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

Protein crystallography data

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

Other elements in 3dp3:

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:

Bromine (Br) 4 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 6 binding sites of Chlorine 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 Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 3dp3

Go back to Chlorine Binding Sites List in 3dp3
Chlorine 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 3Q


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl160

b:41.9
occ:1.00
 N A:GLY67 3.0 12.9 1.0
O B:HOH166 3.1 15.4 1.0
O B:HOH231 3.4 28.1 1.0
CE1 A:HIS58 3.5 15.0 1.0
NE2 A:HIS58 3.5 13.9 1.0
CA A:PRO66 3.6 14.4 1.0
O B:HOH167 3.8 21.8 1.0
C A:PRO66 3.8 13.9 1.0
CA A:GLY67 3.9 12.9 1.0
O A:HOH222 4.3 26.7 1.0
O A:HOH232 4.5 37.7 1.0
O A:PHE65 4.5 15.0 1.0
CB A:PRO66 4.5 12.8 1.0
N A:PRO66 4.6 12.2 1.0
ND1 A:HIS58 4.8 13.3 1.0
CD2 A:HIS58 4.8 14.4 1.0
CG2 A:ILE64 4.9 15.9 1.0
C A:PHE65 4.9 13.6 1.0

Chlorine binding site 2 out of 6 in 3dp3

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Chlorine 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 3Q


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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
B:Cl160

b:58.3
occ:1.00
 O B:HOH200 2.9 26.3 1.0
O A:HOH166 3.1 15.4 1.0
N B:GLY67 3.1 14.9 1.0
CE1 B:HIS58 3.5 12.2 1.0
NE2 B:HIS58 3.7 13.9 1.0
O A:HOH164 3.8 15.6 1.0
CA B:PRO66 3.9 14.6 1.0
CA B:GLY67 3.9 12.8 1.0
C B:PRO66 4.0 15.2 1.0
O B:HOH204 4.3 23.4 1.0
O B:PHE65 4.4 15.3 1.0
ND1 B:HIS58 4.7 11.9 1.0
CD1 A:PHE101 4.8 35.9 1.0
CG2 B:ILE64 4.8 15.9 1.0
N B:PRO66 4.8 13.4 1.0
CB B:PRO66 4.9 13.9 1.0

Chlorine binding site 3 out of 6 in 3dp3

Go back to Chlorine Binding Sites List in 3dp3
Chlorine 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 3Q


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl160

b:34.3
occ:1.00
 O D:HOH162 2.9 17.4 1.0
N C:GLY67 3.2 15.7 1.0
CD1 D:PHE101 3.8 29.1 1.0
CA C:GLY67 3.9 15.2 1.0
CE1 C:HIS58 3.9 18.7 1.0
CB D:PHE101 4.0 28.3 1.0
NE2 C:HIS58 4.0 18.6 1.0
O D:HOH164 4.0 18.3 1.0
N D:PHE101 4.1 29.9 1.0
C C:PRO66 4.2 15.6 1.0
CA C:PRO66 4.2 15.4 1.0
CG D:PHE101 4.4 29.2 1.0
O C:HOH201 4.5 17.6 1.0
CA D:PHE101 4.7 28.4 1.0
O C:PHE65 4.8 16.4 1.0
CE1 D:PHE101 4.9 29.6 1.0
CA D:TYR100 4.9 33.9 1.0

Chlorine binding site 4 out of 6 in 3dp3

Go back to Chlorine Binding Sites List in 3dp3
Chlorine 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 3Q


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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
D:Cl160

b:60.5
occ:1.00
 O C:HOH204 3.0 35.9 1.0
O C:HOH168 3.1 14.2 1.0
N D:GLY67 3.1 13.6 1.0
CE1 D:HIS58 3.6 17.2 1.0
NE2 D:HIS58 3.8 17.3 1.0
CA D:PRO66 3.9 13.6 1.0
CA D:GLY67 4.0 13.1 1.0
C D:PRO66 4.0 14.6 1.0
O C:HOH166 4.1 20.1 1.0
O D:HOH205 4.2 24.0 1.0
O C:HOH213 4.4 34.7 1.0
O D:PHE65 4.6 15.7 1.0
CB D:PRO66 4.8 13.6 1.0
ND1 D:HIS58 4.8 18.2 1.0
N D:PRO66 4.9 13.3 1.0

Chlorine binding site 5 out of 6 in 3dp3

Go back to Chlorine Binding Sites List in 3dp3
Chlorine 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 3Q


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 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
E:Cl160

b:41.0
occ:1.00
 O F:HOH236 2.8 30.6 1.0
N E:GLY67 3.2 16.4 1.0
O F:HOH192 3.4 16.9 1.0
NE2 E:HIS58 3.6 16.2 1.0
CE1 E:HIS58 3.7 17.4 1.0
CA E:GLY67 3.9 15.8 1.0
O F:HOH200 4.0 19.3 1.0
N F:PHE101 4.0 24.6 1.0
CB F:PHE101 4.0 23.7 1.0
CA E:PRO66 4.2 16.1 1.0
C E:PRO66 4.2 16.7 1.0
CD2 F:PHE101 4.2 25.4 1.0
O E:HOH203 4.5 18.6 1.0
CG F:PHE101 4.6 25.3 1.0
O E:PHE65 4.7 16.9 1.0
CA F:PHE101 4.7 23.8 1.0
O F:VAL99 4.7 30.0 1.0
CG2 E:ILE64 4.8 15.9 1.0
CA F:TYR100 4.8 28.1 1.0
C F:TYR100 4.9 26.4 1.0
O E:HOH165 4.9 15.8 1.0
ND1 E:HIS58 4.9 16.0 1.0
CD2 E:HIS58 5.0 16.2 1.0

Chlorine binding site 6 out of 6 in 3dp3

Go back to Chlorine Binding Sites List in 3dp3
Chlorine 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 3Q


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 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
F:Cl160

b:37.7
occ:1.00
 O E:HOH216 2.8 20.5 1.0
N F:GLY67 3.1 16.4 1.0
O E:HOH164 3.4 10.8 1.0
O E:HOH222 3.6 21.5 1.0
CE1 F:HIS58 3.8 17.9 1.0
CA F:GLY67 3.8 15.7 1.0
CB E:PHE101 3.9 23.7 1.0
NE2 F:HIS58 4.0 17.1 1.0
N E:PHE101 4.0 24.0 1.0
O E:HOH204 4.1 21.7 1.0
C F:PRO66 4.1 16.0 1.0
CA F:PRO66 4.2 17.3 1.0
CD2 E:PHE101 4.2 23.7 1.0
O F:HOH228 4.3 17.6 1.0
CG E:PHE101 4.6 22.8 1.0
CA E:PHE101 4.6 22.9 1.0
O F:PHE65 4.8 18.2 1.0
O E:VAL99 4.9 29.6 1.0
CA E:TYR100 5.0 25.7 1.0
C E:TYR100 5.0 25.4 1.0

Reference:

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
Page generated: Fri Jul 11 04:36:26 2025

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