Bromine in PDB 3dp3: Crystal Structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (Fabz) From Helicobacter Pylori in Complex with Compound 3Q

The structure of Crystal Structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (Fabz) From Helicobacter Pylori in Complex with Compound 3Q, PDB code: 3dp3 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 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	73.897, 100.226, 186.630, 90.00, 90.00, 90.00
R / Rfree (%)	20.3 / 23.1

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

Chlorine

(Cl)

6 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 3Q (pdb code 3dp3). 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 3Q, PDB code: 3dp3:
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 3Q


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 3Q within 5.0Å range: probe atom residue distance (Å) B Occ A:Br163 b:72.1 occ:1.00 BRAG A:4BB163 0.0 72.1 1.0 CAR A:4BB163 1.9 65.7 1.0 O A:HOH217 2.8 35.1 1.0 CAN A:4BB163 2.8 63.6 1.0 CAU A:4BB163 2.8 68.2 1.0 OAE A:4BB163 3.1 67.3 1.0 CB A:PHE59 3.7 17.1 1.0 CB B:PRO22 3.8 16.4 1.0 NH1 B:ARG158 3.9 35.8 1.0 CG A:PHE59 3.9 16.1 1.0 CZ B:ARG158 3.9 36.3 1.0 NE B:ARG158 4.1 36.7 1.0 CAT A:4BB163 4.1 59.6 1.0 CAX A:4BB163 4.2 67.7 1.0 CD B:ARG158 4.2 35.7 1.0 CD2 A:PHE59 4.4 17.3 1.0 CD1 A:PHE59 4.4 16.5 1.0 CB A:LYS62 4.5 25.2 1.0 NH2 B:ARG158 4.5 36.0 1.0 CG B:PRO22 4.5 17.3 1.0 CAV A:4BB163 4.7 64.4 1.0 O A:PRO60 4.7 23.8 1.0 CG B:ARG158 4.9 34.7 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 3Q


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 3Q within 5.0Å range: probe atom residue distance (Å) B Occ A:Br163 b:77.5 occ:1.00 BRAH A:4BB163 0.0 77.5 1.0 CAX A:4BB163 1.9 67.7 1.0 CAV A:4BB163 2.8 64.4 1.0 CAU A:4BB163 2.9 68.2 1.0 OAF A:4BB163 3.0 63.0 1.0 OAE A:4BB163 3.1 67.3 1.0 CG B:ARG158 3.8 34.7 1.0 CG A:LYS62 4.0 29.7 1.0 CAT A:4BB163 4.1 59.6 1.0 CAR A:4BB163 4.2 65.7 1.0 C B:ARG158 4.3 35.0 1.0 CE A:LYS62 4.3 33.5 1.0 CAN A:4BB163 4.7 63.6 1.0 CD B:ARG158 4.7 35.7 1.0 CD A:LYS62 4.7 31.7 1.0 CA B:ARG158 4.9 34.0 1.0 CB B:ARG158 4.9 33.9 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 3Q


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 3Q within 5.0Å range: probe atom residue distance (Å) B Occ C:Br162 b:59.6 occ:1.00 BRAG C:4BB162 0.0 59.6 1.0 CAR C:4BB162 1.9 53.6 1.0 CAU C:4BB162 2.8 54.6 1.0 CAN C:4BB162 2.9 51.3 1.0 OAE C:4BB162 3.0 54.7 1.0 O C:ILE20 3.7 17.4 1.0 CG1 C:VAL99 3.8 26.8 1.0 CAX C:4BB162 4.1 54.4 1.0 CAT C:4BB162 4.2 47.1 1.0 CD1 C:PHE83 4.2 18.7 1.0 CD C:PRO22 4.3 14.8 1.0 CB C:PHE83 4.4 19.6 1.0 CG C:PHE83 4.5 19.8 1.0 CD2 C:LEU21 4.5 19.9 1.0 CAV C:4BB162 4.7 51.5 1.0 C C:ILE20 4.7 17.8 1.0 O C:LYS97 4.7 27.4 1.0 CG2 C:ILE20 4.8 17.9 1.0 CA C:LEU21 4.8 18.5 1.0 O C:GLY79 4.9 19.0 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 3Q


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 3Q within 5.0Å range: probe atom residue distance (Å) B Occ C:Br162 b:60.8 occ:1.00 BRAH C:4BB162 0.0 60.8 1.0 CAX C:4BB162 1.9 54.4 1.0 O C:HOH222 2.7 19.4 1.0 CAU C:4BB162 2.8 54.6 1.0 CAV C:4BB162 2.9 51.5 1.0 OAE C:4BB162 3.0 54.7 1.0 OAF C:4BB162 3.1 49.2 1.0 CG2 C:VAL99 3.5 28.8 1.0 CE2 C:PHE101 3.7 28.2 1.0 CE1 C:HIS23 3.8 16.8 1.0 CA C:GLN76 3.9 16.0 1.0 O C:ALA75 3.9 13.6 1.0 CA C:GLY79 4.0 16.6 1.0 CAR C:4BB162 4.1 53.6 1.0 CAT C:4BB162 4.2 47.1 1.0 CD2 C:PHE101 4.4 27.1 1.0 C C:ALA75 4.4 15.7 1.0 N C:GLN76 4.4 16.0 1.0 NE2 C:HIS23 4.4 16.1 1.0 O C:GLN76 4.4 17.6 1.0 CG C:GLN76 4.5 15.5 1.0 N C:GLY79 4.5 17.6 1.0 CD2 C:LEU21 4.6 19.9 1.0 C C:GLN76 4.6 16.9 1.0 CZ C:PHE101 4.7 29.2 1.0 CAN C:4BB162 4.7 51.3 1.0 ND1 C:HIS23 4.7 14.8 1.0 CB C:VAL99 4.7 29.2 1.0 CB C:GLN76 4.7 14.9 1.0 O C:VAL99 4.8 30.3 1.0 CG1 C:VAL99 4.8 26.8 1.0 C C:GLY79 4.9 16.7 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