Fluorine in PDB 7mso: Crystal Structure of Polo Box Domain in Complex with Cyclic Peptide Inhibitor

Enzymatic activity of Crystal Structure of Polo Box Domain in Complex with Cyclic Peptide Inhibitor

All present enzymatic activity of Crystal Structure of Polo Box Domain in Complex with Cyclic Peptide Inhibitor:
2.7.11.21;

Protein crystallography data

The structure of Crystal Structure of Polo Box Domain in Complex with Cyclic Peptide Inhibitor, PDB code: 7mso was solved by D.C.Lim, M.B.Yaffe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 14.83 / 1.85
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 57.282, 64.652, 70.163, 90, 92.49, 90
R / Rfree (%) 16.3 / 21

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Polo Box Domain in Complex with Cyclic Peptide Inhibitor (pdb code 7mso). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of Polo Box Domain in Complex with Cyclic Peptide Inhibitor, PDB code: 7mso:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 7mso

Go back to Fluorine Binding Sites List in 7mso
Fluorine binding site 1 out of 6 in the Crystal Structure of Polo Box Domain in Complex with Cyclic Peptide Inhibitor


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 Polo Box Domain in Complex with Cyclic Peptide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F1

b:35.3
occ:1.00
 F3 E:ZO11 0.0 35.3 1.0
C32 E:ZO11 1.3 32.1 1.0
F2 E:ZO11 2.1 37.0 1.0
F1 E:ZO11 2.1 35.1 1.0
C22 E:ZO11 2.3 20.4 1.0
C21 E:ZO11 2.9 23.1 1.0
C23 E:ZO11 3.5 24.1 1.0
O E:HOH112 3.5 34.7 1.0
C20 E:ZO11 4.2 22.4 1.0
C24 E:ZO11 4.6 25.0 1.0
C25 E:ZO11 5.0 20.4 1.0

Fluorine binding site 2 out of 6 in 7mso

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Fluorine binding site 2 out of 6 in the Crystal Structure of Polo Box Domain in Complex with Cyclic Peptide Inhibitor


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 Polo Box Domain in Complex with Cyclic Peptide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F1

b:35.1
occ:1.00
 F1 E:ZO11 0.0 35.1 1.0
C32 E:ZO11 1.3 32.1 1.0
F3 E:ZO11 2.1 35.3 1.0
F2 E:ZO11 2.2 37.0 1.0
C22 E:ZO11 2.3 20.4 1.0
C21 E:ZO11 2.9 23.1 1.0
C23 E:ZO11 3.4 24.1 1.0
O A:HOH739 3.4 29.8 1.0
CZ A:PHE535 3.5 23.0 1.0
CD A:ARG516 3.7 21.5 1.0
CE2 A:PHE535 3.8 25.2 1.0
NH1 A:ARG516 3.9 25.2 1.0
CE1 A:PHE535 4.0 30.3 1.0
C20 E:ZO11 4.2 22.4 1.0
NE A:ARG516 4.3 21.6 1.0
CZ A:ARG516 4.4 24.6 1.0
CD2 A:PHE535 4.4 30.4 1.0
C24 E:ZO11 4.5 25.0 1.0
CD1 A:PHE535 4.6 32.0 1.0
CH2 A:TRP414 4.7 22.2 1.0
CG A:PHE535 4.8 28.6 1.0
CG A:ARG516 4.9 23.4 1.0
C25 E:ZO11 4.9 20.4 1.0
O E:HOH112 4.9 34.7 1.0

Fluorine binding site 3 out of 6 in 7mso

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Fluorine binding site 3 out of 6 in the Crystal Structure of Polo Box Domain in Complex with Cyclic Peptide Inhibitor


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 Polo Box Domain in Complex with Cyclic Peptide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F1

b:37.0
occ:1.00
 F2 E:ZO11 0.0 37.0 1.0
C32 E:ZO11 1.3 32.1 1.0
F3 E:ZO11 2.1 35.3 1.0
F1 E:ZO11 2.2 35.1 1.0
C22 E:ZO11 2.3 20.4 1.0
C23 E:ZO11 2.7 24.1 1.0
C21 E:ZO11 3.6 23.1 1.0
NH1 A:ARG516 3.6 25.2 1.0
O A:HOH739 3.7 29.8 1.0
C24 E:ZO11 4.1 25.0 1.0
CZ A:ARG516 4.4 24.6 1.0
C20 E:ZO11 4.7 22.4 1.0
CD A:ARG516 4.9 21.5 1.0
NE A:ARG516 4.9 21.6 1.0
C25 E:ZO11 4.9 20.4 1.0

