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Fluorine in PDB 5hdu: Bace-1 Incomplex with (7AR)-7A-(4-(3-Cyanophenyl)Thiophen-2-Yl)-6-(5- Fluoro-4-Methoxypyrimidin-2-Yl)-3-Methyl-4-Oxooctahydro-2H-Pyrrolo[3, 4-D]Pyrimidin-2-Iminium

Enzymatic activity of Bace-1 Incomplex with (7AR)-7A-(4-(3-Cyanophenyl)Thiophen-2-Yl)-6-(5- Fluoro-4-Methoxypyrimidin-2-Yl)-3-Methyl-4-Oxooctahydro-2H-Pyrrolo[3, 4-D]Pyrimidin-2-Iminium

All present enzymatic activity of Bace-1 Incomplex with (7AR)-7A-(4-(3-Cyanophenyl)Thiophen-2-Yl)-6-(5- Fluoro-4-Methoxypyrimidin-2-Yl)-3-Methyl-4-Oxooctahydro-2H-Pyrrolo[3, 4-D]Pyrimidin-2-Iminium:
3.4.23.46;

Protein crystallography data

The structure of Bace-1 Incomplex with (7AR)-7A-(4-(3-Cyanophenyl)Thiophen-2-Yl)-6-(5- Fluoro-4-Methoxypyrimidin-2-Yl)-3-Methyl-4-Oxooctahydro-2H-Pyrrolo[3, 4-D]Pyrimidin-2-Iminium, PDB code: 5hdu was solved by P.Orth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.91 / 1.58
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 86.410, 89.450, 131.240, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / 21.4

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Bace-1 Incomplex with (7AR)-7A-(4-(3-Cyanophenyl)Thiophen-2-Yl)-6-(5- Fluoro-4-Methoxypyrimidin-2-Yl)-3-Methyl-4-Oxooctahydro-2H-Pyrrolo[3, 4-D]Pyrimidin-2-Iminium (pdb code 5hdu). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Bace-1 Incomplex with (7AR)-7A-(4-(3-Cyanophenyl)Thiophen-2-Yl)-6-(5- Fluoro-4-Methoxypyrimidin-2-Yl)-3-Methyl-4-Oxooctahydro-2H-Pyrrolo[3, 4-D]Pyrimidin-2-Iminium, PDB code: 5hdu:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 5hdu

Go back to Fluorine Binding Sites List in 5hdu
Fluorine binding site 1 out of 2 in the Bace-1 Incomplex with (7AR)-7A-(4-(3-Cyanophenyl)Thiophen-2-Yl)-6-(5- Fluoro-4-Methoxypyrimidin-2-Yl)-3-Methyl-4-Oxooctahydro-2H-Pyrrolo[3, 4-D]Pyrimidin-2-Iminium


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Bace-1 Incomplex with (7AR)-7A-(4-(3-Cyanophenyl)Thiophen-2-Yl)-6-(5- Fluoro-4-Methoxypyrimidin-2-Yl)-3-Methyl-4-Oxooctahydro-2H-Pyrrolo[3, 4-D]Pyrimidin-2-Iminium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:25.8
occ:1.00
 F A:60W502 0.0 25.8 1.0
C14 A:60W502 1.3 26.7 1.0
C12 A:60W502 2.4 28.0 1.0
C15 A:60W502 2.4 23.6 1.0
O1 A:60W502 2.7 31.4 1.0
OD1 A:ASN98 3.0 18.4 1.0
O A:HOH758 3.1 17.1 1.0
CG A:ASN98 3.4 19.2 1.0
CG2 A:VAL130 3.4 44.5 1.0
CG A:ARG189 3.4 31.0 1.0
N4 A:60W502 3.6 24.6 1.0
N5 A:60W502 3.6 19.6 1.0
CB A:ASN98 3.7 14.0 1.0
CB A:ARG189 3.9 20.0 1.0
C11 A:60W502 4.0 20.5 1.0
O A:HOH602 4.0 28.8 1.0
CZ2 A:TRP137 4.0 31.1 1.0
C13 A:60W502 4.1 34.8 1.0
ND2 A:ASN98 4.3 16.4 1.0
N A:ARG189 4.6 17.7 1.0
CB A:VAL130 4.7 44.7 1.0
CG1 A:VAL130 4.7 44.7 1.0
CH2 A:TRP137 4.8 29.9 1.0
N A:ASN98 4.8 12.8 1.0
CD A:ARG189 4.8 48.8 1.0
CA A:ARG189 4.9 17.8 1.0
CA A:ASN98 4.9 13.2 1.0
CE2 A:TRP137 4.9 32.5 1.0

