Atomistry » Fluorine » PDB 6jsf-6kjv » 6jt4
Atomistry »
  Fluorine »
    PDB 6jsf-6kjv »
      6jt4 »

Fluorine in PDB 6jt4: Crystal Structure of BACE1 in Complex with N-{3-[(4S,6S)-2-Amino-4- Methyl-6-(Trifluoromethyl)-5,6-Dihydro-4H-1,3-Thiazin-4-Yl]-4- Fluorophenyl}-5-(Fluoromethoxy)Pyrazine-2-Carboxamide

Enzymatic activity of Crystal Structure of BACE1 in Complex with N-{3-[(4S,6S)-2-Amino-4- Methyl-6-(Trifluoromethyl)-5,6-Dihydro-4H-1,3-Thiazin-4-Yl]-4- Fluorophenyl}-5-(Fluoromethoxy)Pyrazine-2-Carboxamide

All present enzymatic activity of Crystal Structure of BACE1 in Complex with N-{3-[(4S,6S)-2-Amino-4- Methyl-6-(Trifluoromethyl)-5,6-Dihydro-4H-1,3-Thiazin-4-Yl]-4- Fluorophenyl}-5-(Fluoromethoxy)Pyrazine-2-Carboxamide:
3.4.23.46;

Protein crystallography data

The structure of Crystal Structure of BACE1 in Complex with N-{3-[(4S,6S)-2-Amino-4- Methyl-6-(Trifluoromethyl)-5,6-Dihydro-4H-1,3-Thiazin-4-Yl]-4- Fluorophenyl}-5-(Fluoromethoxy)Pyrazine-2-Carboxamide, PDB code: 6jt4 was solved by K.Anan, Y.Iso, T.Oguma, K.Nakahara, S.Suzuki, T.Yamamoto, E.Matsuoka, H.Ito, G.Sakaguchi, S.Ando, K.Morimoto, N.Kanegawa, Y.Kido, T.Kawachi, T.Fukushima, A.Teisman, V.Urmaliya, D.Dhuyvetter, H.Borghys, N.Austin, A.V.D.Bergh, P.Verboven, F.Bischoff, H.J.M.Gijsen, Y.Yamano, K.I.Kusakabe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.20
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 101.590, 101.590, 170.351, 90.00, 90.00, 120.00
R / Rfree (%) 19.5 / 23.4

Other elements in 6jt4:

The structure of Crystal Structure of BACE1 in Complex with N-{3-[(4S,6S)-2-Amino-4- Methyl-6-(Trifluoromethyl)-5,6-Dihydro-4H-1,3-Thiazin-4-Yl]-4- Fluorophenyl}-5-(Fluoromethoxy)Pyrazine-2-Carboxamide also contains other interesting chemical elements:

Iodine (I) 3 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of BACE1 in Complex with N-{3-[(4S,6S)-2-Amino-4- Methyl-6-(Trifluoromethyl)-5,6-Dihydro-4H-1,3-Thiazin-4-Yl]-4- Fluorophenyl}-5-(Fluoromethoxy)Pyrazine-2-Carboxamide (pdb code 6jt4). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 5 binding sites of Fluorine where determined in the Crystal Structure of BACE1 in Complex with N-{3-[(4S,6S)-2-Amino-4- Methyl-6-(Trifluoromethyl)-5,6-Dihydro-4H-1,3-Thiazin-4-Yl]-4- Fluorophenyl}-5-(Fluoromethoxy)Pyrazine-2-Carboxamide, PDB code: 6jt4:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5;

Fluorine binding site 1 out of 5 in 6jt4

Go back to Fluorine Binding Sites List in 6jt4
Fluorine binding site 1 out of 5 in the Crystal Structure of BACE1 in Complex with N-{3-[(4S,6S)-2-Amino-4- Methyl-6-(Trifluoromethyl)-5,6-Dihydro-4H-1,3-Thiazin-4-Yl]-4- Fluorophenyl}-5-(Fluoromethoxy)Pyrazine-2-Carboxamide


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 BACE1 in Complex with N-{3-[(4S,6S)-2-Amino-4- Methyl-6-(Trifluoromethyl)-5,6-Dihydro-4H-1,3-Thiazin-4-Yl]-4- Fluorophenyl}-5-(Fluoromethoxy)Pyrazine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F506

