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Fluorine in PDB 6dmi: A Multiconformer Ligand Model of 5T5 Bound to Bace-1

Enzymatic activity of A Multiconformer Ligand Model of 5T5 Bound to Bace-1

All present enzymatic activity of A Multiconformer Ligand Model of 5T5 Bound to Bace-1:
3.4.23.46;

Protein crystallography data

The structure of A Multiconformer Ligand Model of 5T5 Bound to Bace-1, PDB code: 6dmi was solved by B.M.Hudson, G.Van Zundert, D.Keedy, R.Fonseca, A.Heliou, P.Suresh, K.Borrelli, T.Day, J.S.Fraser, H.Van Den Bedem, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.70 / 1.90
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 102.320, 102.320, 169.820, 90.00, 90.00, 120.00
R / Rfree (%) 19.2 / 22.6

Other elements in 6dmi:

The structure of A Multiconformer Ligand Model of 5T5 Bound to Bace-1 also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms
Sodium (Na) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the A Multiconformer Ligand Model of 5T5 Bound to Bace-1 (pdb code 6dmi). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the A Multiconformer Ligand Model of 5T5 Bound to Bace-1, PDB code: 6dmi:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 6dmi

Go back to Fluorine Binding Sites List in 6dmi
Fluorine binding site 1 out of 6 in the A Multiconformer Ligand Model of 5T5 Bound to Bace-1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of A Multiconformer Ligand Model of 5T5 Bound to Bace-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F504

b:33.5
occ:0.32
 F23 A:5T5504 0.0 33.5 0.3
F23 A:5T5504 1.2 33.3 0.3
C12 A:5T5504 1.4 34.0 0.3
C12 A:5T5504 1.9 31.9 0.3
F23 A:5T5504 2.1 31.8 0.3
F24 A:5T5504 2.3 37.0 0.3
O16 A:5T5504 2.3 35.1 0.3
C12 A:5T5504 2.7 29.4 0.3
O16 A:5T5504 2.8 34.8 0.3
C21 A:5T5504 2.9 33.4 0.3
C25 A:5T5504 2.9 29.4 0.3
O A:HOH769 2.9 34.7 1.0
F24 A:5T5504 3.0 27.9 0.3
O16 A:5T5504 3.1 32.1 0.3
O A:HOH765 3.3 37.5 1.0
C26 A:5T5504 3.4 28.7 0.3
C25 A:5T5504 3.5 29.3 0.3
C21 A:5T5504 3.5 30.6 0.3
C21 A:5T5504 3.6 32.0 0.3
NH2 A:ARG189 3.7 53.0 1.0
CZ A:ARG189 3.8 57.1 1.0
NE A:ARG189 3.9 45.9 1.0
CB A:SER96 4.0 22.1 1.0
F24 A:5T5504 4.0 31.1 0.3
C26 A:5T5504 4.1 31.2 0.3
C18 A:5T5504 4.2 28.2 0.3
CG A:ARG189 4.2 36.0 1.0
CG1 A:VAL130 4.5 38.8 1.0
O A:ILE187 4.5 24.4 1.0
C19 A:5T5504 4.5 27.9 0.3
NH1 A:ARG189 4.5 52.4 1.0
C25 A:5T5504 4.6 31.6 0.3
CD A:ARG189 4.7 37.4 1.0
C18 A:5T5504 4.8 28.1 0.3
O A:HOH675 4.8 17.0 1.0
OD1 A:ASN98 4.8 26.0 1.0
CA A:SER96 4.9 19.8 1.0
C26 A:5T5504 5.0 31.6 0.3

Fluorine binding site 2 out of 6 in 6dmi

Go back to Fluorine Binding Sites List in 6dmi
Fluorine binding site 2 out of 6 in the A Multiconformer Ligand Model of 5T5 Bound to Bace-1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of A Multiconformer Ligand Model of 5T5 Bound to Bace-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F504

