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Fluorine in PDB 3u5k: Crystal Structure of the First Bromodomain of Human BRD4 in Complex with Midazolam

Protein crystallography data

The structure of Crystal Structure of the First Bromodomain of Human BRD4 in Complex with Midazolam, PDB code: 3u5k was solved by P.Filippakopoulos, S.Picaud, I.Felletar, O.Fedorov, F.Von Delft, C.H.Arrowsmith, A.M.Edwards, J.Weigelt, C.Bountra, S.Knapp, Structuralgenomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.68 / 1.80
Space group P 31
Cell size a, b, c (Å), α, β, γ (°) 89.550, 89.550, 64.411, 90.00, 90.00, 120.00
R / Rfree (%) 21 / 26

Other elements in 3u5k:

The structure of Crystal Structure of the First Bromodomain of Human BRD4 in Complex with Midazolam also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of the First Bromodomain of Human BRD4 in Complex with Midazolam (pdb code 3u5k). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of the First Bromodomain of Human BRD4 in Complex with Midazolam, PDB code: 3u5k:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 3u5k

Go back to Fluorine Binding Sites List in 3u5k
Fluorine binding site 1 out of 4 in the Crystal Structure of the First Bromodomain of Human BRD4 in Complex with Midazolam


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 First Bromodomain of Human BRD4 in Complex with Midazolam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1

b:34.5
occ:1.00
FAB A:08J1 0.0 34.5 1.0
CAQ A:08J1 1.3 27.9 1.0
CAF A:08J1 2.3 35.1 1.0
CAT A:08J1 2.4 37.5 1.0
NAM A:08J1 2.8 19.7 1.0
CAO A:08J1 2.9 24.9 1.0
CAD A:08J1 3.6 41.4 1.0
CAG A:08J1 3.7 29.4 1.0
CAL A:08J1 4.0 27.1 1.0
O A:HOH187 4.1 13.1 1.0
CAE A:08J1 4.1 37.1 1.0
CAU A:08J1 4.2 30.2 1.0
CAK A:08J1 4.7 25.4 1.0

Fluorine binding site 2 out of 4 in 3u5k

Go back to Fluorine Binding Sites List in 3u5k
Fluorine binding site 2 out of 4 in the Crystal Structure of the First Bromodomain of Human BRD4 in Complex with Midazolam


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 First Bromodomain of Human BRD4 in Complex with Midazolam within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F2

b:52.1
occ:1.00
FAB B:08J2 0.0 52.1 1.0
CAQ B:08J2 1.4 36.0 1.0
CAT B:08J2 2.4 32.9 1.0
CAF B:08J2 2.4 28.6 1.0
O B:HOH232 2.8 24.8 1.0
CAO B:08J2 2.8 31.8 1.0
NAM B:08J2 2.9 29.4 1.0
CAG B:08J2 3.6 25.5 1.0
CAD B:08J2 3.7 54.5 1.0
CAU B:08J2 4.0 20.5 1.0
O B:HOH231 4.0 30.4 1.0
CAK B:08J2 4.1 32.6 1.0
CAL B:08J2 4.1 24.8 1.0
CAE B:08J2 4.1 49.6 1.0
CD2 B:LEU92 5.0 27.5 1.0

Fluorine binding site 3 out of 4 in 3u5k

Go back to Fluorine Binding Sites List in 3u5k
Fluorine binding site 3 out of 4 in the Crystal Structure of the First Bromodomain of Human BRD4 in Complex with Midazolam


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 First Bromodomain of Human BRD4 in Complex with Midazolam within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F3

b:40.8
occ:1.00
FAB C:08J3 0.0 40.8 1.0
CAQ C:08J3 1.4 60.2 1.0
CAF C:08J3 2.4 33.7 1.0
CAT C:08J3 2.4 53.0 1.0
NAM C:08J3 2.4 18.7 1.0
CAO C:08J3 2.7 34.6 1.0
CAL C:08J3 3.6 34.1 1.0
CAD C:08J3 3.6 42.0 1.0
CAG C:08J3 3.7 34.1 1.0
O C:HOH199 3.7 14.7 1.0
CAU C:08J3 4.0 25.8 1.0
CAE C:08J3 4.1 42.5 1.0
CAK C:08J3 4.5 26.8 1.0
CAS C:08J3 4.8 47.6 1.0
CB C:ILE146 4.8 22.7 1.0
CG2 C:ILE146 4.9 17.0 1.0

Fluorine binding site 4 out of 4 in 3u5k

Go back to Fluorine Binding Sites List in 3u5k
Fluorine binding site 4 out of 4 in the Crystal Structure of the First Bromodomain of Human BRD4 in Complex with Midazolam


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of the First Bromodomain of Human BRD4 in Complex with Midazolam within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F4

b:28.8
occ:1.00
FAB D:08J4 0.0 28.8 1.0
CAQ D:08J4 1.3 30.3 1.0
CAF D:08J4 2.4 59.8 1.0
CAT D:08J4 2.4 38.8 1.0
NAM D:08J4 2.6 18.4 1.0
CAO D:08J4 2.8 38.6 1.0
CAG D:08J4 3.6 21.3 1.0
CAD D:08J4 3.7 41.1 1.0
O D:HOH175 3.8 13.8 1.0
CAL D:08J4 3.9 28.8 1.0
CAU D:08J4 4.1 41.2 1.0
CAE D:08J4 4.1 36.0 1.0
CAK D:08J4 4.6 32.1 1.0
CB D:ILE146 4.9 23.1 1.0
CAS D:08J4 5.0 29.2 1.0

Reference:

P.Filippakopoulos, S.Picaud, O.Fedorov, M.Keller, M.Wrobel, O.Morgenstern, F.Bracher, S.Knapp. Benzodiazepines and Benzotriazepines As Protein Interaction Inhibitors Targeting Bromodomains of the Bet Family. Bioorg.Med.Chem. V. 20 1878 2012.
ISSN: ISSN 0968-0896
PubMed: 22137933
DOI: 10.1016/J.BMC.2011.10.080
Page generated: Sun Dec 13 11:56:11 2020

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