Fluorine in PDB 5qad: Oxa-48 in Complex with Compound 8A

All present enzymatic activity of Oxa-48 in Complex with Compound 8A:
3.5.2.6;

The structure of Oxa-48 in Complex with Compound 8A, PDB code: 5qad was solved by B.A.Lund, H.K.S.Leiros, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.88 / 1.75
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	88.919, 108.895, 124.888, 90.00, 90.00, 90.00
R / Rfree (%)	15.7 / 18.4

The structure of Oxa-48 in Complex with Compound 8A also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Fluorine atom in the Oxa-48 in Complex with Compound 8A (pdb code 5qad). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Oxa-48 in Complex with Compound 8A, PDB code: 5qad:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Oxa-48 in Complex with Compound 8A


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Oxa-48 in Complex with Compound 8A within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:37.0 occ:0.87 F A:WVV301 0.0 37.0 0.9 C5 A:WVV301 1.4 24.6 0.9 C6 A:WVV301 2.3 25.5 0.9 C4 A:WVV301 2.4 24.9 0.9 H11 A:EDO307 2.4 60.5 1.0 H1 A:WVV301 2.6 30.6 0.9 H5 A:WVV301 2.6 36.5 0.9 C3 A:WVV301 2.9 36.0 0.9 C10 A:WVV301 3.0 30.4 0.9 C1 A:EDO307 3.5 50.4 1.0 C7 A:WVV301 3.6 33.8 0.9 O A:HOH647 3.6 42.3 1.0 C9 A:WVV301 3.6 26.3 0.9 HD11 A:ILE102 3.6 40.6 1.0 HO1 A:EDO307 3.6 68.3 1.0 HD2 A:TYR211 3.7 23.1 1.0 O1 A:EDO307 3.9 56.9 1.0 HG13 A:ILE102 3.9 29.2 1.0 O A:HOH653 3.9 56.4 1.0 H12 A:EDO307 4.0 60.5 1.0 C2 A:WVV301 4.0 27.3 0.9 HH2 A:TRP105 4.1 17.3 1.0 C8 A:WVV301 4.1 29.5 0.9 C11 A:WVV301 4.2 27.6 0.9 O A:HOH683 4.2 34.8 1.0 HZ2 A:TRP105 4.3 18.1 1.0 CD1 A:ILE102 4.3 33.8 1.0 HD12 A:ILE102 4.3 40.6 1.0 HE2 A:TYR211 4.3 22.4 1.0 CD2 A:TYR211 4.4 19.2 1.0 H A:WVV301 4.5 32.8 0.9 C2 A:EDO307 4.5 50.9 1.0 H2 A:WVV301 4.5 40.5 0.9 H4 A:WVV301 4.5 31.6 0.9 H21 A:EDO307 4.5 61.1 1.0 CH2 A:TRP105 4.5 14.4 1.0 CG1 A:ILE102 4.5 24.3 1.0 O A:HOH624 4.5 50.2 1.0 H22 A:EDO307 4.6 61.1 1.0 CZ2 A:TRP105 4.6 15.0 1.0 H6 A:WVV301 4.7 33.2 0.9 CE2 A:TYR211 4.8 18.6 1.0 O A:HOH408 4.8 27.5 1.0 HG12 A:ILE102 4.8 29.2 1.0 C1 A:WVV301 5.0 28.2 0.9

Fluorine binding site 2 out of 4 in the Oxa-48 in Complex with Compound 8A


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Oxa-48 in Complex with Compound 8A within 5.0Å range: probe atom residue distance (Å) B Occ B:F301 b:34.5 occ:0.87 F B:WVV301 0.0 34.5 0.9 C5 B:WVV301 1.4 35.5 0.9 C6 B:WVV301 2.3 33.0 0.9 C4 B:WVV301 2.4 20.9 0.9 H1 B:WVV301 2.6 39.7 0.9 H5 B:WVV301 2.7 29.9 0.9 C3 B:WVV301 2.9 23.8 0.9 C10 B:WVV301 3.0 24.9 0.9 C7 B:WVV301 3.6 24.9 0.9 HD2 B:TYR211 3.6 22.0 1.0 C9 B:WVV301 3.6 22.4 0.9 O B:HOH636 3.6 28.3 1.0 HD11 B:ILE102 3.7 32.5 1.0 HG13 B:ILE102 3.9 27.7 1.0 C2 B:WVV301 4.0 25.5 0.9 O B:HOH630 4.0 51.6 1.0 C8 B:WVV301 4.1 29.3 0.9 HH2 B:TRP105 4.1 17.3 1.0 C11 B:WVV301 4.2 25.7 0.9 O B:HOH600 4.3 53.5 1.0 HZ2 B:TRP105 4.3 17.4 1.0 HE2 B:TYR211 4.3 20.4 1.0 O B:HOH640 4.3 28.2 1.0 HD12 B:ILE102 4.4 32.5 1.0 CD2 B:TYR211 4.4 18.3 1.0 CD1 B:ILE102 4.4 27.1 1.0 H B:WVV301 4.4 30.6 0.9 H2 B:WVV301 4.5 29.9 0.9 H4 B:WVV301 4.5 27.0 0.9 CH2 B:TRP105 4.5 14.3 1.0 CG1 B:ILE102 4.6 23.0 1.0 CZ2 B:TRP105 4.6 14.5 1.0 CE2 B:TYR211 4.7 17.0 1.0 H6 B:WVV301 4.7 30.9 0.9 O B:HOH412 4.8 22.2 1.0 HG12 B:ILE102 4.9 27.7 1.0 C1 B:WVV301 5.0 34.1 0.9 HB3 B:TYR211 5.0 17.4 1.0

