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Fluorine in PDB 7d36: Crystal Structure of BACE1 in Complex with N-{3-[(3S)-1-Amino-5- Fluoro-3-Methyl-3,4-Dihydro-2,6-Naphthyridin-3-Yl]-4-Fluorophenyl}-5- Cyano-3-Methylpyridine-2-Carboxamide

Enzymatic activity of Crystal Structure of BACE1 in Complex with N-{3-[(3S)-1-Amino-5- Fluoro-3-Methyl-3,4-Dihydro-2,6-Naphthyridin-3-Yl]-4-Fluorophenyl}-5- Cyano-3-Methylpyridine-2-Carboxamide

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

Protein crystallography data

The structure of Crystal Structure of BACE1 in Complex with N-{3-[(3S)-1-Amino-5- Fluoro-3-Methyl-3,4-Dihydro-2,6-Naphthyridin-3-Yl]-4-Fluorophenyl}-5- Cyano-3-Methylpyridine-2-Carboxamide, PDB code: 7d36 was solved by K.Nakahara, Y.Mitsuoka, S.Kasuya, T.Yamamoto, S.Yamamoto, H.Ito, Y.Kido, K.I.Kusakabe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.30
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 102.531, 102.531, 170.115, 90, 90, 120
R / Rfree (%) 21.3 / 26.5

Other elements in 7d36:

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

Iodine (I) 4 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of BACE1 in Complex with N-{3-[(3S)-1-Amino-5- Fluoro-3-Methyl-3,4-Dihydro-2,6-Naphthyridin-3-Yl]-4-Fluorophenyl}-5- Cyano-3-Methylpyridine-2-Carboxamide (pdb code 7d36). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of BACE1 in Complex with N-{3-[(3S)-1-Amino-5- Fluoro-3-Methyl-3,4-Dihydro-2,6-Naphthyridin-3-Yl]-4-Fluorophenyl}-5- Cyano-3-Methylpyridine-2-Carboxamide, PDB code: 7d36:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 7d36

Go back to Fluorine Binding Sites List in 7d36
Fluorine binding site 1 out of 2 in the Crystal Structure of BACE1 in Complex with N-{3-[(3S)-1-Amino-5- Fluoro-3-Methyl-3,4-Dihydro-2,6-Naphthyridin-3-Yl]-4-Fluorophenyl}-5- Cyano-3-Methylpyridine-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-[(3S)-1-Amino-5- Fluoro-3-Methyl-3,4-Dihydro-2,6-Naphthyridin-3-Yl]-4-Fluorophenyl}-5- Cyano-3-Methylpyridine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F508

b:54.7
occ:1.00
 F1 A:GUC508 0.0 54.7 1.0
C11 A:GUC508 1.4 56.0 1.0
C10 A:GUC508 2.4 56.2 1.0
C12 A:GUC508 2.5 55.4 1.0
CE2 A:TYR71 2.8 63.6 1.0
CZ A:TYR71 2.9 64.0 1.0
C15 A:GUC508 3.0 54.0 1.0
C14 A:GUC508 3.0 55.4 1.0
OH A:TYR71 3.1 64.6 1.0
C16 A:GUC508 3.2 56.0 1.0
CE1 A:PHE108 3.4 37.6 1.0
CD2 A:TYR71 3.5 61.7 1.0
CD1 A:PHE108 3.6 36.8 1.0
C9 A:GUC508 3.6 56.0 1.0
C13 A:GUC508 3.7 54.7 1.0
CE1 A:TYR71 3.7 63.6 1.0
C8 A:GUC508 4.2 55.7 1.0
CG A:TYR71 4.2 61.4 1.0
C17 A:GUC508 4.2 58.1 1.0
CD1 A:TYR71 4.3 62.6 1.0
N5 A:GUC508 4.5 54.2 1.0
F2 A:GUC508 4.6 62.0 1.0
CD1 A:ILE118 4.7 40.0 1.0
CZ A:PHE108 4.7 37.9 1.0
CD1 A:TRP76 4.8 40.7 1.0
O A:HOH608 4.8 45.4 1.0
C21 A:GUC508 4.8 59.8 1.0
NE1 A:TRP76 5.0 40.8 1.0
CG A:PHE108 5.0 37.6 1.0

Fluorine binding site 2 out of 2 in 7d36

Go back to Fluorine Binding Sites List in 7d36
Fluorine binding site 2 out of 2 in the Crystal Structure of BACE1 in Complex with N-{3-[(3S)-1-Amino-5- Fluoro-3-Methyl-3,4-Dihydro-2,6-Naphthyridin-3-Yl]-4-Fluorophenyl}-5- Cyano-3-Methylpyridine-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-[(3S)-1-Amino-5- Fluoro-3-Methyl-3,4-Dihydro-2,6-Naphthyridin-3-Yl]-4-Fluorophenyl}-5- Cyano-3-Methylpyridine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F508

b:62.0
occ:1.00
 F2 A:GUC508 0.0 62.0 1.0
C21 A:GUC508 1.3 59.8 1.0
N3 A:GUC508 2.4 60.7 1.0
C17 A:GUC508 2.4 58.1 1.0
C16 A:GUC508 3.0 56.0 1.0
CD1 A:TYR71 3.4 62.6 1.0
CG A:TYR71 3.5 61.4 1.0
CB A:TYR71 3.6 59.9 1.0
C20 A:GUC508 3.6 59.0 1.0
C18 A:GUC508 3.8 57.0 1.0
CE1 A:TYR71 4.2 63.6 1.0
C19 A:GUC508 4.2 57.8 1.0
CD2 A:TYR71 4.3 61.7 1.0
C14 A:GUC508 4.3 55.4 1.0
C12 A:GUC508 4.5 55.4 1.0
F1 A:GUC508 4.6 54.7 1.0
C11 A:GUC508 4.6 56.0 1.0
CA A:TYR71 4.7 59.6 1.0
CZ A:TYR71 4.8 64.0 1.0
CE2 A:TYR71 4.9 63.6 1.0
C22 A:GUC508 5.0 55.3 1.0

Reference:

K.Nakahara, Y.Mitsuoka, S.Kasuya, T.Yamamoto, S.Yamamoto, H.Ito, Y.Kido, K.I.Kusakabe. Balancing Potency and Basicity By Incorporating Fluoropyridine Moieties: Discovery of A 1-Amino-3,4-Dihydro-2,6-Naphthyridine BACE1 Inhibitor That Affords Robust and Sustained Central A Beta Reduction. Eur.J.Med.Chem. V. 216 13270 2021.
ISSN: ISSN 0223-5234
PubMed: 33765486
DOI: 10.1016/J.EJMECH.2021.113270
Page generated: Tue Jul 15 19:02:56 2025

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