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Fluorine in PDB 6kzu: Macrocyclization of An All-D Linear Peptide Improves Target Affinity and Imparts Cellular Activity: A Novel Stapled Alpha-Helical Peptide Modality

Enzymatic activity of Macrocyclization of An All-D Linear Peptide Improves Target Affinity and Imparts Cellular Activity: A Novel Stapled Alpha-Helical Peptide Modality

All present enzymatic activity of Macrocyclization of An All-D Linear Peptide Improves Target Affinity and Imparts Cellular Activity: A Novel Stapled Alpha-Helical Peptide Modality:
2.3.2.27;

Protein crystallography data

The structure of Macrocyclization of An All-D Linear Peptide Improves Target Affinity and Imparts Cellular Activity: A Novel Stapled Alpha-Helical Peptide Modality, PDB code: 6kzu was solved by S.Jiang, C.J.Brown, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.49 / 1.79
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 82.567, 82.567, 54.783, 90.00, 90.00, 120.00
R / Rfree (%) 19.9 / 23.6

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Macrocyclization of An All-D Linear Peptide Improves Target Affinity and Imparts Cellular Activity: A Novel Stapled Alpha-Helical Peptide Modality (pdb code 6kzu). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Macrocyclization of An All-D Linear Peptide Improves Target Affinity and Imparts Cellular Activity: A Novel Stapled Alpha-Helical Peptide Modality, PDB code: 6kzu:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 6kzu

Go back to Fluorine Binding Sites List in 6kzu
Fluorine binding site 1 out of 4 in the Macrocyclization of An All-D Linear Peptide Improves Target Affinity and Imparts Cellular Activity: A Novel Stapled Alpha-Helical Peptide Modality


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Macrocyclization of An All-D Linear Peptide Improves Target Affinity and Imparts Cellular Activity: A Novel Stapled Alpha-Helical Peptide Modality within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F3

b:31.9
occ:1.00
F1 B:E033 0.0 31.9 1.0
CH2 B:E033 1.3 31.7 1.0
CZ3 B:E033 2.4 31.1 1.0
CZ2 B:E033 2.4 31.5 1.0
CG1 A:VAL93 3.2 27.2 1.0
CD2 B:TDF7 3.3 25.8 1.0
CE2 B:TDF7 3.3 26.0 1.0
CD1 A:ILE61 3.5 27.1 1.0
CG2 A:ILE61 3.5 25.2 1.0
CE2 B:E033 3.6 32.8 1.0
CE3 B:E033 3.6 32.6 1.0
CG2 A:VAL75 3.7 30.9 1.0
CB A:ILE61 4.0 26.1 1.0
CD2 B:E033 4.1 32.5 1.0
CG1 A:ILE61 4.3 26.8 1.0
CG B:TDF7 4.3 25.2 1.0
CZ B:TDF7 4.3 25.4 1.0
CB A:VAL93 4.6 27.1 1.0
CB B:DTY4 4.8 28.9 1.0
NE1 B:E033 4.9 32.4 1.0
F19 B:TDF7 4.9 27.1 1.0

Fluorine binding site 2 out of 4 in 6kzu

Go back to Fluorine Binding Sites List in 6kzu
Fluorine binding site 2 out of 4 in the Macrocyclization of An All-D Linear Peptide Improves Target Affinity and Imparts Cellular Activity: A Novel Stapled Alpha-Helical Peptide Modality


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Macrocyclization of An All-D Linear Peptide Improves Target Affinity and Imparts Cellular Activity: A Novel Stapled Alpha-Helical Peptide Modality within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F7

b:27.1
occ:1.00
F19 B:TDF7 0.0 27.1 1.0
C13 B:TDF7 1.3 27.2 1.0
F21 B:TDF7 2.1 25.3 1.0
F20 B:TDF7 2.2 25.0 1.0
CZ B:TDF7 2.3 25.4 1.0
CE2 B:TDF7 2.7 26.0 1.0
CD1 A:ILE99 3.5 24.0 1.0
CE2 A:PHE91 3.6 27.4 1.0
CE1 B:TDF7 3.6 24.6 1.0
CG1 A:ILE99 3.6 23.1 1.0
CG2 A:ILE99 3.7 22.4 1.0
CZ A:PHE91 3.9 27.4 1.0
CZ A:PHE86 4.1 38.6 1.0
CD2 B:TDF7 4.1 25.8 1.0
CD1 A:ILE61 4.3 27.1 1.0
CB A:ILE99 4.3 22.3 1.0
CD2 A:PHE91 4.6 27.8 1.0
CD1 B:TDF7 4.7 24.4 1.0
CE1 A:PHE86 4.8 39.0 1.0
CD2 B:DLE11 4.9 23.4 1.0
F1 B:E033 4.9 31.9 1.0
CG B:TDF7 5.0 25.2 1.0

