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Bromine in PDB 5hkb: Crystal Structure of the Cftr Inhibitory Factor Cif Bound to the Inhibitor KB2115

Protein crystallography data

The structure of Crystal Structure of the Cftr Inhibitory Factor Cif Bound to the Inhibitor KB2115, PDB code: 5hkb 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) 19.92 / 1.65
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 84.168, 169.494, 175.568, 90.00, 90.00, 90.00
R / Rfree (%) 19 / 21.5

Bromine Binding Sites:

The binding sites of Bromine atom in the Crystal Structure of the Cftr Inhibitory Factor Cif Bound to the Inhibitor KB2115 (pdb code 5hkb). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 8 binding sites of Bromine where determined in the Crystal Structure of the Cftr Inhibitory Factor Cif Bound to the Inhibitor KB2115, PDB code: 5hkb:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Bromine binding site 1 out of 8 in 5hkb

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Bromine binding site 1 out of 8 in the Crystal Structure of the Cftr Inhibitory Factor Cif Bound to the Inhibitor KB2115


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 the Cftr Inhibitory Factor Cif Bound to the Inhibitor KB2115 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br401

b:17.1
occ:0.72
 BR2 A:64L401 0.0 17.1 0.7
C17 A:64L401 1.9 21.2 0.7
C18 A:64L401 2.9 28.1 0.7
C7 A:64L401 2.9 18.6 0.7
O4 A:64L401 3.1 16.9 0.7
CG2 A:VAL175 3.7 14.4 1.0
C8 A:64L401 3.8 12.3 0.7
N A:LEU174 3.9 9.3 1.0
N A:VAL175 4.0 8.1 1.0
OG A:SER173 4.0 9.5 1.0
CB A:LEU174 4.1 11.4 1.0
CD A:PRO165 4.1 6.0 1.0
C9 A:64L401 4.1 8.1 0.7
C6 A:64L401 4.2 22.5 0.7
C4 A:64L401 4.2 31.3 0.7
CB A:PHE164 4.3 6.9 1.0
CG1 A:VAL175 4.3 7.4 1.0
CA A:LEU174 4.3 11.5 1.0
C A:LEU174 4.4 7.7 1.0
CG A:PRO165 4.4 8.0 1.0
CB A:VAL175 4.4 10.3 1.0
O A:PRO165 4.5 7.2 1.0
CG A:PHE164 4.6 10.9 1.0
C5 A:64L401 4.7 23.9 0.7
C13 A:64L401 4.7 12.0 0.7
N A:PRO165 4.8 7.2 1.0
CA A:VAL175 4.8 8.0 1.0
CD1 A:PHE164 4.9 13.8 1.0
C A:SER173 4.9 10.8 1.0
CG A:LEU174 5.0 12.7 1.0

Bromine binding site 2 out of 8 in 5hkb

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Bromine binding site 2 out of 8 in the Crystal Structure of the Cftr Inhibitory Factor Cif Bound to the Inhibitor KB2115


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 the Cftr Inhibitory Factor Cif Bound to the Inhibitor KB2115 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br401

b:26.4
occ:0.72
 BR1 A:64L401 0.0 26.4 0.7
C6 A:64L401 1.9 22.5 0.7
C7 A:64L401 2.9 18.6 0.7
C5 A:64L401 2.9 23.9 0.7
O4 A:64L401 3.1 16.9 0.7
SD A:MET272 3.2 13.6 0.4
C8 A:64L401 3.4 12.3 0.7
CE A:MET272 3.4 11.6 0.4
CG A:PHE275 3.6 7.3 1.0
CE A:MET272 3.6 10.5 0.6
CZ A:PHE164 3.7 16.3 1.0
CD1 A:PHE275 3.7 7.1 1.0
CE1 A:PHE164 3.7 16.7 1.0
CG A:MET272 3.8 7.2 0.6
CB A:PHE275 3.8 5.8 1.0
C9 A:64L401 3.9 8.1 0.7
CD2 A:PHE275 4.0 7.0 1.0
CB A:MET272 4.1 4.2 0.6
C13 A:64L401 4.1 12.0 0.7
C17 A:64L401 4.1 21.2 0.7
CB A:MET272 4.2 3.8 0.4
C4 A:64L401 4.2 31.3 0.7
CE1 A:PHE275 4.2 8.1 1.0
CG A:MET272 4.3 5.3 0.4
SD A:MET272 4.4 5.8 0.6
CE2 A:PHE164 4.5 15.8 1.0
CE2 A:PHE275 4.5 9.1 1.0
CD1 A:PHE164 4.5 13.8 1.0
CA A:MET272 4.6 4.2 0.4
CA A:MET272 4.6 3.4 0.6
CZ A:PHE275 4.6 8.3 1.0
O A:MET272 4.6 5.8 1.0
C18 A:64L401 4.7 28.1 0.7
C10 A:64L401 4.8 12.0 0.7

