Bromine in PDB 6d19: Crystal Structure of Kpc-2 Complexed with Compound 9

All present enzymatic activity of Crystal Structure of Kpc-2 Complexed with Compound 9:
3.5.2.6;

The structure of Crystal Structure of Kpc-2 Complexed with Compound 9, PDB code: 6d19 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)	41.05 / 1.45
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.500, 59.740, 77.620, 90.00, 90.00, 90.00
R / Rfree (%)	15.6 / 19.4

The binding sites of Bromine atom in the Crystal Structure of Kpc-2 Complexed with Compound 9 (pdb code 6d19). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 3 binding sites of Bromine where determined in the Crystal Structure of Kpc-2 Complexed with Compound 9, PDB code: 6d19:
Jump to Bromine binding site number: 1; 2; 3;

Bromine binding site 1 out of 3 in the Crystal Structure of Kpc-2 Complexed with Compound 9


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 Kpc-2 Complexed with Compound 9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Br301 b:28.7 occ:0.81 BR05 A:YKG301 0.0 28.7 0.8 C04 A:YKG301 1.9 29.4 0.8 C03 A:YKG301 2.7 29.5 0.8 C06 A:YKG301 2.9 26.1 0.8 C08 A:YKG301 3.1 22.3 0.8 C07 A:YKG301 3.4 23.4 0.8 O A:HOH412 3.5 31.1 1.0 O12 A:YKG301 3.5 19.5 0.8 CD1 A:TRP105 3.5 33.6 1.0 O A:SER130 3.5 23.6 1.0 CG A:TRP105 3.5 35.9 1.0 OG A:SER70 3.6 21.3 1.0 OG A:SER130 3.6 23.1 1.0 NE1 A:TRP105 3.7 35.6 1.0 NZ A:LYS73 3.7 21.5 1.0 CB A:SER130 3.8 22.7 1.0 CD2 A:TRP105 3.8 38.4 1.0 O A:HOH541 3.9 27.8 1.0 CE2 A:TRP105 3.9 38.5 1.0 P09 A:YKG301 3.9 18.7 0.8 C02 A:YKG301 4.0 31.1 0.8 ND2 A:ASN132 4.1 26.2 1.0 CB A:TRP105 4.1 31.5 1.0 C17 A:YKG301 4.2 28.1 0.8 O11 A:YKG301 4.3 19.2 0.8 OD1 A:ASN132 4.3 23.2 1.0 C A:SER130 4.5 22.3 1.0 CG A:ASN132 4.5 21.7 1.0 CE3 A:TRP105 4.5 40.4 1.0 C18 A:YKG301 4.6 30.0 0.8 CB A:SER70 4.7 19.1 1.0 CZ2 A:TRP105 4.7 40.6 1.0 CA A:SER130 4.7 20.5 1.0 C13 A:YKG301 4.8 24.0 0.8 O A:TRP105 5.0 26.3 1.0

Bromine binding site 2 out of 3 in the Crystal Structure of Kpc-2 Complexed with Compound 9


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 Kpc-2 Complexed with Compound 9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Br302 b:98.3 occ:0.82 BR05 A:YKG302 0.0 98.3 0.8 C04 A:YKG302 1.9 93.7 0.8 C03 A:YKG302 2.8 92.3 0.8 C06 A:YKG302 2.9 91.1 0.8 C08 A:YKG302 3.0 92.3 0.8 C07 A:YKG302 3.3 90.7 0.8 CZ2 A:TRP165 3.5 30.3 1.0 CH2 A:TRP165 3.6 29.3 1.0 CE2 A:TRP165 4.0 28.8 1.0 C17 A:YKG302 4.1 89.7 0.8 C02 A:YKG302 4.1 91.2 0.8 CZ3 A:TRP165 4.2 30.1 1.0 O11 A:YKG302 4.2 95.4 0.8 P09 A:YKG302 4.2 94.5 0.8 CD2 A:TRP165 4.5 27.5 1.0 O12 A:YKG302 4.6 94.9 0.8 CE3 A:TRP165 4.6 28.4 1.0 C18 A:YKG302 4.6 90.4 0.8 NE1 A:TRP165 4.6 29.9 1.0 C13 A:YKG302 4.7 89.0 0.8

Bromine binding site 3 out of 3 in the Crystal Structure of Kpc-2 Complexed with Compound 9


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 Kpc-2 Complexed with Compound 9 within 5.0Å range: probe atom residue distance (Å) B Occ A:Br303 b:84.9 occ:0.78 BR05 A:YKG303 0.0 84.9 0.8 C04 A:YKG303 1.9 80.6 0.8 C03 A:YKG303 2.8 78.8 0.8 C06 A:YKG303 2.8 78.3 0.8 C08 A:YKG303 3.0 81.0 0.8 C07 A:YKG303 3.2 79.1 0.8 CB A:ALA82 3.9 30.3 1.0 C17 A:YKG303 4.0 76.3 0.8 CD1 A:PHE151 4.0 26.6 1.0 C02 A:YKG303 4.0 77.6 0.8 O11 A:YKG303 4.1 83.9 0.8 P09 A:YKG303 4.2 83.4 0.8 NE A:ARG83 4.2 61.9 1.0 C A:ALA82 4.3 35.1 1.0 N A:ARG83 4.3 39.0 1.0 CE1 A:PHE151 4.4 27.0 1.0 CG A:ARG83 4.4 53.8 1.0 O A:ALA82 4.5 36.1 1.0 C13 A:YKG303 4.5 78.0 0.8 C18 A:YKG303 4.5 76.8 0.8 CA A:ARG83 4.6 41.9 1.0 O10 A:YKG303 4.7 83.2 0.8 CD A:ARG83 4.8 58.0 1.0 CA A:ALA82 4.8 32.0 1.0 CZ A:ARG83 4.9 64.3 1.0 NH2 A:ARG83 4.9 64.9 1.0 O A:ALA79 5.0 28.6 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