Atomistry » Sodium » PDB 7cfs-7d5w » 7d5b
Atomistry »
  Sodium »
    PDB 7cfs-7d5w »
      7d5b »

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

Last articles

Mg in 1KTG
Mg in 1KWO
Mg in 1KW1
Mg in 1KP8
Mg in 1KVK
Mg in 1KV8
Mg in 1KUV
Mg in 1KSZ
Mg in 1KSJ
Mg in 1KSH
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy