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Fluorine in PDB 4k9h: Bace-1 Inhibitor Complex

Enzymatic activity of Bace-1 Inhibitor Complex

All present enzymatic activity of Bace-1 Inhibitor Complex:
3.4.23.46;

Protein crystallography data

The structure of Bace-1 Inhibitor Complex, PDB code: 4k9h was solved by S.R.Jordan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.00 / 2.29
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 82.538, 103.304, 100.856, 90.00, 104.01, 90.00
R / Rfree (%) 19.9 / 24.8

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Bace-1 Inhibitor Complex (pdb code 4k9h). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 9 binding sites of Fluorine where determined in the Bace-1 Inhibitor Complex, PDB code: 4k9h:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Fluorine binding site 1 out of 9 in 4k9h

Go back to Fluorine Binding Sites List in 4k9h
Fluorine binding site 1 out of 9 in the Bace-1 Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Bace-1 Inhibitor Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:54.1
occ:1.00
 F2 A:1QU401 0.0 54.1 1.0
C32 A:1QU401 1.3 53.5 1.0
F3 A:1QU401 2.1 52.4 1.0
F1 A:1QU401 2.1 59.5 1.0
C16 A:1QU401 2.5 47.4 1.0
C17 A:1QU401 2.9 35.8 1.0
C15 A:1QU401 3.7 34.8 1.0
O A:PRO70 4.0 35.7 1.0
NE A:ARG128 4.2 64.5 1.0
CG1 A:VAL69 4.3 35.8 1.0
C18 A:1QU401 4.3 36.2 1.0
O A:ILE126 4.4 32.0 1.0
NH2 A:ARG128 4.5 59.6 1.0
CZ A:ARG128 4.7 67.5 1.0
CD A:PRO70 4.8 33.8 1.0
C14 A:1QU401 4.9 39.4 1.0
CG A:ARG128 4.9 49.9 1.0
C A:PRO70 5.0 34.8 1.0
CD A:ARG128 5.0 51.2 1.0

Fluorine binding site 2 out of 9 in 4k9h

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Fluorine binding site 2 out of 9 in the Bace-1 Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Bace-1 Inhibitor Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:52.4
occ:1.00
 F3 A:1QU401 0.0 52.4 1.0
C32 A:1QU401 1.3 53.5 1.0
F2 A:1QU401 2.1 54.1 1.0
F1 A:1QU401 2.1 59.5 1.0
C16 A:1QU401 2.5 47.4 1.0
C15 A:1QU401 3.0 34.8 1.0
C17 A:1QU401 3.6 35.8 1.0
CD1 A:ILE126 3.9 36.1 1.0
O A:ILE126 3.9 32.0 1.0
O A:GLY34 4.0 35.7 1.0
CB A:SER35 4.0 32.3 1.0
CB A:ILE126 4.1 38.7 1.0
CA A:SER35 4.1 30.6 1.0
OH A:TYR198 4.3 39.6 1.0
C14 A:1QU401 4.4 39.4 1.0
CG1 A:ILE126 4.4 39.0 1.0
CE1 A:TYR198 4.4 37.8 1.0
CZ A:TYR198 4.6 34.6 1.0
C18 A:1QU401 4.8 36.2 1.0
C A:ILE126 4.8 34.9 1.0
CG2 A:ILE126 4.8 35.3 1.0
C A:GLY34 4.9 34.4 1.0
N A:SER36 5.0 26.8 1.0

Fluorine binding site 3 out of 9 in 4k9h

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Fluorine binding site 3 out of 9 in the Bace-1 Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Bace-1 Inhibitor Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:59.5
occ:1.00
 F1 A:1QU401 0.0 59.5 1.0
C32 A:1QU401 1.3 53.5 1.0
F2 A:1QU401 2.1 54.1 1.0
F3 A:1QU401 2.1 52.4 1.0
C16 A:1QU401 2.3 47.4 1.0
C15 A:1QU401 3.0 34.8 1.0
C17 A:1QU401 3.3 35.8 1.0
CD1 A:TYR71 3.5 37.1 1.0
CE1 A:TYR71 3.5 36.7 1.0
CB A:SER35 3.5 32.3 1.0
CG1 A:VAL69 3.8 35.8 1.0
C14 A:1QU401 4.3 39.4 1.0
CA A:SER35 4.4 30.6 1.0
O3 A:1QU401 4.4 35.8 1.0
O A:PRO70 4.4 35.7 1.0
C18 A:1QU401 4.5 36.2 1.0
O A:GLY34 4.5 35.7 1.0
CG A:TYR71 4.6 38.0 1.0
CZ A:TYR71 4.6 37.4 1.0
OG A:SER35 4.6 38.0 1.0
C19 A:1QU401 4.9 40.1 1.0

Fluorine binding site 4 out of 9 in 4k9h

Go back to Fluorine Binding Sites List in 4k9h
Fluorine binding site 4 out of 9 in the Bace-1 Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Bace-1 Inhibitor Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:46.9
occ:1.00
 F2 B:1QU401 0.0 46.9 1.0
C32 B:1QU401 1.3 45.0 1.0
F3 B:1QU401 2.1 50.5 1.0
F1 B:1QU401 2.1 50.4 1.0
C16 B:1QU401 2.2 40.0 1.0
C15 B:1QU401 2.8 38.7 1.0
C17 B:1QU401 3.3 33.7 1.0
O B:ILE126 3.9 39.7 1.0
OH B:TYR198 3.9 49.2 1.0
CB B:ILE126 3.9 32.3 1.0
CD1 B:ILE126 4.1 31.1 1.0
C14 B:1QU401 4.1 42.1 1.0
O B:GLY34 4.1 29.4 1.0
CE1 B:TYR198 4.3 37.5 1.0
CG1 B:ILE126 4.4 32.8 1.0
CB B:SER35 4.4 34.6 1.0
C18 B:1QU401 4.4 40.9 1.0
CA B:SER35 4.4 33.2 1.0
CZ B:TYR198 4.5 35.2 1.0
CG2 B:ILE126 4.6 32.5 1.0
C B:ILE126 4.8 33.1 1.0
C19 B:1QU401 4.8 39.0 1.0
CA B:ILE126 4.9 35.0 1.0
NH2 B:ARG128 5.0 54.9 1.0

Fluorine binding site 5 out of 9 in 4k9h

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Fluorine binding site 5 out of 9 in the Bace-1 Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Bace-1 Inhibitor Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:50.5
occ:1.00
 F3 B:1QU401 0.0 50.5 1.0
C32 B:1QU401 1.3 45.0 1.0
F2 B:1QU401 2.1 46.9 1.0
F1 B:1QU401 2.2 50.4 1.0
C16 B:1QU401 2.4 40.0 1.0
C15 B:1QU401 3.1 38.7 1.0
CB B:SER35 3.1 34.6 1.0
CE1 B:TYR71 3.5 29.2 1.0
C17 B:1QU401 3.6 33.7 1.0
CG1 B:VAL69 3.7 36.0 1.0
CD1 B:TYR71 3.7 34.5 1.0
CA B:SER35 3.9 33.2 1.0
O B:GLY34 4.2 29.4 1.0
OG B:SER35 4.3 38.0 1.0
C14 B:1QU401 4.4 42.1 1.0
O3 B:1QU401 4.5 30.1 1.0
CZ B:TYR71 4.6 30.4 1.0
O B:ILE126 4.7 39.7 1.0
C18 B:1QU401 4.7 40.9 1.0
N B:SER36 4.9 31.9 1.0
N B:SER35 4.9 29.2 1.0
CG B:TYR71 4.9 32.3 1.0
C B:SER35 5.0 30.0 1.0
C B:GLY34 5.0 29.1 1.0

Fluorine binding site 6 out of 9 in 4k9h

Go back to Fluorine Binding Sites List in 4k9h
Fluorine binding site 6 out of 9 in the Bace-1 Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Bace-1 Inhibitor Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:50.4
occ:1.00
 F1 B:1QU401 0.0 50.4 1.0
C32 B:1QU401 1.3 45.0 1.0
F2 B:1QU401 2.1 46.9 1.0
F3 B:1QU401 2.2 50.5 1.0
C16 B:1QU401 2.4 40.0 1.0
C17 B:1QU401 2.7 33.7 1.0
CG1 B:VAL69 3.6 36.0 1.0
NH2 B:ARG128 3.6 54.9 1.0
C15 B:1QU401 3.7 38.7 1.0
O B:PRO70 4.0 37.3 1.0
NE B:ARG128 4.1 52.8 1.0
C18 B:1QU401 4.1 40.9 1.0
CZ B:ARG128 4.1 58.8 1.0
O B:ILE126 4.5 39.7 1.0
CD B:PRO70 4.7 37.7 1.0
CD1 B:TYR71 4.8 34.5 1.0
C14 B:1QU401 4.8 42.1 1.0
C B:PRO70 4.9 36.1 1.0
CE1 B:TYR71 4.9 29.2 1.0
CB B:VAL69 5.0 33.8 1.0

