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Zinc in PDB 5tfu: Structure of Cytochrome P450 2D6 (CYP2D6) BACE1 Inhibitor Complex

Enzymatic activity of Structure of Cytochrome P450 2D6 (CYP2D6) BACE1 Inhibitor Complex

All present enzymatic activity of Structure of Cytochrome P450 2D6 (CYP2D6) BACE1 Inhibitor Complex:
1.14.14.1;

Protein crystallography data

The structure of Structure of Cytochrome P450 2D6 (CYP2D6) BACE1 Inhibitor Complex, PDB code: 5tfu was solved by M.H.Hsu, E.F.Johnson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.07 / 2.75
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 57.105, 191.756, 246.838, 90.00, 90.00, 90.00
R / Rfree (%) 21.2 / 25

Other elements in 5tfu:

The structure of Structure of Cytochrome P450 2D6 (CYP2D6) BACE1 Inhibitor Complex also contains other interesting chemical elements:

Fluorine (F) 20 atoms
Iron (Fe) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Cytochrome P450 2D6 (CYP2D6) BACE1 Inhibitor Complex (pdb code 5tfu). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Structure of Cytochrome P450 2D6 (CYP2D6) BACE1 Inhibitor Complex, PDB code: 5tfu:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 5tfu

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Zinc binding site 1 out of 5 in the Structure of Cytochrome P450 2D6 (CYP2D6) BACE1 Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Cytochrome P450 2D6 (CYP2D6) BACE1 Inhibitor Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn602

b:31.5
occ:1.00
 OE2 A:GLU273 2.0 33.9 1.0
NE2 A:HIS258 2.0 26.5 1.0
OD2 A:ASP270 2.0 42.8 1.0
CD A:GLU273 2.8 37.5 1.0
CE1 A:HIS258 2.9 36.3 1.0
CG A:ASP270 2.9 33.8 1.0
CD2 A:HIS258 3.1 32.6 1.0
CG A:GLU273 3.1 33.7 1.0
OD1 A:ASP270 3.2 35.3 1.0
O A:CYS191 3.6 44.5 1.0
OE1 A:GLU273 3.9 34.7 1.0
ND1 A:HIS258 4.0 36.6 1.0
CG A:HIS258 4.1 30.1 1.0
C A:CYS191 4.2 32.1 1.0
CB A:ASP270 4.3 31.9 1.0
CB A:GLU273 4.5 29.5 1.0
O A:HOH722 4.5 40.5 1.0
NH2 A:ARG269 4.6 37.8 1.0
CA A:GLY192 4.6 31.3 1.0
CB A:ARG269 4.6 41.2 1.0
N A:GLY192 4.6 36.6 1.0
NE A:ARG269 4.6 58.8 1.0
N A:ASP270 4.8 34.9 1.0

Zinc binding site 2 out of 5 in 5tfu

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Zinc binding site 2 out of 5 in the Structure of Cytochrome P450 2D6 (CYP2D6) BACE1 Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Cytochrome P450 2D6 (CYP2D6) BACE1 Inhibitor Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn603

b:41.4
occ:1.00
 OD2 A:ASP422 2.0 46.2 1.0
OD2 B:ASP422 2.0 41.8 1.0
ND1 B:HIS426 2.0 41.6 1.0
ND1 A:HIS426 2.0 44.5 1.0
CG B:HIS426 3.0 48.9 1.0
CE1 A:HIS426 3.0 48.2 1.0
CG A:HIS426 3.0 47.0 1.0
CE1 B:HIS426 3.0 46.7 1.0
CG B:ASP422 3.1 39.6 1.0
CG A:ASP422 3.1 37.7 1.0
CB B:HIS426 3.2 42.3 1.0
CB A:HIS426 3.4 38.7 1.0
OD1 A:ASP422 3.5 40.0 1.0
OD1 B:ASP422 3.5 41.3 1.0
CB B:GLN424 4.0 51.3 1.0
NE2 A:HIS426 4.1 54.2 1.0
CB A:GLN424 4.1 54.8 1.0
CD2 A:HIS426 4.1 41.8 1.0
CD2 B:HIS426 4.1 46.8 1.0
NE2 B:HIS426 4.1 57.9 1.0
CB B:ASP422 4.3 39.5 1.0
CB A:ASP422 4.3 37.5 1.0
O A:HOH731 4.4 46.6 1.0
CA B:HIS426 4.5 36.0 1.0
CA A:HIS426 4.7 39.0 1.0
N B:HIS426 4.7 37.8 1.0
N A:HIS426 4.8 38.3 1.0
CG B:GLN424 4.8 59.8 1.0
CG A:GLN424 4.8 60.7 1.0

