Fluorine in PDB 6uvp: Bace-1 in Complex with Compound #3

Enzymatic activity of Bace-1 in Complex with Compound #3

All present enzymatic activity of Bace-1 in Complex with Compound #3:
3.4.23.46;

Protein crystallography data

The structure of Bace-1 in Complex with Compound #3, PDB code: 6uvp was solved by J.Hendle, D.E.Timm, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.56
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 86.548, 90.294, 131.583, 90.00, 90.00, 90.00
R / Rfree (%) 13.8 / 18.2

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Bace-1 in Complex with Compound #3 (pdb code 6uvp). 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 Compound #3, PDB code: 6uvp:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 6uvp

Go back to Fluorine Binding Sites List in 6uvp
Fluorine binding site 1 out of 6 in the Bace-1 in Complex with Compound #3


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 Compound #3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:24.8
occ:1.00
 F22 A:QJJ401 0.0 24.8 1.0
C4 A:QJJ401 1.3 17.9 1.0
C3 A:QJJ401 2.3 15.5 1.0
C1 A:QJJ401 2.4 21.0 1.0
O A:SER10 2.5 11.7 1.0
N A:GLY13 3.4 9.6 1.0
CA A:GLY13 3.4 11.5 1.0
C A:SER10 3.4 9.7 1.0
OG1 A:THR232 3.5 9.9 1.0
N16 A:QJJ401 3.5 19.3 1.0
C2 A:QJJ401 3.7 21.4 1.0
CB A:ALA335 3.9 10.8 1.0
CA A:SER10 3.9 9.3 1.0
CA A:THR232 4.0 7.8 1.0
O A:LYS9 4.0 11.4 1.0
C5 A:QJJ401 4.0 19.9 1.0
N A:THR232 4.1 7.8 1.0
O A:SER229 4.1 12.0 1.0
C A:THR231 4.2 9.1 1.0
C A:GLN12 4.2 13.1 1.0
O A:THR231 4.3 10.0 1.0
CB A:THR232 4.3 8.6 1.0
N A:GLN12 4.4 12.5 1.0
C A:GLY11 4.5 12.4 1.0
N A:GLY11 4.5 10.2 1.0
C A:GLY13 4.6 9.9 1.0
O A:HOH705 4.6 11.7 1.0
CA A:GLN12 4.8 13.0 1.0
O A:GLY11 4.9 17.8 1.0
CA A:GLY11 4.9 11.5 1.0
N A:THR231 4.9 9.3 1.0
C A:LYS9 4.9 9.7 1.0
CB A:SER10 4.9 9.6 1.0
N A:SER10 4.9 8.9 1.0
N A:TYR14 4.9 7.5 1.0
O A:GLN12 5.0 15.3 1.0

Fluorine binding site 2 out of 6 in 6uvp

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Fluorine binding site 2 out of 6 in the Bace-1 in Complex with Compound #3


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 Compound #3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F402

b:33.4
occ:1.00
 F22 A:QJM402 0.0 33.4 1.0
C4 A:QJM402 1.3 28.3 1.0
C3 A:QJM402 2.3 29.8 1.0
C1 A:QJM402 2.4 34.9 1.0
O A:HOH1018 2.6 37.6 1.0
O A:HOH503 3.3 29.4 1.0
O B:HOH615 3.5 23.5 1.0
N16 A:QJM402 3.6 21.8 1.0
C2 A:QJM402 3.7 29.9 1.0
CG B:GLN55 3.9 24.4 1.0
O B:HOH1037 4.0 43.2 1.0
OE1 B:GLN55 4.0 26.9 1.0
C5 A:QJM402 4.1 23.2 1.0
O A:HOH885 4.1 42.7 1.0
O A:HOH928 4.2 43.6 1.0
CD B:GLN55 4.3 31.7 1.0
CG A:GLU364 4.6 13.4 0.5
OE2 A:GLU364 4.6 23.3 0.5
CB B:GLN55 4.7 17.4 1.0
O B:HOH1005 4.8 39.2 1.0
CA B:GLN55 5.0 12.9 1.0
CD A:GLU364 5.0 15.4 0.5

Fluorine binding site 3 out of 6 in 6uvp

Go back to Fluorine Binding Sites List in 6uvp
Fluorine binding site 3 out of 6 in the Bace-1 in Complex with Compound #3