Fluorine binding site 7 out of 9 in 4k9h

Go back to Fluorine Binding Sites List in 4k9h
Fluorine binding site 7 out of 9 in the Bace-1 Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Bace-1 Inhibitor Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F401

b:55.2
occ:1.00
 F2 C:1QU401 0.0 55.2 1.0
C32 C:1QU401 1.3 47.5 1.0
F1 C:1QU401 2.1 49.5 1.0
F3 C:1QU401 2.2 39.7 1.0
C16 C:1QU401 2.3 40.9 1.0
C17 C:1QU401 2.6 38.5 1.0
C15 C:1QU401 3.6 38.1 1.0
NE C:ARG128 3.9 66.9 1.0
C18 C:1QU401 4.0 34.6 1.0
O C:PRO70 4.1 38.0 1.0
CG1 C:VAL69 4.1 40.2 1.0
NH2 C:ARG128 4.1 76.5 1.0
CZ C:ARG128 4.4 79.2 1.0
O C:ILE126 4.6 31.4 1.0
C14 C:1QU401 4.7 37.6 1.0
C19 C:1QU401 4.8 36.3 1.0
CD C:ARG128 4.9 56.0 1.0
OH C:TYR198 5.0 43.6 1.0

Fluorine binding site 8 out of 9 in 4k9h

Go back to Fluorine Binding Sites List in 4k9h
Fluorine binding site 8 out of 9 in the Bace-1 Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Bace-1 Inhibitor Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F401

b:39.7
occ:1.00
 F3 C:1QU401 0.0 39.7 1.0
C32 C:1QU401 1.4 47.5 1.0
F1 C:1QU401 2.2 49.5 1.0
F2 C:1QU401 2.2 55.2 1.0
C16 C:1QU401 2.5 40.9 1.0
C15 C:1QU401 3.0 38.1 1.0
C17 C:1QU401 3.6 38.5 1.0
O C:ILE126 3.8 31.4 1.0
CB C:SER35 3.9 30.8 1.0
CA C:SER35 3.9 31.7 1.0
CD1 C:ILE126 4.0 38.4 1.0
O C:GLY34 4.0 35.6 1.0
CG1 C:ILE126 4.1 40.9 1.0
CB C:ILE126 4.1 39.3 1.0
OH C:TYR198 4.3 43.6 1.0
C14 C:1QU401 4.4 37.6 1.0
CE1 C:TYR198 4.5 38.2 1.0
CZ C:TYR198 4.7 38.3 1.0
C18 C:1QU401 4.8 34.6 1.0
C C:ILE126 4.8 33.5 1.0
N C:SER36 4.9 28.9 1.0
C C:GLY34 4.9 29.1 1.0
N C:SER35 4.9 28.2 1.0
C C:SER35 4.9 31.5 1.0

Fluorine binding site 9 out of 9 in 4k9h

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Fluorine binding site 9 out of 9 in the Bace-1 Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Bace-1 Inhibitor Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F401

b:49.5
occ:1.00
 F1 C:1QU401 0.0 49.5 1.0
C32 C:1QU401 1.3 47.5 1.0
F2 C:1QU401 2.1 55.2 1.0
F3 C:1QU401 2.2 39.7 1.0
C16 C:1QU401 2.2 40.9 1.0
C15 C:1QU401 2.9 38.1 1.0
C17 C:1QU401 3.2 38.5 1.0
CB C:SER35 3.4 30.8 1.0
CE1 C:TYR71 3.4 28.3 1.0
CD1 C:TYR71 3.5 25.7 1.0
CG1 C:VAL69 3.7 40.2 1.0
C14 C:1QU401 4.2 37.6 1.0
CA C:SER35 4.3 31.7 1.0
C18 C:1QU401 4.3 34.6 1.0
O C:GLY34 4.4 35.6 1.0
O3 C:1QU401 4.5 34.3 1.0
CG C:TYR71 4.5 27.5 1.0
CZ C:TYR71 4.6 26.2 1.0
OG C:SER35 4.6 32.7 1.0
O C:PRO70 4.7 38.0 1.0
C19 C:1QU401 4.7 36.3 1.0
CA C:TYR71 5.0 34.7 1.0

Reference:

L.D.Pennington, D.A.Whittington, M.D.Bartberger, S.R.Jordan, H.Monenschein, T.T.Nguyen, B.H.Yang, Q.M.Xue, F.Vounatsos, R.C.Wahl, K.Chen, S.Wood, M.Citron, V.F.Patel, S.A.Hitchcock, W.Zhong. Hydroxyethylamine-Based Inhibitors of BACE1: P1-P3 Macrocyclization Can Improve Potency, Selectivity, and Cell Activity. Bioorg.Med.Chem.Lett. V. 23 4459 2013.
ISSN: ISSN 0960-894X
PubMed: 23769639
DOI: 10.1016/J.BMCL.2013.05.028
Page generated: Mon Jul 14 22:48:09 2025

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