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Fluorine in PDB 5he7: Bace-1 in Complex with (4AR,7AS)-7A-(2,4-Difluorophenyl)-6-(5-Fluoro- 4-Methoxy-6-Methylpyrimidin-2-Yl)-2-Imino-3-Methyloctahydro-4H- Pyrrolo[3,4-D]Pyrimidin-4-One

Enzymatic activity of Bace-1 in Complex with (4AR,7AS)-7A-(2,4-Difluorophenyl)-6-(5-Fluoro- 4-Methoxy-6-Methylpyrimidin-2-Yl)-2-Imino-3-Methyloctahydro-4H- Pyrrolo[3,4-D]Pyrimidin-4-One

All present enzymatic activity of Bace-1 in Complex with (4AR,7AS)-7A-(2,4-Difluorophenyl)-6-(5-Fluoro- 4-Methoxy-6-Methylpyrimidin-2-Yl)-2-Imino-3-Methyloctahydro-4H- Pyrrolo[3,4-D]Pyrimidin-4-One:
3.4.23.46;

Protein crystallography data

The structure of Bace-1 in Complex with (4AR,7AS)-7A-(2,4-Difluorophenyl)-6-(5-Fluoro- 4-Methoxy-6-Methylpyrimidin-2-Yl)-2-Imino-3-Methyloctahydro-4H- Pyrrolo[3,4-D]Pyrimidin-4-One, PDB code: 5he7 was solved by P.Orth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.88 / 1.71
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 86.530, 89.270, 131.360, 90.00, 90.00, 90.00
R / Rfree (%) 19 / 21.6

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Bace-1 in Complex with (4AR,7AS)-7A-(2,4-Difluorophenyl)-6-(5-Fluoro- 4-Methoxy-6-Methylpyrimidin-2-Yl)-2-Imino-3-Methyloctahydro-4H- Pyrrolo[3,4-D]Pyrimidin-4-One (pdb code 5he7). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Bace-1 in Complex with (4AR,7AS)-7A-(2,4-Difluorophenyl)-6-(5-Fluoro- 4-Methoxy-6-Methylpyrimidin-2-Yl)-2-Imino-3-Methyloctahydro-4H- Pyrrolo[3,4-D]Pyrimidin-4-One, PDB code: 5he7:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 5he7

Go back to Fluorine Binding Sites List in 5he7
Fluorine binding site 1 out of 6 in the Bace-1 in Complex with (4AR,7AS)-7A-(2,4-Difluorophenyl)-6-(5-Fluoro- 4-Methoxy-6-Methylpyrimidin-2-Yl)-2-Imino-3-Methyloctahydro-4H- Pyrrolo[3,4-D]Pyrimidin-4-One


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 (4AR,7AS)-7A-(2,4-Difluorophenyl)-6-(5-Fluoro- 4-Methoxy-6-Methylpyrimidin-2-Yl)-2-Imino-3-Methyloctahydro-4H- Pyrrolo[3,4-D]Pyrimidin-4-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:25.0
occ:1.00
 F2 A:60X501 0.0 25.0 1.0
C17 A:60X501 1.4 21.7 1.0
C16 A:60X501 2.3 19.4 1.0
C12 A:60X501 2.4 16.9 1.0
OH A:TYR132 2.8 66.8 1.0
C6 A:60X501 2.9 16.7 1.0
C5 A:60X501 3.0 16.5 1.0
CZ A:TYR132 3.0 64.2 1.0
C10 A:60X501 3.0 15.8 1.0
CE2 A:TYR132 3.4 56.8 1.0
CE1 A:PHE169 3.4 26.4 1.0
CD1 A:PHE169 3.5 26.3 1.0
C15 A:60X501 3.6 22.7 1.0
C13 A:60X501 3.6 17.1 1.0
CE1 A:TYR132 3.6 58.5 1.0
N2 A:60X501 3.8 17.1 1.0
C11 A:60X501 4.0 17.3 1.0
CD1 A:ILE179 4.0 20.5 1.0
C14 A:60X501 4.1 19.2 1.0
C9 A:60X501 4.2 20.8 1.0
CD2 A:TYR132 4.3 56.0 1.0
N3 A:60X501 4.3 14.1 1.0
CD1 A:TYR132 4.5 57.5 1.0
CZ A:PHE169 4.6 24.4 1.0
CG A:PHE169 4.6 23.2 1.0
F1 A:60X501 4.7 29.6 1.0
O1 A:60X501 4.7 24.1 1.0
O A:HOH967 4.7 51.6 1.0
O A:HOH636 4.7 33.9 1.0
CG A:TYR132 4.8 55.5 1.0
C2 A:60X501 4.8 19.8 1.0
N1 A:60X501 5.0 20.4 1.0