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 Compound #3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:21.0
occ:1.00
 F22 B:QJJ401 0.0 21.0 1.0
C4 B:QJJ401 1.3 18.7 1.0
C3 B:QJJ401 2.3 16.9 1.0
C1 B:QJJ401 2.4 16.8 1.0
O B:SER10 2.6 12.4 1.0
N B:GLY13 3.4 10.0 1.0
CA B:GLY13 3.4 10.1 1.0
C B:SER10 3.5 12.6 1.0
OG1 B:THR232 3.5 11.2 1.0
N16 B:QJJ401 3.6 16.0 1.0
C2 B:QJJ401 3.7 20.6 1.0
CB B:ALA335 3.9 11.3 1.0
CA B:THR232 4.0 8.7 1.0
CA B:SER10 4.0 11.0 1.0
C5 B:QJJ401 4.1 17.1 1.0
O B:LYS9 4.1 11.6 1.0
N B:THR232 4.1 9.7 1.0
O B:SER229 4.1 13.6 1.0
C B:THR231 4.2 9.6 1.0
O B:THR231 4.2 10.9 1.0
C B:GLN12 4.2 13.6 1.0
CB B:THR232 4.3 8.0 1.0
N B:GLN12 4.3 13.0 1.0
C B:GLY11 4.5 13.8 1.0
C B:GLY13 4.6 10.6 1.0
N B:GLY11 4.6 11.0 1.0
O B:HOH699 4.6 12.5 1.0
CA B:GLN12 4.8 14.2 1.0
N B:THR231 4.9 9.8 1.0
O B:GLY11 4.9 15.3 1.0
CB B:SER10 4.9 11.9 1.0
N B:TYR14 4.9 8.8 1.0
C B:LYS9 4.9 9.7 1.0
O B:GLN12 5.0 15.3 1.0
CA B:GLY11 5.0 12.5 1.0

Fluorine binding site 4 out of 6 in 6uvp

Go back to Fluorine Binding Sites List in 6uvp
Fluorine binding site 4 out of 6 in the Bace-1 in Complex with Compound #3


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 Compound #3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F402

b:38.4
occ:1.00
 F22 B:QJJ402 0.0 38.4 1.0
C4 B:QJJ402 1.3 32.3 1.0
C3 B:QJJ402 2.3 30.6 1.0
C1 B:QJJ402 2.4 39.5 1.0
N16 B:QJJ402 3.6 28.5 1.0
C2 B:QJJ402 3.6 33.8 1.0
OG A:SER164 3.7 32.0 1.0
CB A:SER164 3.8 27.5 1.0
C5 B:QJJ402 4.0 26.5 1.0
O A:HOH904 4.1 44.6 1.0
O A:HOH690 4.4 28.6 1.0
O B:HOH634 4.5 42.1 1.0
O B:HOH754 4.7 32.0 1.0
CA A:SER164 5.0 19.4 1.0

Fluorine binding site 5 out of 6 in 6uvp

Go back to Fluorine Binding Sites List in 6uvp
Fluorine binding site 5 out of 6 in the Bace-1 in Complex with Compound #3


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 Compound #3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F403

b:50.0
occ:1.00
 F22 B:QJJ403 0.0 50.0 1.0
C4 B:QJJ403 1.3 41.0 1.0
C3 B:QJJ403 2.3 30.3 1.0
C1 B:QJJ403 2.4 40.8 1.0
N16 B:QJJ403 3.6 26.0 1.0
C2 B:QJJ403 3.6 34.4 1.0
OG B:SER164 3.8 30.9 1.0
CB B:SER164 3.8 26.5 1.0
O B:HOH885 3.8 37.9 1.0
C5 B:QJJ403 4.0 26.4 1.0
O B:HOH666 4.2 28.4 1.0
CA B:SER164 5.0 18.9 1.0

Fluorine binding site 6 out of 6 in 6uvp

Go back to Fluorine Binding Sites List in 6uvp
Fluorine binding site 6 out of 6 in the Bace-1 in Complex with Compound #3


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 Compound #3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F404

b:37.2
occ:1.00
 F22 B:QJM404 0.0 37.2 1.0
C4 B:QJM404 1.3 30.3 1.0
C3 B:QJM404 2.3 27.3 1.0
C1 B:QJM404 2.4 34.6 1.0
N16 B:QJM404 3.6 24.3 1.0
C2 B:QJM404 3.6 31.6 1.0
C5 B:QJM404 4.0 23.2 1.0
O B:HOH957 4.1 42.5 1.0
O B:HOH883 4.3 43.5 1.0
O B:HOH524 4.5 44.6 1.0

Reference:

L.L.Winneroski, J.A.Erickson, S.J.Green, J.E.Lopez, S.L.Stout, W.J.Porter, D.E.Timm, J.E.Audia, M.Barberis, J.P.Beck, L.N.Boggs, A.R.Borders, R.D.Boyer, R.A.Brier, E.J.Hembre, J.Hendle, P.Garcia-Losada, J.M.Minguez, B.M.Mathes, P.C.May, S.A.Monk, Z.Rankovic, Y.Shi, B.M.Watson, Z.Yang, D.J.Mergott. Preparation and Biological Evaluation of BACE1 Inhibitors: Leveraging Trans-Cyclopropyl Moieties As Ligand Efficient Conformational Constraints. Bioorg.Med.Chem. V. 28 15194 2020.
ISSN: ESSN 1464-3391
PubMed: 31786008
DOI: 10.1016/J.BMC.2019.115194
Page generated: Sun Dec 13 13:18:45 2020

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