Bromine in PDB 6o5t: Crystal Structure of Vim-2 with Compound 16

The structure of Crystal Structure of Vim-2 with Compound 16, PDB code: 6o5t was solved by A.Akhtar, Y.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.59 / 2.10
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	102.389, 79.185, 67.501, 90.00, 130.60, 90.00
R / Rfree (%)	17.9 / 23.6

The structure of Crystal Structure of Vim-2 with Compound 16 also contains other interesting chemical elements:

Zinc

(Zn)

8 atoms

The binding sites of Bromine atom in the Crystal Structure of Vim-2 with Compound 16 (pdb code 6o5t). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 6 binding sites of Bromine where determined in the Crystal Structure of Vim-2 with Compound 16, PDB code: 6o5t:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6;

Bromine binding site 1 out of 6 in the Crystal Structure of Vim-2 with Compound 16


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Crystal Structure of Vim-2 with Compound 16 within 5.0Å range: probe atom residue distance (Å) B Occ A:Br503 b:84.9 occ:0.76 BR01 A:L8J503 0.0 84.9 0.8 C02 A:L8J503 1.9 55.1 0.8 C03 A:L8J503 2.9 45.3 0.8 C06 A:L8J503 2.9 52.9 0.8 O B:ASP63 3.2 57.7 1.0 CE2 A:TYR67 4.0 51.3 1.0 OH B:TYR67 4.0 64.5 1.0 CB B:ALA65 4.0 48.4 1.0 C04 A:L8J503 4.2 54.9 0.8 CB B:ASP63 4.2 57.8 1.0 C07 A:L8J503 4.2 59.0 0.8 C B:ASP63 4.3 51.3 1.0 N B:ALA65 4.5 48.8 1.0 CD2 A:TYR67 4.6 46.0 1.0 NE A:ARG205 4.7 42.7 1.0 CD A:ARG205 4.8 27.7 1.0 C08 A:L8J503 4.8 54.4 0.8 CA B:ASP63 4.9 46.9 1.0 CA B:ALA65 4.9 48.2 1.0 CZ A:TYR67 5.0 55.3 1.0

Bromine binding site 2 out of 6 in the Crystal Structure of Vim-2 with Compound 16


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Crystal Structure of Vim-2 with Compound 16 within 5.0Å range: probe atom residue distance (Å) B Occ A:Br503 b:68.0 occ:0.76 BR05 A:L8J503 0.0 68.0 0.8 C04 A:L8J503 1.9 54.9 0.8 C08 A:L8J503 2.9 54.4 0.8 C03 A:L8J503 2.9 45.3 0.8 O12 A:L8J503 3.0 45.6 0.8 C10 A:L8J503 3.1 47.3 0.8 NH2 A:ARG205 3.2 44.3 1.0 C09 A:L8J503 3.2 58.0 0.8 CD2 A:HIS240 3.3 20.4 1.0 NE2 A:HIS240 3.4 24.9 1.0 CG A:HIS240 3.4 22.0 1.0 ND1 A:HIS240 3.4 16.6 1.0 CE1 A:HIS240 3.4 28.1 1.0 P11 A:L8J503 3.6 39.9 0.8 CB A:HIS240 4.1 18.0 1.0 C07 A:L8J503 4.1 59.0 0.8 C02 A:L8J503 4.2 55.1 0.8 CZ A:ARG205 4.2 49.0 1.0 CD2 A:TYR67 4.4 46.0 1.0 O13 A:L8J503 4.5 27.9 0.8 NH1 A:ARG205 4.6 49.0 1.0 CB A:TYR67 4.6 36.5 1.0 CG A:TYR67 4.6 43.5 1.0 C15 A:L8J503 4.6 58.4 0.8 C06 A:L8J503 4.7 52.9 0.8 O14 A:L8J503 4.7 29.9 0.8 ZN A:ZN502 4.8 22.9 1.0 O A:PRO68 4.9 22.8 1.0

