Bromine in PDB 3dp1: Crystal Structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (Fabz) From Helicobacter Pylori in Complex with Compound 3N

The structure of Crystal Structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (Fabz) From Helicobacter Pylori in Complex with Compound 3N, PDB code: 3dp1 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 (°)	73.853, 100.210, 186.112, 90.00, 90.00, 90.00
R / Rfree (%)	19.9 / 23.5

The structure of Crystal Structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (Fabz) From Helicobacter Pylori in Complex with Compound 3N 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 3N (pdb code 3dp1). 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 3N, PDB code: 3dp1:
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 3N


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 3N within 5.0Å range: probe atom residue distance (Å) B Occ B:Br162 b:73.3 occ:1.00 BRAE B:2RB162 0.0 73.3 1.0 CAQ B:2RB162 1.9 58.5 1.0 CAT B:2RB162 2.8 60.4 1.0 CAL B:2RB162 2.9 57.1 1.0 OAC B:2RB162 3.0 60.6 1.0 O A:HOH227 3.2 23.4 1.0 CB A:PHE59 3.5 14.0 1.0 CG A:PHE59 3.7 13.3 1.0 CB B:PRO22 4.0 12.3 1.0 CD1 A:PHE59 4.1 12.3 1.0 CD B:ARG158 4.1 33.2 1.0 NE B:ARG158 4.1 33.2 1.0 CAW B:2RB162 4.1 59.5 1.0 CAS B:2RB162 4.2 54.2 1.0 CZ B:ARG158 4.2 33.2 1.0 CD2 A:PHE59 4.2 14.3 1.0 NH1 B:ARG158 4.2 32.5 1.0 CB A:LYS62 4.3 24.7 1.0 CG B:PRO22 4.6 11.9 1.0 CAU B:2RB162 4.7 57.5 1.0 CD1 B:ILE98 4.7 26.6 1.0 CG B:ARG158 4.8 32.3 1.0 O A:PRO60 4.8 23.2 1.0 CE1 A:PHE59 4.9 15.6 1.0 NH2 B:ARG158 4.9 32.1 1.0 CG A:LYS62 4.9 27.9 1.0 CE2 A:PHE59 5.0 14.8 1.0 CA A:PHE59 5.0 14.8 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 3N


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 3N within 5.0Å range: probe atom residue distance (Å) B Occ B:Br162 b:78.9 occ:1.00 BRAF B:2RB162 0.0 78.9 1.0 CAW B:2RB162 1.9 59.5 1.0 CAT B:2RB162 2.8 60.4 1.0 CAU B:2RB162 2.9 57.5 1.0 OAC B:2RB162 3.0 60.6 1.0 OAD B:2RB162 3.1 56.6 1.0 CG B:ARG158 3.7 32.3 1.0 C B:ARG158 4.0 31.8 1.0 CG A:LYS62 4.1 27.9 1.0 CAQ B:2RB162 4.2 58.5 1.0 CAS B:2RB162 4.2 54.2 1.0 O B:ARG158 4.4 32.6 1.0 CE A:LYS62 4.4 33.0 1.0 CA B:ARG158 4.6 31.6 1.0 CD B:ARG158 4.7 33.2 1.0 CAL B:2RB162 4.7 57.1 1.0 CB B:ARG158 4.8 31.5 1.0 CD A:LYS62 4.9 30.9 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 3N


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 3N within 5.0Å range: probe atom residue distance (Å) B Occ C:Br161 b:65.6 occ:1.00 BRAE C:2RB161 0.0 65.6 1.0 CAQ C:2RB161 1.9 53.0 1.0 CAL C:2RB161 2.9 51.5 1.0 CAT C:2RB161 2.9 54.0 1.0 OAC C:2RB161 3.1 53.2 1.0 CG1 C:VAL99 3.4 24.9 1.0 CD C:PRO22 3.9 11.2 1.0 O C:ILE20 4.0 13.6 1.0 CAS C:2RB161 4.2 48.4 1.0 CAW C:2RB161 4.2 54.4 1.0 CD2 C:LEU21 4.4 16.1 1.0 N C:VAL99 4.5 25.9 1.0 O C:LYS97 4.5 23.6 1.0 CAU C:2RB161 4.7 51.8 1.0 CA C:ILE98 4.7 25.5 1.0 CG C:PRO22 4.7 11.3 1.0 CA C:LEU21 4.7 14.2 1.0 CB C:VAL99 4.8 26.1 1.0 C C:ILE98 4.9 25.7 1.0 C C:LYS97 4.9 23.7 1.0 C C:ILE20 5.0 14.6 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 3N


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 3N within 5.0Å range: probe atom residue distance (Å) B Occ C:Br161 b:74.3 occ:1.00 BRAF C:2RB161 0.0 74.3 1.0 CAW C:2RB161 1.9 54.4 1.0 CAU C:2RB161 2.8 51.8 1.0 CAT C:2RB161 2.9 54.0 1.0 OAD C:2RB161 3.0 50.0 1.0 OAC C:2RB161 3.1 53.2 1.0 CE2 C:PHE101 3.4 23.7 1.0 CE1 C:HIS23 3.5 12.0 1.0 CD2 C:PHE101 3.9 23.5 1.0 NE2 C:HIS23 3.9 11.4 1.0 O C:ALA75 4.1 10.3 1.0 CA C:GLN76 4.1 13.8 1.0 O C:VAL99 4.1 26.9 1.0 CAS C:2RB161 4.1 48.4 1.0 CAQ C:2RB161 4.2 53.0 1.0 C C:ALA75 4.4 12.0 1.0 O C:HOH166 4.4 15.8 1.0 CG C:GLN76 4.4 14.4 1.0 N C:GLN76 4.4 13.3 1.0 CZ C:PHE101 4.6 25.0 1.0 CG2 C:VAL99 4.6 25.3 1.0 ND1 C:HIS23 4.6 9.4 1.0 CAL C:2RB161 4.7 51.5 1.0 CA C:GLY79 4.8 14.5 1.0 CG1 C:VAL99 4.8 24.9 1.0 O C:HOH227 4.8 28.4 1.0 CB C:GLN76 4.9 12.9 1.0 CB C:ALA75 5.0 8.5 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