3.4 18.9 1.0
N A:GLY13 3.5 19.3 1.0
C8 A:0GT401 3.6 22.6 0.5
C8 A:0GT401 3.7 24.2 0.5
O A:GLY11 3.7 23.8 1.0
O A:HOH821 3.8 48.7 1.0
O A:HOH548 3.8 23.1 1.0
CA A:GLY13 3.9 18.3 1.0
C A:GLN12 3.9 21.9 1.0
N A:THR220 4.1 13.5 1.0
C A:GLY11 4.1 22.1 1.0
CA A:GLN12 4.2 22.7 1.0
C A:GLY218 4.2 18.3 1.0
C14 A:0GT401 4.3 20.8 0.5
N A:GLN12 4.3 21.3 1.0
CB A:THR220 4.4 15.7 1.0
C14 A:0GT401 4.4 22.5 0.5
C15 A:0GT401 4.4 20.3 0.5
C15 A:0GT401 4.4 21.9 0.5
CA A:THR220 4.6 13.9 1.0
O A:GLN12 4.6 23.3 1.0
C A:THR219 4.6 14.9 1.0
C9 A:0GT401 4.7 22.4 0.5
CA A:THR219 4.8 16.9 1.0
C9 A:0GT401 4.8 24.5 0.5
N A:THR219 5.0 15.7 1.0

Fluorine binding site 2 out of 4 in 3vg1

Go back to Fluorine Binding Sites List in 3vg1
Fluorine binding site 2 out of 4 in the Crystal Structure of Human Beta Secretase in Complex with Nvp-BUR436, Derived From A Soaking Experiment


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 Beta Secretase in Complex with Nvp-BUR436, Derived From A Soaking Experiment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:26.2
occ:0.50
 F1 A:0GT401 0.0 26.2 0.5
C2 A:0GT401 1.4 25.0 0.5
C5 A:0GT401 1.4 26.1 0.5
F4 A:0GT401 2.2 24.7 0.5
C5 A:0GT401 2.4 24.5 0.5
C2 A:0GT401 2.6 27.0 0.5
C8 A:0GT401 2.6 24.2 0.5
F1 A:0GT401 2.7 29.0 0.5
O A:GLN12 2.8 23.3 1.0
C A:GLN12 2.9 21.9 1.0
C8 A:0GT401 2.9 22.6 0.5
N A:GLY13 3.3 19.3 1.0
C9 A:0GT401 3.5 24.5 0.5
CA A:GLY13 3.5 18.3 1.0
F4 A:0GT401 3.5 28.1 0.5
CZ2 A:TRP115 3.5 18.5 1.0
CA A:GLN12 3.5 22.7 1.0
C9 A:0GT401 3.6 22.4 0.5
C14 A:0GT401 3.7 22.5 0.5
CD1 A:ILE110 3.7 30.3 1.0
NE1 A:TRP115 3.8 17.8 1.0
C14 A:0GT401 3.8 20.8 0.5
CD1 A:LEU30 3.8 14.3 1.0
CE2 A:TRP115 4.0 18.3 1.0
CD2 A:LEU30 4.2 15.1 1.0
C15 A:0GT401 4.2 21.9 0.5
C15 A:0GT401 4.3 20.3 0.5
N11 A:0GT401 4.5 22.3 0.5
N A:GLN12 4.5 21.3 1.0
O A:GLY11 4.6 23.8 1.0
O A:GLY218 4.6 22.2 1.0
N11 A:0GT401 4.6 23.9 0.5
CB A:GLN12 4.6 24.1 1.0
C13 A:0GT401 4.6 21.8 0.5
CH2 A:TRP115 4.6 16.7 1.0
CG A:LEU30 4.7 13.9 1.0
C13 A:0GT401 4.7 23.4 0.5
C A:GLY13 4.7 17.8 1.0
C A:GLY11 5.0 22.1 1.0
CG1 A:ILE110 5.0 30.1 1.0

Fluorine binding site 3 out of 4 in 3vg1

Go back to Fluorine Binding Sites List in 3vg1
Fluorine binding site 3 out of 4 in the Crystal Structure of Human Beta Secretase in Complex with Nvp-BUR436, Derived From A Soaking Experiment


