Bromine in PDB 3doy: Crystal Structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (Fabz) From Helicobacter Pylori in Complex with Compound 3I

The structure of Crystal Structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (Fabz) From Helicobacter Pylori in Complex with Compound 3I, PDB code: 3doy was solved by L.Zhang, L.He, X.Liu, H.Liu, X.Shen, H.Jiang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	73.975, 100.370, 186.622, 90.00, 90.00, 90.00
R / Rfree (%)	20 / 23.8

The structure of Crystal Structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (Fabz) From Helicobacter Pylori in Complex with Compound 3I also contains other interesting chemical elements:

Chlorine

(Cl)

8 atoms

The binding sites of Bromine atom in the Crystal Structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (Fabz) From Helicobacter Pylori in Complex with Compound 3I (pdb code 3doy). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 4 binding sites of Bromine where determined in the Crystal Structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (Fabz) From Helicobacter Pylori in Complex with Compound 3I, PDB code: 3doy:
Jump to Bromine binding site number: 1; 2; 3; 4;

Bromine binding site 1 out of 4 in the Crystal Structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (Fabz) From Helicobacter Pylori in Complex with Compound 3I


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 (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (Fabz) From Helicobacter Pylori in Complex with Compound 3I within 5.0Å range: probe atom residue distance (Å) B Occ A:Br3001 b:59.1 occ:1.00 BRAE A:2BE3001 0.0 59.1 1.0 CAS A:2BE3001 1.9 60.1 1.0 CAQ A:2BE3001 2.8 61.8 1.0 CAL A:2BE3001 2.9 59.3 1.0 OAB A:2BE3001 3.0 63.1 1.0 CB A:PHE59 3.7 16.2 1.0 CG A:PHE59 3.7 15.1 1.0 O A:HOH3206 3.8 25.3 1.0 CB B:PRO22 3.9 15.6 1.0 CD2 A:PHE59 3.9 14.1 1.0 NE B:ARG158 4.0 36.0 1.0 CZ B:ARG158 4.1 36.1 1.0 CAV A:2BE3001 4.2 61.1 1.0 CAU A:2BE3001 4.2 57.4 1.0 CD1 A:PHE59 4.2 15.3 1.0 NH2 B:ARG158 4.3 36.0 1.0 CD B:ARG158 4.5 34.9 1.0 CG B:PRO22 4.5 16.0 1.0 CB A:LYS62 4.5 24.8 1.0 CD1 B:ILE98 4.5 24.6 1.0 CE2 A:PHE59 4.6 15.2 1.0 CAR A:2BE3001 4.7 60.1 1.0 NH1 B:ARG158 4.7 36.3 1.0 CE1 A:PHE59 4.9 16.2 1.0 CG B:ARG158 5.0 33.3 1.0

Bromine binding site 2 out of 4 in the Crystal Structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (Fabz) From Helicobacter Pylori in Complex with Compound 3I


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 (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (Fabz) From Helicobacter Pylori in Complex with Compound 3I within 5.0Å range: probe atom residue distance (Å) B Occ A:Br3001 b:64.2 occ:1.00 BRAF A:2BE3001 0.0 64.2 1.0 CAV A:2BE3001 1.9 61.1 1.0 CAQ A:2BE3001 2.9 61.8 1.0 CAR A:2BE3001 2.9 60.1 1.0 OAB A:2BE3001 3.0 63.1 1.0 OAC A:2BE3001 3.0 60.5 1.0 C B:ARG158 3.7 31.5 1.0 CG B:ARG158 4.0 33.3 1.0 CAS A:2BE3001 4.2 60.1 1.0 CAU A:2BE3001 4.2 57.4 1.0 CG A:LYS62 4.2 28.5 1.0 CA B:ARG158 4.3 31.5 1.0 CE A:LYS62 4.4 31.2 1.0 NZ A:LYS62 4.5 31.9 1.0 CB B:ARG158 4.6 32.0 1.0 CAL A:2BE3001 4.7 59.3 1.0 O B:ARG158 4.8 31.8 1.0 CD A:LYS62 4.9 30.2 1.0

