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Fluorine in PDB 6c2i: Structure of Bace-1 (Beta-Secretase) in Complex with : N-(3-((1R,5S, 6R)-3-Amino-5-Methyl-2-Oxa-4-Azabicyclo[4.1.0]Hept-3-En-5-Yl)-4- Fluorophenyl)-5-Methoxypyrazine-2-Carboxamide

Enzymatic activity of Structure of Bace-1 (Beta-Secretase) in Complex with : N-(3-((1R,5S, 6R)-3-Amino-5-Methyl-2-Oxa-4-Azabicyclo[4.1.0]Hept-3-En-5-Yl)-4- Fluorophenyl)-5-Methoxypyrazine-2-Carboxamide

All present enzymatic activity of Structure of Bace-1 (Beta-Secretase) in Complex with : N-(3-((1R,5S, 6R)-3-Amino-5-Methyl-2-Oxa-4-Azabicyclo[4.1.0]Hept-3-En-5-Yl)-4- Fluorophenyl)-5-Methoxypyrazine-2-Carboxamide:
3.4.23.46;

Protein crystallography data

The structure of Structure of Bace-1 (Beta-Secretase) in Complex with : N-(3-((1R,5S, 6R)-3-Amino-5-Methyl-2-Oxa-4-Azabicyclo[4.1.0]Hept-3-En-5-Yl)-4- Fluorophenyl)-5-Methoxypyrazine-2-Carboxamide, PDB code: 6c2i was solved by E.A.Sickmier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.99 / 1.95
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 101.952, 101.952, 172.155, 90.00, 90.00, 120.00
R / Rfree (%) 15.8 / 18.4

Other elements in 6c2i:

The structure of Structure of Bace-1 (Beta-Secretase) in Complex with : N-(3-((1R,5S, 6R)-3-Amino-5-Methyl-2-Oxa-4-Azabicyclo[4.1.0]Hept-3-En-5-Yl)-4- Fluorophenyl)-5-Methoxypyrazine-2-Carboxamide also contains other interesting chemical elements:

Iodine (I) 3 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of Bace-1 (Beta-Secretase) in Complex with : N-(3-((1R,5S, 6R)-3-Amino-5-Methyl-2-Oxa-4-Azabicyclo[4.1.0]Hept-3-En-5-Yl)-4- Fluorophenyl)-5-Methoxypyrazine-2-Carboxamide (pdb code 6c2i). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total only one binding site of Fluorine was determined in the Structure of Bace-1 (Beta-Secretase) in Complex with : N-(3-((1R,5S, 6R)-3-Amino-5-Methyl-2-Oxa-4-Azabicyclo[4.1.0]Hept-3-En-5-Yl)-4- Fluorophenyl)-5-Methoxypyrazine-2-Carboxamide, PDB code: 6c2i:

Fluorine binding site 1 out of 1 in 6c2i

Go back to Fluorine Binding Sites List in 6c2i
Fluorine binding site 1 out of 1 in the Structure of Bace-1 (Beta-Secretase) in Complex with : N-(3-((1R,5S, 6R)-3-Amino-5-Methyl-2-Oxa-4-Azabicyclo[4.1.0]Hept-3-En-5-Yl)-4- Fluorophenyl)-5-Methoxypyrazine-2-Carboxamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of Bace-1 (Beta-Secretase) in Complex with : N-(3-((1R,5S, 6R)-3-Amino-5-Methyl-2-Oxa-4-Azabicyclo[4.1.0]Hept-3-En-5-Yl)-4- Fluorophenyl)-5-Methoxypyrazine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F407

b:23.8
occ:1.00
 F7 A:EJ7407 0.0 23.8 1.0
C4 A:EJ7407 1.3 23.1 1.0
C3 A:EJ7407 2.3 17.8 1.0
C5 A:EJ7407 2.4 19.0 1.0
H90 A:EJ7407 2.5 22.0 1.0
H31 A:EJ7407 2.5 21.5 1.0
HE1 A:PHE107 2.5 27.4 1.0
H103 A:EJ7407 2.6 30.2 1.0
H102 A:EJ7407 2.7 30.2 1.0
HD1 A:PHE107 2.8 23.7 1.0
C10 A:EJ7407 2.9 25.1 1.0
C9 A:EJ7407 2.9 19.8 1.0
CE1 A:PHE107 3.2 22.8 1.0
C11 A:EJ7407 3.3 18.2 1.0
HE2 A:TYR70 3.3 37.5 1.0
CD1 A:PHE107 3.4 19.7 1.0
CE2 A:TYR70 3.5 31.1 1.0
C6 A:EJ7407 3.6 17.4 1.0
C2 A:EJ7407 3.6 20.2 1.0
HD2 A:TYR70 3.7 40.4 1.0
CD2 A:TYR70 3.7 33.6 1.0
H101 A:EJ7407 3.9 30.2 1.0
HD12 A:ILE117 4.1 36.2 1.0
C1 A:EJ7407 4.1 19.4 1.0
CZ A:TYR70 4.2 31.4 1.0
N15 A:EJ7407 4.3 20.4 1.0
HD13 A:ILE117 4.3 36.2 1.0
H21 A:EJ7407 4.4 24.3 1.0
H61 A:EJ7407 4.4 20.9 1.0
CZ A:PHE107 4.5 20.7 1.0
CG A:TYR70 4.5 32.0 1.0
CD1 A:ILE117 4.6 30.1 1.0
C12 A:EJ7407 4.6 21.0 1.0
OH A:TYR70 4.7 48.3 1.0
C17 A:EJ7407 4.7 17.6 1.0
HA A:PHE107 4.7 27.7 1.0
CG A:PHE107 4.7 16.9 1.0
HD1 A:TRP75 4.8 26.6 1.0
HD11 A:ILE117 4.8 36.2 1.0
HZ A:PHE107 4.8 24.9 1.0
CE1 A:TYR70 4.9 38.4 1.0

Reference:

J.D.Low, M.D.Bartberger, Y.Cheng, D.Whittington, Q.Xue, S.Wood, J.R.Allen, A.E.Minatti. Diastereoselective Synthesis of Fused Cyclopropyl-3-Amino-2,4-Oxazine Beta-Amyloid Cleaving Enzyme (Bace) Inhibitors and Their Biological Evaluation. Bioorg. Med. Chem. Lett. V. 28 1111 2018.
ISSN: ESSN 1464-3405
PubMed: 29426770
DOI: 10.1016/J.BMCL.2018.01.056
Page generated: Tue Jul 15 10:19:44 2025

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