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Iodine in PDB 4wy6: Crystal Structure of Human Bace-1 Bound to Compound 36

Enzymatic activity of Crystal Structure of Human Bace-1 Bound to Compound 36

All present enzymatic activity of Crystal Structure of Human Bace-1 Bound to Compound 36:
3.4.23.46;

Protein crystallography data

The structure of Crystal Structure of Human Bace-1 Bound to Compound 36, PDB code: 4wy6 was solved by F.F.Vajdos, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.41 / 2.10
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 102.871, 102.871, 170.884, 90.00, 90.00, 120.00
R / Rfree (%) 18.5 / 20.1

Other elements in 4wy6:

The structure of Crystal Structure of Human Bace-1 Bound to Compound 36 also contains other interesting chemical elements:

Fluorine (F) 3 atoms

Iodine Binding Sites:

The binding sites of Iodine atom in the Crystal Structure of Human Bace-1 Bound to Compound 36 (pdb code 4wy6). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 5 binding sites of Iodine where determined in the Crystal Structure of Human Bace-1 Bound to Compound 36, PDB code: 4wy6:
Jump to Iodine binding site number: 1; 2; 3; 4; 5;

Iodine binding site 1 out of 5 in 4wy6

Go back to Iodine Binding Sites List in 4wy6
Iodine binding site 1 out of 5 in the Crystal Structure of Human Bace-1 Bound to Compound 36


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 Human Bace-1 Bound to Compound 36 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I402

b:42.7
occ:1.00
 O A:HOH770 3.4 34.8 1.0
OG A:SER105 3.5 33.7 1.0
O A:HOH563 3.5 40.8 1.0
CD2 A:HIS45 3.8 36.2 1.0
CA A:GLU104 3.9 29.9 1.0
N A:SER105 3.9 29.1 1.0
N A:GLU104 3.9 30.6 1.0
C A:GLU104 4.0 32.4 1.0
C A:THR103 4.0 35.1 1.0
O A:THR103 4.1 36.2 1.0
CE2 A:PHE109 4.1 34.2 1.0
CG2 A:ILE102 4.3 29.7 1.0
CB A:SER105 4.3 30.1 1.0
CB A:HIS45 4.4 30.9 1.0
CG A:HIS45 4.4 34.2 1.0
O A:ILE102 4.6 31.6 1.0
CA A:SER105 4.7 28.9 1.0
CD2 A:PHE109 4.7 32.7 1.0
O A:GLU104 4.7 32.2 1.0
CA A:THR103 4.8 31.9 1.0
C A:ILE102 4.9 32.5 1.0
NE2 A:HIS45 4.9 36.3 1.0
N A:THR103 4.9 31.4 1.0
CB A:ALA43 5.0 34.0 1.0

Iodine binding site 2 out of 5 in 4wy6

Go back to Iodine Binding Sites List in 4wy6
Iodine binding site 2 out of 5 in the Crystal Structure of Human Bace-1 Bound to Compound 36


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 Human Bace-1 Bound to Compound 36 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I403

b:59.6
occ:0.50
 O A:HOH549 3.1 30.8 1.0
O A:HOH501 3.5 50.1 1.0
CE A:LYS239 4.1 70.8 1.0
CE2 A:TYR222 4.2 36.4 1.0
O A:HOH605 4.3 35.3 1.0
NZ A:LYS239 4.5 78.0 1.0
CB A:LYS239 4.6 37.7 1.0
CD2 A:TYR222 4.7 35.0 1.0
N A:LYS239 4.8 33.5 1.0
CB A:LYS238 4.9 32.1 1.0
O A:HOH600 5.0 31.3 1.0

Iodine binding site 3 out of 5 in 4wy6

Go back to Iodine Binding Sites List in 4wy6
Iodine binding site 3 out of 5 in the Crystal Structure of Human Bace-1 Bound to Compound 36


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 Human Bace-1 Bound to Compound 36 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I404

b:66.1
occ:1.00
 O A:HOH575 3.2 65.2 1.0
O A:HOH524 3.4 34.6 1.0
O A:HOH769 3.5 28.7 1.0
N A:LYS107 3.6 30.1 1.0
O A:HOH533 3.7 50.6 1.0
NE2 A:HIS45 4.1 36.3 1.0
CA A:ASP106 4.3 31.3 1.0
CE2 A:PHE47 4.3 47.9 1.0
CA A:LYS107 4.3 29.7 1.0
OD1 A:ASP106 4.4 54.0 1.0
C A:ASP106 4.4 33.1 1.0
O A:SER105 4.5 32.2 1.0
CE1 A:HIS45 4.6 36.0 1.0
CZ A:PHE47 4.8 46.1 1.0

Iodine binding site 4 out of 5 in 4wy6

Go back to Iodine Binding Sites List in 4wy6
Iodine binding site 4 out of 5 in the Crystal Structure of Human Bace-1 Bound to Compound 36


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 Human Bace-1 Bound to Compound 36 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I405

b:0.5
occ:1.00
 NH1 A:ARG349 3.2 69.2 1.0
O A:HOH516 3.5 47.1 1.0
O A:HOH519 3.6 30.5 1.0
CZ A:ARG349 4.0 80.9 1.0
NH2 A:ARG349 4.1 70.4 1.0
CD1 A:LEU149 4.6 39.6 1.0
CD1 A:ILE179 4.8 45.9 1.0
OD2 A:ASP346 4.9 44.3 1.0

Iodine binding site 5 out of 5 in 4wy6

Go back to Iodine Binding Sites List in 4wy6
Iodine binding site 5 out of 5 in the Crystal Structure of Human Bace-1 Bound to Compound 36


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 Human Bace-1 Bound to Compound 36 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I406

b:0.7
occ:1.00
 O A:ARG96 3.5 35.9 1.0
NE2 A:GLN143 4.1 38.1 1.0
O A:HOH715 4.1 44.7 1.0
OE2 A:GLU134 4.2 51.0 1.0
O A:HOH736 4.2 54.1 1.0
C A:ARG96 4.4 38.1 1.0
OG A:SER139 4.4 42.6 1.0
CG2 A:THR82 4.6 36.6 1.0
CG A:ARG96 4.6 39.9 1.0
CA A:ALA97 4.8 33.5 1.0
OD1 A:ASN98 4.8 37.0 1.0
ND2 A:ASN98 4.9 29.8 1.0
O A:HOH617 4.9 36.1 1.0
CB A:ARG96 4.9 36.5 1.0
N A:ASN98 5.0 29.6 1.0
N A:ALA97 5.0 34.3 1.0

Reference:

C.R.Butler, M.A.Brodney, E.M.Beck, G.Barreiro, C.E.Nolan, F.Pan, F.F.Vajdos, K.Parris, A.H.Varghese, C.J.Helal, R.Lira, S.D.Doran, D.Riddell, L.M.Buzon, J.K.Dutra, L.A.Martinez-Alsina, K.Ogilvie, J.C.Murray, J.M.Young, K.Atchison, A.Robshaw, C.Gonzales, J.Wang, Y.Zhang, B.T.O'neill. Discovery of A Series of Efficient, Centrally Efficacious BACE1 Inhibitors Through Structure-Based Drug Design. J.Med.Chem. 2015.
ISSN: ISSN 0022-2623
PubMed: 25695670
DOI: 10.1021/JM501833T
Page generated: Sun Aug 11 20:09:14 2024

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