b:31.8
occ:0.34
 F23 A:5T5504 0.0 31.8 0.3
C12 A:5T5504 1.4 29.4 0.3
F23 A:5T5504 1.6 33.3 0.3
F24 A:5T5504 1.7 27.9 0.3
C12 A:5T5504 1.8 31.9 0.3
F23 A:5T5504 2.1 33.5 0.3
F24 A:5T5504 2.2 31.1 0.3
O16 A:5T5504 2.3 32.1 0.3
C12 A:5T5504 2.6 34.0 0.3
O A:HOH769 2.8 34.7 1.0
O16 A:5T5504 2.9 35.1 0.3
O16 A:5T5504 3.2 34.8 0.3
OD1 A:ASN98 3.3 26.0 1.0
C21 A:5T5504 3.4 30.6 0.3
C26 A:5T5504 3.6 28.7 0.3
CG A:ARG189 3.6 36.0 1.0
C21 A:5T5504 3.6 33.4 0.3
O A:HOH675 3.7 17.0 1.0
CG1 A:VAL130 3.9 38.8 1.0
F24 A:5T5504 4.0 37.0 0.3
CG A:ASN98 4.0 24.9 1.0
CB A:ASN98 4.1 21.3 1.0
C21 A:5T5504 4.2 32.0 0.3
CZ2 A:TRP137 4.2 26.6 1.0
C25 A:5T5504 4.2 29.4 0.3
NE1 A:TRP137 4.3 32.0 1.0
C26 A:5T5504 4.4 31.2 0.3
C25 A:5T5504 4.4 29.3 0.3
CB A:SER96 4.5 22.1 1.0
NE A:ARG189 4.5 45.9 1.0
CB A:ARG189 4.5 35.7 1.0
CE2 A:TRP137 4.6 31.9 1.0
CD A:ARG189 4.7 37.4 1.0
C25 A:5T5504 4.7 31.6 0.3
N A:ASN98 4.7 20.6 1.0
CZ A:ARG189 4.8 57.1 1.0
CG2 A:VAL130 4.9 32.7 1.0
N A:ARG189 4.9 30.1 1.0
O A:ILE187 4.9 24.4 1.0
C19 A:5T5504 5.0 27.9 0.3
CB A:VAL130 5.0 38.0 1.0
N A:SER97 5.0 15.5 1.0

Fluorine binding site 3 out of 6 in 6dmi

Go back to Fluorine Binding Sites List in 6dmi
Fluorine binding site 3 out of 6 in the A Multiconformer Ligand Model of 5T5 Bound to Bace-1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of A Multiconformer Ligand Model of 5T5 Bound to Bace-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F504

b:33.3
occ:0.34
 F23 A:5T5504 0.0 33.3 0.3
C12 A:5T5504 1.1 34.0 0.3
F23 A:5T5504 1.2 33.5 0.3
C12 A:5T5504 1.4 31.9 0.3
F23 A:5T5504 1.6 31.8 0.3
O16 A:5T5504 1.6 35.1 0.3
C12 A:5T5504 2.3 29.4 0.3
F24 A:5T5504 2.3 27.9 0.3
O16 A:5T5504 2.3 34.8 0.3
O16 A:5T5504 2.3 32.1 0.3
F24 A:5T5504 2.4 37.0 0.3
C21 A:5T5504 2.7 33.4 0.3
C21 A:5T5504 3.2 30.6 0.3
CG1 A:VAL130 3.3 38.8 1.0
C25 A:5T5504 3.3 29.4 0.3
F24 A:5T5504 3.4 31.1 0.3
C21 A:5T5504 3.4 32.0 0.3
C26 A:5T5504 3.5 28.7 0.3
O A:HOH769 3.6 34.7 1.0
CZ A:ARG189 3.7 57.1 1.0
CG A:ARG189 3.7 36.0 1.0
C26 A:5T5504 3.7 31.2 0.3
C25 A:5T5504 3.8 29.3 0.3
NE A:ARG189 3.8 45.9 1.0
NH2 A:ARG189 3.9 53.0 1.0
NH1 A:ARG189 4.1 52.4 1.0
C25 A:5T5504 4.2 31.6 0.3
CD A:ARG189 4.4 37.4 1.0
NE1 A:TRP137 4.5 32.0 1.0
O A:HOH765 4.5 37.5 1.0
OD1 A:ASN98 4.6 26.0 1.0
CB A:VAL130 4.6 38.0 1.0
C18 A:5T5504 4.7 28.2 0.3
C26 A:5T5504 4.7 31.6 0.3
C19 A:5T5504 4.8 27.9 0.3
CB A:SER96 4.9 22.1 1.0
O A:HOH675 4.9 17.0 1.0
CG2 A:VAL130 4.9 32.7 1.0
C19 A:5T5504 5.0 30.1 0.3
CB A:ARG189 5.0 35.7 1.0

