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Sodium 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:

Chlorine (Cl) 1 atom
Fluorine (F) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 2 binding sites of Sodium where 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:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7d5b

Go back to Sodium Binding Sites List in 7d5b
Sodium binding site 1 out of 2 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 Sodium with other atoms in the Na 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:Na404

b:42.4
occ:1.00
 O A:HOH572 2.3 27.4 1.0
O A:PRO39 2.4 18.2 1.0
O A:HOH804 2.6 35.8 1.0
O A:ARG72 2.7 22.0 1.0
NE2 A:GLN41 3.2 16.6 1.0
C A:ARG72 3.3 20.1 1.0
C A:PRO39 3.5 15.5 1.0
N A:PRO39 3.5 18.9 1.0
C A:THR38 3.7 16.2 1.0
O A:THR38 3.7 17.4 1.0
CD A:PRO39 3.7 21.1 1.0
CG A:GLN41 3.7 16.5 1.0
N A:SER73 3.8 16.2 1.0
CA A:SER73 3.9 16.6 1.0
CG A:PRO39 3.9 25.2 1.0
CD A:GLN41 3.9 14.8 1.0
CB A:ARG72 3.9 24.9 1.0
CA A:PRO39 4.0 18.0 1.0
N A:THR38 4.2 15.1 1.0
CA A:ARG72 4.2 19.7 1.0
O A:HOH820 4.3 41.3 1.0
CB A:SER73 4.3 15.1 1.0
O A:HOH519 4.4 35.4 1.0
CB A:PRO39 4.5 20.3 1.0
CA A:THR38 4.5 17.1 1.0
N A:PRO40 4.6 18.1 1.0
C A:PRO40 4.6 18.5 1.0
C A:GLY37 4.7 13.9 1.0
N A:GLN41 4.7 16.8 1.0
O A:PRO40 4.8 18.6 1.0
O A:ILE36 4.8 14.9 0.5
O A:HOH762 4.9 51.3 1.0
O A:ILE36 4.9 15.4 0.5
CA A:PRO40 4.9 16.8 1.0
CB A:GLN41 4.9 16.9 1.0
OG A:SER73 4.9 14.8 1.0
O A:HOH739 4.9 30.3 1.0

Sodium binding site 2 out of 2 in 7d5b

Go back to Sodium Binding Sites List in 7d5b
Sodium binding site 2 out of 2 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 Sodium with other atoms in the Na binding site number 2 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
D:Na303

b:39.5
occ:1.00
 OG D:SER257 2.2 28.0 1.0
O D:ILE192 2.7 15.4 1.0
O A:HOH605 2.9 39.0 1.0
CL A:CL402 3.0 18.4 1.0
OE1 A:GLU150 3.4 18.6 1.0
CB D:SER257 3.4 18.1 1.0
N D:ILE192 3.5 12.0 1.0
N D:ALA258 3.6 13.9 1.0
CB A:GLU150 3.7 13.8 1.0
C D:ILE192 3.7 12.2 1.0
CA D:SER257 3.7 15.0 1.0
C D:SER257 3.9 15.3 1.0
CB D:ALA191 3.9 15.4 1.0
CA D:ILE192 4.0 12.4 1.0
CD A:GLU150 4.0 18.4 1.0
CA D:ALA191 4.1 12.6 1.0
O A:SER148 4.1 18.7 0.5
O A:SER148 4.1 18.2 0.5
C D:ALA191 4.1 11.8 1.0
CB D:ILE192 4.1 13.5 1.0
CB D:ALA258 4.2 16.2 1.0
CA D:ALA258 4.3 15.5 1.0
O A:HOH662 4.3 16.4 1.0
CG A:GLU150 4.4 15.7 1.0
N A:GLU150 4.5 13.0 1.0
CA A:GLU150 4.6 11.8 1.0
OE2 A:GLU150 4.8 17.8 1.0
O D:SER257 4.9 15.8 1.0
O D:HOH489 4.9 28.9 1.0
N D:MET193 4.9 11.4 0.5
N D:MET193 4.9 11.3 0.5

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: Tue Oct 8 16:29:45 2024

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