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 Beta Secretase in Complex with Nvp-BUR436, Derived From A Soaking Experiment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:28.1
occ:0.50
 F4 A:0GT401 0.0 28.1 0.5
C2 A:0GT401 1.4 27.0 0.5
C5 A:0GT401 1.4 24.5 0.5
F1 A:0GT401 2.2 29.0 0.5
C5 A:0GT401 2.4 26.1 0.5
O A:HOH821 2.4 48.7 1.0
C2 A:0GT401 2.5 25.0 0.5
F4 A:0GT401 2.6 24.7 0.5
C8 A:0GT401 2.7 22.6 0.5
C8 A:0GT401 3.1 24.2 0.5
O A:HOH548 3.2 23.1 1.0
O A:GLY11 3.3 23.8 1.0
F1 A:0GT401 3.5 26.2 0.5
C9 A:0GT401 3.5 22.4 0.5
OG1 A:THR220 3.6 18.4 1.0
C14 A:0GT401 3.8 20.8 0.5
C9 A:0GT401 3.8 24.5 0.5
C14 A:0GT401 4.0 22.5 0.5
O A:HOH836 4.1 52.1 1.0
C A:GLY11 4.3 22.1 1.0
O A:HOH688 4.3 38.2 1.0
C15 A:0GT401 4.4 20.3 0.5
O A:GLY218 4.5 22.2 1.0
C15 A:0GT401 4.6 21.9 0.5
CD1 A:ILE110 4.6 30.3 1.0
N11 A:0GT401 4.7 22.3 0.5
CA A:GLN12 4.7 22.7 1.0
N11 A:0GT401 4.8 23.9 0.5
CB A:THR220 4.8 15.7 1.0
C13 A:0GT401 4.8 21.8 0.5
C13 A:0GT401 4.9 23.4 0.5
N A:GLN12 4.9 21.3 1.0
N A:THR220 4.9 13.5 1.0
O A:HOH694 4.9 39.0 1.0

Fluorine binding site 4 out of 4 in 3vg1

Go back to Fluorine Binding Sites List in 3vg1
Fluorine binding site 4 out of 4 in the Crystal Structure of Human Beta Secretase in Complex with Nvp-BUR436, Derived From A Soaking Experiment


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 Beta Secretase in Complex with Nvp-BUR436, Derived From A Soaking Experiment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:24.7
occ:0.50
 F4 A:0GT401 0.0 24.7 0.5
F1 A:0GT401 0.7 29.0 0.5
C2 A:0GT401 1.4 25.0 0.5
C2 A:0GT401 1.8 27.0 0.5
F1 A:0GT401 2.2 26.2 0.5
C5 A:0GT401 2.3 26.1 0.5
C5 A:0GT401 2.4 24.5 0.5
F4 A:0GT401 2.6 28.1 0.5
N A:GLY13 2.8 19.3 1.0
C A:GLN12 3.2 21.9 1.0
CA A:GLY13 3.2 18.3 1.0
O A:HOH528 3.2 18.9 1.0
O A:HOH523 3.3 18.3 1.0
OG1 A:THR220 3.5 18.4 1.0
O A:GLY218 3.5 22.2 1.0
O A:GLY11 3.6 23.8 1.0
CA A:GLN12 3.6 22.7 1.0
C8 A:0GT401 3.7 22.6 0.5
C8 A:0GT401 3.7 24.2 0.5
N A:GLN12 3.9 21.3 1.0
C A:GLY11 3.9 22.1 1.0
O A:GLN12 3.9 23.3 1.0
O A:HOH821 4.3 48.7 1.0
C14 A:0GT401 4.5 20.8 0.5
C14 A:0GT401 4.5 22.5 0.5
O A:HOH548 4.6 23.1 1.0
C A:GLY218 4.6 18.3 1.0
N A:THR220 4.7 13.5 1.0
C15 A:0GT401 4.7 20.3 0.5
C15 A:0GT401 4.7 21.9 0.5
C A:GLY13 4.7 17.8 1.0
C9 A:0GT401 4.8 22.4 0.5
CB A:THR220 4.8 15.7 1.0
CD1 A:LEU30 4.8 14.3 1.0
C9 A:0GT401 4.8 24.5 0.5
CA A:GLY11 5.0 22.7 1.0

Reference:

H.Rueeger, R.Lueoend, O.Rogel, J.M.Rondeau, H.Mobitz, R.Machauer, L.Jacobson, M.Staufenbiel, S.Desrayaud, U.Neumann. Discovery of Cyclic Sulfone Hydroxyethylamines As Potent and Selective Beta-Site App-Cleaving Enzyme 1 (BACE1) Inhibitors: Structure Based Design and in Vivo Reduction of Amyloid Beta-Peptides J.Med.Chem. V. 55 3364 2012.
ISSN: ISSN 0022-2623
PubMed: 22380629
DOI: 10.1021/JM300069Y
Page generated: Wed Jul 31 23:17:23 2024

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