Bromine binding site 3 out of 6 in the Crystal Structure of Vim-2 with Compound 16


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Crystal Structure of Vim-2 with Compound 16 within 5.0Å range: probe atom residue distance (Å) B Occ B:Br503 b:82.7 occ:0.48 BR01 B:L8J503 0.0 82.7 0.5 C02 B:L8J503 1.9 61.5 0.5 C06 B:L8J503 2.9 59.7 0.5 C03 B:L8J503 2.9 61.6 0.5 O17 B:L8J503 3.1 65.8 0.5 OD1 B:ASP63 3.4 66.7 1.0 C04 B:L8J503 4.2 58.1 0.5 C07 B:L8J503 4.2 50.5 0.5 C16 B:L8J503 4.3 65.5 0.5 OG A:SER207 4.4 57.0 1.0 CB A:SER207 4.4 56.1 1.0 OD1 B:ASN210 4.4 39.5 1.0 CE1 B:PHE62 4.5 62.4 1.0 CG B:ASP63 4.7 62.6 1.0 CG B:ASN210 4.8 63.6 1.0 C08 B:L8J503 4.8 53.0 0.5

Bromine binding site 4 out of 6 in the Crystal Structure of Vim-2 with Compound 16


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Crystal Structure of Vim-2 with Compound 16 within 5.0Å range: probe atom residue distance (Å) B Occ B:Br503 b:74.2 occ:0.52 BR01 B:L8J503 0.0 74.2 0.5 C02 B:L8J503 1.9 60.5 0.5 C03 B:L8J503 2.9 59.2 0.5 C06 B:L8J503 2.9 57.3 0.5 O A:ASP63 3.6 50.9 1.0 NE B:ARG205 3.9 43.1 1.0 CB A:ASP63 4.2 51.4 1.0 C04 B:L8J503 4.2 56.1 0.5 C07 B:L8J503 4.3 59.5 0.5 CE2 B:TYR67 4.3 52.8 1.0 CA B:GLY209 4.3 52.2 1.0 OH A:TYR67 4.4 66.0 1.0 CD B:ARG205 4.4 35.7 1.0 CZ B:ARG205 4.6 57.7 1.0 C A:ASP63 4.6 43.4 1.0 NH1 B:ARG205 4.7 54.8 1.0 CG B:ARG205 4.8 38.5 1.0 CB A:ALA65 4.8 41.2 1.0 CD2 B:TYR67 4.8 46.8 1.0 C08 B:L8J503 4.8 61.7 0.5 N B:GLY209 4.9 46.4 1.0 O B:SER207 5.0 42.4 1.0

Bromine binding site 5 out of 6 in the Crystal Structure of Vim-2 with Compound 16


