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Iodine in PDB 6jsn: Crystal Structure of BACE1 in Complex with N-{3-[(5R)-3-Amino-5- Methyl-9,9-Dioxo-2,9LAMBDA6-Dithia-4-Azaspiro[5.5]Undec-3-En-5-Yl]-4- Fluorophenyl}-5-(Fluoromethoxy)Pyrazine-2-Carboxamide

Enzymatic activity of Crystal Structure of BACE1 in Complex with N-{3-[(5R)-3-Amino-5- Methyl-9,9-Dioxo-2,9LAMBDA6-Dithia-4-Azaspiro[5.5]Undec-3-En-5-Yl]-4- Fluorophenyl}-5-(Fluoromethoxy)Pyrazine-2-Carboxamide

All present enzymatic activity of Crystal Structure of BACE1 in Complex with N-{3-[(5R)-3-Amino-5- Methyl-9,9-Dioxo-2,9LAMBDA6-Dithia-4-Azaspiro[5.5]Undec-3-En-5-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-[(5R)-3-Amino-5- Methyl-9,9-Dioxo-2,9LAMBDA6-Dithia-4-Azaspiro[5.5]Undec-3-En-5-Yl]-4- Fluorophenyl}-5-(Fluoromethoxy)Pyrazine-2-Carboxamide, PDB code: 6jsn 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 / 2.60
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 101.705, 101.705, 170.422, 90.00, 90.00, 120.00
R / Rfree (%) 20.1 / 25.9

Other elements in 6jsn:

The structure of Crystal Structure of BACE1 in Complex with N-{3-[(5R)-3-Amino-5- Methyl-9,9-Dioxo-2,9LAMBDA6-Dithia-4-Azaspiro[5.5]Undec-3-En-5-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-[(5R)-3-Amino-5- Methyl-9,9-Dioxo-2,9LAMBDA6-Dithia-4-Azaspiro[5.5]Undec-3-En-5-Yl]-4- Fluorophenyl}-5-(Fluoromethoxy)Pyrazine-2-Carboxamide (pdb code 6jsn). 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-[(5R)-3-Amino-5- Methyl-9,9-Dioxo-2,9LAMBDA6-Dithia-4-Azaspiro[5.5]Undec-3-En-5-Yl]-4- Fluorophenyl}-5-(Fluoromethoxy)Pyrazine-2-Carboxamide, PDB code: 6jsn:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6;

Iodine binding site 1 out of 6 in 6jsn

Go back to Iodine Binding Sites List in 6jsn
Iodine binding site 1 out of 6 in the Crystal Structure of BACE1 in Complex with N-{3-[(5R)-3-Amino-5- Methyl-9,9-Dioxo-2,9LAMBDA6-Dithia-4-Azaspiro[5.5]Undec-3-En-5-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-[(5R)-3-Amino-5- Methyl-9,9-Dioxo-2,9LAMBDA6-Dithia-4-Azaspiro[5.5]Undec-3-En-5-Yl]-4- Fluorophenyl}-5-(Fluoromethoxy)Pyrazine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I501

b:54.7
occ:0.64
 OG A:SER129 3.5 34.9 1.0
N A:GLU128 3.7 43.5 1.0
CA A:GLU128 3.7 44.2 1.0
N A:SER129 3.7 38.4 1.0
C A:GLU128 3.8 41.0 1.0
C A:THR127 3.9 43.7 1.0
CD2 A:HIS69 4.0 40.6 1.0
CG2 A:ILE126 4.1 33.1 1.0
CB A:HIS69 4.1 39.0 1.0
CE2 A:PHE133 4.2 32.1 1.0
O A:THR127 4.2 48.0 1.0
CB A:SER129 4.3 36.7 1.0
CG A:HIS69 4.4 39.5 1.0
O A:GLU128 4.5 39.4 1.0
CA A:THR127 4.5 40.5 1.0
N A:THR127 4.6 38.2 1.0
CA A:SER129 4.6 37.5 1.0
O A:ILE126 4.8 37.7 1.0
C A:ILE126 4.8 36.1 1.0
CD2 A:PHE133 4.8 34.5 1.0
CB A:ALA67 5.0 36.7 1.0

Iodine binding site 2 out of 6 in 6jsn

Go back to Iodine Binding Sites List in 6jsn
Iodine binding site 2 out of 6 in the Crystal Structure of BACE1 in Complex with N-{3-[(5R)-3-Amino-5- Methyl-9,9-Dioxo-2,9LAMBDA6-Dithia-4-Azaspiro[5.5]Undec-3-En-5-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-[(5R)-3-Amino-5- Methyl-9,9-Dioxo-2,9LAMBDA6-Dithia-4-Azaspiro[5.5]Undec-3-En-5-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:0.73
 NH2 A:ARG373 2.4 32.3 1.0
CZ A:ARG373 3.6 45.2 1.0
O A:HOH602 3.6 26.6 1.0
CD1 A:ILE203 4.2 43.2 1.0
CD1 A:LEU173 4.3 38.5 1.0
NH1 A:ARG373 4.3 45.9 1.0
NE A:ARG373 4.5 47.9 1.0
OD2 A:ASP370 5.0 41.3 1.0