Fluorine binding site 2 out of 6 in 5he7

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Fluorine binding site 2 out of 6 in the Bace-1 in Complex with (4AR,7AS)-7A-(2,4-Difluorophenyl)-6-(5-Fluoro- 4-Methoxy-6-Methylpyrimidin-2-Yl)-2-Imino-3-Methyloctahydro-4H- Pyrrolo[3,4-D]Pyrimidin-4-One


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 (4AR,7AS)-7A-(2,4-Difluorophenyl)-6-(5-Fluoro- 4-Methoxy-6-Methylpyrimidin-2-Yl)-2-Imino-3-Methyloctahydro-4H- Pyrrolo[3,4-D]Pyrimidin-4-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:29.6
occ:1.00
 F1 A:60X501 0.0 29.6 1.0
C15 A:60X501 1.4 22.7 1.0
C16 A:60X501 2.3 19.4 1.0
C14 A:60X501 2.3 19.2 1.0
CZ2 A:TRP176 3.1 23.8 1.0
CD1 A:ILE171 3.3 37.9 1.0
CH2 A:TRP176 3.4 23.9 1.0
C17 A:60X501 3.6 21.7 1.0
C13 A:60X501 3.6 17.1 1.0
O A:HOH636 3.7 33.9 1.0
O A:HOH951 3.7 48.3 1.0
CG1 A:ILE171 4.1 34.8 1.0
C12 A:60X501 4.1 16.9 1.0
CE2 A:TRP176 4.3 24.5 1.0
O A:PHE169 4.3 29.8 1.0
CD1 A:LEU91 4.5 24.5 1.0
O A:HOH912 4.5 35.6 1.0
F2 A:60X501 4.7 25.0 1.0
CZ3 A:TRP176 4.8 23.1 1.0
O A:HOH645 4.8 34.2 1.0
NE1 A:TRP176 4.9 22.2 1.0
O A:GLN73 4.9 20.7 1.0
CD1 A:ILE179 5.0 20.5 1.0

Fluorine binding site 3 out of 6 in 5he7

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Fluorine binding site 3 out of 6 in the Bace-1 in Complex with (4AR,7AS)-7A-(2,4-Difluorophenyl)-6-(5-Fluoro- 4-Methoxy-6-Methylpyrimidin-2-Yl)-2-Imino-3-Methyloctahydro-4H- Pyrrolo[3,4-D]Pyrimidin-4-One


