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Iodine in PDB 6jse: Crystal Structure of BACE1 in Complex with N-(3-((4S,5R)-2-Amino-4- Methyl-5-Phenyl-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,5R)-2-Amino-4- Methyl-5-Phenyl-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,5R)-2-Amino-4- Methyl-5-Phenyl-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,5R)-2-Amino-4- Methyl-5-Phenyl-5,6-Dihydro-4H-1,3-Thiazin-4-Yl)-4-Fluorophenyl)-5- (Fluoromethoxy)Pyrazine-2-Carboxamide, PDB code: 6jse was solved by K.Fujimoto, E.Matsuoka, N.Asada, G.Tadano, T.Yamamoto, K.Nakahara, K.Fuchino, H.Ito, N.Kanegawa, D.Moechars, H.J.M.Gijsen, K.I.Kusakabe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.00
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 101.788, 101.788, 170.425, 90.00, 90.00, 120.00
R / Rfree (%) 18.9 / 20.8

Other elements in 6jse:

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

Iodine binding site 1 out of 6 in 6jse

Go back to Iodine Binding Sites List in 6jse
Iodine binding site 1 out of 6 in the Crystal Structure of BACE1 in Complex with N-(3-((4S,5R)-2-Amino-4- Methyl-5-Phenyl-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 Iodine with other atoms in the I binding site number 1 of Crystal Structure of BACE1 in Complex with N-(3-((4S,5R)-2-Amino-4- Methyl-5-Phenyl-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:I501

b:30.8
occ:0.69
 O A:HOH779 3.2 30.5 1.0
O A:HOH780 3.3 39.5 1.0
OG A:SER129 3.6 30.1 1.0
N A:SER129 3.8 30.4 1.0
CA A:GLU128 3.8 33.8 1.0
CD2 A:HIS69 3.9 29.9 1.0
N A:GLU128 3.9 32.2 1.0
C A:GLU128 3.9 32.0 1.0
C A:THR127 4.0 31.9 1.0
O A:THR127 4.0 32.5 1.0
CE2 A:PHE133 4.2 28.9 1.0
CB A:SER129 4.2 29.3 1.0
CB A:HIS69 4.2 30.7 1.0
CG2 A:ILE126 4.3 24.7 1.0
CG A:HIS69 4.4 30.5 1.0
O A:ILE126 4.5 26.7 1.0
CA A:SER129 4.6 30.4 1.0
O A:GLU128 4.7 31.3 1.0
CA A:THR127 4.7 30.5 1.0
CB A:ALA67 4.8 30.0 1.0
CD2 A:PHE133 4.8 29.1 1.0
C A:ILE126 4.8 27.0 1.0
N A:THR127 4.8 29.0 1.0

Iodine binding site 2 out of 6 in 6jse

Go back to Iodine Binding Sites List in 6jse
Iodine binding site 2 out of 6 in the Crystal Structure of BACE1 in Complex with N-(3-((4S,5R)-2-Amino-4- Methyl-5-Phenyl-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 Iodine with other atoms in the I binding site number 2 of Crystal Structure of BACE1 in Complex with N-(3-((4S,5R)-2-Amino-4- Methyl-5-Phenyl-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:I502

b:83.9
occ:0.78
 NH2 A:ARG373 2.4 40.4 1.0
O A:HOH614 3.6 31.1 1.0
CZ A:ARG373 3.6 44.2 1.0
O A:HOH699 3.7 39.8 1.0
CD1 A:LEU173 4.3 34.8 1.0
NH1 A:ARG373 4.3 44.6 1.0
NE A:ARG373 4.5 43.6 1.0
CD1 A:ILE203 4.8 37.4 1.0
OD2 A:ASP370 4.8 28.6 1.0

Iodine binding site 3 out of 6 in 6jse

Go back to Iodine Binding Sites List in 6jse
Iodine binding site 3 out of 6 in the Crystal Structure of BACE1 in Complex with N-(3-((4S,5R)-2-Amino-4- Methyl-5-Phenyl-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 Iodine with other atoms in the I binding site number 3 of Crystal Structure of BACE1 in Complex with N-(3-((4S,5R)-2-Amino-4- Methyl-5-Phenyl-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:I503

b:40.7
occ:0.62
 O A:HOH755 3.4 43.8 1.0
O A:HOH657 3.4 35.5 1.0
N A:LYS131 3.5 29.7 1.0
O A:HOH623 3.6 24.8 1.0
NE2 A:HIS69 3.9 30.0 1.0
CA A:ASP130 4.2 30.9 1.0
CA A:LYS131 4.3 29.8 1.0
CE2 A:PHE71 4.3 43.0 1.0
OD1 A:ASP130 4.4 38.6 1.0
C A:ASP130 4.4 30.1 1.0
CE1 A:HIS69 4.5 29.5 1.0
O A:SER129 4.7 30.5 1.0
CZ A:PHE71 4.7 42.5 1.0
CG A:ASP130 5.0 37.1 1.0
O A:HOH641 5.0 35.2 1.0
N A:PHE132 5.0 28.9 1.0

