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Iodine in PDB 6jsf: Crystal Structure of BACE1 in Complex with N-(3-((4S,5S)-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,5S)-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,5S)-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,5S)-2-Amino-4- Methyl-5-Phenyl-5,6-Dihydro-4H-1,3-Thiazin-4-Yl)-4-Fluorophenyl)-5- (Fluoromethoxy)Pyrazine-2-Carboxamide, PDB code: 6jsf 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 / 2.30
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 102.535, 102.535, 170.350, 90.00, 90.00, 120.00
R / Rfree (%) 18.3 / 21.3

Other elements in 6jsf:

The structure of Crystal Structure of BACE1 in Complex with N-(3-((4S,5S)-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,5S)-2-Amino-4- Methyl-5-Phenyl-5,6-Dihydro-4H-1,3-Thiazin-4-Yl)-4-Fluorophenyl)-5- (Fluoromethoxy)Pyrazine-2-Carboxamide (pdb code 6jsf). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 7 binding sites of Iodine where determined in the Crystal Structure of BACE1 in Complex with N-(3-((4S,5S)-2-Amino-4- Methyl-5-Phenyl-5,6-Dihydro-4H-1,3-Thiazin-4-Yl)-4-Fluorophenyl)-5- (Fluoromethoxy)Pyrazine-2-Carboxamide, PDB code: 6jsf:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7;

Iodine binding site 1 out of 7 in 6jsf

Go back to Iodine Binding Sites List in 6jsf
Iodine binding site 1 out of 7 in the Crystal Structure of BACE1 in Complex with N-(3-((4S,5S)-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,5S)-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:38.5
occ:0.84
 O A:HOH726 3.3 38.0 1.0
OG A:SER129 3.4 30.7 1.0
O A:HOH724 3.5 46.8 1.0
N A:SER129 3.8 33.5 1.0
CA A:GLU128 3.8 38.5 1.0
N A:GLU128 3.8 39.2 1.0
C A:GLU128 3.9 35.6 1.0
C A:THR127 3.9 38.6 1.0
CD2 A:HIS69 3.9 33.2 1.0
O A:THR127 4.1 41.0 1.0
CB A:SER129 4.1 31.8 1.0
CE2 A:PHE133 4.1 31.1 1.0
CG2 A:ILE126 4.1 31.7 1.0
CB A:HIS69 4.2 33.4 1.0
CG A:HIS69 4.4 33.9 1.0
O A:ILE126 4.5 34.4 1.0
CA A:SER129 4.5 33.9 1.0
CA A:THR127 4.6 38.0 1.0
O A:GLU128 4.6 34.6 1.0
N A:THR127 4.7 35.6 1.0
C A:ILE126 4.7 34.5 1.0
CD2 A:PHE133 4.9 31.2 1.0
CB A:ALA67 5.0 33.5 1.0

Iodine binding site 2 out of 7 in 6jsf

Go back to Iodine Binding Sites List in 6jsf
Iodine binding site 2 out of 7 in the Crystal Structure of BACE1 in Complex with N-(3-((4S,5S)-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,5S)-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:70.8
occ:0.81
 NH2 A:ARG373 2.4 55.0 1.0
NH1 A:ARG373 3.1 55.4 1.0
CZ A:ARG373 3.1 55.2 1.0
O A:HOH689 3.4 36.3 1.0
O A:HOH615 3.5 24.6 1.0
NH2 A:ARG20 3.7 55.3 1.0
NH1 A:ARG20 3.9 59.1 1.0
CZ A:ARG20 4.3 59.0 1.0
NE A:ARG373 4.3 52.9 1.0
CD1 A:LEU173 4.5 39.9 1.0
CD1 A:ILE203 4.8 38.6 1.0
OD2 A:ASP370 4.9 34.8 1.0

Iodine binding site 3 out of 7 in 6jsf

Go back to Iodine Binding Sites List in 6jsf
Iodine binding site 3 out of 7 in the Crystal Structure of BACE1 in Complex with N-(3-((4S,5S)-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,5S)-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:48.0
occ:0.61
 O A:HOH642 3.2 40.8 1.0
O A:HOH752 3.5 49.6 0.5
N A:LYS131 3.6 35.9 1.0
O A:HOH668 3.6 26.4 1.0
O A:HOH727 3.7 50.6 1.0
NE2 A:HIS69 3.9 32.9 1.0
CA A:ASP130 4.1 37.3 1.0
O A:SER129 4.3 36.7 1.0
C A:ASP130 4.4 36.0 1.0
CE2 A:PHE71 4.4 44.5 1.0
CE1 A:HIS69 4.4 33.9 1.0
CA A:LYS131 4.5 35.5 1.0
OD1 A:ASP130 4.6 50.3 1.0
CZ A:PHE71 4.7 45.3 1.0
N A:ASP130 4.9 36.1 1.0
C A:SER129 4.9 34.9 1.0