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Bace-1 in Complex with (4AR,7AS)-7A-(2,4-Difluorophenyl)-6-(5-Fluoro- 4-Methoxy-6-Methylpyrimidin-2-Yl)-2-Imino-3-Methyloctahydro-4H- Pyrrolo[3,4-D]Pyrimidin-4-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:27.3
occ:1.00
 F A:60X501 0.0 27.3 1.0
C A:60X501 1.3 24.6 1.0
C3 A:60X501 2.4 25.7 1.0
C1 A:60X501 2.4 23.2 1.0
O A:60X501 2.7 28.1 1.0
C18 A:60X501 3.0 21.8 1.0
OD1 A:ASN98 3.1 16.0 1.0
O A:HOH795 3.1 17.9 1.0
CG A:ASN98 3.4 21.0 1.0
N1 A:60X501 3.6 20.4 1.0
CG A:ARG189 3.6 25.1 1.0
CB A:ASN98 3.6 12.1 1.0
N A:60X501 3.6 20.4 1.0
CZ2 A:TRP137 3.9 27.8 1.0
CG1 A:VAL130 4.0 36.9 1.0
C2 A:60X501 4.0 19.8 1.0
CG2 A:VAL130 4.0 36.9 1.0
C4 A:60X501 4.1 29.6 1.0
CB A:ARG189 4.1 19.4 1.0
ND2 A:ASN98 4.4 14.0 1.0
CE2 A:TRP137 4.6 29.2 1.0
CB A:VAL130 4.6 36.9 1.0
NE1 A:TRP137 4.6 28.8 1.0
N A:ASN98 4.6 11.8 1.0
N A:ARG189 4.7 18.4 1.0
CA A:ASN98 4.8 12.2 1.0
CH2 A:TRP137 4.8 26.4 1.0
CB A:SER96 4.8 14.2 1.0
CD A:ARG189 5.0 32.9 1.0

Fluorine binding site 4 out of 6 in 5he7

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Fluorine binding site 4 out of 6 in the Bace-1 in Complex with (4AR,7AS)-7A-(2,4-Difluorophenyl)-6-(5-Fluoro- 4-Methoxy-6-Methylpyrimidin-2-Yl)-2-Imino-3-Methyloctahydro-4H- Pyrrolo[3,4-D]Pyrimidin-4-One


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Bace-1 in Complex with (4AR,7AS)-7A-(2,4-Difluorophenyl)-6-(5-Fluoro- 4-Methoxy-6-Methylpyrimidin-2-Yl)-2-Imino-3-Methyloctahydro-4H- Pyrrolo[3,4-D]Pyrimidin-4-One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F501

b:19.6
occ:1.00
 F2 B:60X501 0.0 19.6 1.0
C17 B:60X501 1.4 17.3 1.0
C16 B:60X501 2.3 17.4 1.0
C12 B:60X501 2.4 13.6 1.0
OH B:TYR132 2.9 25.7 1.0
C6 B:60X501 2.9 13.4 1.0
C5 B:60X501 3.0 13.6 1.0
C10 B:60X501 3.0 13.2 1.0
CZ B:TYR132 3.2 27.8 1.0
CD1 B:PHE169 3.3 18.4 1.0
O B:HOH845 3.4 34.8 1.0
C15 B:60X501 3.6 19.4 1.0
CE1 B:PHE169 3.6 18.2 1.0
C13 B:60X501 3.6 14.1 1.0
CE2 B:TYR132 3.6 22.8 1.0
N2 B:60X501 3.8 13.7 1.0
CE1 B:TYR132 3.9 22.4 1.0
CD1 B:ILE179 4.0 16.3 1.0
C11 B:60X501 4.0 15.8 1.0
C14 B:60X501 4.1 15.5 1.0
C9 B:60X501 4.2 18.2 1.0
CG B:PHE169 4.3 15.4 1.0
N3 B:60X501 4.3 13.2 1.0
O B:HOH950 4.5 48.4 1.0
CA B:PHE169 4.6 14.8 1.0
CD2 B:TYR132 4.6 22.1 1.0
O1 B:60X501 4.7 23.5 1.0
F1 B:60X501 4.7 22.5 1.0
O B:PHE169 4.7 18.7 1.0
CZ B:PHE169 4.7 16.9 1.0
CD1 B:TYR132 4.8 23.2 1.0
O B:HOH855 4.8 22.7 1.0
CB B:PHE169 4.8 15.2 1.0
C2 B:60X501 4.8 15.7 1.0

Fluorine binding site 5 out of 6 in 5he7

Go back to Fluorine Binding Sites List in 5he7
Fluorine binding site 5 out of 6 in the Bace-1 in Complex with (4AR,7AS)-7A-(2,4-Difluorophenyl)-6-(5-Fluoro- 4-Methoxy-6-Methylpyrimidin-2-Yl)-2-Imino-3-Methyloctahydro-4H- Pyrrolo[3,4-D]Pyrimidin-4-One


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Bace-1 in Complex with (4AR,7AS)-7A-(2,4-Difluorophenyl)-6-(5-Fluoro- 4-Methoxy-6-Methylpyrimidin-2-Yl)-2-Imino-3-Methyloctahydro-4H- Pyrrolo[3,4-D]Pyrimidin-4-One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F501

b:22.5
occ:1.00
 F1 B:60X501 0.0 22.5 1.0
C15 B:60X501 1.4 19.4 1.0
C16 B:60X501 2.3 17.4 1.0
C14 B:60X501 2.3 15.5 1.0
CZ2 B:TRP176 3.1 16.9 1.0
O B:HOH855 3.3 22.7 1.0
CD1 B:ILE171 3.3 26.1 1.0
O B:HOH1055 3.4 50.7 1.0
CH2 B:TRP176 3.5 17.4 1.0
C17 B:60X501 3.6 17.3 1.0
O B:HOH968 3.6 40.2 1.0
C13 B:60X501 3.6 14.1 1.0
O B:PHE169 3.8 18.7 1.0
CG1 B:ILE171 3.9 23.1 1.0
C12 B:60X501 4.1 13.6 1.0
CD1 B:LEU91 4.2 21.3 1.0
O B:HOH944 4.3 32.4 1.0
CE2 B:TRP176 4.4 17.5 1.0
F2 B:60X501 4.7 19.6 1.0
O B:HOH845 4.8 34.8 1.0
CZ3 B:TRP176 4.8 16.3 1.0
CD1 B:ILE179 4.8 16.3 1.0
O B:GLN73 4.8 21.2 1.0
O B:HOH699 5.0 29.7 1.0

Fluorine binding site 6 out of 6 in 5he7

Go back to Fluorine Binding Sites List in 5he7
Fluorine binding site 6 out of 6 in the Bace-1 in Complex with (4AR,7AS)-7A-(2,4-Difluorophenyl)-6-(5-Fluoro- 4-Methoxy-6-Methylpyrimidin-2-Yl)-2-Imino-3-Methyloctahydro-4H- Pyrrolo[3,4-D]Pyrimidin-4-One


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Bace-1 in Complex with (4AR,7AS)-7A-(2,4-Difluorophenyl)-6-(5-Fluoro- 4-Methoxy-6-Methylpyrimidin-2-Yl)-2-Imino-3-Methyloctahydro-4H- Pyrrolo[3,4-D]Pyrimidin-4-One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F501

b:19.9
occ:1.00
 F B:60X501 0.0 19.9 1.0
C B:60X501 1.3 17.2 1.0
C3 B:60X501 2.4 16.8 1.0
C1 B:60X501 2.4 14.8 1.0
O B:60X501 2.7 16.5 1.0
C18 B:60X501 2.9 17.0 1.0
O B:HOH809 3.0 16.1 1.0
OD1 B:ASN98 3.1 12.1 1.0
CG B:ASN98 3.4 17.8 1.0
CZ2 B:TRP137 3.5 16.9 1.0
CB B:ASN98 3.6 11.9 1.0
N1 B:60X501 3.6 15.5 1.0
N B:60X501 3.6 14.9 1.0
CG B:ARG189 3.7 17.0 1.0
C2 B:60X501 4.0 15.7 1.0
CG1 B:VAL130 4.1 17.2 1.0
NE1 B:TRP137 4.1 16.5 1.0
C4 B:60X501 4.1 16.4 1.0
CE2 B:TRP137 4.2 16.9 1.0
CB B:ARG189 4.2 14.3 1.0
CG2 B:VAL130 4.2 18.7 1.0
ND2 B:ASN98 4.4 15.3 1.0
N B:ASN98 4.5 10.6 1.0
CH2 B:TRP137 4.6 16.7 1.0
CB B:SER96 4.6 14.2 1.0
CA B:ASN98 4.7 10.9 1.0
CB B:VAL130 4.7 17.1 1.0
N B:ARG189 4.8 13.9 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 09:50:14 2024

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