Fluorine in PDB 6v1p: Structure of Vim-2 Bound to QPX7728 at 1.20 A

The structure of Structure of Vim-2 Bound to QPX7728 at 1.20 A, PDB code: 6v1p was solved by O.A.Pemberton, Y.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.20 / 1.20
Space group	P 21 2 21
Cell size a, b, c (Å), α, β, γ (°)	66.670, 79.120, 77.110, 90.00, 90.00, 90.00
R / Rfree (%)	14.3 / 16.8

The structure of Structure of Vim-2 Bound to QPX7728 at 1.20 A also contains other interesting chemical elements:

Zinc

(Zn)

6 atoms

The binding sites of Fluorine atom in the Structure of Vim-2 Bound to QPX7728 at 1.20 A (pdb code 6v1p). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Structure of Vim-2 Bound to QPX7728 at 1.20 A, PDB code: 6v1p:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Structure of Vim-2 Bound to QPX7728 at 1.20 A


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of Vim-2 Bound to QPX7728 at 1.20 A within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:10.6 occ:1.00 F06 A:QNA401 0.0 10.6 1.0 C05 A:QNA401 1.4 9.3 1.0 C04 A:QNA401 2.4 8.2 1.0 C07 A:QNA401 2.4 9.8 1.0 O01 A:QNA401 2.7 8.2 1.0 C02 A:QNA401 2.8 8.2 1.0 N A:ASN233 3.4 9.0 1.0 NH2 A:ARG228 3.5 12.7 1.0 CA A:GLY232 3.6 9.8 1.0 O A:HOH654 3.6 14.6 1.0 C08 A:QNA401 3.7 10.0 1.0 C10 A:QNA401 3.7 7.8 1.0 CE2 A:TYR67 3.7 10.7 1.0 C3 A:GOL407 3.8 23.5 1.0 C A:GLY232 3.9 9.2 1.0 O A:HOH656 3.9 14.8 1.0 O03 A:QNA401 4.0 7.3 1.0 CZ A:ARG228 4.1 11.1 1.0 CD2 A:TYR67 4.1 10.3 1.0 C09 A:QNA401 4.2 8.9 1.0 O3 A:GOL407 4.3 22.6 1.0 CB A:ASN233 4.3 11.2 1.0 NE A:ARG228 4.4 10.6 1.0 CA A:ASN233 4.4 9.7 1.0 CZ A:TYR67 4.5 10.9 1.0 C2 A:GOL407 4.6 24.2 1.0 C1 A:GOL407 4.7 25.4 1.0 O11 A:QNA401 4.8 7.7 1.0 OH A:TYR67 4.8 13.2 1.0 CD2 A:HIS263 4.8 8.3 1.0 N A:GLY232 4.9 9.7 1.0 NH1 A:ARG228 4.9 11.0 1.0 NE2 A:HIS263 5.0 7.5 1.0

Fluorine binding site 2 out of 2 in the Structure of Vim-2 Bound to QPX7728 at 1.20 A


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of Vim-2 Bound to QPX7728 at 1.20 A within 5.0Å range: probe atom residue distance (Å) B Occ B:F401 b:10.4 occ:1.00 F06 B:QNA401 0.0 10.4 1.0 C05 B:QNA401 1.4 9.1 1.0 C07 B:QNA401 2.4 10.0 1.0 C04 B:QNA401 2.4 8.7 1.0 O01 B:QNA401 2.7 8.3 1.0 C02 B:QNA401 2.9 8.2 1.0 N B:ASN233 3.4 8.9 1.0 NH2 B:ARG228 3.6 12.2 1.0 CA B:GLY232 3.6 10.1 1.0 O B:HOH646 3.6 12.0 1.0 CE2 B:TYR67 3.6 11.2 1.0 C08 B:QNA401 3.7 9.1 1.0 C10 B:QNA401 3.7 8.1 1.0 C3 B:GOL407 3.8 22.3 1.0 O B:HOH647 3.9 13.3 1.0 C B:GLY232 3.9 10.0 1.0 O03 B:QNA401 4.1 7.8 1.0 CD2 B:TYR67 4.1 10.8 1.0 C09 B:QNA401 4.2 8.7 1.0 CZ B:ARG228 4.2 10.4 1.0 CB B:ASN233 4.2 10.7 1.0 O3 B:GOL407 4.3 20.9 1.0 CA B:ASN233 4.4 10.3 1.0 NE B:ARG228 4.5 9.8 1.0 CZ B:TYR67 4.5 11.2 1.0 C2 B:GOL407 4.6 23.4 1.0 C1 B:GOL407 4.7 24.6 1.0 OH B:TYR67 4.7 13.1 1.0 O11 B:QNA401 4.8 7.1 1.0 CD2 B:HIS263 4.8 7.1 1.0 NE2 B:HIS263 5.0 7.0 1.0 N B:GLY232 5.0 9.5 1.0

S.J.Hecker, K.R.Reddy, O.Lomovskaya, D.C.Griffith, D.Rubio-Aparicio, K.Nelson, R.Tsivkovski, D.Sun, M.Sabet, Z.Tarazi, J.Parkinson, M.Totrov, S.H.Boyer, T.W.Glinka, O.A.Pemberton, Y.Chen, M.N.Dudley. Discovery of Cyclic Boronic Acid QPX7728, An Ultra-Broad-Spectrum Inhibitor of Serine and Metallo Beta-Lactamases. J.Med.Chem. 2020.
ISSN: ISSN 0022-2623
PubMed: 32150407
DOI: 10.1021/ACS.JMEDCHEM.9B01976