Bromine binding site 3 out of 8 in 5hkb

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Bromine binding site 3 out of 8 in the Crystal Structure of the Cftr Inhibitory Factor Cif Bound to the Inhibitor KB2115


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 the Cftr Inhibitory Factor Cif Bound to the Inhibitor KB2115 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br401

b:18.9
occ:0.84
 BR2 B:64L401 0.0 18.9 0.8
C17 B:64L401 2.0 13.3 0.8
C18 B:64L401 2.9 16.6 0.8
C7 B:64L401 2.9 11.6 0.8
O B:HOH713 3.1 22.5 1.0
O4 B:64L401 3.1 11.7 0.8
O B:HOH685 3.3 14.0 1.0
CG2 B:VAL175 3.7 10.5 1.0
C8 B:64L401 3.9 8.6 0.8
C9 B:64L401 4.1 5.3 0.8
CB B:PHE164 4.1 7.1 1.0
C6 B:64L401 4.1 12.4 0.8
CD B:PRO165 4.2 10.9 1.0
C4 B:64L401 4.2 19.9 0.8
CG1 B:VAL175 4.2 6.2 1.0
CG B:PHE164 4.3 6.4 1.0
OG B:SER173 4.4 16.7 1.0
CB B:LEU174 4.4 7.7 1.0
N B:LEU174 4.5 6.4 1.0
CB B:VAL175 4.6 8.5 1.0
CD1 B:PHE164 4.6 8.5 1.0
N B:VAL175 4.7 7.4 1.0
C5 B:64L401 4.7 11.2 0.8
CG B:PRO165 4.8 15.1 1.0
CA B:PHE164 4.8 6.5 1.0
N B:PRO165 4.8 7.6 1.0
CA B:LEU174 4.9 5.7 1.0
CD2 B:PHE164 4.9 8.5 1.0
O B:PRO165 4.9 8.8 1.0
C13 B:64L401 4.9 3.5 0.8

Bromine binding site 4 out of 8 in 5hkb

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Bromine binding site 4 out of 8 in the Crystal Structure of the Cftr Inhibitory Factor Cif Bound to the Inhibitor KB2115


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 the Cftr Inhibitory Factor Cif Bound to the Inhibitor KB2115 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br401

b:16.4
occ:0.84
 BR1 B:64L401 0.0 16.4 0.8
C6 B:64L401 1.9 12.4 0.8
C5 B:64L401 2.7 11.2 0.8
C7 B:64L401 2.8 11.6 0.8
O4 B:64L401 3.0 11.7 0.8
C8 B:64L401 3.4 8.6 0.8
CZ B:PHE164 3.6 8.4 1.0
CG B:PHE275 3.6 7.3 1.0
CE B:MET272 3.6 9.3 1.0
CD1 B:PHE275 3.6 4.9 1.0
CG B:MET272 3.8 4.4 1.0
C9 B:64L401 3.9 5.3 0.8
CB B:PHE275 3.9 6.2 1.0
CE1 B:PHE164 3.9 8.5 1.0
C13 B:64L401 4.0 3.5 0.8
C4 B:64L401 4.0 19.9 0.8
C17 B:64L401 4.0 13.3 0.8
CD2 B:PHE275 4.0 6.9 1.0
SD B:MET272 4.1 5.9 1.0
CB B:MET272 4.1 3.7 1.0
CE1 B:PHE275 4.1 6.5 1.0
CE2 B:PHE164 4.3 4.7 1.0
CE2 B:PHE275 4.5 8.3 1.0
C18 B:64L401 4.5 16.6 0.8
CZ B:PHE275 4.5 5.7 1.0
CA B:MET272 4.8 4.7 1.0
C10 B:64L401 4.8 5.6 0.8
CD B:PRO155 4.8 3.9 1.0
O B:MET272 4.8 6.2 1.0
CD1 B:PHE164 4.8 8.5 1.0
C12 B:64L401 4.9 1.9 0.8

