Fluorine in PDB 5m8g: Tubulin-MTD265 Complex
Protein crystallography data
The structure of Tubulin-MTD265 Complex, PDB code: 5m8g
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)
|
49.29 /
2.15
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
104.768,
157.508,
179.235,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
17.1 /
20.8
|
Other elements in 5m8g:
The structure of Tubulin-MTD265 Complex also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Tubulin-MTD265 Complex
(pdb code 5m8g). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the
Tubulin-MTD265 Complex, PDB code: 5m8g:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
6;
Fluorine binding site 1 out
of 6 in 5m8g
Go back to
Fluorine Binding Sites List in 5m8g
Fluorine binding site 1 out
of 6 in the Tubulin-MTD265 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 Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F501
b:60.6
occ:1.00
|
FAZ
|
B:918501
|
0.0
|
60.6
|
1.0
|
CAO
|
B:918501
|
1.3
|
57.7
|
1.0
|
FBB
|
B:918501
|
2.1
|
56.0
|
1.0
|
FBA
|
B:918501
|
2.1
|
44.7
|
1.0
|
CAN
|
B:918501
|
2.2
|
47.3
|
1.0
|
N3
|
B:918501
|
2.8
|
39.0
|
1.0
|
CAH
|
B:918501
|
3.0
|
45.5
|
1.0
|
CAM
|
B:918501
|
3.2
|
41.0
|
1.0
|
C4
|
B:918501
|
3.3
|
37.9
|
1.0
|
CAU
|
B:918501
|
3.4
|
42.5
|
1.0
|
CD1
|
B:LEU248
|
3.7
|
70.2
|
1.0
|
CD2
|
B:LEU255
|
3.7
|
46.8
|
1.0
|
C2
|
B:918501
|
3.8
|
39.7
|
1.0
|
SG
|
B:CYS241
|
3.9
|
63.1
|
1.0
|
CB
|
B:CYS241
|
4.0
|
50.5
|
1.0
|
NAG
|
B:918501
|
4.1
|
46.0
|
1.0
|
CB
|
B:ALA250
|
4.1
|
53.2
|
1.0
|
CAJ
|
B:918501
|
4.3
|
48.2
|
1.0
|
CAL
|
B:918501
|
4.4
|
48.5
|
1.0
|
CD2
|
B:LEU248
|
4.4
|
66.8
|
1.0
|
CG
|
B:LEU248
|
4.6
|
69.9
|
1.0
|
C5
|
B:918501
|
4.6
|
37.2
|
1.0
|
CAT
|
B:918501
|
4.6
|
47.4
|
1.0
|
NZ
|
B:LYS352
|
4.7
|
75.0
|
1.0
|
NAK
|
B:918501
|
4.8
|
44.5
|
1.0
|
CB
|
B:LEU248
|
4.9
|
69.4
|
1.0
|
N1
|
B:918501
|
4.9
|
34.2
|
1.0
|
CB
|
B:ALA354
|
4.9
|
41.6
|
1.0
|
|
Fluorine binding site 2 out
of 6 in 5m8g
Go back to
Fluorine Binding Sites List in 5m8g
Fluorine binding site 2 out
of 6 in the Tubulin-MTD265 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 Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F501
b:44.7
occ:1.00
|
FBA
|
B:918501
|
0.0
|
44.7
|
1.0
|
CAO
|
B:918501
|
1.3
|
57.7
|
1.0
|
FAZ
|
B:918501
|
2.1
|
60.6
|
1.0
|
FBB
|
B:918501
|
2.1
|
56.0
|
1.0
|
CAN
|
B:918501
|
2.2
|
47.3
|
1.0
|
CAH
|
B:918501
|
2.8
|
45.5
|
1.0
|
C4
|
B:918501
|
2.8
|
37.9
|
1.0
|
N3
|
B:918501
|
2.9
|
39.0
|
1.0
|
CAM
|
B:918501
|
3.4
|
41.0
|
1.0
|
C5
|
B:918501
|
3.7
|
37.2
|
1.0
|
CG
|
B:LYS352
|
3.7
|
45.1
|
1.0
|
C2
|
B:918501
|
3.7
|
39.7
|
1.0
|
CB
|
B:ALA354
|
3.8
