Fluorine in PDB 2fdp: Crystal Structure of Beta-Secretase Complexed with An Amino- Ethylene Inhibitor

All present enzymatic activity of Crystal Structure of Beta-Secretase Complexed with An Amino- Ethylene Inhibitor:
3.4.23.46;

The structure of Crystal Structure of Beta-Secretase Complexed with An Amino- Ethylene Inhibitor, PDB code: 2fdp was solved by W.Yang, W.Lu, Y.Lu, M.Zhong, J.Sun, A.E.Thomas, J.M.Wilkinson, R.V.Fucini, M.Lam, M.Randal, X.P.Shi, J.W.Jacobs, R.S.Mcdowell, E.M.Gordon, M.D.Ballinger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	81.189, 102.188, 99.530, 90.00, 103.21, 90.00
R / Rfree (%)	22.5 / 25.4

The binding sites of Fluorine atom in the Crystal Structure of Beta-Secretase Complexed with An Amino- Ethylene Inhibitor (pdb code 2fdp). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of Beta-Secretase Complexed with An Amino- Ethylene Inhibitor, PDB code: 2fdp:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Crystal Structure of Beta-Secretase Complexed with An Amino- Ethylene Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Beta-Secretase Complexed with An Amino- Ethylene Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F386 b:18.2 occ:1.00 F1 A:FRP386 0.0 18.2 1.0 C23 A:FRP386 1.3 16.8 1.0 C24 A:FRP386 2.4 15.4 1.0 C22 A:FRP386 2.4 17.0 1.0 NE A:ARG128 3.0 26.9 1.0 O A:ILE126 3.2 19.7 1.0 CG A:ARG128 3.3 21.5 1.0 C25 A:FRP386 3.6 15.1 1.0 C27 A:FRP386 3.6 16.4 1.0 CD A:ARG128 3.7 24.0 1.0 CZ A:ARG128 3.7 27.9 1.0 NH2 A:ARG128 3.8 28.3 1.0 CG1 A:VAL69 4.1 16.1 1.0 C26 A:FRP386 4.1 15.2 1.0 C A:ILE126 4.4 19.3 1.0 CD A:PRO70 4.7 14.0 1.0 CB A:ARG128 4.7 19.7 1.0 O A:PRO70 4.8 16.9 1.0 NH1 A:ARG128 4.9 27.7 1.0 CG2 A:VAL69 4.9 15.7 1.0 N A:ARG128 4.9 17.5 1.0 CB A:VAL69 5.0 15.4 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of Beta-Secretase Complexed with An Amino- Ethylene Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Beta-Secretase Complexed with An Amino- Ethylene Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:F386 b:16.0 occ:1.00 F1 B:FRP386 0.0 16.0 1.0 C23 B:FRP386 1.3 14.6 1.0 C24 B:FRP386 2.4 14.8 1.0 C22 B:FRP386 2.4 14.8 1.0 O B:ILE126 3.1 16.9 1.0 NE B:ARG128 3.2 19.6 1.0 CG B:ARG128 3.4 17.1 1.0 O B:HOH407 3.5 28.0 1.0 C25 B:FRP386 3.6 14.7 1.0 C27 B:FRP386 3.6 13.8 1.0 CD B:ARG128 3.8 18.5 1.0 CZ B:ARG128 4.1 19.1 1.0 C26 B:FRP386 4.1 13.5 1.0 CG1 B:VAL69 4.2 12.3 1.0 NH2 B:ARG128 4.3 18.8 1.0 C B:ILE126 4.4 16.9 1.0 CD B:PRO70 4.6 11.3 1.0 CB B:ARG128 4.7 16.1 1.0 CG2 B:VAL69 4.8 11.7 1.0 N B:ARG128 4.9 14.2 1.0 CB B:VAL69 4.9 12.1 1.0 OD1 B:ASN37 4.9 16.7 1.0 O B:PRO70 5.0 12.0 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of Beta-Secretase Complexed with An Amino- Ethylene Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Beta-Secretase Complexed with An Amino- Ethylene Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ C:F386 b:19.8 occ:1.00 F1 C:FRP386 0.0 19.8 1.0 C23 C:FRP386 1.3 16.8 1.0 C22 C:FRP386 2.4 16.0 1.0 C24 C:FRP386 2.4 15.8 1.0 NE C:ARG128 3.2 22.8 1.0 O C:ILE126 3.2 17.0 1.0 CG C:ARG128 3.2 19.4 1.0 C25 C:FRP386 3.6 16.0 1.0 C27 C:FRP386 3.6 16.0 1.0 CD C:ARG128 3.8 21.2 1.0 CZ C:ARG128 3.9 23.8 1.0 NH2 C:ARG128 4.1 23.7 1.0 C26 C:FRP386 4.1 15.6 1.0 CG1 C:VAL69 4.1 17.6 1.0 C C:ILE126 4.4 16.6 1.0 CB C:ARG128 4.5 17.1 1.0 CD C:PRO70 4.5 16.5 1.0 N C:ARG128 4.7 14.4 1.0 O C:PRO70 4.8 16.8 1.0 CG2 C:VAL69 4.9 17.7 1.0 NH1 C:ARG128 5.0 23.8 1.0

W.Yang, W.Lu, Y.Lu, M.Zhong, J.Sun, A.E.Thomas, J.M.Wilkinson, R.V.Fucini, M.Lam, M.Randal, X.P.Shi, J.W.Jacobs, R.S.Mcdowell, E.M.Gordon, M.D.Ballinger. Aminoethylenes: A Tetrahedral Intermediate Isostere Yielding Potent Inhibitors of the Aspartyl Protease Bace-1. J.Med.Chem. V. 49 839 2006.
ISSN: ISSN 0022-2623
PubMed: 16451048
DOI: 10.1021/JM0509142