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Fluorine in PDB 5hdx: Bace-1 in Complex with (7AR)-7A-(5-Cyanothiophen-2-Yl)-6-(4-Ethoxy-5- Fluoro-6-Methylpyrimidin-2-Yl)-3-Methyl-4-Oxooctahydro-2H-Pyrrolo[3, 4-D]Pyrimidin-2-Iminium

Enzymatic activity of Bace-1 in Complex with (7AR)-7A-(5-Cyanothiophen-2-Yl)-6-(4-Ethoxy-5- Fluoro-6-Methylpyrimidin-2-Yl)-3-Methyl-4-Oxooctahydro-2H-Pyrrolo[3, 4-D]Pyrimidin-2-Iminium

All present enzymatic activity of Bace-1 in Complex with (7AR)-7A-(5-Cyanothiophen-2-Yl)-6-(4-Ethoxy-5- Fluoro-6-Methylpyrimidin-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 in Complex with (7AR)-7A-(5-Cyanothiophen-2-Yl)-6-(4-Ethoxy-5- Fluoro-6-Methylpyrimidin-2-Yl)-3-Methyl-4-Oxooctahydro-2H-Pyrrolo[3, 4-D]Pyrimidin-2-Iminium, PDB code: 5hdx was solved by P.Orth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 72.10 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 86.273, 89.353, 131.319, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 19.2

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Bace-1 in Complex with (7AR)-7A-(5-Cyanothiophen-2-Yl)-6-(4-Ethoxy-5- Fluoro-6-Methylpyrimidin-2-Yl)-3-Methyl-4-Oxooctahydro-2H-Pyrrolo[3, 4-D]Pyrimidin-2-Iminium (pdb code 5hdx). 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 in Complex with (7AR)-7A-(5-Cyanothiophen-2-Yl)-6-(4-Ethoxy-5- Fluoro-6-Methylpyrimidin-2-Yl)-3-Methyl-4-Oxooctahydro-2H-Pyrrolo[3, 4-D]Pyrimidin-2-Iminium, PDB code: 5hdx:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 5hdx

Go back to Fluorine Binding Sites List in 5hdx
Fluorine binding site 1 out of 2 in the Bace-1 in Complex with (7AR)-7A-(5-Cyanothiophen-2-Yl)-6-(4-Ethoxy-5- Fluoro-6-Methylpyrimidin-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 in Complex with (7AR)-7A-(5-Cyanothiophen-2-Yl)-6-(4-Ethoxy-5- Fluoro-6-Methylpyrimidin-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:F501

b:37.0
occ:1.00
 F25 A:60U501 0.0 37.0 1.0
C15 A:60U501 1.3 31.9 1.0
C11 A:60U501 2.3 37.8 1.0
C17 A:60U501 2.4 27.3 1.0
O27 A:60U501 2.6 43.9 1.0
C28 A:60U501 2.9 20.8 1.0
CG A:ARG189 2.9 22.7 1.0
NE A:ARG189 3.1 41.3 1.0
O A:HOH671 3.2 27.0 1.0
O A:HOH829 3.2 17.5 1.0
CD A:ARG189 3.5 33.7 1.0
CZ A:ARG189 3.6 55.7 1.0
N8 A:60U501 3.6 33.6 1.0
O A:ILE187 3.6 15.7 1.0
N12 A:60U501 3.6 28.7 1.0
C29 A:60U501 3.8 47.8 1.0
NH1 A:ARG189 3.9 39.8 1.0
CG1 A:VAL130 3.9 35.3 1.0
C7 A:60U501 4.0 26.9 1.0
CB A:ARG189 4.2 18.1 1.0
O A:HOH669 4.4 35.5 1.0
NH2 A:ARG189 4.4 43.6 1.0
OD1 A:ASN98 4.6 16.6 1.0
N A:ARG189 4.7 15.6 1.0
C A:ILE187 4.8 17.1 1.0
C30 A:60U501 4.8 48.0 1.0
CG2 A:VAL130 4.9 35.5 1.0

Fluorine binding site 2 out of 2 in 5hdx

Go back to Fluorine Binding Sites List in 5hdx
Fluorine binding site 2 out of 2 in the Bace-1 in Complex with (7AR)-7A-(5-Cyanothiophen-2-Yl)-6-(4-Ethoxy-5- Fluoro-6-Methylpyrimidin-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 in Complex with (7AR)-7A-(5-Cyanothiophen-2-Yl)-6-(4-Ethoxy-5- Fluoro-6-Methylpyrimidin-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:F501

b:25.2
occ:1.00
 F25 B:60U501 0.0 25.2 1.0
C15 B:60U501 1.3 19.1 1.0
C11 B:60U501 2.4 27.0 1.0
C17 B:60U501 2.4 17.5 1.0
O27 B:60U501 2.6 32.2 1.0
C28 B:60U501 2.8 13.9 1.0
CG B:ARG189 2.9 20.2 1.0
NE B:ARG189 2.9 27.9 1.0
O B:HOH644 3.2 23.7 1.0
O B:HOH755 3.3 18.5 1.0
CZ B:ARG189 3.4 41.9 1.0
CD B:ARG189 3.5 24.5 1.0
O B:ILE187 3.5 15.0 1.0
N12 B:60U501 3.6 20.0 1.0
N8 B:60U501 3.6 24.6 1.0
NH2 B:ARG189 3.7 24.8 1.0
CG1 B:VAL130 4.0 18.7 1.0
C7 B:60U501 4.0 20.0 1.0
C29 B:60U501 4.0 35.7 1.0
NH1 B:ARG189 4.2 31.8 1.0
CB B:ARG189 4.2 15.3 1.0
O B:HOH665 4.3 33.4 1.0
OD1 B:ASN98 4.6 12.7 1.0
N B:ARG189 4.7 15.3 1.0
C B:ILE187 4.8 14.6 1.0
C30 B:60U501 4.8 36.2 1.0
CG2 B:VAL130 4.8 18.5 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 09:46:56 2024

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