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of Crystal Structure of Vim-2 with Compound 16 within 5.0Å range: probe atom residue distance (Å) B Occ B:Br503 b:82.0 occ:0.48 BR05 B:L8J503 0.0 82.0 0.5 C15 B:L8J503 0.7 67.4 0.5 C09 B:L8J503 0.8 65.8 0.5 C10 B:L8J503 1.8 54.8 0.5 C16 B:L8J503 1.9 65.5 0.5 C04 B:L8J503 1.9 58.1 0.5 C08 B:L8J503 2.0 61.7 0.5 N18 B:L8J503 2.6 60.4 0.5 C07 B:L8J503 2.6 59.5 0.5 C08 B:L8J503 2.8 53.0 0.5 O17 B:L8J503 2.9 65.8 0.5 C03 B:L8J503 2.9 61.6 0.5 O14 B:L8J503 3.0 42.1 0.5 P11 B:L8J503 3.0 53.9 0.5 C10 B:L8J503 3.1 45.9 0.5 C09 B:L8J503 3.2 50.6 0.5 C04 B:L8J503 3.3 56.1 0.5 O14 B:L8J503 3.8 47.4 0.5 CB B:ASN210 3.8 53.1 1.0 P11 B:L8J503 3.9 49.6 0.5 BR05 B:L8J503 4.0 73.3 0.5 O13 B:L8J503 4.0 48.1 0.5 C06 B:L8J503 4.0 57.3 0.5 O12 B:L8J503 4.1 42.5 0.5 C07 B:L8J503 4.1 50.5 0.5 C02 B:L8J503 4.2 61.5 0.5 O12 B:L8J503 4.2 42.1 0.5 C03 B:L8J503 4.5 59.2 0.5 CD1 B:PHE62 4.6 62.2 1.0 C15 B:L8J503 4.6 40.6 0.5 C06 B:L8J503 4.7 59.7 0.5 CG B:ASN210 4.7 63.6 1.0 ND2 B:ASN210 4.7 51.8 1.0 C02 B:L8J503 4.8 60.5 0.5 CE1 B:PHE62 4.8 62.4 1.0 N B:ASN210 4.8 57.0 1.0 O B:HOH607 4.9 40.5 1.0 CZ B:TYR67 4.9 50.7 1.0 CA B:ASN210 5.0 51.4 1.0 CE1 B:TYR67 5.0 51.2 1.0

Bromine binding site 6 out of 6 in the Crystal Structure of Vim-2 with Compound 16


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 6 of Crystal Structure of Vim-2 with Compound 16 within 5.0Å range: probe atom residue distance (Å) B Occ B:Br503 b:73.3 occ:0.52 BR05 B:L8J503 0.0 73.3 0.5 C04 B:L8J503 1.9 56.1 0.5 C08 B:L8J503 2.9 61.7 0.5 C03 B:L8J503 2.9 59.2 0.5 O12 B:L8J503 3.0 42.5 0.5 C10 B:L8J503 3.1 54.8 0.5 C09 B:L8J503 3.3 65.8 0.5 NE2 B:HIS240 3.3 28.8 1.0 O B:HOH607 3.4 40.5 1.0 CD2 B:HIS240 3.4 24.0 1.0 CE1 B:HIS240 3.5 29.8 1.0 P11 B:L8J503 3.6 53.9 0.5 CG B:HIS240 3.6 25.1 1.0 ND1 B:HIS240 3.7 22.5 1.0 O12 B:L8J503 3.8 42.1 0.5 NH2 B:ARG205 4.0 43.6 1.0 BR05 B:L8J503 4.0 82.0 0.5 C07 B:L8J503 4.1 59.5 0.5 C02 B:L8J503 4.2 60.5 0.5 NH1 B:ARG205 4.2 54.8 1.0 CZ B:ARG205 4.2 57.7 1.0 ZN B:ZN502 4.3 27.0 1.0 CD2 B:TYR67 4.3 46.8 1.0 O14 B:L8J503 4.4 42.1 0.5 CB B:HIS240 4.5 27.9 1.0 CG B:TYR67 4.5 43.5 1.0 CB B:TYR67 4.6 33.6 1.0 C15 B:L8J503 4.6 67.4 0.5 C06 B:L8J503 4.7 57.3 0.5 O B:HOH652 4.8 25.1 1.0 O13 B:L8J503 4.8 48.1 0.5 P11 B:L8J503 4.9 49.6 0.5 C10 B:L8J503 4.9 45.9 0.5 CE2 B:TYR67 4.9 52.8 1.0

O.A.Pemberton, P.Jaishankar, A.Akhtar, J.L.Adams, L.N.Shaw, A.R.Renslo, Y.Chen. Heteroaryl Phosphonates As Noncovalent Inhibitors of Both Serine- and Metallocarbapenemases. J.Med.Chem. V. 62 8480 2019.
ISSN: ISSN 0022-2623
PubMed: 31483651
DOI: 10.1021/ACS.JMEDCHEM.9B00728