b:26.8
occ:1.00
 F1 A:C86506 0.0 26.8 1.0
C10 A:C86506 1.3 27.1 1.0
O2 A:C86506 2.2 26.7 1.0
O A:HOH752 2.9 35.0 1.0
C9 A:C86506 3.0 26.8 1.0
N5 A:C86506 3.1 27.3 1.0
N A:GLY13 3.1 21.9 1.0
CA A:GLY13 3.4 22.6 1.0
N A:GLY11 3.6 31.4 1.0
N A:GLN12 3.9 25.4 1.0
CE1 A:TYR14 3.9 22.5 1.0
CA A:GLY11 3.9 29.0 1.0
C A:GLY11 4.0 28.1 1.0
C8 A:C86506 4.2 26.2 1.0
C A:GLY13 4.2 21.5 1.0
O A:LYS9 4.3 31.9 1.0
C A:GLN12 4.3 24.1 1.0
C11 A:C86506 4.3 26.3 1.0
CD1 A:TYR14 4.4 21.8 1.0
NH2 A:ARG307 4.5 37.2 1.0
O A:GLY13 4.6 22.2 1.0
C A:SER10 4.6 33.8 1.0
OG1 A:THR232 4.7 24.5 1.0
CZ A:TYR14 4.7 23.4 1.0
CA A:GLN12 4.7 25.7 1.0
OE2 A:GLU339 4.7 29.6 1.0
O A:GLY11 4.7 27.3 1.0
CB A:ALA335 4.7 22.2 1.0
CA A:SER10 4.8 36.0 1.0
OH A:TYR14 4.9 24.9 1.0

Fluorine binding site 2 out of 5 in 6jt4

Go back to Fluorine Binding Sites List in 6jt4
Fluorine binding site 2 out of 5 in the Crystal Structure of BACE1 in Complex with N-{3-[(4S,6S)-2-Amino-4- Methyl-6-(Trifluoromethyl)-5,6-Dihydro-4H-1,3-Thiazin-4-Yl]-4- Fluorophenyl}-5-(Fluoromethoxy)Pyrazine-2-Carboxamide


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 BACE1 in Complex with N-{3-[(4S,6S)-2-Amino-4- Methyl-6-(Trifluoromethyl)-5,6-Dihydro-4H-1,3-Thiazin-4-Yl]-4- Fluorophenyl}-5-(Fluoromethoxy)Pyrazine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F506

b:22.6
occ:1.00
 F2 A:C86506 0.0 22.6 1.0
C14 A:C86506 1.3 23.8 1.0
C13 A:C86506 2.3 22.6 1.0
C3 A:C86506 2.4 23.0 1.0
C15 A:C86506 2.8 23.4 1.0
C2 A:C86506 2.9 23.6 1.0
C16 A:C86506 3.1 23.3 1.0
CE1 A:PHE108 3.2 23.9 1.0
CD1 A:PHE108 3.3 24.1 1.0
CE2 A:TYR71 3.5 45.6 1.0
CZ A:TYR71 3.6 42.7 1.0
C12 A:C86506 3.6 23.8 1.0
C4 A:C86506 3.6 23.2 1.0
OH A:TYR71 3.7 44.5 1.0
C17 A:C86506 4.0 24.5 1.0
CD1 A:ILE118 4.0 19.6 0.5
C5 A:C86506 4.1 24.0 1.0
CD2 A:TYR71 4.1 47.4 1.0
CE1 A:TYR71 4.3 43.0 1.0
N2 A:C86506 4.3 23.0 1.0
CZ A:PHE108 4.4 23.7 1.0
F4 A:C86506 4.5 30.0 1.0
CG A:PHE108 4.6 23.7 1.0
CG A:TYR71 4.7 46.0 1.0
CD1 A:TYR71 4.8 43.8 1.0
C18 A:C86506 4.9 27.1 1.0

Fluorine binding site 3 out of 5 in 6jt4

Go back to Fluorine Binding Sites List in 6jt4
Fluorine binding site 3 out of 5 in the Crystal Structure of BACE1 in Complex with N-{3-[(4S,6S)-2-Amino-4- Methyl-6-(Trifluoromethyl)-5,6-Dihydro-4H-1,3-Thiazin-4-Yl]-4- Fluorophenyl}-5-(Fluoromethoxy)Pyrazine-2-Carboxamide


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 BACE1 in Complex with N-{3-[(4S,6S)-2-Amino-4- Methyl-6-(Trifluoromethyl)-5,6-Dihydro-4H-1,3-Thiazin-4-Yl]-4- Fluorophenyl}-5-(Fluoromethoxy)Pyrazine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F506

b:28.3
occ:1.00
 F3 A:C86506 0.0 28.3 1.0
C18 A:C86506 1.3 27.1 1.0
F4 A:C86506 2.1 30.0 1.0
F5 A:C86506 2.1 25.1 1.0
C17 A:C86506 2.4 24.5 1.0
C16 A:C86506 2.9 23.3 1.0
S1 A:C86506 3.1 22.5 1.0
O A:HOH804 3.3 45.6 1.0
O A:HOH625 3.5 57.2 1.0
CD1 A:TYR71 3.8 43.8 1.0
O A:HOH790 3.9 48.4 1.0
C1 A:C86506 4.1 21.4 1.0
C2 A:C86506 4.3 23.6 1.0
CE1 A:TYR71 4.4 43.0 1.0
CG A:TYR71 4.5 46.0 1.0
O A:HOH757 4.6 44.6 1.0
CB A:TYR71 4.6 48.9 1.0
N2 A:C86506 4.6 23.0 1.0
O A:HOH720 4.9 41.8 1.0