Bromine binding site 3 out of 4 in the Crystal Structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (Fabz) From Helicobacter Pylori in Complex with Compound 3I


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 (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (Fabz) From Helicobacter Pylori in Complex with Compound 3I within 5.0Å range: probe atom residue distance (Å) B Occ C:Br3002 b:56.9 occ:1.00 BRAE C:2BE3002 0.0 56.9 1.0 CAS C:2BE3002 1.9 58.0 1.0 CAL C:2BE3002 2.8 56.3 1.0 CAQ C:2BE3002 2.9 59.1 1.0 OAB C:2BE3002 3.1 60.6 1.0 CG2 C:VAL99 3.8 20.6 1.0 CD C:PRO22 3.9 12.9 1.0 O C:ILE20 4.0 15.7 1.0 CAU C:2BE3002 4.2 54.2 1.0 CAV C:2BE3002 4.2 59.6 1.0 O C:LYS97 4.3 26.0 1.0 N C:VAL99 4.4 25.0 1.0 CA C:ILE98 4.6 25.7 1.0 CD2 C:LEU21 4.6 15.1 1.0 C C:LYS97 4.6 25.1 1.0 CB C:VAL99 4.7 22.6 1.0 CAR C:2BE3002 4.7 56.8 1.0 CG C:PRO22 4.7 14.5 1.0 C C:ILE98 4.8 25.1 1.0 N C:ILE98 4.8 25.6 1.0 CA C:LEU21 4.9 15.2 1.0 NH2 C:ARG158 4.9 28.5 1.0 CD1 C:PHE83 4.9 15.0 1.0 CB C:LYS97 5.0 24.0 1.0

Bromine binding site 4 out of 4 in the Crystal Structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (Fabz) From Helicobacter Pylori in Complex with Compound 3I


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 (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (Fabz) From Helicobacter Pylori in Complex with Compound 3I within 5.0Å range: probe atom residue distance (Å) B Occ C:Br3002 b:62.4 occ:1.00 BRAF C:2BE3002 0.0 62.4 1.0 CAV C:2BE3002 1.9 59.6 1.0 CAQ C:2BE3002 2.9 59.1 1.0 CAR C:2BE3002 2.9 56.8 1.0 OAB C:2BE3002 3.0 60.6 1.0 OAC C:2BE3002 3.1 57.7 1.0 CE1 C:PHE101 3.4 26.4 1.0 CE1 C:HIS23 3.5 12.6 1.0 CD1 C:PHE101 4.0 25.4 1.0 NE2 C:HIS23 4.0 12.7 1.0 CA C:GLN76 4.0 13.2 1.0 O C:ALA75 4.1 9.9 1.0 CAS C:2BE3002 4.2 58.0 1.0 CAU C:2BE3002 4.2 54.2 1.0 CB C:VAL99 4.4 22.6 1.0 O C:VAL99 4.4 25.9 1.0 CA C:GLY79 4.4 15.9 1.0 CG C:GLN76 4.4 13.4 1.0 C C:ALA75 4.5 12.0 1.0 N C:GLN76 4.5 13.0 1.0 CZ C:PHE101 4.5 26.5 1.0 ND1 C:HIS23 4.6 12.2 1.0 CG1 C:VAL99 4.6 22.0 1.0 O C:HOH3006 4.7 13.9 1.0 CAL C:2BE3002 4.7 56.3 1.0 O C:GLN76 4.7 15.0 1.0 CB C:GLN76 4.8 12.9 1.0 CD2 C:LEU21 4.8 15.1 1.0 C C:GLN76 4.9 13.2 1.0 N C:GLY79 4.9 15.1 1.0

L.He, L.Zhang, X.Liu, X.Li, M.Zheng, H.Li, K.Yu, K.Chen, X.Shen, H.Jiang, H.Liu. Discovering Potent Inhibitors Against the Beta-Hydroxyacyl-Acyl Carrier Protein Dehydratase (Fabz) of Helicobacter Pylori: Structure-Based Design, Synthesis, Bioassay, and Crystal Structure Determination. J.Med.Chem. V. 52 2465 2009.
ISSN: ISSN 0022-2623
PubMed: 19309082
DOI: 10.1021/JM8015602