Bromine binding site 5 out of 8 in 5hkb

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Bromine binding site 5 out of 8 in the Crystal Structure of the Cftr Inhibitory Factor Cif Bound to the Inhibitor KB2115


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 the Cftr Inhibitory Factor Cif Bound to the Inhibitor KB2115 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Br401

b:18.3
occ:0.68
 BR2 C:64L401 0.0 18.3 0.7
C17 C:64L401 1.9 20.3 0.7
C18 C:64L401 2.8 27.0 0.7
C7 C:64L401 2.9 19.8 0.7
O4 C:64L401 3.2 19.0 0.7
CG2 C:VAL175 3.5 14.6 1.0
O C:HOH699 3.5 21.9 1.0
C8 C:64L401 3.9 13.8 0.7
OG C:SER173 3.9 10.9 1.0
N C:LEU174 4.0 9.3 1.0
N C:VAL175 4.0 9.9 1.0
CD C:PRO165 4.0 6.7 1.0
C4 C:64L401 4.1 31.6 0.7
C6 C:64L401 4.2 19.3 0.7
CB C:PHE164 4.2 7.5 1.0
C9 C:64L401 4.3 6.8 0.7
CB C:LEU174 4.3 11.9 1.0
O C:HOH856 4.4 39.5 1.0
CA C:LEU174 4.4 11.9 1.0
CG C:PRO165 4.5 9.9 1.0
C C:LEU174 4.5 9.3 1.0
O C:PRO165 4.5 7.5 1.0
CB C:VAL175 4.5 13.2 1.0
CG C:PHE164 4.6 9.9 1.0
C5 C:64L401 4.7 22.8 0.7
CG1 C:VAL175 4.7 12.4 1.0
N C:PRO165 4.7 8.3 1.0
C13 C:64L401 4.8 9.9 0.7
CA C:VAL175 4.8 9.8 1.0
CD1 C:PHE164 4.9 11.5 1.0
CA C:PHE164 4.9 7.8 1.0
C C:SER173 5.0 11.6 1.0

Bromine binding site 6 out of 8 in 5hkb

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Bromine binding site 6 out of 8 in the Crystal Structure of the Cftr Inhibitory Factor Cif Bound to the Inhibitor KB2115


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 the Cftr Inhibitory Factor Cif Bound to the Inhibitor KB2115 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Br401

b:24.4
occ:0.68
 BR1 C:64L401 0.0 24.4 0.7
C6 C:64L401 1.9 19.3 0.7
C7 C:64L401 2.8 19.8 0.7
C5 C:64L401 2.9 22.8 0.7
O4 C:64L401 2.9 19.0 0.7
SD C:MET272 3.2 12.5 0.4
C8 C:64L401 3.4 13.8 0.7
CE C:MET272 3.4 10.7 0.4
CG C:PHE275 3.5 5.5 1.0
CE C:MET272 3.6 8.6 0.6
CD1 C:PHE275 3.7 6.5 1.0
CB C:PHE275 3.7 6.9 1.0
CG C:MET272 3.8 5.7 0.6
CE1 C:PHE164 3.8 14.5 1.0
CZ C:PHE164 3.8 14.1 1.0
C9 C:64L401 3.9 6.8 0.7
CD2 C:PHE275 4.0 8.5 1.0
CB C:MET272 4.0 4.5 0.6
C13 C:64L401 4.1 9.9 0.7
C17 C:64L401 4.1 20.3 0.7
C4 C:64L401 4.2 31.6 0.7
CB C:MET272 4.2 3.3 0.4
CE1 C:PHE275 4.3 6.3 1.0
CG C:MET272 4.3 4.2 0.4
SD C:MET272 4.3 5.7 0.6
CE2 C:PHE275 4.5 8.1 1.0
CA C:MET272 4.5 5.1 0.6
CA C:MET272 4.5 4.8 0.4
CD1 C:PHE164 4.5 11.5 1.0
O C:MET272 4.6 6.2 1.0
CE2 C:PHE164 4.6 15.2 1.0
C18 C:64L401 4.7 27.0 0.7
CZ C:PHE275 4.7 7.7 1.0
C10 C:64L401 4.9 8.0 0.7

Bromine binding site 7 out of 8 in 5hkb

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Bromine binding site 7 out of 8 in the Crystal Structure of the Cftr Inhibitory Factor Cif Bound to the Inhibitor KB2115


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 7 of Crystal Structure of the Cftr Inhibitory Factor Cif Bound to the Inhibitor KB2115 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Br401

b:18.2
occ:0.83
 BR2 D:64L401 0.0 18.2 0.8
C17 D:64L401 1.9 11.2 0.8
C7 D:64L401 2.8 9.2 0.8
C18 D:64L401 2.9 13.2 0.8
O4 D:64L401 3.0 9.9 0.8
CG2 D:VAL175 3.6 11.6 1.0
C8 D:64L401 3.8 8.9 0.8
CG1 D:VAL175 3.9 9.9 1.0
CB D:PHE164 4.0 5.3 1.0
C9 D:64L401 4.0 3.9 0.8
C6 D:64L401 4.1 8.9 0.8
C4 D:64L401 4.2 15.1 0.8
CG D:PHE164 4.2 5.3 1.0
CD D:PRO165 4.3 8.7 1.0
CB D:VAL175 4.4 8.3 1.0
O D:HOH848 4.4 38.2 1.0
CB D:LEU174 4.5 7.3 1.0
CD1 D:PHE164 4.6 8.9 1.0
N D:LEU174 4.6 7.3 1.0
O D:HOH794 4.6 26.7 1.0
C5 D:64L401 4.7 12.3 0.8
N D:VAL175 4.7 5.5 1.0
CA D:PHE164 4.7 6.0 1.0
CD2 D:PHE164 4.8 6.6 1.0
C13 D:64L401 4.8 5.4 0.8
O D:HOH769 4.8 22.6 1.0
CG D:PRO165 4.8 11.9 1.0
N D:PRO165 4.8 8.2 1.0
O D:PRO165 5.0 7.5 1.0
CA D:LEU174 5.0 4.2 1.0

Bromine binding site 8 out of 8 in 5hkb

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Bromine binding site 8 out of 8 in the Crystal Structure of the Cftr Inhibitory Factor Cif Bound to the Inhibitor KB2115


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 8 of Crystal Structure of the Cftr Inhibitory Factor Cif Bound to the Inhibitor KB2115 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Br401

b:15.1
occ:0.83
 BR1 D:64L401 0.0 15.1 0.8
C6 D:64L401 1.9 8.9 0.8
C7 D:64L401 2.8 9.2 0.8
C5 D:64L401 2.8 12.3 0.8
O4 D:64L401 3.1 9.9 0.8
C8 D:64L401 3.4 8.9 0.8
CE D:MET272 3.6 6.6 1.0
CG D:PHE275 3.6 4.5 1.0
CZ D:PHE164 3.6 6.2 1.0
CD1 D:PHE275 3.7 4.3 1.0
CG D:MET272 3.7 5.8 1.0
C9 D:64L401 3.9 3.9 0.8
C13 D:64L401 4.0 5.4 0.8
CB D:PHE275 4.0 4.9 1.0
CD2 D:PHE275 4.0 5.5 1.0
CE1 D:PHE164 4.0 6.8 1.0
SD D:MET272 4.1 5.5 1.0
C17 D:64L401 4.1 11.2 0.8
CB D:MET272 4.1 4.9 1.0
C4 D:64L401 4.2 15.1 0.8
CE1 D:PHE275 4.2 5.6 1.0
CE2 D:PHE164 4.2 6.5 1.0
CE2 D:PHE275 4.5 6.6 1.0
CZ D:PHE275 4.5 6.6 1.0
C18 D:64L401 4.7 13.2 0.8
CA D:MET272 4.7 5.4 1.0
CD D:PRO155 4.7 5.0 1.0
C10 D:64L401 4.8 2.3 0.8
C12 D:64L401 4.9 5.1 0.8
O D:MET272 4.9 5.7 1.0
CD1 D:PHE164 4.9 8.9 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: Wed Jul 10 23:48:30 2024

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