Atomistry » Iodine » PDB 6eql-6k60 » 6jse
Atomistry »
  Iodine »
    PDB 6eql-6k60 »
      6jse »

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy