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

The structure of Crystal Structure of (3R)-Hydroxyacyl-Acyl Carrier Protein Dehydratase (Fabz) From Helicobacter Pylori in Complex with Compound 3K, PDB code: 3doz 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 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	73.737, 100.215, 186.564, 90.00, 90.00, 90.00
R / Rfree (%)	21 / 25.5

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


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 3K within 5.0Å range: probe atom residue distance (Å) B Occ B:Br163 b:63.2 occ:1.00 BRAD B:3BE163 0.0 63.2 1.0 CAP B:3BE163 1.9 53.2 1.0 CAI B:3BE163 2.8 53.5 1.0 CAK B:3BE163 2.9 53.0 1.0 O A:ARG110 3.3 19.4 1.0 C A:ARG110 3.7 19.4 1.0 CE2 B:TYR100 4.0 31.9 1.0 O A:PHE109 4.1 19.4 1.0 CAH B:3BE163 4.1 55.2 1.0 CAU B:3BE163 4.2 51.0 1.0 N A:ILE111 4.3 18.8 1.0 CA A:ARG110 4.4 19.3 1.0 CZ B:TYR100 4.4 32.5 1.0 CD A:PRO112 4.4 17.6 1.0 CA A:ILE111 4.5 17.6 1.0 CD2 B:TYR100 4.5 31.8 1.0 OH B:TYR100 4.5 32.3 1.0 C A:PHE109 4.6 19.7 1.0 CAJ B:3BE163 4.7 54.4 1.0 N A:ARG110 4.7 19.8 1.0 N A:PRO112 4.8 18.6 1.0 C A:ILE111 4.8 18.3 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 3K


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 3K within 5.0Å range: probe atom residue distance (Å) B Occ B:Br163 b:58.6 occ:1.00 BRAE B:3BE163 0.0 58.6 1.0 CAQ B:3BE163 1.9 57.8 1.0 CAR B:3BE163 2.8 59.9 1.0 CAL B:3BE163 2.9 56.6 1.0 OAB B:3BE163 3.0 60.2 1.0 CB A:PHE59 3.6 19.7 1.0 CG A:PHE59 3.6 18.9 1.0 CB B:PRO22 3.9 16.4 1.0 CD1 A:PHE59 4.1 17.9 1.0 CD2 A:PHE59 4.1 18.9 1.0 CD B:ARG158 4.1 37.2 1.0 CAV B:3BE163 4.1 59.6 1.0 CAT B:3BE163 4.2 55.2 1.0 CG B:PRO22 4.2 16.6 1.0 NE B:ARG158 4.2 36.2 1.0 NH1 B:ARG158 4.3 35.2 1.0 CZ B:ARG158 4.3 36.5 1.0 CB A:LYS62 4.4 27.9 1.0 CG A:LYS62 4.7 29.8 1.0 CAS B:3BE163 4.7 58.3 1.0 CD1 B:ILE98 4.7 22.9 1.0 CG B:ARG158 4.8 38.2 1.0 CE1 A:PHE59 4.8 19.1 1.0 CE2 A:PHE59 4.8 18.5 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 3K


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 3K within 5.0Å range: probe atom residue distance (Å) B Occ B:Br163 b:62.2 occ:1.00 BRAF B:3BE163 0.0 62.2 1.0 CAV B:3BE163 1.9 59.6 1.0 CAR B:3BE163 2.8 59.9 1.0 CAS B:3BE163 2.9 58.3 1.0 O B:ARG158 3.0 40.8 1.0 OAB B:3BE163 3.0 60.2 1.0 OAC B:3BE163 3.0 58.3 1.0 CG B:ARG158 3.5 38.2 1.0 C B:ARG158 3.6 41.6 1.0 CA B:ARG158 4.0 39.8 1.0 CE A:LYS62 4.1 33.2 1.0 CAQ B:3BE163 4.2 57.8 1.0 CAT B:3BE163 4.2 55.2 1.0 CB B:ARG158 4.3 38.2 1.0 N B:GLU159 4.4 44.0 1.0 CD B:ARG158 4.6 37.2 1.0 CAL B:3BE163 4.7 56.6 1.0 CD A:LYS62 4.8 32.2 1.0 CA B:GLU159 4.8 45.7 1.0 CG A:LYS62 4.9 29.8 1.0 NZ A:LYS62 5.0 35.4 1.0 OE1 B:GLU159 5.0 45.3 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 3K


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 3K within 5.0Å range: probe atom residue distance (Å) B Occ C:Br162 b:65.3 occ:1.00 BRAD C:3BE162 0.0 65.3 1.0 CAP C:3BE162 1.9 57.3 1.0 CAI C:3BE162 2.8 57.1 1.0 CAK C:3BE162 2.9 55.3 1.0 CZ C:ARG158 3.8 33.4 1.0 CB C:PRO22 3.8 14.3 1.0 CB D:PHE59 3.9 17.9 1.0 NH1 C:ARG158 3.9 33.0 1.0 CG D:PHE59 3.9 18.8 1.0 NE C:ARG158 3.9 34.3 1.0 CAH C:3BE162 4.1 58.3 1.0 CD1 D:PHE59 4.2 18.4 1.0 CAU C:3BE162 4.2 54.6 1.0 CD C:ARG158 4.2 34.5 1.0 NH2 C:ARG158 4.3 33.6 1.0 CD2 D:PHE59 4.4 19.8 1.0 CG C:PRO22 4.5 15.1 1.0 CAJ C:3BE162 4.7 57.8 1.0 CB D:LYS62 4.7 28.3 1.0 CE1 D:PHE59 4.8 19.7 1.0 CAG C:3BE162 4.9 59.9 1.0 CG C:ARG158 4.9 34.8 1.0 CG2 C:ILE98 5.0 28.8 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 3K


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 3K within 5.0Å range: probe atom residue distance (Å) B Occ C:Br162 b:62.4 occ:1.00 BRAE C:3BE162 0.0 62.4 1.0 CAQ C:3BE162 1.9 62.2 1.0 CAR C:3BE162 2.8 65.5 1.0 CAL C:3BE162 2.9 62.0 1.0 OAB C:3BE162 3.0 65.2 1.0 O C:LYS97 3.5 25.0 1.0 O C:ILE20 3.7 18.4 1.0 CG2 C:VAL99 4.0 23.4 1.0 C C:LYS97 4.1 25.3 1.0 CAV C:3BE162 4.1 65.5 1.0 CAT C:3BE162 4.2 59.8 1.0 CD1 C:PHE83 4.2 15.6 1.0 O C:ALA94 4.3 21.7 1.0 CD C:PRO22 4.4 15.4 1.0 NH2 C:ARG158 4.4 33.6 1.0 CB C:LYS97 4.5 25.7 1.0 CA C:ILE98 4.6 26.0 1.0 N C:ILE98 4.6 25.3 1.0 CAS C:3BE162 4.7 63.2 1.0 CG C:PHE83 4.8 15.8 1.0 CE1 C:PHE83 4.8 14.9 1.0 N C:VAL99 4.9 26.1 1.0 CA C:LYS97 4.9 25.1 1.0 C C:ILE98 4.9 26.2 1.0 C C:ILE20 4.9 19.3 1.0 CB C:PHE83 5.0 18.6 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 3K


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 3K within 5.0Å range: probe atom residue distance (Å) B Occ C:Br162 b:71.2 occ:1.00 BRAF C:3BE162 0.0 71.2 1.0 CAV C:3BE162 1.9 65.5 1.0 CAS C:3BE162 2.9 63.2 1.0 CAR C:3BE162 2.9 65.5 1.0 OAC C:3BE162 3.0 63.9 1.0 OAB C:3BE162 3.1 65.2 1.0 O C:HOH213 3.2 25.3 1.0 CE1 C:HIS23 3.6 14.8 1.0 CE2 C:PHE101 3.9 28.3 1.0 CA C:GLY79 4.0 20.5 1.0 CB C:VAL99 4.0 24.9 1.0 CAT C:3BE162 4.2 59.8 1.0 CAQ C:3BE162 4.2 62.2 1.0 CD2 C:LEU21 4.2 15.9 1.0 CA C:GLN76 4.4 17.8 1.0 NE2 C:HIS23 4.4 15.2 1.0 CG2 C:VAL99 4.4 23.4 1.0 O C:ALA75 4.5 15.7 1.0 O C:GLN76 4.5 19.0 1.0 ND1 C:HIS23 4.5 13.7 1.0 CG1 C:VAL99 4.6 25.0 1.0 O C:VAL99 4.6 28.8 1.0 CD2 C:PHE101 4.7 27.3 1.0 C C:GLY79 4.7 21.2 1.0 CAL C:3BE162 4.7 62.0 1.0 CZ C:PHE101 4.8 28.5 1.0 N C:GLY79 4.8 19.7 1.0 CG C:GLN76 4.8 17.5 1.0 C C:GLN76 4.9 18.8 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