Bromine in PDB 3dp2: Crystal Structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (Fabz) From Helicobacter Pylori in Complex with Compound 3J

The structure of Crystal Structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (Fabz) From Helicobacter Pylori in Complex with Compound 3J, PDB code: 3dp2 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 (°)	73.970, 100.323, 186.417, 90.00, 90.00, 90.00
R / Rfree (%)	19.7 / 23

The structure of Crystal Structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (Fabz) From Helicobacter Pylori in Complex with Compound 3J 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 3J (pdb code 3dp2). 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 (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (Fabz) From Helicobacter Pylori in Complex with Compound 3J, PDB code: 3dp2:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6;

Bromine binding site 1 out of 6 in the Crystal Structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (Fabz) From Helicobacter Pylori in Complex with Compound 3J


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 3J within 5.0Å range: probe atom residue distance (Å) B Occ B:Br162 b:68.3 occ:1.00 BRAD B:4BE162 0.0 68.3 1.0 CAP B:4BE162 1.9 45.3 1.0 CAI B:4BE162 2.8 46.4 1.0 CAH B:4BE162 2.9 46.0 1.0 O A:PHE109 3.4 16.1 1.0 O A:ARG110 3.7 13.5 1.0 C A:ARG110 3.7 12.8 1.0 C A:PHE109 3.8 14.2 1.0 N A:ILE111 4.0 13.9 1.0 CAK B:4BE162 4.1 46.0 1.0 CAJ B:4BE162 4.2 44.8 1.0 CB A:PHE109 4.2 12.9 1.0 CA A:ARG110 4.2 13.6 1.0 N A:ARG110 4.2 15.2 1.0 CA A:ILE111 4.3 13.2 1.0 CE2 B:TYR100 4.3 28.4 1.0 N A:PRO112 4.3 14.5 1.0 CD A:PRO112 4.3 14.5 1.0 C A:ILE111 4.4 14.6 1.0 CD2 B:TYR100 4.5 27.1 1.0 CAU B:4BE162 4.7 44.0 1.0 CA A:PHE109 4.7 14.2 1.0 O A:HOH204 4.7 34.2 1.0 O B:HOH188 4.7 21.6 1.0 O A:HOH187 4.8 14.2 1.0 O A:ILE111 4.9 14.4 1.0 O A:HOH216 5.0 20.9 1.0 CZ B:TYR100 5.0 29.0 1.0

Bromine binding site 2 out of 6 in the Crystal Structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (Fabz) From Helicobacter Pylori in Complex with Compound 3J


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 3J within 5.0Å range: probe atom residue distance (Å) B Occ B:Br162 b:66.2 occ:1.00 BRAE B:4BE162 0.0 66.2 1.0 CAQ B:4BE162 1.9 53.0 1.0 CAR B:4BE162 2.8 52.9 1.0 CAL B:4BE162 2.9 51.9 1.0 O A:HOH199 3.0 23.4 1.0 OAB B:4BE162 3.0 57.3 1.0 CB A:PHE59 3.7 13.6 1.0 CG A:PHE59 3.8 12.7 1.0 CB B:PRO22 3.8 11.0 1.0 NE B:ARG158 3.9 31.7 1.0 CZ B:ARG158 4.0 32.0 1.0 NH2 B:ARG158 4.1 31.0 1.0 CD2 A:PHE59 4.1 11.7 1.0 CAV B:4BE162 4.1 52.8 1.0 CAT B:4BE162 4.2 51.0 1.0 CD1 A:PHE59 4.3 13.2 1.0 CG B:PRO22 4.4 11.5 1.0 CB A:LYS62 4.5 22.6 1.0 CD B:ARG158 4.6 31.7 1.0 CAS B:4BE162 4.7 51.4 1.0 NH1 B:ARG158 4.7 30.9 1.0 CE2 A:PHE59 4.9 13.0 1.0 O A:PRO60 4.9 19.1 1.0 CD1 B:ILE98 4.9 20.3 1.0

Bromine binding site 3 out of 6 in the Crystal Structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (Fabz) From Helicobacter Pylori in Complex with Compound 3J


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 3J within 5.0Å range: probe atom residue distance (Å) B Occ B:Br162 b:70.2 occ:1.00 BRAF B:4BE162 0.0 70.2 1.0 CAV B:4BE162 1.9 52.8 1.0 OE2 B:GLU159 2.7 39.5 1.0 CAS B:4BE162 2.9 51.4 1.0 CAR B:4BE162 2.9 52.9 1.0 OAC B:4BE162 3.0 51.5 1.0 OAB B:4BE162 3.1 57.3 1.0 N B:GLU159 3.1 34.6 1.0 CA B:GLU159 3.6 37.1 1.0 CD B:GLU159 3.6 39.0 1.0 CG B:ARG158 3.9 29.8 1.0 CAT B:4BE162 4.2 51.0 1.0 CAQ B:4BE162 4.2 53.0 1.0 OE1 B:GLU159 4.2 38.5 1.0 C B:ARG158 4.2 32.8 1.0 CG A:LYS62 4.3 26.6 1.0 CE A:LYS62 4.5 32.5 1.0 CA B:ARG158 4.5 29.9 1.0 CG B:GLU159 4.6 38.8 1.0 O B:GLU159 4.6 40.0 1.0 C B:GLU159 4.6 38.3 1.0 CB B:GLU159 4.6 37.9 1.0 CB B:ARG158 4.6 29.6 1.0 CAL B:4BE162 4.7 51.9 1.0 CD A:LYS62 4.9 29.6 1.0