Fluorine binding site 4 out of 6 in 7mso

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Fluorine binding site 4 out of 6 in the Crystal Structure of Polo Box Domain in Complex with Cyclic Peptide Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Polo Box Domain in Complex with Cyclic Peptide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F1

b:35.9
occ:1.00
 F3 F:ZO11 0.0 35.9 1.0
C32 F:ZO11 1.3 34.5 1.0
F1 F:ZO11 2.2 32.2 1.0
F2 F:ZO11 2.2 30.9 1.0
C22 F:ZO11 2.3 22.0 1.0
C23 F:ZO11 2.7 23.8 1.0
C21 F:ZO11 3.6 19.9 1.0
NH1 B:ARG516 3.7 20.1 1.0
O B:HOH746 3.7 27.0 1.0
C24 F:ZO11 4.1 25.3 1.0
CZ B:ARG516 4.5 26.4 1.0
C20 F:ZO11 4.8 19.6 1.0
C25 F:ZO11 5.0 23.7 1.0

Fluorine binding site 5 out of 6 in 7mso

Go back to Fluorine Binding Sites List in 7mso
Fluorine binding site 5 out of 6 in the Crystal Structure of Polo Box Domain in Complex with Cyclic Peptide Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of Polo Box Domain in Complex with Cyclic Peptide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F1

b:32.2
occ:1.00
 F1 F:ZO11 0.0 32.2 1.0
C32 F:ZO11 1.3 34.5 1.0
F3 F:ZO11 2.2 35.9 1.0
F2 F:ZO11 2.2 30.9 1.0
C22 F:ZO11 2.3 22.0 1.0
C21 F:ZO11 2.8 19.9 1.0
C23 F:ZO11 3.5 23.8 1.0
O F:HOH110 3.5 34.0 1.0
C20 F:ZO11 4.2 19.6 1.0
C24 F:ZO11 4.6 25.3 1.0
C25 F:ZO11 4.9 23.7 1.0

Fluorine binding site 6 out of 6 in 7mso

Go back to Fluorine Binding Sites List in 7mso
Fluorine binding site 6 out of 6 in the Crystal Structure of Polo Box Domain in Complex with Cyclic Peptide Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of Polo Box Domain in Complex with Cyclic Peptide Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F1

b:30.9
occ:1.00
 F2 F:ZO11 0.0 30.9 1.0
C32 F:ZO11 1.4 34.5 1.0
F1 F:ZO11 2.2 32.2 1.0
F3 F:ZO11 2.2 35.9 1.0
C22 F:ZO11 2.3 22.0 1.0
C21 F:ZO11 2.9 19.9 1.0
C23 F:ZO11 3.3 23.8 1.0
O B:HOH746 3.4 27.0 1.0
CZ B:PHE535 3.6 27.5 1.0
CD B:ARG516 3.7 24.7 1.0
NH1 B:ARG516 3.8 20.1 1.0
CE2 B:PHE535 3.8 25.1 1.0
CE1 B:PHE535 4.1 28.9 1.0
C20 F:ZO11 4.2 19.6 1.0
NE B:ARG516 4.3 24.3 1.0
CZ B:ARG516 4.3 26.4 1.0
CD2 B:PHE535 4.4 25.4 1.0
C24 F:ZO11 4.5 25.3 1.0
CD1 B:PHE535 4.7 28.7 1.0
CH2 B:TRP414 4.7 16.9 1.0
CG B:PHE535 4.8 30.4 1.0
C25 F:ZO11 4.9 23.7 1.0
O F:HOH110 4.9 34.0 1.0
CG B:ARG516 5.0 27.0 1.0

Reference:

S.Ryu, J.E.Park, Y.J.Ham, D.C.Lim, N.P.Kwiatkowski, D.H.Kim, D.Bhunia, N.D.Kim, M.B.Yaffe, W.Son, N.Kim, T.I.Choi, P.Swain, C.H.Kim, J.Y.Lee, N.S.Gray, K.S.Lee, T.Sim. Novel Macrocyclic Peptidomimetics Targeting the Polo-Box Domain of Polo-Like Kinase 1. J.Med.Chem. V. 65 1915 2022.
ISSN: ISSN 0022-2623
PubMed: 35029981
DOI: 10.1021/ACS.JMEDCHEM.1C01359
Page generated: Fri Aug 2 09:48:01 2024

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