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Iodine in PDB 6c2i: Structure of Bace-1 (Beta-Secretase) in Complex with : N-(3-((1R,5S, 6R)-3-Amino-5-Methyl-2-Oxa-4-Azabicyclo[4.1.0]Hept-3-En-5-Yl)-4- Fluorophenyl)-5-Methoxypyrazine-2-Carboxamide

Enzymatic activity of Structure of Bace-1 (Beta-Secretase) in Complex with : N-(3-((1R,5S, 6R)-3-Amino-5-Methyl-2-Oxa-4-Azabicyclo[4.1.0]Hept-3-En-5-Yl)-4- Fluorophenyl)-5-Methoxypyrazine-2-Carboxamide

All present enzymatic activity of Structure of Bace-1 (Beta-Secretase) in Complex with : N-(3-((1R,5S, 6R)-3-Amino-5-Methyl-2-Oxa-4-Azabicyclo[4.1.0]Hept-3-En-5-Yl)-4- Fluorophenyl)-5-Methoxypyrazine-2-Carboxamide:
3.4.23.46;

Protein crystallography data

The structure of Structure of Bace-1 (Beta-Secretase) in Complex with : N-(3-((1R,5S, 6R)-3-Amino-5-Methyl-2-Oxa-4-Azabicyclo[4.1.0]Hept-3-En-5-Yl)-4- Fluorophenyl)-5-Methoxypyrazine-2-Carboxamide, PDB code: 6c2i was solved by E.A.Sickmier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.99 / 1.95
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 101.952, 101.952, 172.155, 90.00, 90.00, 120.00
R / Rfree (%) 15.8 / 18.4

Other elements in 6c2i:

The structure of Structure of Bace-1 (Beta-Secretase) in Complex with : N-(3-((1R,5S, 6R)-3-Amino-5-Methyl-2-Oxa-4-Azabicyclo[4.1.0]Hept-3-En-5-Yl)-4- Fluorophenyl)-5-Methoxypyrazine-2-Carboxamide also contains other interesting chemical elements:

Fluorine (F) 1 atom

Iodine Binding Sites:

The binding sites of Iodine atom in the Structure of Bace-1 (Beta-Secretase) in Complex with : N-(3-((1R,5S, 6R)-3-Amino-5-Methyl-2-Oxa-4-Azabicyclo[4.1.0]Hept-3-En-5-Yl)-4- Fluorophenyl)-5-Methoxypyrazine-2-Carboxamide (pdb code 6c2i). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 3 binding sites of Iodine where determined in the Structure of Bace-1 (Beta-Secretase) in Complex with : N-(3-((1R,5S, 6R)-3-Amino-5-Methyl-2-Oxa-4-Azabicyclo[4.1.0]Hept-3-En-5-Yl)-4- Fluorophenyl)-5-Methoxypyrazine-2-Carboxamide, PDB code: 6c2i:
Jump to Iodine binding site number: 1; 2; 3;

Iodine binding site 1 out of 3 in 6c2i

Go back to Iodine Binding Sites List in 6c2i
Iodine binding site 1 out of 3 in the Structure of Bace-1 (Beta-Secretase) in Complex with : N-(3-((1R,5S, 6R)-3-Amino-5-Methyl-2-Oxa-4-Azabicyclo[4.1.0]Hept-3-En-5-Yl)-4- Fluorophenyl)-5-Methoxypyrazine-2-Carboxamide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Structure of Bace-1 (Beta-Secretase) in Complex with : N-(3-((1R,5S, 6R)-3-Amino-5-Methyl-2-Oxa-4-Azabicyclo[4.1.0]Hept-3-En-5-Yl)-4- Fluorophenyl)-5-Methoxypyrazine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I401

b:24.1
occ:0.60
 HA A:GLU103 3.1 28.7 1.0
O A:HOH787 3.1 21.7 1.0
HG A:SER104 3.1 29.5 1.0
HD2 A:HIS44 3.2 33.5 1.0
HG22 A:ILE101 3.4 20.5 1.0
HB2 A:HIS44 3.4 24.9 1.0
HE2 A:PHE108 3.4 27.8 1.0
OG A:SER104 3.5 24.5 1.0
H A:SER104 3.6 25.5 1.0
CA A:GLU103 3.7 23.9 1.0
N A:SER104 3.7 21.2 1.0
C A:GLU103 3.8 19.8 1.0
N A:GLU103 3.8 19.2 1.0
HB3 A:SER104 3.9 21.1 1.0
CD2 A:HIS44 3.9 27.9 1.0
C A:THR102 3.9 26.1 1.0
O A:THR102 4.1 29.0 1.0
HB3 A:ALA42 4.1 21.9 1.0
CB A:SER104 4.2 17.5 1.0
H A:GLU103 4.2 23.1 1.0
CG2 A:ILE101 4.2 17.0 1.0
CB A:HIS44 4.3 20.7 1.0
CE2 A:PHE108 4.3 23.1 1.0
HG21 A:ILE101 4.4 20.5 1.0
CG A:HIS44 4.4 23.1 1.0
HD2 A:PHE108 4.5 27.8 1.0
HA A:THR102 4.5 26.7 1.0
CA A:SER104 4.5 19.4 1.0
O A:GLU103 4.6 15.9 1.0
O A:ILE101 4.6 17.4 1.0
HG23 A:ILE101 4.6 20.5 1.0
CA A:THR102 4.7 22.2 1.0
HB3 A:HIS44 4.8 24.9 1.0
CD2 A:PHE108 4.9 23.1 1.0
C A:ILE101 4.9 18.8 1.0
H A:HIS44 4.9 21.8 1.0
N A:THR102 4.9 17.6 1.0

Iodine binding site 2 out of 3 in 6c2i

Go back to Iodine Binding Sites List in 6c2i
Iodine binding site 2 out of 3 in the Structure of Bace-1 (Beta-Secretase) in Complex with : N-(3-((1R,5S, 6R)-3-Amino-5-Methyl-2-Oxa-4-Azabicyclo[4.1.0]Hept-3-En-5-Yl)-4- Fluorophenyl)-5-Methoxypyrazine-2-Carboxamide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Structure of Bace-1 (Beta-Secretase) in Complex with : N-(3-((1R,5S, 6R)-3-Amino-5-Methyl-2-Oxa-4-Azabicyclo[4.1.0]Hept-3-En-5-Yl)-4- Fluorophenyl)-5-Methoxypyrazine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I402

b:33.1
occ:0.54
 H A:LYS106 2.6 24.4 1.0
HA A:ASP105 3.1 26.6 1.0
HE2 A:HIS44 3.2 35.6 1.0
O A:HOH586 3.4 41.4 1.0
N A:LYS106 3.4 20.3 1.0
O A:HOH622 3.5 17.1 1.0
O A:HOH504 3.5 30.3 1.0
NE2 A:HIS44 3.9 29.6 1.0
HE1 A:HIS44 3.9 29.6 1.0
HE2 A:PHE46 4.0 48.5 1.0
HA A:LYS106 4.0 31.5 1.0
CA A:ASP105 4.0 22.1 1.0
C A:ASP105 4.2 23.6 1.0
CE1 A:HIS44 4.3 24.6 1.0
CA A:LYS106 4.3 26.2 1.0
OD1 A:ASP105 4.3 34.3 1.0
H A:PHE107 4.3 27.8 1.0
O A:SER104 4.4 22.2 1.0
CE2 A:PHE46 4.6 40.3 1.0
HG3 A:LYS106 4.6 33.0 1.0
O A:HOH527 4.7 34.7 1.0
N A:ASP105 4.8 21.4 1.0
CG A:ASP105 4.9 34.7 1.0
C A:SER104 4.9 25.0 1.0
HD2 A:PHE46 4.9 45.0 1.0
CB A:ASP105 5.0 28.6 1.0

Iodine binding site 3 out of 3 in 6c2i

Go back to Iodine Binding Sites List in 6c2i
Iodine binding site 3 out of 3 in the Structure of Bace-1 (Beta-Secretase) in Complex with : N-(3-((1R,5S, 6R)-3-Amino-5-Methyl-2-Oxa-4-Azabicyclo[4.1.0]Hept-3-En-5-Yl)-4- Fluorophenyl)-5-Methoxypyrazine-2-Carboxamide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Structure of Bace-1 (Beta-Secretase) in Complex with : N-(3-((1R,5S, 6R)-3-Amino-5-Methyl-2-Oxa-4-Azabicyclo[4.1.0]Hept-3-En-5-Yl)-4- Fluorophenyl)-5-Methoxypyrazine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I403

b:29.1
occ:0.36
 O A:HOH675 3.2 21.5 1.0
HE3 A:LYS238 3.2 59.9 1.0
HG3 A:LYS238 3.3 43.5 1.0
HE2 A:TYR221 3.5 32.5 1.0
O A:HOH574 3.7 31.5 1.0
HB3 A:LYS237 3.8 28.8 1.0
O A:HOH785 4.0 20.7 1.0
CE A:LYS238 4.1 49.9 1.0
CG A:LYS238 4.2 36.2 1.0
H A:LYS238 4.2 27.7 1.0
HD2 A:LYS238 4.2 51.2 1.0
HD2 A:TYR221 4.3 28.7 1.0
HD3 A:LYS237 4.3 36.6 1.0
CE2 A:TYR221 4.4 27.0 1.0
CD A:LYS238 4.4 42.6 1.0
HZ1 A:LYS238 4.5 81.7 1.0
HB2 A:LYS238 4.6 31.5 1.0
HE2 A:LYS238 4.7 59.9 1.0
CB A:LYS237 4.8 23.9 1.0
HG2 A:LYS238 4.8 43.5 1.0
CD2 A:TYR221 4.8 23.8 1.0
NZ A:LYS238 4.8 68.0 1.0
N A:LYS238 4.9 23.0 1.0
HZ3 A:LYS238 4.9 81.7 1.0
CB A:LYS238 5.0 26.2 1.0

Reference:

J.D.Low, M.D.Bartberger, Y.Cheng, D.Whittington, Q.Xue, S.Wood, J.R.Allen, A.E.Minatti. Diastereoselective Synthesis of Fused Cyclopropyl-3-Amino-2,4-Oxazine Beta-Amyloid Cleaving Enzyme (Bace) Inhibitors and Their Biological Evaluation. Bioorg. Med. Chem. Lett. V. 28 1111 2018.
ISSN: ESSN 1464-3405
PubMed: 29426770
DOI: 10.1016/J.BMCL.2018.01.056
Page generated: Sun Aug 11 22:46:20 2024

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