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Fluorine in PDB 4j53: Crystal Structure of PLK1 in Complex with Tak-960

Enzymatic activity of Crystal Structure of PLK1 in Complex with Tak-960

All present enzymatic activity of Crystal Structure of PLK1 in Complex with Tak-960:
2.7.11.21;

Protein crystallography data

The structure of Crystal Structure of PLK1 in Complex with Tak-960, PDB code: 4j53 was solved by D.J.Hosfield, R.J.Skene, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.35 / 2.50
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 66.649, 66.649, 153.960, 90.00, 90.00, 120.00
R / Rfree (%) 18 / 24

Other elements in 4j53:

The structure of Crystal Structure of PLK1 in Complex with Tak-960 also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of PLK1 in Complex with Tak-960 (pdb code 4j53). 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 PLK1 in Complex with Tak-960, PDB code: 4j53:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 4j53

Go back to Fluorine Binding Sites List in 4j53
Fluorine binding site 1 out of 3 in the Crystal Structure of PLK1 in Complex with Tak-960


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 PLK1 in Complex with Tak-960 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F403

b:72.2
occ:1.00
F17 A:1J4403 0.0 72.2 1.0
C16 A:1J4403 1.3 72.3 1.0
C18 A:1J4403 2.3 70.2 1.0
C5 A:1J4403 2.4 75.1 1.0
C6 A:1J4403 2.9 73.8 1.0
N8 A:1J4403 3.1 75.6 1.0
O A:LEU59 3.1 56.3 1.0
O A:HOH630 3.1 50.6 1.0
O A:HOH613 3.2 41.8 1.0
C19 A:1J4403 3.6 71.2 1.0
C4 A:1J4403 3.7 76.5 1.0
NH2 A:ARG136 3.7 60.4 1.0
C38 A:1J4403 3.7 69.8 1.0
NE A:ARG136 3.8 54.6 1.0
O7 A:1J4403 3.9 76.2 1.0
C A:LEU59 4.0 59.2 1.0
CZ A:ARG136 4.1 58.8 1.0
C3 A:1J4403 4.1 75.8 1.0
O A:HOH527 4.3 51.5 1.0
C10 A:1J4403 4.3 79.3 1.0
C9 A:1J4403 4.3 80.2 1.0
C37 A:1J4403 4.3 70.3 1.0
CB A:LEU59 4.3 55.1 1.0
C34 A:1J4403 4.5 68.4 1.0
CA A:LEU59 4.5 58.2 1.0
N40 A:1J4403 4.6 62.9 1.0
N20 A:1J4403 4.8 69.8 1.0
CD A:ARG136 4.8 52.5 1.0
CG A:ARG136 4.8 49.5 1.0

Fluorine binding site 2 out of 3 in 4j53

Go back to Fluorine Binding Sites List in 4j53
Fluorine binding site 2 out of 3 in the Crystal Structure of PLK1 in Complex with Tak-960


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 PLK1 in Complex with Tak-960 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F403

b:77.2
occ:1.00
F30 A:1J4403 0.0 77.2 1.0
C29 A:1J4403 1.3 71.5 1.0
F31 A:1J4403 2.2 71.0 1.0
C27 A:1J4403 2.3 70.1 1.0
C32 A:1J4403 2.3 71.5 1.0
O28 A:1J4403 2.5 68.2 1.0
O A:HOH610 2.7 57.4 1.0
N33 A:1J4403 3.2 67.6 1.0
CD A:LYS82 3.4 49.4 1.0
N25 A:1J4403 3.5 67.8 1.0
SG A:CYS67 3.7 53.7 1.0
CE A:LYS82 4.1 48.1 1.0
C35 A:1J4403 4.1 67.6 1.0
C39 A:1J4403 4.2 64.9 1.0
C34 A:1J4403 4.2 68.4 1.0
C24 A:1J4403 4.2 63.1 1.0
CG A:LYS82 4.6 49.5 1.0
C26 A:1J4403 4.6 67.1 1.0
CD1 A:LEU130 4.7 35.4 1.0
CZ A:PHE183 4.7 29.0 1.0
O A:HOH501 4.8 32.2 1.0
C38 A:1J4403 4.9 69.8 1.0
CB A:LYS82 4.9 48.7 1.0
C36 A:1J4403 4.9 69.3 1.0
CB A:CYS67 4.9 54.9 1.0
O A:HOH578 5.0 61.4 1.0

Fluorine binding site 3 out of 3 in 4j53

Go back to Fluorine Binding Sites List in 4j53
Fluorine binding site 3 out of 3 in the Crystal Structure of PLK1 in Complex with Tak-960


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 PLK1 in Complex with Tak-960 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F403

b:71.0
occ:1.00
F31 A:1J4403 0.0 71.0 1.0
C29 A:1J4403 1.3 71.5 1.0
F30 A:1J4403 2.2 77.2 1.0
C32 A:1J4403 2.3 71.5 1.0
C27 A:1J4403 2.3 70.1 1.0
O28 A:1J4403 2.9 68.2 1.0
N25 A:1J4403 3.2 67.8 1.0
SG A:CYS67 3.4 53.7 1.0
N33 A:1J4403 3.5 67.6 1.0
C24 A:1J4403 3.7 63.1 1.0
CD A:LYS82 3.8 49.4 1.0
CD1 A:LEU130 3.8 35.4 1.0
C39 A:1J4403 3.9 64.9 1.0
CB A:LYS82 3.9 48.7 1.0
CB A:CYS67 4.0 54.9 1.0
CB A:ALA80 4.3 42.3 1.0
CG A:LYS82 4.4 49.5 1.0
C26 A:1J4403 4.5 67.1 1.0
CA A:LYS82 4.6 49.2 1.0
C23 A:1J4403 4.7 59.9 1.0
C34 A:1J4403 4.7 68.4 1.0
O A:HOH610 4.8 57.4 1.0
N A:LYS82 4.8 50.4 1.0
N40 A:1J4403 4.9 62.9 1.0
CG A:LEU130 5.0 36.7 1.0
CE A:LYS82 5.0 48.1 1.0

Reference:

Z.Nie, V.Feher, S.Natala, C.Mcbride, A.Kiryanov, B.Jones, B.Lam, Y.Liu, S.Kaldor, J.Stafford, K.Hikami, N.Uchiyama, T.Kawamoto, Y.Hikichi, S.Matsumoto, N.Amano, L.Zhang, D.Hosfield, R.Skene, H.Zou, X.Cao, T.Ichikawa. Discovery of Tak-960: An Orally Available Small Molecule Inhibitor of Polo-Like Kinase 1 (PLK1). Bioorg.Med.Chem.Lett. V. 23 3662 2013.
ISSN: ISSN 0960-894X
PubMed: 23664874
DOI: 10.1016/J.BMCL.2013.02.083
Page generated: Sun Dec 13 12:05:14 2020

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