Atomistry » Iodine » PDB 7ben-7fgj » 7d36
Atomistry »
  Iodine »
    PDB 7ben-7fgj »
      7d36 »

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

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