Bromine binding site 4 out of 6 in the Crystal Structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (Fabz) From Helicobacter Pylori in Complex with Compound 3J


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 3J within 5.0Å range: probe atom residue distance (Å) B Occ C:Br161 b:72.4 occ:1.00 BRAD C:4BE161 0.0 72.4 1.0 CAP C:4BE161 1.9 47.6 1.0 CAI C:4BE161 2.8 47.9 1.0 CAH C:4BE161 2.9 47.6 1.0 O D:HOH210 3.7 29.6 1.0 CD C:ARG158 4.0 28.9 1.0 CB D:LYS62 4.0 23.3 1.0 NE C:ARG158 4.1 29.6 1.0 CAK C:4BE161 4.1 46.3 1.0 CAJ C:4BE161 4.2 45.8 1.0 CB D:PHE59 4.2 14.7 1.0 CG D:LYS62 4.2 25.8 1.0 CZ C:ARG158 4.2 29.4 1.0 NH1 C:ARG158 4.3 29.7 1.0 CG C:ARG158 4.5 28.4 1.0 CG D:PHE59 4.5 16.2 1.0 CAU C:4BE161 4.7 43.8 1.0 O D:PRO60 4.7 19.1 1.0 CD1 D:PHE59 4.8 16.0 1.0 CB C:PRO22 4.8 10.8 1.0 NH2 C:ARG158 4.9 28.4 1.0

Bromine binding site 5 out of 6 in the Crystal Structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (Fabz) From Helicobacter Pylori in Complex with Compound 3J


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 (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (Fabz) From Helicobacter Pylori in Complex with Compound 3J within 5.0Å range: probe atom residue distance (Å) B Occ C:Br161 b:63.1 occ:1.00 BRAE C:4BE161 0.0 63.1 1.0 CAQ C:4BE161 1.9 54.6 1.0 CAR C:4BE161 2.8 54.0 1.0 CAL C:4BE161 2.9 52.4 1.0 OAB C:4BE161 3.0 59.5 1.0 O C:ILE20 3.8 12.6 1.0 CD C:PRO22 4.0 10.3 1.0 CG2 C:VAL99 4.0 20.3 1.0 CAV C:4BE161 4.1 52.9 1.0 CAT C:4BE161 4.2 49.7 1.0 O C:LYS97 4.3 22.3 1.0 CD1 C:PHE83 4.6 14.1 1.0 C C:LYS97 4.6 22.5 1.0 N C:VAL99 4.6 22.9 1.0 CA C:ILE98 4.6 23.3 1.0 CAS C:4BE161 4.7 51.0 1.0 O C:ALA94 4.8 19.6 1.0 CD2 C:LEU21 4.8 12.7 1.0 N C:ILE98 4.8 22.9 1.0 NH2 C:ARG158 4.8 28.4 1.0 C C:ILE20 4.8 14.7 1.0 CA C:LEU21 4.8 13.9 1.0 CG C:PRO22 4.8 11.2 1.0 C C:ILE98 4.9 22.2 1.0 CB C:VAL99 4.9 21.5 1.0 CG C:PHE83 4.9 14.8 1.0 CB C:PHE83 4.9 15.3 1.0 CB C:LYS97 4.9 22.6 1.0 O C:HOH205 5.0 24.3 1.0

Bromine binding site 6 out of 6 in the Crystal Structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (Fabz) From Helicobacter Pylori in Complex with Compound 3J


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 (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (Fabz) From Helicobacter Pylori in Complex with Compound 3J within 5.0Å range: probe atom residue distance (Å) B Occ C:Br161 b:70.6 occ:1.00 BRAF C:4BE161 0.0 70.6 1.0 CAV C:4BE161 1.9 52.9 1.0 O C:HOH185 2.8 18.6 1.0 CAR C:4BE161 2.9 54.0 1.0 CAS C:4BE161 2.9 51.0 1.0 OAC C:4BE161 3.1 48.3 1.0 OAB C:4BE161 3.1 59.5 1.0 CE1 C:PHE101 3.7 22.7 1.0 CA C:GLY79 3.7 15.7 1.0 O C:ALA75 3.7 11.7 1.0 CA C:GLN76 3.8 13.1 1.0 CE1 C:HIS23 4.0 10.6 1.0 CAQ C:4BE161 4.2 54.6 1.0 CAT C:4BE161 4.2 49.7 1.0 N C:GLY79 4.2 15.3 1.0 O C:GLN76 4.2 16.1 1.0 C C:ALA75 4.3 11.8 1.0 CB C:VAL99 4.3 21.5 1.0 N C:GLN76 4.4 13.1 1.0 CD1 C:PHE101 4.4 21.5 1.0 CD2 C:LEU21 4.4 12.7 1.0 C C:GLN76 4.5 14.3 1.0 CG C:GLN76 4.5 13.7 1.0 C C:GLY79 4.6 16.1 1.0 CG1 C:VAL99 4.6 21.6 1.0 CZ C:PHE101 4.6 23.2 1.0 CB C:GLN76 4.7 14.1 1.0 CAL C:4BE161 4.7 52.4 1.0 NE2 C:HIS23 4.7 10.3 1.0 O C:VAL99 4.8 24.9 1.0 ND1 C:HIS23 4.9 10.4 1.0 CG2 C:VAL99 4.9 20.3 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