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Fluorine in PDB 4inb: Crystal Structure of the N-Terminal Domain of Hiv-1 Capsid in Complex with Benzodiazepine Inhibitor

Protein crystallography data

The structure of Crystal Structure of the N-Terminal Domain of Hiv-1 Capsid in Complex with Benzodiazepine Inhibitor, PDB code: 4inb was solved by R.Coulombe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 22.42 / 1.80
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 68.950, 89.210, 39.270, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Other elements in 4inb:

The structure of Crystal Structure of the N-Terminal Domain of Hiv-1 Capsid in Complex with Benzodiazepine Inhibitor also contains other interesting chemical elements:

Sodium (Na) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of the N-Terminal Domain of Hiv-1 Capsid in Complex with Benzodiazepine Inhibitor (pdb code 4inb). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of the N-Terminal Domain of Hiv-1 Capsid in Complex with Benzodiazepine Inhibitor, PDB code: 4inb:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 4inb

Go back to Fluorine Binding Sites List in 4inb
Fluorine binding site 1 out of 3 in the Crystal Structure of the N-Terminal Domain of Hiv-1 Capsid in Complex with Benzodiazepine Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of the N-Terminal Domain of Hiv-1 Capsid in Complex with Benzodiazepine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F201

b:27.9
occ:1.00
F26 A:1F6201 0.0 27.9 1.0
C25 A:1F6201 1.4 27.0 1.0
F28 A:1F6201 2.2 33.2 1.0
F27 A:1F6201 2.2 31.2 1.0
C1 A:1F6201 2.4 23.2 1.0
C2 A:1F6201 2.8 21.6 1.0
CZ2 A:TRP23 3.7 25.7 1.0
CD1 A:LEU138 3.7 20.8 1.0
C6 A:1F6201 3.7 19.8 1.0
CG1 A:VAL36 3.7 29.9 1.0
CD1 A:PHE40 3.9 23.4 1.0
CB A:PHE40 4.1 22.4 1.0
CG A:PHE40 4.1 21.8 1.0
NE1 A:TRP23 4.2 23.9 1.0
CD2 A:LEU138 4.2 19.8 1.0
C3 A:1F6201 4.2 20.8 1.0
CE2 A:TRP23 4.3 24.8 1.0
CG2 A:VAL27 4.4 29.5 1.0
CG A:LEU138 4.6 18.7 1.0
CE1 A:PHE40 4.6 23.6 1.0
CH2 A:TRP23 4.7 26.8 1.0
C18 A:1F6201 4.8 22.2 1.0
C23 A:1F6201 4.8 23.3 1.0
C5 A:1F6201 4.8 18.3 1.0
N7 A:1F6201 5.0 21.7 1.0

Fluorine binding site 2 out of 3 in 4inb

Go back to Fluorine Binding Sites List in 4inb
Fluorine binding site 2 out of 3 in the Crystal Structure of the N-Terminal Domain of Hiv-1 Capsid in Complex with Benzodiazepine Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of the N-Terminal Domain of Hiv-1 Capsid in Complex with Benzodiazepine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F201

b:31.2
occ:1.00
F27 A:1F6201 0.0 31.2 1.0
C25 A:1F6201 1.4 27.0 1.0
F26 A:1F6201 2.2 27.9 1.0
F28 A:1F6201 2.2 33.2 1.0
C1 A:1F6201 2.4 23.2 1.0
C6 A:1F6201 2.9 19.8 1.0
CD1 A:PHE40 3.3 23.4 1.0
CE1 A:PHE40 3.3 23.6 1.0
C2 A:1F6201 3.6 21.6 1.0
CD2 A:LEU56 3.6 18.2 1.0
CD1 A:LEU138 3.8 20.8 1.0
CG A:PHE40 4.0 21.8 1.0
CD2 A:LEU138 4.0 19.8 1.0
CZ A:PHE40 4.1 22.8 1.0
C5 A:1F6201 4.3 18.3 1.0
CG A:LEU138 4.5 18.7 1.0
NE1 A:TRP23 4.5 23.9 1.0
CD2 A:PHE40 4.6 22.9 1.0
CB A:PHE40 4.7 22.4 1.0
CE2 A:PHE40 4.7 23.8 1.0
CG2 A:ILE134 4.8 15.6 1.0
C3 A:1F6201 4.8 20.8 1.0
CZ2 A:TRP23 4.9 25.7 1.0
CG A:LEU56 5.0 16.1 1.0

Fluorine binding site 3 out of 3 in 4inb

Go back to Fluorine Binding Sites List in 4inb
Fluorine binding site 3 out of 3 in the Crystal Structure of the N-Terminal Domain of Hiv-1 Capsid in Complex with Benzodiazepine Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of the N-Terminal Domain of Hiv-1 Capsid in Complex with Benzodiazepine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F201

b:33.2
occ:1.00
F28 A:1F6201 0.0 33.2 1.0
C25 A:1F6201 1.4 27.0 1.0
F26 A:1F6201 2.2 27.9 1.0
F27 A:1F6201 2.2 31.2 1.0
C1 A:1F6201 2.4 23.2 1.0
NE1 A:TRP23 2.8 23.9 1.0
C6 A:1F6201 3.2 19.8 1.0
C2 A:1F6201 3.3 21.6 1.0
CG2 A:VAL59 3.5 17.3 1.0
CE2 A:TRP23 3.5 24.8 1.0
CZ2 A:TRP23 3.7 25.7 1.0
CG2 A:VAL27 3.8 29.5 1.0
CD1 A:TRP23 3.9 22.7 1.0
CG1 A:VAL59 4.0 20.7 1.0
CB A:VAL59 4.1 16.8 1.0
CD1 A:PHE40 4.1 23.4 1.0
CE1 A:PHE40 4.5 23.6 1.0
C5 A:1F6201 4.5 18.3 1.0
C3 A:1F6201 4.6 20.8 1.0
CD2 A:TRP23 4.8 24.4 1.0
CG A:TRP23 4.9 23.4 1.0
CG A:PHE40 4.9 21.8 1.0

Reference:

N.Goudreau, R.Coulombe, A.M.Faucher, C.Grand-Maitre, J.E.Lacoste, C.T.Lemke, E.Malenfant, Y.Bousquet, L.Fader, B.Simoneau, J.F.Mercier, S.Titolo, S.W.Mason. Monitoring Binding of Hiv-1 Capsid Assembly Inhibitors Using (19) F Ligand-and (15) N Protein-Based uc(Nmr) and X-Ray Crystallography: Early Hit Validation of A Benzodiazepine Series. Chemmedchem V. 8 405 2013.
ISSN: ISSN 1860-7179
PubMed: 23401268
DOI: 10.1002/CMDC.201200580
Page generated: Sun Dec 13 12:04:41 2020

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