Fluorine in PDB 8c0f: Tubulin-PTC596 Complex

Protein crystallography data

The structure of Tubulin-PTC596 Complex, PDB code: 8c0f was solved by A.E.Prota, T.Muehlethaler, M.Weetall, M.O.Steinmetz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.55 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 104.68, 158.26, 180.54, 90, 90, 90
R / Rfree (%) 19.4 / 22.5

Other elements in 8c0f:

The structure of Tubulin-PTC596 Complex also contains other interesting chemical elements:

Calcium (Ca) 2 atoms
Magnesium (Mg) 5 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Tubulin-PTC596 Complex (pdb code 8c0f). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 5 binding sites of Fluorine where determined in the Tubulin-PTC596 Complex, PDB code: 8c0f:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5;

Fluorine binding site 1 out of 5 in 8c0f

Go back to Fluorine Binding Sites List in 8c0f
Fluorine binding site 1 out of 5 in the Tubulin-PTC596 Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Tubulin-PTC596 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F505

b:64.9
occ:0.84
 F24 B:SOZ505 0.0 64.9 0.8
C21 B:SOZ505 1.3 65.2 0.8
C22 B:SOZ505 2.3 57.8 0.8
C20 B:SOZ505 2.4 72.6 0.8
H201 B:SOZ505 2.5 87.2 0.8
H221 B:SOZ505 2.6 69.4 0.8
CB B:ALA316 3.3 53.7 1.0
O B:ALA317 3.4 71.0 1.0
N B:ALA317 3.4 57.5 1.0
O B:LYS352 3.5 56.9 1.0
C18 B:SOZ505 3.6 64.5 0.8
C19 B:SOZ505 3.6 66.3 0.8
CA B:ALA316 3.7 60.1 1.0
CG B:LYS352 3.7 71.7 1.0
C B:ALA316 3.9 58.6 1.0
C B:LYS352 4.0 62.9 1.0
CB B:ALA354 4.1 59.8 1.0
C B:ALA317 4.1 60.0 1.0
CB B:LYS352 4.1 60.7 1.0
C17 B:SOZ505 4.1 66.8 0.8
N B:ALA354 4.2 60.4 1.0
H191 B:SOZ505 4.4 79.6 0.8
CA B:ALA317 4.4 56.5 1.0
N B:THR353 4.4 62.0 1.0
C B:THR353 4.5 60.9 1.0
H61 B:SOZ505 4.5 75.2 0.8
CA B:THR353 4.6 65.5 1.0
CA B:LYS352 4.7 61.2 1.0
H51 B:SOZ505 4.7 80.3 0.8
C6 B:SOZ505 4.7 62.6 0.8
CA B:ALA354 4.8 61.4 1.0
CG1 B:ILE318 4.8 85.9 1.0
C5 B:SOZ505 4.8 66.9 0.8
N14 B:SOZ505 4.9 64.9 0.8
O B:ALA316 4.9 59.5 1.0
CD1 B:LEU248 5.0 78.8 1.0

Fluorine binding site 2 out of 5 in 8c0f

Go back to Fluorine Binding Sites List in 8c0f
Fluorine binding site 2 out of 5 in the Tubulin-PTC596 Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Tubulin-PTC596 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F505

b:69.7
occ:0.84
 F27 B:SOZ505 0.0 69.7 0.8
C26 B:SOZ505 1.4 56.6 0.8
F29 B:SOZ505 2.2 51.1 0.8
F28 B:SOZ505 2.2 58.2 0.8
C1 B:SOZ505 2.4 55.1 0.8
H21 B:SOZ505 2.5 64.7 0.8
C2 B:SOZ505 2.8 53.8 0.8
CB B:LYS352 3.0 60.7 1.0
N B:LYS352 3.1 51.6 1.0
C B:VAL351 3.5 51.6 1.0
O B:ASN350 3.5 54.6 1.0
CA B:LYS352 3.5 61.2 1.0
C B:ASN350 3.6 54.0 1.0
C6 B:SOZ505 3.6 62.6 0.8
O B:HOH701 3.6 70.2 1.0
O B:VAL315 3.7 59.5 1.0
N B:VAL351 3.7 52.2 1.0
CG2 A:VAL181 3.8 65.2 1.0
H61 B:SOZ505 3.8 75.2 0.8
CA B:VAL351 3.9 54.0 1.0
C3 B:SOZ505 4.1 50.8 0.8
O B:VAL351 4.2 61.0 1.0
CA B:ASN350 4.2 52.0 1.0
CG B:LYS352 4.3 71.7 1.0
O B:ASN349 4.3 59.2 1.0
H31 B:SOZ505 4.7 61.0 0.8
C B:VAL315 4.7 58.4 1.0
C5 B:SOZ505 4.7 66.9 0.8
CD B:LYS352 4.8 73.3 1.0
C B:LYS352 4.9 62.9 1.0
N B:VAL315 4.9 48.9 1.0
C4 B:SOZ505 4.9 61.0 0.8

Fluorine binding site 3 out of 5 in 8c0f

Go back to Fluorine Binding Sites List in 8c0f
Fluorine binding site 3 out of 5 in the Tubulin-PTC596 Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Tubulin-PTC596 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F505

b:58.2
occ:0.84
 F28 B:SOZ505 0.0 58.2 0.8
C26 B:SOZ505 1.4 56.6 0.8
F29 B:SOZ505 2.2 51.1 0.8
F27 B:SOZ505 2.2 69.7 0.8
C1 B:SOZ505 2.3 55.1 0.8
H61 B:SOZ505 2.4 75.2 0.8
O B:VAL315 2.6 59.5 1.0
C6 B:SOZ505 2.7 62.6 0.8
C B:VAL315 3.2 58.4 1.0
SD B:MET259 3.3 57.5 1.0
CB B:LYS352 3.5 60.7 1.0
C2 B:SOZ505 3.6 53.8 0.8
N B:ALA316 3.7 51.9 1.0
N B:LYS352 3.7 51.6 1.0
CA B:ALA316 3.8 60.1 1.0
N B:VAL315 3.8 48.9 1.0
CB B:ALA316 3.9 53.7 1.0
H21 B:SOZ505 3.9 64.7 0.8
O B:ASN350 4.0 54.6 1.0
C5 B:SOZ505 4.1 66.9 0.8
CA B:VAL315 4.2 52.5 1.0
CA B:LYS352 4.2 61.2 1.0
CB B:THR314 4.4 53.1 1.0
C B:VAL351 4.6 51.6 1.0
C B:ASN350 4.6 54.0 1.0
CE B:MET259 4.6 47.0 1.0
CG B:MET259 4.6 57.0 1.0
H51 B:SOZ505 4.6 80.3 0.8
CA B:VAL351 4.7 54.0 1.0
CG B:LYS352 4.7 71.7 1.0
C B:THR314 4.7 50.2 1.0
C3 B:SOZ505 4.7 50.8 0.8
O B:ASN258 4.9 58.7 1.0
OG1 B:THR314 4.9 49.0 1.0
O B:LYS352 4.9 56.9 1.0
C4 B:SOZ505 4.9 61.0 0.8
N B:VAL351 5.0 52.2 1.0
CA B:THR314 5.0 47.8 1.0

Fluorine binding site 4 out of 5 in 8c0f

Go back to Fluorine Binding Sites List in 8c0f
Fluorine binding site 4 out of 5 in the Tubulin-PTC596 Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Tubulin-PTC596 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F505

b:51.1
occ:0.84
 F29 B:SOZ505 0.0 51.1 0.8
C26 B:SOZ505 1.4 56.6 0.8
F27 B:SOZ505 2.2 69.7 0.8
F28 B:SOZ505 2.2 58.2 0.8
C1 B:SOZ505 2.4 55.1 0.8
O B:ASN258 3.0 58.7 1.0
C2 B:SOZ505 3.1 53.8 0.8
H21 B:SOZ505 3.2 64.7 0.8
C6 B:SOZ505 3.3 62.6 0.8
H61 B:SOZ505 3.4 75.2 0.8
CG2 A:VAL181 3.4 65.2 1.0
C B:ASN258 3.6 47.6 1.0
CB B:THR314 3.7 53.1 1.0
CB B:ASN258 3.8 51.2 1.0
O B:ASN350 3.9 54.6 1.0
SD B:MET259 4.0 57.5 1.0
CG2 B:THR314 4.0 42.3 1.0
CA B:ASN258 4.3 47.3 1.0
C B:ASN350 4.4 54.0 1.0
N B:MET259 4.4 45.9 1.0
C3 B:SOZ505 4.4 50.8 0.8
OG1 B:THR314 4.4 49.0 1.0
O B:VAL315 4.5 59.5 1.0
C5 B:SOZ505 4.5 66.9 0.8
CA B:MET259 4.5 43.5 1.0
N B:VAL315 4.6 48.9 1.0
CA B:THR314 4.6 47.8 1.0
CA B:ASN350 4.7 52.0 1.0
CB A:VAL181 4.7 57.5 1.0
CB B:LYS352 4.8 60.7 1.0
CG B:MET259 4.8 57.0 1.0
CG B:ASN258 4.9 54.6 1.0
C4 B:SOZ505 5.0 61.0 0.8

Fluorine binding site 5 out of 5 in 8c0f

Go back to Fluorine Binding Sites List in 8c0f
Fluorine binding site 5 out of 5 in the Tubulin-PTC596 Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Tubulin-PTC596 Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F505

b:58.9
occ:0.84
 F30 B:SOZ505 0.0 58.9 0.8
C13 B:SOZ505 1.3 62.6 0.8
C12 B:SOZ505 2.4 57.8 0.8
C8 B:SOZ505 2.4 55.7 0.8
H71 B:SOZ505 2.5 71.9 0.8
H312 B:SOZ505 2.5 77.8 0.8
N31 B:SOZ505 2.8 64.8 0.8
N7 B:SOZ505 2.8 59.8 0.8
CB B:LYS254 3.4 44.6 1.0
CD B:LYS254 3.4 47.5 1.0
O B:HOH697 3.5 64.1 1.0
N11 B:SOZ505 3.6 51.1 0.8
N9 B:SOZ505 3.6 52.7 0.8
H311 B:SOZ505 3.6 77.8 0.8
O B:HOH678 3.8 64.5 1.0
CD2 B:LEU248 3.9 56.2 1.0
C10 B:SOZ505 4.0 53.4 0.8
CG B:LYS254 4.0 46.2 1.0
OD1 A:ASN101 4.1 59.4 1.0
C4 B:SOZ505 4.3 61.0 0.8
O A:THR179 4.3 111.4 1.0
CG B:LEU248 4.7 77.0 1.0
CA B:LYS254 4.7 43.4 1.0
CE B:LYS254 4.7 49.3 1.0
C B:LYS254 4.7 53.7 1.0
CD1 B:LEU248 4.7 78.8 1.0
CB B:LEU248 4.7 84.7 1.0
H31 B:SOZ505 4.8 61.0 0.8
ND2 B:ASN258 4.8 60.8 1.0
NZ B:LYS254 4.9 54.6 1.0
O B:LYS254 5.0 42.5 1.0

Reference:

F.Jernigan, A.Branstrom, J.D.Baird, L.Cao, M.Dali, B.Furia, M.J.Kim, K.O'keefe, R.Kong, O.L.Laskin, J.M.Colacino, M.Pykett, A.Mollin, J.Sheedy, M.Dumble, Y.-C.Moon, R.Sheridan, T.Muehlethaler, R.J.Spiegel, A.E.Prota, M.O.Steinmetz, M.Weetall. Preclinical and Early Clinical Development of PTC596, A Novel Small-Molecule Tubulin-Binding Agent Mol Cancer Ther V. 20 1846 2021.
ISSN: ISSN 1535-7163
PubMed: 34315764
DOI: 10.1158/1535-7163.MCT-20-0774
Page generated: Fri Aug 2 17:01:17 2024

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