Fluorine binding site 2 out of 2 in 5hdu

Go back to Fluorine Binding Sites List in 5hdu
Fluorine binding site 2 out of 2 in the Bace-1 Incomplex with (7AR)-7A-(4-(3-Cyanophenyl)Thiophen-2-Yl)-6-(5- Fluoro-4-Methoxypyrimidin-2-Yl)-3-Methyl-4-Oxooctahydro-2H-Pyrrolo[3, 4-D]Pyrimidin-2-Iminium


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Bace-1 Incomplex with (7AR)-7A-(4-(3-Cyanophenyl)Thiophen-2-Yl)-6-(5- Fluoro-4-Methoxypyrimidin-2-Yl)-3-Methyl-4-Oxooctahydro-2H-Pyrrolo[3, 4-D]Pyrimidin-2-Iminium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F502

b:20.5
occ:1.00
 F B:60W502 0.0 20.5 1.0
C14 B:60W502 1.3 17.8 1.0
C12 B:60W502 2.4 18.9 1.0
C15 B:60W502 2.4 16.7 1.0
O1 B:60W502 2.7 21.6 1.0
OD1 B:ASN98 3.0 15.7 1.0
O B:HOH770 3.0 15.3 1.0
CG B:ASN98 3.3 18.0 1.0
CZ2 B:TRP137 3.5 21.2 1.0
CB B:ASN98 3.5 13.2 1.0
N4 B:60W502 3.6 17.6 1.0
N5 B:60W502 3.6 16.1 1.0
CG B:ARG189 3.6 23.6 1.0
CG1 B:VAL130 3.9 25.4 1.0
C11 B:60W502 4.0 18.3 1.0
CB B:ARG189 4.1 16.9 1.0
CG2 B:VAL130 4.1 24.3 1.0
NE1 B:TRP137 4.1 21.5 1.0
C13 B:60W502 4.1 19.7 1.0
CE2 B:TRP137 4.2 21.9 1.0
ND2 B:ASN98 4.3 14.7 1.0
O B:HOH619 4.3 43.0 1.0
N B:ASN98 4.5 11.5 1.0
CH2 B:TRP137 4.5 19.0 1.0
CB B:VAL130 4.6 24.5 1.0
CA B:ASN98 4.6 12.2 1.0
N B:ARG189 4.7 15.0 1.0
CB B:SER96 4.8 14.8 1.0

Reference:

M.Mandal, Y.Wu, J.Misiaszek, G.Li, A.Buevich, J.P.Caldwell, X.Liu, R.D.Mazzola, P.Orth, C.Strickland, J.Voigt, H.Wang, Z.Zhu, X.Chen, M.Grzelak, L.A.Hyde, R.Kuvelkar, P.T.Leach, G.Terracina, L.Zhang, Q.Zhang, M.S.Michener, B.Smith, K.Cox, D.Grotz, L.Favreau, K.Mitra, I.Kazakevich, B.A.Mckittrick, W.Greenlee, M.E.Kennedy, E.M.Parker, J.N.Cumming, A.W.Stamford. Structure-Based Design of An Iminoheterocyclic Beta-Site Amyloid Precursor Protein Cleaving Enzyme (Bace) Inhibitor That Lowers Central A Beta in Nonhuman Primates. J.Med.Chem. V. 59 3231 2016.
ISSN: ISSN 0022-2623
PubMed: 26937601
DOI: 10.1021/ACS.JMEDCHEM.5B01995
Page generated: Thu Aug 1 09:46:45 2024

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