Fluorine binding site 3 out of 4 in the Oxa-48 in Complex with Compound 8A


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Oxa-48 in Complex with Compound 8A within 5.0Å range: probe atom residue distance (Å) B Occ C:F301 b:59.7 occ:0.87 F C:WVV301 0.0 59.7 0.9 C5 C:WVV301 1.4 44.8 0.9 C6 C:WVV301 2.3 47.6 0.9 C4 C:WVV301 2.4 37.1 0.9 H1 C:WVV301 2.6 57.1 0.9 H5 C:WVV301 2.8 45.1 0.9 C3 C:WVV301 2.9 37.4 0.9 C10 C:WVV301 3.0 37.5 0.9 C7 C:WVV301 3.6 40.8 0.9 HD2 C:TYR211 3.6 31.2 1.0 C9 C:WVV301 3.6 37.6 0.9 HD11 C:ILE102 3.6 43.1 1.0 HG13 C:ILE102 3.9 39.7 1.0 C2 C:WVV301 4.0 39.1 0.9 HH2 C:TRP105 4.0 20.7 1.0 HZ2 C:TRP105 4.1 23.3 1.0 C8 C:WVV301 4.1 35.3 0.9 C11 C:WVV301 4.2 36.9 0.9 O C:HOH645 4.3 33.8 1.0 CD1 C:ILE102 4.3 35.9 1.0 HD12 C:ILE102 4.3 43.1 1.0 H C:WVV301 4.4 46.9 0.9 CD2 C:TYR211 4.4 26.0 1.0 O C:HOH408 4.4 36.1 1.0 H2 C:WVV301 4.5 49.0 0.9 CH2 C:TRP105 4.5 17.2 1.0 CZ2 C:TRP105 4.5 19.4 1.0 HE2 C:TYR211 4.5 26.2 1.0 H4 C:WVV301 4.5 45.1 0.9 CG1 C:ILE102 4.6 33.0 1.0 H6 C:WVV301 4.8 44.3 0.9 HB3 C:TYR211 4.8 21.5 1.0 CE2 C:TYR211 4.8 21.8 1.0 HG12 C:ILE102 4.9 39.7 1.0 C1 C:WVV301 4.9 44.5 0.9 O C:HOH414 5.0 29.7 1.0

Fluorine binding site 4 out of 4 in the Oxa-48 in Complex with Compound 8A


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Oxa-48 in Complex with Compound 8A within 5.0Å range: probe atom residue distance (Å) B Occ D:F301 b:53.7 occ:0.87 F D:WVV301 0.0 53.7 0.9 C5 D:WVV301 1.4 48.6 0.9 C6 D:WVV301 2.3 51.0 0.9 C4 D:WVV301 2.4 41.2 0.9 H1 D:WVV301 2.6 61.2 0.9 H5 D:WVV301 2.7 52.2 0.9 C3 D:WVV301 2.9 43.5 0.9 C10 D:WVV301 3.0 43.4 0.9 O D:HOH633 3.2 38.5 1.0 HD11 D:ILE102 3.5 48.5 1.0 C7 D:WVV301 3.6 39.6 0.9 C9 D:WVV301 3.6 39.7 0.9 HD2 D:TYR211 3.7 30.1 1.0 HG13 D:ILE102 3.8 60.6 1.0 HH2 D:TRP105 3.9 27.2 1.0 C2 D:WVV301 4.0 44.1 0.9 HZ2 D:TRP105 4.0 24.0 1.0 O D:HOH629 4.1 43.6 1.0 C8 D:WVV301 4.1 39.8 0.9 CD1 D:ILE102 4.2 40.4 1.0 C11 D:WVV301 4.2 43.1 0.9 HD12 D:ILE102 4.2 48.5 1.0 CH2 D:TRP105 4.3 22.6 1.0 CZ2 D:TRP105 4.4 20.0 1.0 H D:WVV301 4.4 52.9 0.9 CG1 D:ILE102 4.5 50.5 1.0 H2 D:WVV301 4.5 47.6 0.9 H4 D:WVV301 4.5 47.6 0.9 CD2 D:TYR211 4.5 25.1 1.0 O D:HOH408 4.6 29.4 1.0 HE2 D:TYR211 4.7 27.1 1.0 HG12 D:ILE102 4.7 60.6 1.0 H6 D:WVV301 4.7 51.8 0.9 HB3 D:TYR211 4.9 21.5 1.0 C1 D:WVV301 4.9 47.1 0.9

S.Akhter, B.A.Lund, A.Ismael, M.Langer, J.Isaksson, T.Christopeit, H.S.Leiros, A.Bayer. A Focused Fragment Library Targeting the Antibiotic Resistance Enzyme - Oxacillinase-48: Synthesis, Structural Evaluation and Inhibitor Design. Eur J Med Chem V. 145 634 2018.
ISSN: ISSN 1768-3254
PubMed: 29348071
DOI: 10.1016/J.EJMECH.2017.12.085