Chlorine in PDB 7d5b: BACE2 Xaperone Complex with N-{3-[(5R)-3-Amino-2,5-Dimethyl-1,1-Dioxo- 5,6-Dihydro-2H-1LAMBDA6,2,4-Thiadiazin-5-Yl]-4-Fluorophenyl}-5- Fluoropyridine-2-Carboxamide

Enzymatic activity of BACE2 Xaperone Complex with N-{3-[(5R)-3-Amino-2,5-Dimethyl-1,1-Dioxo- 5,6-Dihydro-2H-1LAMBDA6,2,4-Thiadiazin-5-Yl]-4-Fluorophenyl}-5- Fluoropyridine-2-Carboxamide

All present enzymatic activity of BACE2 Xaperone Complex with N-{3-[(5R)-3-Amino-2,5-Dimethyl-1,1-Dioxo- 5,6-Dihydro-2H-1LAMBDA6,2,4-Thiadiazin-5-Yl]-4-Fluorophenyl}-5- Fluoropyridine-2-Carboxamide:
3.4.23.45;

Protein crystallography data

The structure of BACE2 Xaperone Complex with N-{3-[(5R)-3-Amino-2,5-Dimethyl-1,1-Dioxo- 5,6-Dihydro-2H-1LAMBDA6,2,4-Thiadiazin-5-Yl]-4-Fluorophenyl}-5- Fluoropyridine-2-Carboxamide, PDB code: 7d5b was solved by K.Fujimoto, S.Yoshida, G.Tadano, N.Asada, K.Fuchino, S.Suzuki, E.Matsuoka, T.Yamamoto, S.Yamamoto, S.Ando, N.Kanegawa, Y.Tonomura, H.Ito, D.Moechars, F.J.R.Rombouts, H.J.M.Gijsen, K.I.Kusakabe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 61.70 / 1.31
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 63.807, 74.396, 110.408, 90, 90, 90
R / Rfree (%) 19.5 / 22.2

Other elements in 7d5b:

The structure of BACE2 Xaperone Complex with N-{3-[(5R)-3-Amino-2,5-Dimethyl-1,1-Dioxo- 5,6-Dihydro-2H-1LAMBDA6,2,4-Thiadiazin-5-Yl]-4-Fluorophenyl}-5- Fluoropyridine-2-Carboxamide also contains other interesting chemical elements:

Sodium (Na) 2 atoms
Fluorine (F) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the BACE2 Xaperone Complex with N-{3-[(5R)-3-Amino-2,5-Dimethyl-1,1-Dioxo- 5,6-Dihydro-2H-1LAMBDA6,2,4-Thiadiazin-5-Yl]-4-Fluorophenyl}-5- Fluoropyridine-2-Carboxamide (pdb code 7d5b). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total only one binding site of Chlorine was determined in the BACE2 Xaperone Complex with N-{3-[(5R)-3-Amino-2,5-Dimethyl-1,1-Dioxo- 5,6-Dihydro-2H-1LAMBDA6,2,4-Thiadiazin-5-Yl]-4-Fluorophenyl}-5- Fluoropyridine-2-Carboxamide, PDB code: 7d5b:

Chlorine binding site 1 out of 1 in 7d5b

Go back to Chlorine Binding Sites List in 7d5b
Chlorine binding site 1 out of 1 in the BACE2 Xaperone Complex with N-{3-[(5R)-3-Amino-2,5-Dimethyl-1,1-Dioxo- 5,6-Dihydro-2H-1LAMBDA6,2,4-Thiadiazin-5-Yl]-4-Fluorophenyl}-5- Fluoropyridine-2-Carboxamide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of BACE2 Xaperone Complex with N-{3-[(5R)-3-Amino-2,5-Dimethyl-1,1-Dioxo- 5,6-Dihydro-2H-1LAMBDA6,2,4-Thiadiazin-5-Yl]-4-Fluorophenyl}-5- Fluoropyridine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:18.4
occ:1.00
 NA D:NA303 3.0 39.5 1.0
O D:HOH489 3.0 28.9 1.0
ND2 A:ASN114 3.2 12.6 1.0
N D:ILE192 3.3 12.0 1.0
N A:GLU150 3.5 13.0 1.0
O A:SER148 3.7 18.7 0.5
O A:SER148 3.7 18.2 0.5
NZ A:LYS79 3.7 15.8 1.0
CA D:ALA191 3.7 12.6 1.0
O D:SER190 3.8 14.9 0.5
CB A:GLU150 3.8 13.8 1.0
O D:SER190 3.8 15.0 0.5
OD1 A:ASN114 3.9 14.2 1.0
CG A:ASN114 4.0 13.2 1.0
C D:ALA191 4.0 11.8 1.0
CG1 D:ILE192 4.1 14.0 1.0
CB D:ILE192 4.1 13.5 1.0
O A:HOH605 4.2 39.0 1.0
CA A:LEU149 4.3 15.3 1.0
CA D:ILE192 4.3 12.4 1.0
CA A:GLU150 4.3 11.8 1.0
C A:LEU149 4.4 14.9 1.0
CD1 D:ILE192 4.4 16.5 1.0
CB D:ALA191 4.5 15.4 1.0
CD1 A:LEU149 4.5 17.0 1.0
O D:ILE192 4.6 15.4 1.0
C D:SER190 4.7 12.8 0.5
C D:SER190 4.7 13.4 0.5
N D:ALA191 4.7 12.4 1.0
C A:SER148 4.7 15.8 0.5
C A:SER148 4.7 15.9 0.5
CE A:LYS79 4.7 29.6 1.0
N A:LEU149 5.0 14.5 1.0
C D:ILE192 5.0 12.2 1.0

Reference:

K.Fujimoto, S.Yoshida, G.Tadano, N.Asada, K.Fuchino, S.Suzuki, E.Matsuoka, T.Yamamoto, S.Yamamoto, S.Ando, N.Kanegawa, Y.Tonomura, H.Ito, D.Moechars, F.J.R.Rombouts, H.J.M.Gijsen, K.I.Kusakabe. Structure-Based Approaches to Improving Selectivity Through Utilizing Explicit Water Molecules: Discovery of Selective Beta-Secretase (BACE1) Inhibitors Over BACE2. J.Med.Chem. 2021.
ISSN: ISSN 0022-2623
PubMed: 33719429
DOI: 10.1021/ACS.JMEDCHEM.0C01858
Page generated: Sat Apr 3 14:37:47 2021

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