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Chlorine in PDB 5hka: Crystal Structure of the Cftr Inhibitory Factor Cif Bound to An Amide Inhibitor

Protein crystallography data

The structure of Crystal Structure of the Cftr Inhibitory Factor Cif Bound to An Amide Inhibitor, PDB code: 5hka was solved by K.L.Hvorecny, D.R.Madden, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.97 / 2.05
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 168.971, 83.711, 88.879, 90.00, 100.68, 90.00
R / Rfree (%) 16.2 / 19.7

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of the Cftr Inhibitory Factor Cif Bound to An Amide Inhibitor (pdb code 5hka). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Crystal Structure of the Cftr Inhibitory Factor Cif Bound to An Amide Inhibitor, PDB code: 5hka:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 5hka

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Chlorine binding site 1 out of 8 in the Crystal Structure of the Cftr Inhibitory Factor Cif Bound to An Amide Inhibitor


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 the Cftr Inhibitory Factor Cif Bound to An Amide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl401

b:32.0
occ:0.70
 CL2 A:64N401 0.0 32.0 0.7
C21 A:64N401 1.8 70.8 0.7
C22 A:64N401 2.6 70.2 0.7
O A:HOH586 2.8 28.2 1.0
C7 A:64N401 2.9 70.6 0.7
O2 A:64N401 3.3 65.6 0.7
CD2 A:LEU174 3.5 45.9 1.0
N A:LEU174 3.7 19.8 1.0
CB A:LEU174 3.9 32.4 1.0
C4 A:64N401 4.0 71.6 0.7
CG A:PRO165 4.0 19.8 1.0
CD A:PRO165 4.0 18.8 1.0
C6 A:64N401 4.1 71.9 0.7
C8 A:64N401 4.2 54.0 0.7
CG A:LEU174 4.2 39.6 1.0
CB A:SER173 4.3 17.1 1.0
CA A:LEU174 4.3 24.0 1.0
C5 A:64N401 4.5 71.0 0.7
CG2 A:THR168 4.6 19.8 1.0
C A:SER173 4.7 19.4 1.0
CA A:SER173 4.7 18.0 1.0
C9 A:64N401 4.7 42.7 0.7
C1 A:64N401 4.8 73.5 0.7
O A:PRO165 4.8 15.0 1.0
CD1 A:PHE164 4.8 20.6 0.6
N A:VAL175 4.9 18.4 1.0
N A:PRO165 4.9 16.1 1.0
C2 A:64N401 5.0 74.4 0.7

Chlorine binding site 2 out of 8 in 5hka

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Chlorine binding site 2 out of 8 in the Crystal Structure of the Cftr Inhibitory Factor Cif Bound to An Amide Inhibitor


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 the Cftr Inhibitory Factor Cif Bound to An Amide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl401

b:0.9
occ:0.70
 CL1 A:64N401 0.0 0.9 0.7
C6 A:64N401 1.7 71.9 0.7
C5 A:64N401 2.6 71.0 0.7
C7 A:64N401 2.7 70.6 0.7
O2 A:64N401 3.0 65.6 0.7
CE1 A:PHE164 3.1 20.9 0.6
SD A:MET272 3.2 9.6 0.3
C8 A:64N401 3.3 54.0 0.7
CE A:MET272 3.4 19.1 0.3
C9 A:64N401 3.6 42.7 0.7
CZ A:PHE164 3.6 20.5 0.4
CZ A:PHE164 3.6 20.2 0.6
CB A:PHE275 3.8 15.2 1.0
CG A:PHE275 3.8 17.7 1.0
CE1 A:PHE164 3.9 21.9 0.4
CD1 A:PHE164 3.9 20.6 0.6
C4 A:64N401 4.0 71.6 0.7
C21 A:64N401 4.0 70.8 0.7
CG A:MET272 4.1 14.4 0.6
CE2 A:PHE164 4.1 21.1 0.4
CE A:MET272 4.1 20.7 0.6
CB A:MET272 4.2 12.8 0.6
C13 A:64N401 4.2 50.7 0.7
O A:MET272 4.2 13.4 1.0
CD2 A:PHE275 4.2 19.0 1.0
CD1 A:PHE275 4.3 18.1 1.0
CA A:MET272 4.3 12.3 0.6
CA A:MET272 4.4 12.7 0.3
CB A:MET272 4.4 12.6 0.3
CG A:MET272 4.5 14.7 0.3
C22 A:64N401 4.5 70.2 0.7
C10 A:64N401 4.6 43.2 0.7
CD1 A:PHE164 4.6 20.9 0.4
C A:MET272 4.7 14.6 1.0
CD2 A:PHE164 4.8 20.4 0.4
CE2 A:PHE164 4.8 21.2 0.6
SD A:MET272 4.9 19.6 0.6
CE2 A:PHE275 4.9 17.0 1.0
CE1 A:PHE275 5.0 17.9 1.0

Chlorine binding site 3 out of 8 in 5hka

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Chlorine binding site 3 out of 8 in the Crystal Structure of the Cftr Inhibitory Factor Cif Bound to An Amide Inhibitor


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 the Cftr Inhibitory Factor Cif Bound to An Amide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl401

b:39.9
occ:0.87
 CL2 B:64N401 0.0 39.9 0.9
C21 B:64N401 1.7 26.6 0.9
C7 B:64N401 2.6 17.3 0.9
C22 B:64N401 2.8 27.8 0.9
O2 B:64N401 2.8 21.0 0.9
C8 B:64N401 3.3 15.6 0.9
CG B:PHE275 3.3 16.1 1.0
CB B:PHE275 3.4 13.6 1.0
CG B:MET272 3.6 13.4 1.0
CE B:MET272 3.6 20.4 1.0
CD1 B:PHE275 3.6 15.4 1.0
C9 B:64N401 3.7 16.3 0.9
CB B:MET272 3.7 11.0 1.0
CZ B:PHE164 3.8 14.2 1.0
CD2 B:PHE275 3.8 16.4 1.0
CE1 B:PHE164 3.9 17.4 1.0
C6 B:64N401 3.9 23.4 0.9
C4 B:64N401 4.0 33.3 0.9
O B:MET272 4.0 15.9 1.0
CA B:MET272 4.1 14.9 1.0
SD B:MET272 4.2 20.0 1.0
C13 B:64N401 4.2 12.0 0.9
CE1 B:PHE275 4.3 16.8 1.0
CE2 B:PHE275 4.5 16.6 1.0
C5 B:64N401 4.5 32.1 0.9
C B:MET272 4.6 16.9 1.0
CZ B:PHE275 4.7 16.8 1.0
CE2 B:PHE164 4.7 14.3 1.0
C10 B:64N401 4.8 10.1 0.9
CA B:PHE275 4.9 17.5 1.0
CD1 B:PHE164 4.9 17.6 1.0

Chlorine binding site 4 out of 8 in 5hka

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Chlorine binding site 4 out of 8 in the Crystal Structure of the Cftr Inhibitory Factor Cif Bound to An Amide Inhibitor


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 the Cftr Inhibitory Factor Cif Bound to An Amide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl401

b:34.1
occ:0.87
 CL1 B:64N401 0.0 34.1 0.9
C6 B:64N401 1.7 23.4 0.9
C7 B:64N401 2.7 17.3 0.9
C5 B:64N401 2.7 32.1 0.9
O2 B:64N401 3.0 21.0 0.9
C8 B:64N401 3.5 15.6 0.9
O B:HOH648 3.6 30.0 1.0
CG B:PHE164 3.8 15.8 1.0
CD1 B:PHE164 3.8 17.6 1.0
CG2 B:VAL175 3.8 17.2 1.0
CB B:PHE164 3.9 16.1 1.0
C21 B:64N401 3.9 26.6 0.9
C9 B:64N401 3.9 16.3 0.9
CB B:LEU174 4.0 21.4 1.0
CG1 B:VAL175 4.0 15.6 1.0
C4 B:64N401 4.0 33.3 0.9
CD B:PRO165 4.1 19.0 1.0
CD1 B:LEU174 4.3 26.1 1.0
C13 B:64N401 4.4 12.0 0.9
CD2 B:PHE164 4.4 15.2 1.0
CE1 B:PHE164 4.4 17.4 1.0
C22 B:64N401 4.5 27.8 0.9
CB B:VAL175 4.5 15.8 1.0
CA B:PHE164 4.6 14.9 1.0
N B:VAL175 4.6 13.4 1.0
CG B:LEU174 4.7 24.4 1.0
N B:LEU174 4.7 14.8 1.0
CA B:LEU174 4.7 17.0 1.0
CG B:PRO165 4.9 19.5 1.0
N B:PRO165 4.9 18.2 1.0
C B:LEU174 4.9 14.9 1.0
CE2 B:PHE164 5.0 14.3 1.0
CZ B:PHE164 5.0 14.2 1.0