Iodine binding site 3 out of 6 in 6jsn

Go back to Iodine Binding Sites List in 6jsn
Iodine binding site 3 out of 6 in the Crystal Structure of BACE1 in Complex with N-{3-[(5R)-3-Amino-5- Methyl-9,9-Dioxo-2,9LAMBDA6-Dithia-4-Azaspiro[5.5]Undec-3-En-5-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-[(5R)-3-Amino-5- Methyl-9,9-Dioxo-2,9LAMBDA6-Dithia-4-Azaspiro[5.5]Undec-3-En-5-Yl]-4- Fluorophenyl}-5-(Fluoromethoxy)Pyrazine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I503

b:61.1
occ:0.64
 N A:LYS131 3.5 42.4 1.0
O A:HOH637 3.5 25.8 1.0
NE2 A:HIS69 4.0 37.8 1.0
CE2 A:PHE71 4.1 69.9 1.0
CA A:LYS131 4.2 44.3 1.0
CA A:ASP130 4.3 43.0 1.0
C A:ASP130 4.4 43.4 1.0
O A:SER129 4.4 42.5 1.0
CE1 A:HIS69 4.7 37.2 1.0
CZ A:PHE71 4.7 73.8 1.0
CD2 A:PHE71 4.9 64.2 1.0
C A:SER129 5.0 41.0 1.0
N A:ASP130 5.0 43.5 1.0
CG A:LYS131 5.0 50.2 1.0

Iodine binding site 4 out of 6 in 6jsn

Go back to Iodine Binding Sites List in 6jsn
Iodine binding site 4 out of 6 in the Crystal Structure of BACE1 in Complex with N-{3-[(5R)-3-Amino-5- Methyl-9,9-Dioxo-2,9LAMBDA6-Dithia-4-Azaspiro[5.5]Undec-3-En-5-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-[(5R)-3-Amino-5- Methyl-9,9-Dioxo-2,9LAMBDA6-Dithia-4-Azaspiro[5.5]Undec-3-En-5-Yl]-4- Fluorophenyl}-5-(Fluoromethoxy)Pyrazine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I504

b:99.4
occ:0.50
 CE2 A:TYR246 4.2 35.6 1.0
CB A:LYS262 4.5 48.0 1.0
CD A:LYS263 4.5 57.6 1.0
CD2 A:TYR246 4.6 34.0 1.0
CE A:LYS263 4.6 57.4 1.0
CG A:LYS263 4.8 55.7 1.0
CG A:LYS262 4.8 49.6 1.0

Iodine binding site 5 out of 6 in 6jsn

Go back to Iodine Binding Sites List in 6jsn
Iodine binding site 5 out of 6 in the Crystal Structure of BACE1 in Complex with N-{3-[(5R)-3-Amino-5- Methyl-9,9-Dioxo-2,9LAMBDA6-Dithia-4-Azaspiro[5.5]Undec-3-En-5-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-[(5R)-3-Amino-5- Methyl-9,9-Dioxo-2,9LAMBDA6-Dithia-4-Azaspiro[5.5]Undec-3-En-5-Yl]-4- Fluorophenyl}-5-(Fluoromethoxy)Pyrazine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I505

b:76.6
occ:0.56
 O A:ARG120 3.4 46.4 1.0
NE2 A:GLN167 3.8 39.0 1.0
OE1 A:GLU158 3.8 46.7 1.0
O A:HOH608 4.1 33.9 1.0
OG A:SER163 4.1 38.9 1.0
C A:ARG120 4.3 45.2 1.0
OD1 A:ASN122 4.4 49.6 1.0
CG A:ARG120 4.5 46.2 1.0
CA A:ALA121 4.7 39.3 1.0
CD A:GLU158 4.7 47.3 1.0
CB A:SER163 4.8 38.3 1.0
N A:ALA121 4.9 43.0 1.0
CG A:ASN122 4.9 43.9 1.0
CB A:ARG120 4.9 44.6 1.0
N A:ASN122 4.9 37.6 1.0
ND2 A:ASN122 4.9 44.2 1.0
C A:ALA121 5.0 38.1 1.0

Iodine binding site 6 out of 6 in 6jsn

Go back to Iodine Binding Sites List in 6jsn
Iodine binding site 6 out of 6 in the Crystal Structure of BACE1 in Complex with N-{3-[(5R)-3-Amino-5- Methyl-9,9-Dioxo-2,9LAMBDA6-Dithia-4-Azaspiro[5.5]Undec-3-En-5-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-[(5R)-3-Amino-5- Methyl-9,9-Dioxo-2,9LAMBDA6-Dithia-4-Azaspiro[5.5]Undec-3-En-5-Yl]-4- Fluorophenyl}-5-(Fluoromethoxy)Pyrazine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I506

b:81.3
occ:0.50
 CD1 A:TYR246 4.1 35.8 1.0
CB A:LYS242 4.1 43.3 1.0
CG A:TYR246 4.2 35.1 1.0
CG A:LYS242 4.3 46.9 1.0
CD1 A:TYR408 4.4 57.4 1.0
OE1 A:GLU243 4.4 54.7 1.0
OE2 A:GLU243 4.5 50.9 1.0
CE1 A:TYR408 4.5 59.3 1.0
CD A:GLU243 4.5 52.6 1.0
CB A:TYR246 4.5 35.9 1.0
CE1 A:TYR246 4.6 35.4 1.0
C A:LYS242 4.6 42.1 1.0
O A:LYS242 4.6 41.6 1.0
CD2 A:TYR246 4.8 34.0 1.0
N A:GLU243 4.8 39.9 1.0
CD A:LYS242 4.9 46.2 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 23:18:02 2024

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