Iodine binding site 4 out of 7 in 6jsf

Go back to Iodine Binding Sites List in 6jsf
Iodine binding site 4 out of 7 in the Crystal Structure of BACE1 in Complex with N-(3-((4S,5S)-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,5S)-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:91.2
occ:0.62
 O A:ARG120 3.4 37.9 1.0
NE2 A:GLN167 4.0 37.4 1.0
O A:HOH629 4.2 37.9 1.0
OE1 A:GLU158 4.3 40.9 1.0
C A:ARG120 4.3 39.2 1.0
OG A:SER163 4.4 36.3 1.0
CG A:ARG120 4.5 42.6 1.0
CG2 A:THR106 4.7 34.2 1.0
CA A:ALA121 4.7 36.7 1.0
CB A:ARG120 4.8 41.5 1.0
N A:ALA121 4.8 37.7 1.0
OD1 A:ASN122 4.9 36.5 1.0
N A:ASN122 4.9 35.0 1.0
C A:ALA121 5.0 36.2 1.0

Iodine binding site 5 out of 7 in 6jsf

Go back to Iodine Binding Sites List in 6jsf
Iodine binding site 5 out of 7 in the Crystal Structure of BACE1 in Complex with N-(3-((4S,5S)-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,5S)-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:85.5
occ:0.64
 CD1 A:TYR246 4.1 33.6 1.0
CG A:TYR246 4.2 32.8 1.0
CD1 A:TYR408 4.3 49.1 1.0
CB A:TYR246 4.4 32.4 1.0
CE1 A:TYR408 4.4 53.0 1.0
OE1 A:GLU243 4.4 40.1 1.0
OE2 A:GLU243 4.4 40.1 1.0
O A:LYS242 4.5 35.4 1.0
CD A:GLU243 4.5 39.0 1.0
CB A:LYS242 4.5 39.2 1.0
CG A:LYS242 4.5 42.2 1.0
C A:LYS242 4.6 36.5 1.0
CE1 A:TYR246 4.6 34.6 1.0
CD2 A:TYR246 4.7 33.1 1.0
N A:GLU243 4.8 35.1 1.0
O A:HOH616 4.9 38.4 1.0
CA A:GLU243 4.9 34.8 1.0
CD A:LYS242 5.0 44.3 1.0

Iodine binding site 6 out of 7 in 6jsf

Go back to Iodine Binding Sites List in 6jsf
Iodine binding site 6 out of 7 in the Crystal Structure of BACE1 in Complex with N-(3-((4S,5S)-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,5S)-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:49.9
occ:0.55
 O A:HOH707 3.1 29.8 1.0
O A:HOH616 3.4 38.4 1.0
O A:HOH744 3.9 31.9 1.0
CE2 A:TYR246 4.1 34.3 1.0
CE A:LYS263 4.5 45.9 1.0
NZ A:LYS263 4.5 46.8 1.0
CD2 A:TYR246 4.6 33.1 1.0
CB A:LYS263 4.8 41.0 1.0
CB A:LYS262 4.8 36.5 1.0
N A:LYS263 4.9 37.2 1.0

Iodine binding site 7 out of 7 in 6jsf

Go back to Iodine Binding Sites List in 6jsf
Iodine binding site 7 out of 7 in the Crystal Structure of BACE1 in Complex with N-(3-((4S,5S)-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 7 of Crystal Structure of BACE1 in Complex with N-(3-((4S,5S)-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:I507

b:65.0
occ:0.44
 NE2 A:HIS205 3.2 35.9 1.0
CA A:GLY21 3.6 53.5 1.0
N A:GLY21 3.9 57.0 1.0
O A:ARG20 3.9 62.9 1.0
CD2 A:HIS205 3.9 35.6 1.0
C A:ARG20 3.9 60.5 1.0
CB A:ARG20 4.3 60.3 1.0
CE1 A:HIS205 4.3 35.7 1.0
CA A:ARG20 4.8 60.7 1.0
NE A:ARG20 4.9 61.0 1.0
C A:GLY21 4.9 52.0 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 23:16:47 2024

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