Fluorine binding site 4 out of 6 in 6dmi

Go back to Fluorine Binding Sites List in 6dmi
Fluorine binding site 4 out of 6 in the A Multiconformer Ligand Model of 5T5 Bound to Bace-1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of A Multiconformer Ligand Model of 5T5 Bound to Bace-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F504

b:37.0
occ:0.32
 F24 A:5T5504 0.0 37.0 0.3
C12 A:5T5504 1.4 34.0 0.3
F23 A:5T5504 2.3 33.5 0.3
O16 A:5T5504 2.3 35.1 0.3
F23 A:5T5504 2.4 33.3 0.3
NH2 A:ARG189 2.5 53.0 1.0
C21 A:5T5504 2.9 33.4 0.3
C25 A:5T5504 2.9 29.4 0.3
O16 A:5T5504 3.0 34.8 0.3
CZ A:ARG189 3.1 57.1 1.0
C12 A:5T5504 3.1 31.9 0.3
NH1 A:ARG189 3.5 52.4 1.0
C21 A:5T5504 3.7 32.0 0.3
C25 A:5T5504 3.8 29.3 0.3
O A:HOH765 3.8 37.5 1.0
NE A:ARG189 3.9 45.9 1.0
F23 A:5T5504 4.0 31.8 0.3
O16 A:5T5504 4.1 32.1 0.3
C26 A:5T5504 4.2 31.2 0.3
C18 A:5T5504 4.2 28.2 0.3
C21 A:5T5504 4.2 30.6 0.3
CG1 A:VAL130 4.3 38.8 1.0
F24 A:5T5504 4.4 27.9 0.3
C12 A:5T5504 4.5 29.4 0.3
C26 A:5T5504 4.5 28.7 0.3
O A:PRO131 4.6 51.3 1.0
CB A:TYR132 4.6 58.8 1.0
CD1 A:TYR132 4.7 49.6 1.0
C25 A:5T5504 4.8 31.6 0.3
C26 A:5T5504 4.9 31.6 0.3
C18 A:5T5504 5.0 28.1 0.3

Fluorine binding site 5 out of 6 in 6dmi

Go back to Fluorine Binding Sites List in 6dmi
Fluorine binding site 5 out of 6 in the A Multiconformer Ligand Model of 5T5 Bound to Bace-1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of A Multiconformer Ligand Model of 5T5 Bound to Bace-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F504

b:31.1
occ:0.34
 F24 A:5T5504 0.0 31.1 0.3
C12 A:5T5504 1.4 29.4 0.3
F24 A:5T5504 1.4 27.9 0.3
F23 A:5T5504 2.2 31.8 0.3
O16 A:5T5504 2.2 32.1 0.3
C12 A:5T5504 2.8 31.9 0.3
O A:HOH675 2.8 17.0 1.0
CZ2 A:TRP137 2.9 26.6 1.0
NE1 A:TRP137 3.1 32.0 1.0
CB A:ASN98 3.2 21.3 1.0
C21 A:5T5504 3.3 30.6 0.3
CE2 A:TRP137 3.3 31.9 1.0
F23 A:5T5504 3.4 33.3 0.3
C26 A:5T5504 3.6 28.7 0.3
O16 A:5T5504 3.7 34.8 0.3
OD1 A:ASN98 3.8 26.0 1.0
CG A:ASN98 3.8 24.9 1.0
O16 A:5T5504 3.9 35.1 0.3
F23 A:5T5504 4.0 33.5 0.3
CD1 A:ILE179 4.0 30.9 1.0
CH2 A:TRP137 4.1 31.2 1.0
C21 A:5T5504 4.3 33.4 0.3
CA A:ASN98 4.3 19.0 1.0
O A:HOH769 4.3 34.7 1.0
C26 A:5T5504 4.3 31.2 0.3
CD1 A:TRP137 4.4 35.8 1.0
C25 A:5T5504 4.4 31.6 0.3
C12 A:5T5504 4.4 34.0 0.3
O A:ASN98 4.4 18.0 1.0
CB A:ALA100 4.4 19.0 1.0
C21 A:5T5504 4.4 32.0 0.3
N A:ASN98 4.4 20.6 1.0
CD2 A:TRP137 4.7 29.6 1.0
C A:ASN98 4.7 18.6 1.0
CG1 A:VAL130 4.7 38.8 1.0
CG1 A:ILE179 4.7 28.1 1.0
ND2 A:ASN98 4.8 23.0 1.0
C19 A:5T5504 4.9 27.9 0.3
CB A:SER96 4.9 22.1 1.0
C25 A:5T5504 5.0 29.3 0.3
OG A:SER96 5.0 16.9 1.0

