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Iodine in PDB 5ygy: Crystal Structure of BACE1 in Complex with (S)-N-(3-(2-Amino-6- (Fluoromethyl)-4 -Methyl-4H-1,3-Oxazin-4-Yl)-4-Fluorophenyl)-5- Cyanopicolinamide

Enzymatic activity of Crystal Structure of BACE1 in Complex with (S)-N-(3-(2-Amino-6- (Fluoromethyl)-4 -Methyl-4H-1,3-Oxazin-4-Yl)-4-Fluorophenyl)-5- Cyanopicolinamide

All present enzymatic activity of Crystal Structure of BACE1 in Complex with (S)-N-(3-(2-Amino-6- (Fluoromethyl)-4 -Methyl-4H-1,3-Oxazin-4-Yl)-4-Fluorophenyl)-5- Cyanopicolinamide:
3.4.23.46;

Protein crystallography data

The structure of Crystal Structure of BACE1 in Complex with (S)-N-(3-(2-Amino-6- (Fluoromethyl)-4 -Methyl-4H-1,3-Oxazin-4-Yl)-4-Fluorophenyl)-5- Cyanopicolinamide, PDB code: 5ygy was solved by K.Fuchino, Y.Mitsuoka, M.Masui, N.Kurose, S.Yoshida, K.Komano, T.Yamamoto, M.Ogawa, C.Unemura, M.Hosono, H.Ito, G.Sakaguchi, S.Ando, S.Ohnishi, Y.Kido, T.Fukushima, H.Miyajima, S.Hiroyama, K.Koyabu, D.Dhuyvetter, H.Borghys, H.Gijsen, Y.Yamano, Y.Iso, K.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 (°) 102.149, 102.149, 171.125, 90.00, 90.00, 120.00
R / Rfree (%) 19.1 / 23.5

Other elements in 5ygy:

The structure of Crystal Structure of BACE1 in Complex with (S)-N-(3-(2-Amino-6- (Fluoromethyl)-4 -Methyl-4H-1,3-Oxazin-4-Yl)-4-Fluorophenyl)-5- Cyanopicolinamide 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 (S)-N-(3-(2-Amino-6- (Fluoromethyl)-4 -Methyl-4H-1,3-Oxazin-4-Yl)-4-Fluorophenyl)-5- Cyanopicolinamide (pdb code 5ygy). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 5 binding sites of Iodine where determined in the Crystal Structure of BACE1 in Complex with (S)-N-(3-(2-Amino-6- (Fluoromethyl)-4 -Methyl-4H-1,3-Oxazin-4-Yl)-4-Fluorophenyl)-5- Cyanopicolinamide, PDB code: 5ygy:
Jump to Iodine binding site number: 1; 2; 3; 4; 5;

Iodine binding site 1 out of 5 in 5ygy

Go back to Iodine Binding Sites List in 5ygy
Iodine binding site 1 out of 5 in the Crystal Structure of BACE1 in Complex with (S)-N-(3-(2-Amino-6- (Fluoromethyl)-4 -Methyl-4H-1,3-Oxazin-4-Yl)-4-Fluorophenyl)-5- Cyanopicolinamide


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 (S)-N-(3-(2-Amino-6- (Fluoromethyl)-4 -Methyl-4H-1,3-Oxazin-4-Yl)-4-Fluorophenyl)-5- Cyanopicolinamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I501

b:42.2
occ:1.00
 O A:HOH740 3.3 32.3 1.0
O A:HOH743 3.4 34.8 1.0
OG A:SER105 3.5 30.2 1.0
N A:SER105 3.7 31.2 1.0
CA A:GLU104 3.7 35.6 1.0
N A:GLU104 3.8 35.4 1.0
C A:GLU104 3.9 32.3 1.0
C A:THR103 4.0 35.6 1.0
CD2 A:HIS45 4.0 28.4 1.0
CE2 A:PHE109 4.2 29.6 1.0
O A:THR103 4.2 37.9 1.0
CB A:SER105 4.2 30.4 1.0
CG2 A:ILE102 4.3 28.7 1.0
CB A:HIS45 4.3 29.4 1.0
CG A:HIS45 4.5 29.4 1.0
CA A:SER105 4.6 33.5 1.0
O A:ILE102 4.6 31.7 1.0
CA A:THR103 4.7 34.9 1.0
O A:GLU104 4.7 30.8 1.0
CD2 A:PHE109 4.7 31.4 1.0
N A:THR103 4.8 33.1 1.0
C A:ILE102 4.8 32.0 1.0

Iodine binding site 2 out of 5 in 5ygy

Go back to Iodine Binding Sites List in 5ygy
Iodine binding site 2 out of 5 in the Crystal Structure of BACE1 in Complex with (S)-N-(3-(2-Amino-6- (Fluoromethyl)-4 -Methyl-4H-1,3-Oxazin-4-Yl)-4-Fluorophenyl)-5- Cyanopicolinamide


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 (S)-N-(3-(2-Amino-6- (Fluoromethyl)-4 -Methyl-4H-1,3-Oxazin-4-Yl)-4-Fluorophenyl)-5- Cyanopicolinamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I502

b:62.0
occ:1.00
 O A:HOH726 2.4 22.7 1.0
O A:HOH752 3.3 40.5 1.0
NH1 A:ARG349 3.5 41.1 1.0
O A:HOH655 3.6 28.8 1.0
NH2 A:ARG-4 3.9 72.5 1.0
NH2 A:ARG351 3.9 26.0 1.0
OD2 A:ASP346 4.3 29.0 1.0
CD A:ARG349 4.6 40.0 1.0
CZ A:ARG349 4.7 43.1 1.0
CZ A:ARG-4 4.9 67.6 1.0

Iodine binding site 3 out of 5 in 5ygy

Go back to Iodine Binding Sites List in 5ygy
Iodine binding site 3 out of 5 in the Crystal Structure of BACE1 in Complex with (S)-N-(3-(2-Amino-6- (Fluoromethyl)-4 -Methyl-4H-1,3-Oxazin-4-Yl)-4-Fluorophenyl)-5- Cyanopicolinamide


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 (S)-N-(3-(2-Amino-6- (Fluoromethyl)-4 -Methyl-4H-1,3-Oxazin-4-Yl)-4-Fluorophenyl)-5- Cyanopicolinamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I503

b:68.7
occ:1.00
 N A:LYS107 3.5 31.9 1.0
O A:HOH729 3.5 23.4 1.0
NE2 A:HIS45 3.9 29.2 1.0
CA A:ASP106 4.2 37.8 1.0
C A:ASP106 4.3 33.6 1.0
CA A:LYS107 4.3 34.0 1.0
CE2 A:PHE47 4.4 54.0 1.0
CE1 A:HIS45 4.4 30.0 1.0
O A:SER105 4.5 34.8 1.0
OD1 A:ASP106 4.5 50.4 1.0
CZ A:PHE47 4.9 55.5 1.0
N A:ASP106 5.0 36.0 1.0
N A:PHE108 5.0 34.6 1.0

Iodine binding site 4 out of 5 in 5ygy

Go back to Iodine Binding Sites List in 5ygy
Iodine binding site 4 out of 5 in the Crystal Structure of BACE1 in Complex with (S)-N-(3-(2-Amino-6- (Fluoromethyl)-4 -Methyl-4H-1,3-Oxazin-4-Yl)-4-Fluorophenyl)-5- Cyanopicolinamide


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 (S)-N-(3-(2-Amino-6- (Fluoromethyl)-4 -Methyl-4H-1,3-Oxazin-4-Yl)-4-Fluorophenyl)-5- Cyanopicolinamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I504

b:0.4
occ:1.00
 O A:ARG96 3.5 34.5 1.0
O A:HOH784 3.6 50.3 1.0
OE1 A:GLU134 3.9 38.9 1.0
NE2 A:GLN143 3.9 29.5 1.0
O A:HOH635 3.9 30.1 1.0
OG A:SER139 4.2 29.6 1.0
C A:ARG96 4.4 36.9 1.0
CG A:ARG96 4.5 36.1 1.0
CD A:GLU134 4.8 39.6 1.0
CA A:ALA97 4.8 33.1 1.0
ND2 A:ASN98 4.8 33.4 1.0
CB A:SER139 4.9 31.4 1.0
CB A:ARG96 4.9 34.9 1.0
N A:ALA97 5.0 34.2 1.0
CG2 A:THR82 5.0 32.1 1.0

Iodine binding site 5 out of 5 in 5ygy

Go back to Iodine Binding Sites List in 5ygy
Iodine binding site 5 out of 5 in the Crystal Structure of BACE1 in Complex with (S)-N-(3-(2-Amino-6- (Fluoromethyl)-4 -Methyl-4H-1,3-Oxazin-4-Yl)-4-Fluorophenyl)-5- Cyanopicolinamide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Crystal Structure of BACE1 in Complex with (S)-N-(3-(2-Amino-6- (Fluoromethyl)-4 -Methyl-4H-1,3-Oxazin-4-Yl)-4-Fluorophenyl)-5- Cyanopicolinamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I505

b:0.3
occ:1.00
 CD1 A:TYR222 4.1 42.6 1.0
CG A:TYR222 4.3 39.6 1.0
OE2 A:GLU219 4.3 49.9 1.0
CE1 A:TYR222 4.5 42.2 1.0
CD1 A:TYR384 4.6 57.4 1.0
CB A:LYS218 4.6 47.8 1.0
CG A:LYS218 4.6 51.4 1.0
CB A:TYR222 4.6 39.2 1.0
CD A:GLU219 4.7 50.7 1.0
O A:LYS218 4.7 42.7 1.0
CE1 A:TYR384 4.7 57.8 1.0
O A:HOH643 4.8 42.0 1.0
CD2 A:TYR222 4.8 40.2 1.0
C A:LYS218 4.8 44.8 1.0
OE1 A:GLU219 4.9 50.5 1.0

Reference:

K.Fuchino, Y.Mitsuoka, M.Masui, N.Kurose, S.Yoshida, K.Komano, T.Yamamoto, M.Ogawa, C.Unemura, M.Hosono, H.Ito, G.Sakaguchi, S.Ando, S.Ohnishi, Y.Kido, T.Fukushima, H.Miyajima, S.Hiroyama, K.Koyabu, D.Dhuyvetter, H.Borghys, H.J.M.Gijsen, Y.Yamano, Y.Iso, K.I.Kusakabe. Rational Design of Novel 1,3-Oxazine Based Beta-Secretase (BACE1) Inhibitors: Incorporation of A Double Bond to Reduce P-Gp Efflux Leading to Robust A Beta Reduction in the Brain J. Med. Chem. V. 61 5122 2018.
ISSN: ISSN 1520-4804
PubMed: 29733614
DOI: 10.1021/ACS.JMEDCHEM.8B00002
Page generated: Sun Aug 11 22:22:26 2024

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