Zinc binding site 3 out of 5 in 5tfu

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Zinc binding site 3 out of 5 in the Structure of Cytochrome P450 2D6 (CYP2D6) BACE1 Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Cytochrome P450 2D6 (CYP2D6) BACE1 Inhibitor Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn602

b:34.1
occ:1.00
 NE2 B:HIS258 1.9 25.3 1.0
OE2 B:GLU273 2.0 32.0 1.0
OD2 B:ASP270 2.0 41.7 1.0
CE1 B:HIS258 2.7 38.6 1.0
CD B:GLU273 2.8 37.3 1.0
CG B:ASP270 3.0 32.9 1.0
CD2 B:HIS258 3.1 31.5 1.0
CG B:GLU273 3.1 36.1 1.0
OD1 B:ASP270 3.3 35.8 1.0
O B:CYS191 3.5 49.9 1.0
OE1 B:GLU273 3.9 36.5 1.0
ND1 B:HIS258 3.9 45.6 1.0
C B:CYS191 4.1 38.0 1.0
CG B:HIS258 4.1 31.6 1.0
O B:HOH702 4.2 38.6 1.0
CB B:ASP270 4.3 31.9 1.0
CA B:GLY192 4.5 32.2 1.0
CB B:GLU273 4.5 32.3 1.0
N B:GLY192 4.6 33.8 1.0
CB B:ARG269 4.6 43.6 1.0
NE B:ARG269 4.6 48.6 1.0
NH2 B:ARG269 4.8 40.0 1.0
N B:ASP270 4.8 34.6 1.0
CA B:CYS191 4.9 34.6 1.0

Zinc binding site 4 out of 5 in 5tfu

Go back to Zinc Binding Sites List in 5tfu
Zinc binding site 4 out of 5 in the Structure of Cytochrome P450 2D6 (CYP2D6) BACE1 Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Cytochrome P450 2D6 (CYP2D6) BACE1 Inhibitor Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn602

b:32.9
occ:1.00
 NE2 C:HIS258 2.0 25.2 1.0
OE2 C:GLU273 2.0 26.5 1.0
OD1 C:ASP270 2.0 45.0 1.0
CE1 C:HIS258 2.8 30.9 1.0
CD C:GLU273 2.8 30.8 1.0
CG C:ASP270 2.9 36.7 1.0
CD2 C:HIS258 3.1 36.0 1.0
CG C:GLU273 3.1 27.2 1.0
OD2 C:ASP270 3.2 30.3 1.0
O C:CYS191 3.5 41.1 1.0
OE1 C:GLU273 4.0 29.4 1.0
ND1 C:HIS258 4.0 32.7 1.0
O C:HOH709 4.1 32.8 1.0
CG C:HIS258 4.2 30.5 1.0
C C:CYS191 4.2 31.4 1.0
CB C:ASP270 4.3 34.1 1.0
CA C:GLY192 4.5 32.1 1.0
CB C:ARG269 4.5 37.4 1.0
CB C:GLU273 4.5 31.2 1.0
NE C:ARG269 4.6 45.3 1.0
N C:GLY192 4.6 37.1 1.0
N C:ASP270 4.8 31.6 1.0
NH2 C:ARG269 5.0 31.6 1.0

Zinc binding site 5 out of 5 in 5tfu

Go back to Zinc Binding Sites List in 5tfu
Zinc binding site 5 out of 5 in the Structure of Cytochrome P450 2D6 (CYP2D6) BACE1 Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Cytochrome P450 2D6 (CYP2D6) BACE1 Inhibitor Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn602

b:39.1
occ:1.00
 NE2 D:HIS258 2.0 27.6 1.0
OE2 D:GLU273 2.0 28.0 1.0
OD2 D:ASP270 2.0 42.2 1.0
CE1 D:HIS258 2.8 31.4 1.0
CD D:GLU273 2.9 31.4 1.0
CG D:ASP270 2.9 38.6 1.0
CD2 D:HIS258 3.1 38.0 1.0
OD1 D:ASP270 3.2 38.1 1.0
CG D:GLU273 3.3 25.4 1.0
O D:CYS191 3.6 44.6 1.0
ND1 D:HIS258 4.0 34.9 1.0
OE1 D:GLU273 4.0 34.5 1.0
O D:HOH717 4.1 40.9 1.0
C D:CYS191 4.1 36.5 1.0
CG D:HIS258 4.2 32.2 1.0
O D:HOH705 4.2 40.3 1.0
CB D:ASP270 4.3 43.4 1.0
CA D:GLY192 4.4 36.2 1.0
NH2 D:ARG269 4.5 33.8 1.0
N D:GLY192 4.5 40.2 1.0
NE D:ARG269 4.6 59.6 1.0
CB D:GLU273 4.6 29.5 1.0
CB D:ARG269 4.7 47.0 1.0
N D:ASP270 4.8 41.2 1.0
CZ D:ARG269 4.9 39.7 1.0

Reference:

C.R.Butler, K.Ogilvie, L.Martinez-Alsina, G.Barreiro, E.M.Beck, C.E.Nolan, K.Atchison, E.Benvenuti, L.Buzon, S.Doran, C.Gonzales, C.J.Helal, X.Hou, M.H.Hsu, E.F.Johnson, K.Lapham, L.Lanyon, K.Parris, B.T.O'neill, D.Riddell, A.Robshaw, F.Vajdos, M.A.Brodney. Aminomethyl-Derived Beta Secretase (BACE1) Inhibitors: Engaging GLY230 Without An Anilide Functionality. J. Med. Chem. V. 60 386 2017.
ISSN: ISSN 1520-4804
PubMed: 27997172
DOI: 10.1021/ACS.JMEDCHEM.6B01451
Page generated: Mon Oct 28 08:30:04 2024

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