Fluorine binding site 6 out of 6 in 6dmi

Go back to Fluorine Binding Sites List in 6dmi
Fluorine binding site 6 out of 6 in the A Multiconformer Ligand Model of 5T5 Bound to Bace-1


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of A Multiconformer Ligand Model of 5T5 Bound to Bace-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F504

b:27.9
occ:0.34
 F24 A:5T5504 0.0 27.9 0.3
C12 A:5T5504 0.6 29.4 0.3
O16 A:5T5504 0.9 32.1 0.3
C12 A:5T5504 1.4 31.9 0.3
F24 A:5T5504 1.4 31.1 0.3
F23 A:5T5504 1.7 31.8 0.3
C21 A:5T5504 2.1 30.6 0.3
F23 A:5T5504 2.3 33.3 0.3
O16 A:5T5504 2.3 34.8 0.3
O16 A:5T5504 2.5 35.1 0.3
C26 A:5T5504 2.7 28.7 0.3
C21 A:5T5504 2.9 33.4 0.3
NE1 A:TRP137 2.9 32.0 1.0
F23 A:5T5504 3.0 33.5 0.3
C26 A:5T5504 3.1 31.2 0.3
C12 A:5T5504 3.1 34.0 0.3
C21 A:5T5504 3.1 32.0 0.3
C25 A:5T5504 3.3 31.6 0.3
O A:HOH675 3.4 17.0 1.0
CE2 A:TRP137 3.6 31.9 1.0
CZ2 A:TRP137 3.6 26.6 1.0
C25 A:5T5504 3.8 29.3 0.3
C25 A:5T5504 3.9 29.4 0.3
CG1 A:VAL130 3.9 38.8 1.0
C26 A:5T5504 4.0 31.6 0.3
C19 A:5T5504 4.0 27.9 0.3
CD1 A:TRP137 4.1 35.8 1.0
C19 A:5T5504 4.2 30.1 0.3
O A:HOH769 4.2 34.7 1.0
CD1 A:ILE179 4.3 30.9 1.0
F24 A:5T5504 4.4 37.0 0.3
CB A:ASN98 4.5 21.3 1.0
C18 A:5T5504 4.5 31.0 0.3
OD1 A:ASN98 4.5 26.0 1.0
CB A:SER96 4.6 22.1 1.0
C18 A:5T5504 4.8 28.2 0.3
C11 A:5T5504 4.8 27.0 0.3
CG A:ASN98 4.8 24.9 1.0
CB A:VAL130 4.9 38.0 1.0
OG A:SER96 4.9 16.9 1.0
C11 A:5T5504 4.9 28.4 0.3
C18 A:5T5504 4.9 28.1 0.3
CD2 A:TRP137 5.0 29.6 1.0
CH2 A:TRP137 5.0 31.2 1.0

Reference:

G.C.P.Van Zundert, B.M.Hudson, S.H.P.De Oliveira, D.A.Keedy, R.Fonseca, A.Heliou, P.Suresh, K.Borrelli, T.Day, J.S.Fraser, H.Van Den Bedem. Qfit-Ligand Reveals Widespread Conformational Heterogeneity of Drug-Like Molecules in X-Ray Electron Density Maps. J. Med. Chem. V. 61 11183 2018.
ISSN: ISSN 1520-4804
PubMed: 30457858
DOI: 10.1021/ACS.JMEDCHEM.8B01292
Page generated: Tue Jul 15 10:50:18 2025

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