Chlorine binding site 5 out of 8 in 5hka

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Chlorine binding site 5 out of 8 in the Crystal Structure of the Cftr Inhibitory Factor Cif Bound to An Amide Inhibitor


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 the Cftr Inhibitory Factor Cif Bound to An Amide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl401

b:56.8
occ:0.88
 CL2 C:64N401 0.0 56.8 0.9
C21 C:64N401 1.8 61.4 0.7
C22 C:64N401 2.7 61.1 0.7
C7 C:64N401 2.8 62.3 0.7
O2 C:64N401 3.1 62.6 0.7
CD C:PRO165 3.8 18.7 1.0
CD2 C:PHE164 3.9 14.4 0.4
C8 C:64N401 4.0 54.6 0.7
C4 C:64N401 4.1 62.0 0.7
C6 C:64N401 4.1 62.6 0.7
CG C:PRO165 4.1 20.2 1.0
N C:LEU174 4.3 20.5 1.0
CB C:LEU174 4.3 31.5 1.0
C9 C:64N401 4.4 48.7 0.7
C5 C:64N401 4.6 60.2 0.7
CE2 C:PHE164 4.6 16.1 0.4
CG2 C:VAL175 4.6 28.0 1.0
CG C:LEU174 4.7 34.3 1.0
CB C:PHE164 4.8 13.2 0.4
CB C:PHE164 4.8 13.3 0.6
CG C:PHE164 4.8 13.9 0.4
CA C:LEU174 4.9 26.2 1.0
N C:PRO165 4.9 19.0 1.0
CB C:SER173 4.9 19.4 1.0
CD1 C:LEU174 5.0 33.3 1.0

Chlorine binding site 6 out of 8 in 5hka

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Chlorine binding site 6 out of 8 in the Crystal Structure of the Cftr Inhibitory Factor Cif Bound to An Amide Inhibitor


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 the Cftr Inhibitory Factor Cif Bound to An Amide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl401

b:1.0
occ:0.70
 CL1 C:64N401 0.0 1.0 0.7
C6 C:64N401 1.7 62.6 0.7
CE2 C:PHE164 2.4 16.1 0.4
C5 C:64N401 2.6 60.2 0.7
C7 C:64N401 2.7 62.3 0.7
CZ C:PHE164 2.7 15.4 0.4
O2 C:64N401 3.0 62.6 0.7
SD C:MET272 3.1 10.9 0.3
CZ C:PHE164 3.3 15.2 0.6
C8 C:64N401 3.3 54.6 0.7
CE C:MET272 3.3 30.3 0.3
CE1 C:PHE164 3.5 16.4 0.6
CD2 C:PHE164 3.6 14.4 0.4
CG C:PHE275 3.6 17.7 1.0
C9 C:64N401 3.7 48.7 0.7
CE C:MET272 3.8 30.9 0.6
CD2 C:PHE275 3.8 20.1 1.0
CG C:MET272 3.8 13.2 0.6
CB C:PHE275 3.8 18.6 1.0
CE2 C:PHE164 3.9 13.9 0.6
C4 C:64N401 3.9 62.0 0.7
C13 C:64N401 4.0 49.3 0.7
C21 C:64N401 4.0 61.4 0.7
CB C:MET272 4.0 12.0 0.6
CD1 C:PHE275 4.1 18.0 1.0
CE1 C:PHE164 4.1 14.8 0.4
CD1 C:PHE164 4.3 14.9 0.6
CE2 C:PHE275 4.3 17.7 1.0
CB C:MET272 4.4 11.2 0.3
CG C:MET272 4.4 13.4 0.3
C22 C:64N401 4.5 61.1 0.7
O C:MET272 4.5 14.8 1.0
CA C:MET272 4.5 12.0 0.6
CA C:MET272 4.6 12.0 0.3
SD C:MET272 4.6 20.0 0.6
C10 C:64N401 4.6 48.0 0.7
CE1 C:PHE275 4.6 19.7 1.0
CD2 C:PHE164 4.7 12.8 0.6
CG C:PHE164 4.7 13.9 0.4
CZ C:PHE275 4.7 18.2 1.0
C12 C:64N401 4.9 42.6 0.7
CG C:PHE164 4.9 13.9 0.6
CD1 C:PHE164 4.9 13.5 0.4

Chlorine binding site 7 out of 8 in 5hka

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Chlorine binding site 7 out of 8 in the Crystal Structure of the Cftr Inhibitory Factor Cif Bound to An Amide Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of the Cftr Inhibitory Factor Cif Bound to An Amide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl401

b:33.2
occ:0.94
 CL2 D:64N401 0.0 33.2 0.9
C21 D:64N401 1.7 22.7 0.9
C7 D:64N401 2.7 24.4 0.9
C22 D:64N401 2.7 32.3 0.9
O2 D:64N401 2.9 25.0 0.9
O D:HOH555 3.1 22.8 1.0
C8 D:64N401 3.5 17.5 0.9
O D:HOH669 3.6 7.9 1.0
CG D:PHE164 3.7 16.7 1.0
CD1 D:PHE164 3.7 18.4 1.0
CB D:PHE164 3.8 12.5 1.0
C9 D:64N401 3.9 16.3 0.9
C6 D:64N401 4.0 31.8 0.9
CB D:LEU174 4.0 18.8 1.0
C4 D:64N401 4.0 41.2 0.9
CG1 D:VAL175 4.1 15.0 1.0
CG2 D:VAL175 4.1 18.3 1.0
CD D:PRO165 4.3 19.2 1.0
CD2 D:PHE164 4.3 15.1 1.0
C13 D:64N401 4.3 18.6 0.9
CE1 D:PHE164 4.4 18.8 1.0
C5 D:64N401 4.5 35.6 0.9
CA D:PHE164 4.6 12.6 1.0
CD1 D:LEU174 4.6 20.3 1.0
N D:VAL175 4.7 12.1 1.0
CB D:VAL175 4.7 19.1 1.0
CA D:LEU174 4.8 16.8 1.0
N D:LEU174 4.9 17.4 1.0
CG D:LEU174 4.9 20.1 1.0
CE2 D:PHE164 4.9 12.9 1.0
CZ D:PHE164 4.9 14.8 1.0
C D:LEU174 5.0 16.1 1.0
C10 D:64N401 5.0 16.4 0.9

Chlorine binding site 8 out of 8 in 5hka

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Chlorine binding site 8 out of 8 in the Crystal Structure of the Cftr Inhibitory Factor Cif Bound to An Amide Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Crystal Structure of the Cftr Inhibitory Factor Cif Bound to An Amide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl401

b:44.1
occ:0.94
 CL1 D:64N401 0.0 44.1 0.9
C6 D:64N401 1.7 31.8 0.9
C7 D:64N401 2.6 24.4 0.9
C5 D:64N401 2.7 35.6 0.9
O2 D:64N401 2.8 25.0 0.9
CG D:PHE275 3.2 14.3 1.0
CB D:PHE275 3.3 16.2 1.0
C8 D:64N401 3.4 17.5 0.9
CE D:MET272 3.4 22.7 1.0
CG D:MET272 3.6 13.7 1.0
CD2 D:PHE275 3.6 18.1 1.0
CD1 D:PHE275 3.6 15.6 1.0
C9 D:64N401 3.7 16.3 0.9
CB D:MET272 3.7 13.7 1.0
CZ D:PHE164 3.8 14.8 1.0
C21 D:64N401 3.9 22.7 0.9
CE1 D:PHE164 4.0 18.8 1.0
C4 D:64N401 4.0 41.2 0.9
O D:MET272 4.1 15.8 1.0
CA D:MET272 4.2 14.9 1.0
CE2 D:PHE275 4.3 16.1 1.0
SD D:MET272 4.3 19.0 1.0
C13 D:64N401 4.3 18.6 0.9
CE1 D:PHE275 4.3 17.1 1.0
C22 D:64N401 4.5 32.3 0.9
CZ D:PHE275 4.6 17.5 1.0
C D:MET272 4.7 15.2 1.0
O D:HOH660 4.7 33.9 1.0
CE2 D:PHE164 4.8 12.9 1.0
C10 D:64N401 4.8 16.4 0.9
CA D:PHE275 4.8 15.1 1.0
CD1 D:PHE164 5.0 18.4 1.0

Reference:

S.Kitamura, K.L.Hvorecny, J.Niu, B.D.Hammock, D.R.Madden, C.Morisseau. Rational Design of Potent and Selective Inhibitors of An Epoxide Hydrolase Virulence Factor From Pseudomonas Aeruginosa. J.Med.Chem. V. 59 4790 2016.
ISSN: ISSN 0022-2623
PubMed: 27120257
DOI: 10.1021/ACS.JMEDCHEM.6B00173
Page generated: Fri Jul 26 08:51:44 2024

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