|
41.6
|
1.0
|
NZ
|
B:LYS352
|
4.1
|
75.0
|
1.0
|
CAJ
|
B:918501
|
4.1
|
48.2
|
1.0
|
CD1
|
B:LEU248
|
4.3
|
70.2
|
1.0
|
CAU
|
B:918501
|
4.4
|
42.5
|
1.0
|
C6
|
B:918501
|
4.4
|
38.7
|
1.0
|
CB
|
B:LYS352
|
4.4
|
39.8
|
1.0
|
NAG
|
B:918501
|
4.4
|
46.0
|
1.0
|
N1
|
B:918501
|
4.4
|
34.2
|
1.0
|
CB
|
B:ALA316
|
4.5
|
41.4
|
1.0
|
CAL
|
B:918501
|
4.6
|
48.5
|
1.0
|
CD2
|
B:LEU248
|
4.8
|
66.8
|
1.0
|
NAK
|
B:918501
|
4.8
|
44.5
|
1.0
|
CG1
|
B:ILE318
|
4.9
|
49.0
|
1.0
|
CD
|
B:LYS352
|
4.9
|
51.6
|
1.0
|
|
Fluorine binding site 3 out
of 6 in 5m8g
Go back to
Fluorine Binding Sites List in 5m8g
Fluorine binding site 3 out
of 6 in the Tubulin-MTD265 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 Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F501
b:56.0
occ:1.00
|
FBB
|
B:918501
|
0.0
|
56.0
|
1.0
|
CAO
|
B:918501
|
1.3
|
57.7
|
1.0
|
FAZ
|
B:918501
|
2.1
|
60.6
|
1.0
|
FBA
|
B:918501
|
2.1
|
44.7
|
1.0
|
CAN
|
B:918501
|
2.3
|
47.3
|
1.0
|
CAM
|
B:918501
|
2.6
|
41.0
|
1.0
|
CB
|
B:CYS241
|
3.5
|
50.5
|
1.0
|
CAH
|
B:918501
|
3.6
|
45.5
|
1.0
|
CB
|
B:ALA354
|
3.6
|
41.6
|
1.0
|
CD1
|
B:LEU248
|
3.7
|
70.2
|
1.0
|
SG
|
B:CYS241
|
3.8
|
63.1
|
1.0
|
CG1
|
B:ILE318
|
3.8
|
49.0
|
1.0
|
O
|
B:HOH679
|
3.9
|
50.2
|
1.0
|
CAL
|
B:918501
|
4.0
|
48.5
|
1.0
|
C4
|
B:918501
|
4.3
|
37.9
|
1.0
|
N3
|
B:918501
|
4.3
|
39.0
|
1.0
|
CD1
|
B:ILE318
|
4.5
|
54.7
|
0.8
|
CAJ
|
B:918501
|
4.7
|
48.2
|
1.0
|
NAP
|
B:918501
|
4.8
|
54.8
|
1.0
|
NAK
|
B:918501
|
4.8
|
44.5
|
1.0
|
CA
|
B:CYS241
|
4.9
|
51.1
|
1.0
|
|
Fluorine binding site 4 out
of 6 in 5m8g
Go back to
Fluorine Binding Sites List in 5m8g
Fluorine binding site 4 out
of 6 in the Tubulin-MTD265 Complex
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 4 of Tubulin-MTD265 Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:F501
b:59.5
occ:1.00
|
FAZ
|
D:918501
|
0.0
|
59.5
|
1.0
|
CAO
|
D:918501
|
1.3
|
60.2
|
1.0
|
FBA
|
D:918501
|
2.1
|
56.3
|
1.0
|
FBB
|
D:918501
|
2.1
|
52.9
|
1.0
|
CAN
|
D:918501
|
2.2
|
52.5
|
1.0
|
N3
|
D:918501
|
2.8
|
48.3
|
1.0
|
CAH
|
D:918501
|
3.0
|
44.2
|
1.0
|
CD1
|
D:LEU248
|
3.0
|
92.7
|
1.0
|
CAM
|
D:918501
|
3.2
|
48.7
|
1.0
|
C4
|
D:918501
|
3.3
|
47.1
|
1.0
|
CAU
|
D:918501
|
3.5
|
55.5
|
1.0
|
CD2
|
D:LEU255
|
3.7
|
50.4
|
1.0
|
C2
|
D:918501
|
3.8
|
54.9
|
1.0
|
CB
|
D:CYS241
|
3.9
|
56.5
|
1.0
|
SG
|
D:CYS241
|
3.9
|
68.7
|
1.0
|
NAG
|
D:918501
|
4.1
|
57.4
|
1.0
|
CAJ
|
D:918501
|
4.3
|
47.4
|
1.0
|
CG
|
D:LEU248
|
4.4
|
84.2
|
1.0
|
CAL
|
D:918501
|
4.4
|
51.9
|
1.0
|
CB
|
D:ALA250
|
4.5
|
61.5
|
1.0
|
C5
|
D:918501
|
4.6
|
49.0
|
1.0
|
CB
|
D:ALA354
|
4.6
|
44.3
|
1.0
|
CD2
|
D:LEU248
|
4.7
|
77.8
|
1.0
|
CAT
|
D:918501
|
4.7
|
57.6
|
1.0
|
NAK
|
D:918501
|
4.8
|
56.6
|
1.0
|
N1
|
D:918501
|
4.9
|
44.3
|
1.0
|
CG
|
D:LYS352
|
5.0
|
46.1
|
1.0
|
|
Fluorine binding site 5 out
of 6 in 5m8g
Go back to
Fluorine Binding Sites List in 5m8g
Fluorine binding site 5 out
of 6 in the Tubulin-MTD265 Complex
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 5 of Tubulin-MTD265 Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:F501
b:56.3
occ:1.00
|
FBA
|
D:918501
|
0.0
|
56.3
|
1.0
|
CAO
|
D:918501
|
1.3
|
60.2
|
1.0
|
FBB
|
D:918501
|
2.0
|
52.9
|
1.0
|
FAZ
|
D:918501
|
2.1
|
59.5
|
1.0
|
CAN
|
D:918501
|
2.2
|
52.5
|
1.0
|
CAM
|
D:918501
|
2.6
|
48.7
|
1.0
|
CB
|
D:ALA354
|
3.5
|
44.3
|
1.0
|
CAH
|
D:918501
|
3.5
|
44.2
|
1.0
|
CB
|
D:CYS241
|
3.6
|
56.5
|
1.0
|
CG1
|
D:ILE318
|
3.7
|
60.4
|
1.0
|
CD1
|
D:LEU248
|
3.7
|
92.7
|
1.0
|
SG
|
D:CYS241
|
3.8
|
68.7
|
1.0
|
O
|
D:HOH624
|
3.8
|
50.8
|
1.0
|
CAL
|
D:918501
|
4.0
|
51.9
|
1.0
|
C4
|
D:918501
|
4.2
|
47.1
|
1.0
|
CD1
|
D:ILE318
|
4.3
|
63.0
|
0.6
|
N3
|
D:918501
|
4.4
|
48.3
|
1.0
|
CAJ
|
D:918501
|
4.6
|
47.4
|
1.0
|
NAK
|
D:918501
|
4.8
|
56.6
|
1.0
|
NAP
|
D:918501
|
4.8
|
49.9
|
1.0
|
CA
|
D:CYS241
|
4.9
|
51.0
|
1.0
|
CA
|
D:ALA354
|
4.9
|
48.3
|
1.0
|
CB
|
D:ALA316
|
4.9
|
34.9
|
1.0
|
|
Fluorine binding site 6 out
of 6 in 5m8g
Go back to
Fluorine Binding Sites List in 5m8g
Fluorine binding site 6 out
of 6 in the Tubulin-MTD265 Complex
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 6 of Tubulin-MTD265 Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:F501
b:52.9
occ:1.00
|
FBB
|
D:918501
|
0.0
|
52.9
|
1.0
|
CAO
|
D:918501
|
1.3
|
60.2
|
1.0
|
FBA
|
D:918501
|
2.0
|
56.3
|
1.0
|
FAZ
|
D:918501
|
2.1
|
59.5
|
1.0
|
CAN
|
D:918501
|
2.3
|
52.5
|
1.0
|
CAH
|
D:918501
|
2.8
|
44.2
|
1.0
|
C4
|
D:918501
|
2.9
|
47.1
|
1.0
|
N3
|
D:918501
|
3.0
|
48.3
|
1.0
|
CG
|
D:LYS352
|
3.4
|
46.1
|
1.0
|
CAM
|
D:918501
|
3.4
|
48.7
|
1.0
|
C5
|
D:918501
|
3.7
|
49.0
|
1.0
|
CB
|
D:ALA354
|
3.8
|
44.3
|
1.0
|
C2
|
D:918501
|
3.8
|
54.9
|
1.0
|
CD1
|
D:LEU248
|
3.9
|
92.7
|
1.0
|
CB
|
D:ALA316
|
4.1
|
34.9
|
1.0
|
CAJ
|
D:918501
|
4.1
|
47.4
|
1.0
|
CB
|
D:LYS352
|
4.3
|
44.2
|
1.0
|
C6
|
D:918501
|
4.5
|
50.8
|
1.0
|
N1
|
D:918501
|
4.5
|
44.3
|
1.0
|
CAU
|
D:918501
|
4.5
|
55.5
|
1.0
|
NAG
|
D:918501
|
4.6
|
57.4
|
1.0
|
CE
|
D:LYS352
|
4.6
|
65.5
|
1.0
|
CAL
|
D:918501
|
4.6
|
51.9
|
1.0
|
CD
|
D:LYS352
|
4.6
|
59.5
|
1.0
|
N
|
D:ALA354
|
4.9
|
47.3
|
1.0
|
NAK
|
D:918501
|
4.9
|
56.6
|
1.0
|
CA
|
D:ALA354
|
4.9
|
48.3
|
1.0
|
CG1
|
D:ILE318
|
4.9
|
60.4
|
1.0
|
|
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: Thu Aug 1 11:38:34 2024
|