Fluorine binding site 4 out of 5 in 6jt4

Go back to Fluorine Binding Sites List in 6jt4
Fluorine binding site 4 out of 5 in the Crystal Structure of BACE1 in Complex with N-{3-[(4S,6S)-2-Amino-4- Methyl-6-(Trifluoromethyl)-5,6-Dihydro-4H-1,3-Thiazin-4-Yl]-4- Fluorophenyl}-5-(Fluoromethoxy)Pyrazine-2-Carboxamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of BACE1 in Complex with N-{3-[(4S,6S)-2-Amino-4- Methyl-6-(Trifluoromethyl)-5,6-Dihydro-4H-1,3-Thiazin-4-Yl]-4- Fluorophenyl}-5-(Fluoromethoxy)Pyrazine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F506

b:30.0
occ:1.00
 F4 A:C86506 0.0 30.0 1.0
C18 A:C86506 1.3 27.1 1.0
F3 A:C86506 2.1 28.3 1.0
F5 A:C86506 2.1 25.1 1.0
C17 A:C86506 2.4 24.5 1.0
C16 A:C86506 3.0 23.3 1.0
O A:HOH625 3.4 57.2 1.0
CB A:TYR71 3.4 48.9 1.0
CG A:TYR71 3.5 46.0 1.0
CD1 A:TYR71 3.5 43.8 1.0
S1 A:C86506 3.9 22.5 1.0
CD2 A:TYR71 4.3 47.4 1.0
CE1 A:TYR71 4.3 43.0 1.0
O A:HOH804 4.4 45.6 1.0
C2 A:C86506 4.4 23.6 1.0
F2 A:C86506 4.5 22.6 1.0
O A:HOH786 4.7 46.5 1.0
C3 A:C86506 4.7 23.0 1.0
O A:THR72 4.8 69.2 1.0
C14 A:C86506 4.8 23.8 1.0
OG1 A:THR72 4.8 68.5 1.0
CA A:TYR71 4.8 49.7 1.0
N A:THR72 4.8 63.6 1.0
CE2 A:TYR71 4.9 45.6 1.0
CZ A:TYR71 4.9 42.7 1.0

Fluorine binding site 5 out of 5 in 6jt4

Go back to Fluorine Binding Sites List in 6jt4
Fluorine binding site 5 out of 5 in the Crystal Structure of BACE1 in Complex with N-{3-[(4S,6S)-2-Amino-4- Methyl-6-(Trifluoromethyl)-5,6-Dihydro-4H-1,3-Thiazin-4-Yl]-4- Fluorophenyl}-5-(Fluoromethoxy)Pyrazine-2-Carboxamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of BACE1 in Complex with N-{3-[(4S,6S)-2-Amino-4- Methyl-6-(Trifluoromethyl)-5,6-Dihydro-4H-1,3-Thiazin-4-Yl]-4- Fluorophenyl}-5-(Fluoromethoxy)Pyrazine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F506

b:25.1
occ:1.00
 F5 A:C86506 0.0 25.1 1.0
C18 A:C86506 1.3 27.1 1.0
F4 A:C86506 2.1 30.0 1.0
F3 A:C86506 2.1 28.3 1.0
C17 A:C86506 2.4 24.5 1.0
S1 A:C86506 2.9 22.5 1.0
O A:HOH786 3.4 46.5 1.0
C16 A:C86506 3.7 23.3 1.0
O A:HOH720 3.7 41.8 1.0
O A:HOH790 3.9 48.4 1.0
O A:HOH625 4.1 57.2 1.0
C1 A:C86506 4.5 21.4 1.0
OG1 A:THR72 4.9 68.5 1.0
C2 A:C86506 4.9 23.6 1.0
O A:HOH804 5.0 45.6 1.0

Reference:

K.Anan, Y.Iso, T.Oguma, K.Nakahara, S.Suzuki, T.Yamamoto, E.Matsuoka, H.Ito, G.Sakaguchi, S.Ando, K.Morimoto, N.Kanegawa, Y.Kido, T.Kawachi, T.Fukushima, A.Teisman, V.Urmaliya, D.Dhuyvetter, H.Borghys, N.Austin, A.Van Den Bergh, P.Verboven, F.Bischoff, H.J.M.Gijsen, Y.Yamano, K.Kusakabe. Trifluoromethyl Dihydrothiazine-Based Beta-Secretase (BACE1) Inhibitors with Robust Central Beta-Amyloid Reduction and Minimal Covalent Binding Burden. Chemmedchem V. 14 1894 2019.
ISSN: ESSN 1860-7187
PubMed: 31657130
DOI: 10.1002/CMDC.201900478
Page generated: Thu Aug 1 21:42:26 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy