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Fluorine in PDB 5m8d: Tubulin MTD265-R1 Complex

Protein crystallography data

The structure of Tubulin MTD265-R1 Complex, PDB code: 5m8d was solved by T.Bohnacker, A.E.Prota, M.O.Steinmetz, M.P.Wymann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 68.10 / 2.25
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 104.180, 157.020, 179.980, 90.00, 90.00, 90.00
R / Rfree (%) 17 / 21

Other elements in 5m8d:

The structure of Tubulin MTD265-R1 Complex also contains other interesting chemical elements:

Magnesium (Mg) 5 atoms
Calcium (Ca) 5 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Tubulin MTD265-R1 Complex (pdb code 5m8d). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Tubulin MTD265-R1 Complex, PDB code: 5m8d:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 5m8d

Go back to Fluorine Binding Sites List in 5m8d
Fluorine binding site 1 out of 3 in the Tubulin MTD265-R1 Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Tubulin MTD265-R1 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F501

b:71.6
occ:0.80
FAZ B:UGI501 0.0 71.6 0.8
CAY B:UGI501 1.3 73.2 0.8
FBA B:UGI501 2.0 85.5 0.8
FBB B:UGI501 2.0 62.3 0.8
CAS B:UGI501 2.2 66.3 0.8
CAR B:UGI501 2.6 64.2 0.8
CG1 B:ILE318 3.4 55.4 1.0
CB B:ALA354 3.4 52.8 1.0
CAH B:UGI501 3.6 59.2 0.8
CB B:CYS241 3.6 57.0 1.0
SG B:CYS241 3.7 76.5 1.0
O B:HOH659 3.7 50.3 1.0
CD1 B:ILE318 3.9 55.4 0.7
CAQ B:UGI501 4.0 73.0 0.8
C4 B:UGI501 4.3 50.5 0.8
C5 B:UGI501 4.6 51.4 0.8
CAO B:UGI501 4.7 68.7 0.8
CB B:ILE318 4.7 52.3 1.0
NAX B:UGI501 4.8 77.8 0.8
CD1 B:LEU248 4.8 0.5 1.0
CA B:ALA354 4.8 56.0 1.0
NAP B:UGI501 4.8 71.6 0.8
CG2 B:ILE318 4.9 52.6 1.0
CB B:ALA316 4.9 38.1 1.0
CD2 B:LEU248 5.0 0.8 1.0

Fluorine binding site 2 out of 3 in 5m8d

Go back to Fluorine Binding Sites List in 5m8d
Fluorine binding site 2 out of 3 in the Tubulin MTD265-R1 Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Tubulin MTD265-R1 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F501

b:85.5
occ:0.80
FBA B:UGI501 0.0 85.5 0.8
CAY B:UGI501 1.2 73.2 0.8
FBB B:UGI501 2.0 62.3 0.8
FAZ B:UGI501 2.0 71.6 0.8
CAS B:UGI501 2.2 66.3 0.8
CAH B:UGI501 2.9 59.2 0.8
C5 B:UGI501 2.9 51.4 0.8
CAR B:UGI501 3.2 64.2 0.8
C4 B:UGI501 3.2 50.5 0.8
CD1 B:LEU248 3.5 0.5 1.0
CD2 B:LEU248 3.7 0.8 1.0
SG B:CYS241 3.8 76.5 1.0
CD2 B:LEU255 3.9 64.3 1.0
CB B:CYS241 4.0 57.0 1.0
C6 B:UGI501 4.0 57.7 0.8
CG B:LEU248 4.1 0.9 1.0
CAJ B:UGI501 4.1 43.9 0.8
CAO B:UGI501 4.2 68.7 0.8
CB B:ALA250 4.3 72.1 1.0
CB B:ALA354 4.3 52.8 1.0
N3 B:UGI501 4.3 53.4 0.8
CAQ B:UGI501 4.4 73.0 0.8
NAG B:UGI501 4.5 56.7 0.8
NAP B:UGI501 4.8 71.6 0.8
N1 B:UGI501 5.0 56.3 0.8

Fluorine binding site 3 out of 3 in 5m8d

Go back to Fluorine Binding Sites List in 5m8d
Fluorine binding site 3 out of 3 in the Tubulin MTD265-R1 Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Tubulin MTD265-R1 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F501

b:62.3
occ:0.80
FBB B:UGI501 0.0 62.3 0.8
CAY B:UGI501 1.2 73.2 0.8
FBA B:UGI501 2.0 85.5 0.8
FAZ B:UGI501 2.0 71.6 0.8
CAS B:UGI501 2.2 66.3 0.8
CAH B:UGI501 2.8 59.2 0.8
C4 B:UGI501 2.9 50.5 0.8
C5 B:UGI501 3.3 51.4 0.8
CAR B:UGI501 3.4 64.2 0.8
N3 B:UGI501 3.5 53.4 0.8
CG B:LYS352 3.7 65.3 1.0
CB B:ALA354 3.8 52.8 1.0
CB B:ALA316 4.0 38.1 1.0
C6 B:UGI501 4.1 57.7 0.8
CAO B:UGI501 4.2 68.7 0.8
CD1 B:LEU248 4.2 0.5 1.0
C2 B:UGI501 4.3 56.9 0.8
CB B:LYS352 4.5 50.8 1.0
CAQ B:UGI501 4.6 73.0 0.8
N1 B:UGI501 4.6 56.3 0.8
CG1 B:ILE318 4.6 55.4 1.0
N B:ALA354 4.7 51.8 1.0
O B:LYS352 4.7 52.4 1.0
CA B:ALA316 4.8 54.7 1.0
CA B:ALA354 4.8 56.0 1.0
NAP B:UGI501 4.9 71.6 0.8
CE B:LYS352 4.9 85.2 1.0
CD B:LYS352 4.9 75.8 1.0
CD1 B:ILE318 5.0 55.4 0.7

Reference:

T.Bohnacker, A.E.Prota, F.Beaufils, J.E.Burke, A.Melone, A.J.Inglis, D.Rageot, A.M.Sele, V.Cmiljanovic, N.Cmiljanovic, K.Bargsten, A.Aher, A.Akhmanova, J.F.Diaz, D.Fabbro, M.Zvelebil, R.L.Williams, M.O.Steinmetz, M.P.Wymann. Deconvolution of Buparlisib'S Mechanism of Action Defines Specific PI3K and Tubulin Inhibitors For Therapeutic Intervention. Nat Commun V. 8 14683 2017.
ISSN: ESSN 2041-1723
PubMed: 28276440
DOI: 10.1038/NCOMMS14683
Page generated: Tue Jul 15 05:12:27 2025

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