Atomistry » Iodine » PDB 6axy-6doe » 6c2i
Atomistry »
  Iodine »
    PDB 6axy-6doe »
      6c2i »

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

Last articles

Cl in 3D52
Cl in 3D5K
Cl in 3D4I
Cl in 3D32
Cl in 3D37
Cl in 3D44
Cl in 3D2O
Cl in 3D2Z
Cl in 3D20
Cl in 3D1Z
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy