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Fluorine in PDB 3db6: Crystal Structure of An Activated (Thr->Asp) Polo-Like Kinase 1 (PLK1) Catalytic Domain in Complex with Compound 902

Enzymatic activity of Crystal Structure of An Activated (Thr->Asp) Polo-Like Kinase 1 (PLK1) Catalytic Domain in Complex with Compound 902

All present enzymatic activity of Crystal Structure of An Activated (Thr->Asp) Polo-Like Kinase 1 (PLK1) Catalytic Domain in Complex with Compound 902:
2.7.11.21;

Protein crystallography data

The structure of Crystal Structure of An Activated (Thr->Asp) Polo-Like Kinase 1 (PLK1) Catalytic Domain in Complex with Compound 902, PDB code: 3db6 was solved by R.A.Elling, R.V.Fucini, J.Zhu, K.J.Barr, M.J.Romanowski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.85
Space group I 2 3
Cell size a, b, c (Å), α, β, γ (°) 135.129, 135.129, 135.129, 90.00, 90.00, 90.00
R / Rfree (%) 22.1 / 25.7

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of An Activated (Thr->Asp) Polo-Like Kinase 1 (PLK1) Catalytic Domain in Complex with Compound 902 (pdb code 3db6). 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 An Activated (Thr->Asp) Polo-Like Kinase 1 (PLK1) Catalytic Domain in Complex with Compound 902, PDB code: 3db6:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 3db6

Go back to Fluorine Binding Sites List in 3db6
Fluorine binding site 1 out of 3 in the Crystal Structure of An Activated (Thr->Asp) Polo-Like Kinase 1 (PLK1) Catalytic Domain in Complex with Compound 902


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 An Activated (Thr->Asp) Polo-Like Kinase 1 (PLK1) Catalytic Domain in Complex with Compound 902 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1

b:52.3
occ:1.00
 F9 A:FRS1 0.0 52.3 1.0
C6 A:FRS1 1.3 51.0 1.0
F7 A:FRS1 2.1 51.9 1.0
F8 A:FRS1 2.1 50.2 1.0
C5 A:FRS1 2.3 49.9 1.0
C10 A:FRS1 3.1 48.3 1.0
N11 A:FRS1 3.3 47.8 1.0
CE1 A:PHE102 3.4 39.3 1.0
O4 A:FRS1 3.5 50.2 1.0
CG1 A:VAL114 3.6 46.6 1.0
CG2 A:VAL114 3.7 47.4 1.0
CG1 A:ILE88 4.0 52.9 1.0
C12 A:FRS1 4.0 47.8 1.0
OE1 A:GLU87 4.0 50.7 1.0
CB A:VAL114 4.1 47.4 1.0
CZ A:PHE102 4.2 39.1 1.0
CD1 A:PHE102 4.4 39.0 1.0
C3 A:FRS1 4.4 50.3 1.0
CD A:GLU87 4.5 51.6 1.0
C2 A:FRS1 4.5 50.8 1.0
O13 A:FRS1 4.5 48.0 1.0
CD1 A:ILE88 4.7 53.9 1.0
N14 A:FRS1 4.7 47.2 1.0
OE2 A:GLU87 4.9 50.6 1.0

Fluorine binding site 2 out of 3 in 3db6

Go back to Fluorine Binding Sites List in 3db6
Fluorine binding site 2 out of 3 in the Crystal Structure of An Activated (Thr->Asp) Polo-Like Kinase 1 (PLK1) Catalytic Domain in Complex with Compound 902


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 An Activated (Thr->Asp) Polo-Like Kinase 1 (PLK1) Catalytic Domain in Complex with Compound 902 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1

b:50.2
occ:1.00
 F8 A:FRS1 0.0 50.2 1.0
C6 A:FRS1 1.3 51.0 1.0
F7 A:FRS1 2.1 51.9 1.0
F9 A:FRS1 2.1 52.3 1.0
C5 A:FRS1 2.3 49.9 1.0
CD A:GLU87 3.0 51.6 1.0
OE1 A:GLU87 3.1 50.7 1.0
OE2 A:GLU87 3.1 50.6 1.0
O4 A:FRS1 3.2 50.2 1.0
C10 A:FRS1 3.2 48.3 1.0
CG A:GLU87 3.5 51.6 1.0
N11 A:FRS1 3.6 47.8 1.0
CG1 A:ILE88 3.7 52.9 1.0
CB A:GLU87 3.7 52.5 1.0
O A:MET84 3.9 67.8 1.0
CG A:MET84 3.9 68.6 1.0
N A:ILE88 4.2 51.1 1.0
C2 A:FRS1 4.3 50.8 1.0
C3 A:FRS1 4.4 50.3 1.0
CD1 A:ILE88 4.4 53.9 1.0
C A:GLU87 4.5 51.8 1.0
CA A:MET84 4.6 68.7 1.0
CA A:ILE88 4.6 51.5 1.0
C A:MET84 4.7 67.6 1.0
CA A:GLU87 4.8 53.5 1.0
CB A:ILE88 4.8 51.6 1.0
C12 A:FRS1 4.8 47.8 1.0
CB A:MET84 4.8 68.0 1.0
CE1 A:PHE102 4.9 39.3 1.0

Fluorine binding site 3 out of 3 in 3db6

Go back to Fluorine Binding Sites List in 3db6
Fluorine binding site 3 out of 3 in the Crystal Structure of An Activated (Thr->Asp) Polo-Like Kinase 1 (PLK1) Catalytic Domain in Complex with Compound 902


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 An Activated (Thr->Asp) Polo-Like Kinase 1 (PLK1) Catalytic Domain in Complex with Compound 902 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1

b:51.9
occ:1.00
 F7 A:FRS1 0.0 51.9 1.0
C6 A:FRS1 1.3 51.0 1.0
F9 A:FRS1 2.1 52.3 1.0
F8 A:FRS1 2.1 50.2 1.0
C5 A:FRS1 2.3 49.9 1.0
O4 A:FRS1 2.6 50.2 1.0
CG A:MET84 3.3 68.6 1.0
CG2 A:VAL114 3.4 47.4 1.0
CG1 A:ILE88 3.6 52.9 1.0
C10 A:FRS1 3.7 48.3 1.0
CD1 A:ILE88 3.7 53.9 1.0
SD A:MET84 3.9 69.8 1.0
C2 A:FRS1 4.0 50.8 1.0
N11 A:FRS1 4.5 47.8 1.0
C3 A:FRS1 4.5 50.3 1.0
CB A:VAL114 4.6 47.4 1.0
O A:MET84 4.6 67.8 1.0
CG1 A:VAL114 4.7 46.6 1.0
CE A:MET84 4.7 70.4 1.0
CB A:MET84 4.7 68.0 1.0
CE1 A:PHE102 4.9 39.3 1.0
C1 A:FRS1 4.9 50.9 1.0

Reference:

R.A.Elling, R.V.Fucini, E.J.Hanan, K.J.Barr, J.Zhu, K.Paulvannan, W.Yang, M.J.Romanowski. Structure of the Brachydanio Rerio Polo-Like Kinase 1 (PLK1) Catalytic Domain in Complex with An Extended Inhibitor Targeting the Adaptive Pocket of the Enzyme. Acta Crystallogr.,Sect.F V. 64 686 2008.
ISSN: ESSN 1744-3091
PubMed: 18678933
DOI: 10.1107/S1744309108019623
Page generated: Sun Dec 13 11:44:44 2020

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