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Fluorine in PDB 5kr8: (4~{S},6~{S})-4-[2,4-Bis(Fluoranyl)Phenyl]-6-(3,5-Dimethyl-1,2-Oxazol- 4-Yl)-4-Methyl-5,6-Dihydro-1,3-Thiazin-2-Amine (Compound 5) Bound to BACE1

Enzymatic activity of (4~{S},6~{S})-4-[2,4-Bis(Fluoranyl)Phenyl]-6-(3,5-Dimethyl-1,2-Oxazol- 4-Yl)-4-Methyl-5,6-Dihydro-1,3-Thiazin-2-Amine (Compound 5) Bound to BACE1

All present enzymatic activity of (4~{S},6~{S})-4-[2,4-Bis(Fluoranyl)Phenyl]-6-(3,5-Dimethyl-1,2-Oxazol- 4-Yl)-4-Methyl-5,6-Dihydro-1,3-Thiazin-2-Amine (Compound 5) Bound to BACE1:
3.4.23.46;

Protein crystallography data

The structure of (4~{S},6~{S})-4-[2,4-Bis(Fluoranyl)Phenyl]-6-(3,5-Dimethyl-1,2-Oxazol- 4-Yl)-4-Methyl-5,6-Dihydro-1,3-Thiazin-2-Amine (Compound 5) Bound to BACE1, PDB code: 5kr8 was solved by H.A.Lewis, Y.J.Wu, R.Rajamani, L.A.Thompson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.90 / 2.12
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 102.059, 102.059, 170.843, 90.00, 90.00, 120.00
R / Rfree (%) 21.3 / 24.4

Other elements in 5kr8:

The structure of (4~{S},6~{S})-4-[2,4-Bis(Fluoranyl)Phenyl]-6-(3,5-Dimethyl-1,2-Oxazol- 4-Yl)-4-Methyl-5,6-Dihydro-1,3-Thiazin-2-Amine (Compound 5) Bound to BACE1 also contains other interesting chemical elements:

Iodine (I) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the (4~{S},6~{S})-4-[2,4-Bis(Fluoranyl)Phenyl]-6-(3,5-Dimethyl-1,2-Oxazol- 4-Yl)-4-Methyl-5,6-Dihydro-1,3-Thiazin-2-Amine (Compound 5) Bound to BACE1 (pdb code 5kr8). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the (4~{S},6~{S})-4-[2,4-Bis(Fluoranyl)Phenyl]-6-(3,5-Dimethyl-1,2-Oxazol- 4-Yl)-4-Methyl-5,6-Dihydro-1,3-Thiazin-2-Amine (Compound 5) Bound to BACE1, PDB code: 5kr8:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 5kr8

Go back to Fluorine Binding Sites List in 5kr8
Fluorine binding site 1 out of 2 in the (4~{S},6~{S})-4-[2,4-Bis(Fluoranyl)Phenyl]-6-(3,5-Dimethyl-1,2-Oxazol- 4-Yl)-4-Methyl-5,6-Dihydro-1,3-Thiazin-2-Amine (Compound 5) Bound to BACE1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of (4~{S},6~{S})-4-[2,4-Bis(Fluoranyl)Phenyl]-6-(3,5-Dimethyl-1,2-Oxazol- 4-Yl)-4-Methyl-5,6-Dihydro-1,3-Thiazin-2-Amine (Compound 5) Bound to BACE1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:34.8
occ:1.00
 F22 A:6WE502 0.0 34.8 1.0
C21 A:6WE502 1.3 31.7 1.0
C20 A:6WE502 2.3 27.5 1.0
C16 A:6WE502 2.4 32.7 1.0
C10 A:6WE502 2.9 29.9 1.0
C9 A:6WE502 3.0 26.8 1.0
C15 A:6WE502 3.1 27.6 1.0
CE2 A:TYR119 3.3 46.7 1.0
CE1 A:PHE156 3.3 26.1 1.0
CD1 A:PHE156 3.4 25.0 1.0
CD2 A:TYR119 3.6 40.0 1.0
C19 A:6WE502 3.6 32.4 1.0
C17 A:6WE502 3.6 29.1 1.0
CZ A:TYR119 3.6 45.4 1.0
C8 A:6WE502 3.8 33.6 1.0
OH A:TYR119 4.1 54.2 1.0
C18 A:6WE502 4.1 30.4 1.0
CG A:TYR119 4.2 41.9 1.0
CE1 A:TYR119 4.3 41.9 1.0
N11 A:6WE502 4.4 27.0 1.0
CD1 A:TYR119 4.5 44.5 1.0
CZ A:PHE156 4.6 27.4 1.0
C3 A:6WE502 4.6 33.8 1.0
CG A:PHE156 4.7 26.5 1.0
F23 A:6WE502 4.7 37.4 1.0
C7 A:6WE502 4.8 36.9 1.0
CD1 A:ILE166 4.9 46.6 1.0
C4 A:6WE502 5.0 38.0 1.0
O A:HOH610 5.0 44.0 1.0

Fluorine binding site 2 out of 2 in 5kr8

Go back to Fluorine Binding Sites List in 5kr8
Fluorine binding site 2 out of 2 in the (4~{S},6~{S})-4-[2,4-Bis(Fluoranyl)Phenyl]-6-(3,5-Dimethyl-1,2-Oxazol- 4-Yl)-4-Methyl-5,6-Dihydro-1,3-Thiazin-2-Amine (Compound 5) Bound to BACE1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of (4~{S},6~{S})-4-[2,4-Bis(Fluoranyl)Phenyl]-6-(3,5-Dimethyl-1,2-Oxazol- 4-Yl)-4-Methyl-5,6-Dihydro-1,3-Thiazin-2-Amine (Compound 5) Bound to BACE1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:37.4
occ:1.00
 F23 A:6WE502 0.0 37.4 1.0
C19 A:6WE502 1.3 32.4 1.0
C18 A:6WE502 2.4 30.4 1.0
C20 A:6WE502 2.4 27.5 1.0
O A:HOH610 2.9 44.0 1.0
CZ2 A:TRP163 3.4 28.4 1.0
CH2 A:TRP163 3.5 32.0 1.0
C17 A:6WE502 3.6 29.1 1.0
C21 A:6WE502 3.7 31.7 1.0
O A:PHE156 4.0 30.7 1.0
C16 A:6WE502 4.2 32.7 1.0
CD1 A:ILE158 4.2 36.5 1.0
CD2 A:LEU78 4.4 41.3 1.0
O A:HOH698 4.4 56.8 1.0
CE2 A:TRP163 4.5 30.6 1.0
CG1 A:ILE158 4.7 35.8 1.0
F22 A:6WE502 4.7 34.8 1.0
CZ3 A:TRP163 4.8 31.0 1.0

Reference:

Y.J.Wu, J.Guernon, J.Shi, L.Marcin, M.Higgins, R.Rajamani, J.Muckelbauer, H.Lewis, C.Chang, D.Camac, J.H.Toyn, M.K.Ahlijanian, C.F.Albright, J.E.Macor, L.A.Thompson. Discovery of S3-Truncated, C-6 Heteroaryl Substituted Aminothiazine Beta-Site App Cleaving Enzyme-1 (BACE1) Inhibitors. J.Med.Chem. V. 59 8593 2016.
ISSN: ISSN 0022-2623
PubMed: 27559936
DOI: 10.1021/ACS.JMEDCHEM.6B01012
Page generated: Tue Jul 15 04:53:09 2025

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