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Iodine 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:

Fluorine (F) 2 atoms

Iodine Binding Sites:

The binding sites of Iodine 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 Iodine atom.
In total 4 binding sites of Iodine 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 Iodine binding site number: 1; 2; 3; 4;

Iodine binding site 1 out of 4 in 7d36

Go back to Iodine Binding Sites List in 7d36
Iodine binding site 1 out of 4 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 Iodine with other atoms in the I 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:I501

b:45.2
occ:1.00
 O A:HOH724 3.3 31.3 1.0
O A:HOH737 3.3 48.8 1.0
OG A:SER105 3.5 39.2 1.0
N A:SER105 3.7 38.7 1.0
CA A:GLU104 3.7 38.6 1.0
C A:GLU104 3.8 38.4 1.0
N A:GLU104 3.9 39.2 1.0
C A:THR103 4.0 38.9 1.0
O A:THR103 4.0 40.1 1.0
CE2 A:PHE109 4.1 36.0 1.0
CD2 A:HIS45 4.1 33.1 1.0
CB A:SER105 4.2 38.9 1.0
CB A:HIS45 4.3 34.9 1.0
CG2 A:ILE102 4.4 34.3 1.0
CG A:HIS45 4.5 35.3 1.0
O A:ILE102 4.5 35.9 1.0
O A:GLU104 4.6 38.1 1.0
CA A:SER105 4.6 39.2 1.0
CD2 A:PHE109 4.7 37.7 1.0
CA A:THR103 4.7 38.2 1.0
C A:ILE102 4.9 36.5 1.0
N A:THR103 4.9 37.1 1.0

Iodine binding site 2 out of 4 in 7d36

Go back to Iodine Binding Sites List in 7d36
Iodine binding site 2 out of 4 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 Iodine with other atoms in the I 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:I502

b:71.8
occ:1.00
 N A:LYS107 3.4 40.7 1.0
O A:HOH689 3.5 32.0 1.0
NE2 A:HIS45 3.9 34.7 1.0
CA A:ASP106 4.1 41.4 1.0
C A:ASP106 4.3 41.1 1.0
CA A:LYS107 4.3 40.5 1.0
O A:SER105 4.4 39.8 1.0
CE1 A:HIS45 4.5 35.3 1.0
CE2 A:PHE47 4.6 49.7 1.0
OD1 A:ASP106 4.6 48.5 1.0
N A:ASP106 5.0 40.7 1.0

Iodine binding site 3 out of 4 in 7d36

Go back to Iodine Binding Sites List in 7d36
Iodine binding site 3 out of 4 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 Iodine with other atoms in the I binding site number 3 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:I503

b:70.3
occ:1.00
 O A:HOH755 2.2 28.5 1.0
NH2 A:ARG349 3.1 56.7 1.0
O A:HOH711 3.2 40.5 1.0
NE A:ARG349 3.5 51.0 1.0
O A:HOH635 3.7 39.7 1.0
CZ A:ARG349 3.8 54.6 1.0
NH2 A:ARG351 3.9 31.1 1.0
OD2 A:ASP346 4.4 33.8 1.0
NH2 A:ARG-4 4.4 63.1 1.0
CD A:ARG349 4.8 45.7 1.0

Iodine binding site 4 out of 4 in 7d36

Go back to Iodine Binding Sites List in 7d36
Iodine binding site 4 out of 4 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 Iodine with other atoms in the I binding site number 4 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:I504

b:86.5
occ:1.00
 CB A:LYS238 3.1 52.2 1.0
CG A:LYS238 3.4 54.0 1.0
CD A:LYS238 3.5 56.0 1.0
CA A:LYS238 4.4 52.3 1.0
CE A:LYS238 4.5 57.4 1.0
O A:HOH731 4.6 43.5 1.0
N A:LYS238 4.7 52.0 1.0
N A:LYS239 4.9 51.5 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: Mon Aug 12 00:57:31 2024

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