Iodine binding site 4 out of 6 in 6jse

Go back to Iodine Binding Sites List in 6jse
Iodine binding site 4 out of 6 in the Crystal Structure of BACE1 in Complex with N-(3-((4S,5R)-2-Amino-4- Methyl-5-Phenyl-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 Iodine with other atoms in the I binding site number 4 of Crystal Structure of BACE1 in Complex with N-(3-((4S,5R)-2-Amino-4- Methyl-5-Phenyl-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:I504

b:43.0
occ:0.49
 O A:HOH752 3.2 29.6 1.0
O A:HOH625 3.4 42.5 1.0
CE2 A:TYR246 4.1 33.0 1.0
O A:HOH771 4.1 29.8 1.0
NZ A:LYS263 4.2 44.8 1.0
CG A:LYS263 4.2 39.5 1.0
CD2 A:TYR246 4.6 31.8 1.0
CE A:LYS263 4.8 42.7 1.0
CB A:LYS262 4.9 31.9 1.0

Iodine binding site 5 out of 6 in 6jse

Go back to Iodine Binding Sites List in 6jse
Iodine binding site 5 out of 6 in the Crystal Structure of BACE1 in Complex with N-(3-((4S,5R)-2-Amino-4- Methyl-5-Phenyl-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 Iodine with other atoms in the I binding site number 5 of Crystal Structure of BACE1 in Complex with N-(3-((4S,5R)-2-Amino-4- Methyl-5-Phenyl-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:I505

b:94.5
occ:0.66
 O A:ARG120 3.4 33.0 1.0
OE2 A:GLU158 3.8 37.6 1.0
NE2 A:GLN167 4.1 34.9 1.0
OG A:SER163 4.2 32.1 1.0
C A:ARG120 4.3 33.9 1.0
O A:HOH664 4.4 33.5 1.0
OD1 A:ASN122 4.6 31.6 1.0
CG A:ARG120 4.6 36.1 1.0
N A:ASN122 4.6 30.3 1.0
CA A:ALA121 4.6 32.0 1.0
CG2 A:THR106 4.7 33.4 1.0
O A:HOH608 4.8 26.1 1.0
N A:ALA121 4.8 32.0 1.0
C A:ALA121 4.8 30.9 1.0
ND2 A:ASN122 4.8 31.2 1.0
CG A:ASN122 4.8 31.8 1.0
CB A:SER163 4.9 32.7 1.0
O A:HOH706 4.9 30.4 1.0
CD A:GLU158 4.9 36.6 1.0

Iodine binding site 6 out of 6 in 6jse

Go back to Iodine Binding Sites List in 6jse
Iodine binding site 6 out of 6 in the Crystal Structure of BACE1 in Complex with N-(3-((4S,5R)-2-Amino-4- Methyl-5-Phenyl-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 Iodine with other atoms in the I binding site number 6 of Crystal Structure of BACE1 in Complex with N-(3-((4S,5R)-2-Amino-4- Methyl-5-Phenyl-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:I506

b:90.6
occ:0.66
 CD1 A:TYR246 4.2 32.0 1.0
CD A:LYS242 4.2 40.5 1.0
CG A:TYR246 4.2 31.2 1.0
CG A:LYS242 4.2 40.7 1.0
CD1 A:TYR408 4.3 46.1 1.0
CB A:LYS242 4.3 37.0 1.0
CB A:TYR246 4.3 30.2 1.0
O A:LYS242 4.4 32.8 1.0
CE1 A:TYR408 4.4 47.0 1.0
OE1 A:GLU243 4.5 38.4 1.0
C A:LYS242 4.5 34.4 1.0
CD A:GLU243 4.6 39.6 1.0
OE2 A:GLU243 4.7 41.8 1.0
CE1 A:TYR246 4.7 32.6 1.0
CD2 A:TYR246 4.7 31.8 1.0
N A:GLU243 4.7 33.8 1.0
CA A:GLU243 5.0 34.4 1.0

Reference:

K.Fujimoto, E.Matsuoka, N.Asada, G.Tadano, T.Yamamoto, K.Nakahara, K.Fuchino, H.Ito, N.Kanegawa, D.Moechars, H.J.M.Gijsen, K.I.Kusakabe. Structure-Based Design of Selective Beta-Site Amyloid Precursor Protein Cleaving Enzyme 1 (BACE1) Inhibitors: Targeting the Flap to Gain Selectivity Over BACE2. J.Med.Chem. V. 62 5080 2019.
ISSN: ISSN 0022-2623
PubMed: 31021626
DOI: 10.1021/ACS.JMEDCHEM.9B00309
Page generated: Sun Aug 11 23:16:36 2024

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