Fluorine binding site 3 out of 4 in 6kzu

Go back to Fluorine Binding Sites List in 6kzu
Fluorine binding site 3 out of 4 in the Macrocyclization of An All-D Linear Peptide Improves Target Affinity and Imparts Cellular Activity: A Novel Stapled Alpha-Helical Peptide Modality


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Macrocyclization of An All-D Linear Peptide Improves Target Affinity and Imparts Cellular Activity: A Novel Stapled Alpha-Helical Peptide Modality within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F7

b:25.0
occ:1.00
F20 B:TDF7 0.0 25.0 1.0
C13 B:TDF7 1.3 27.2 1.0
F21 B:TDF7 2.1 25.3 1.0
F19 B:TDF7 2.2 27.1 1.0
CZ B:TDF7 2.4 25.4 1.0
CE1 B:TDF7 2.8 24.6 1.0
CG2 A:ILE99 3.4 22.4 1.0
CD2 A:LEU54 3.5 22.9 1.0
CE2 B:TDF7 3.6 26.0 1.0
CD1 A:LEU57 3.6 26.8 1.0
CB A:LEU57 4.0 23.8 1.0
CD1 B:TDF7 4.2 24.4 1.0
CD1 A:ILE103 4.4 32.5 1.0
CD1 B:DLE11 4.5 22.3 1.0
CG A:LEU57 4.5 25.8 1.0
CB A:ILE99 4.6 22.3 1.0
CG1 A:ILE99 4.7 23.1 1.0
CD2 B:TDF7 4.7 25.8 1.0
CD1 A:ILE99 4.8 24.0 1.0
CG A:LEU54 4.9 22.1 1.0
CZ A:PHE86 5.0 38.6 1.0
CA A:LEU54 5.0 20.6 1.0

Fluorine binding site 4 out of 4 in 6kzu

Go back to Fluorine Binding Sites List in 6kzu
Fluorine binding site 4 out of 4 in the Macrocyclization of An All-D Linear Peptide Improves Target Affinity and Imparts Cellular Activity: A Novel Stapled Alpha-Helical Peptide Modality


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Macrocyclization of An All-D Linear Peptide Improves Target Affinity and Imparts Cellular Activity: A Novel Stapled Alpha-Helical Peptide Modality within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F7

b:25.3
occ:1.00
F21 B:TDF7 0.0 25.3 1.0
C13 B:TDF7 1.3 27.2 1.0
F20 B:TDF7 2.1 25.0 1.0
F19 B:TDF7 2.1 27.1 1.0
CZ B:TDF7 2.3 25.4 1.0
CE1 B:TDF7 3.1 24.6 1.0
CD1 A:ILE61 3.2 27.1 1.0
CE2 B:TDF7 3.3 26.0 1.0
CB A:LEU57 3.4 23.8 1.0
CD1 A:LEU57 3.8 26.8 1.0
CG A:LEU57 4.2 25.8 1.0
C A:LEU57 4.2 24.0 1.0
O A:LEU57 4.3 24.8 1.0
CD1 B:TDF7 4.4 24.4 1.0
CA A:LEU57 4.5 23.5 1.0
N A:GLY58 4.5 22.8 1.0
CG1 A:ILE61 4.5 26.8 1.0
CD2 B:TDF7 4.5 25.8 1.0
CZ A:PHE91 4.6 27.4 1.0
CD2 A:LEU57 4.6 25.7 1.0
CZ A:PHE86 4.7 38.6 1.0
CE1 A:PHE86 4.8 39.0 1.0
CE2 A:PHE91 4.8 27.4 1.0
CG B:TDF7 5.0 25.2 1.0
CA A:GLY58 5.0 23.6 1.0
CG2 A:ILE99 5.0 22.4 1.0

Reference:

K.Srinivasaraghavan, G.A.Pietro, S.Ng, D.Thean, Y.Frosi, S.Chee, S.Jiang, T.Z.Yuen, A.Sadruddin, Y.K.Hung, A.Chandramohan, J.H.Wong, Y.S.Tan, F.J.Ferrer, P.Arumugam, Y.Han, S.Chen, C.J.Brown, C.W.Johannes, B.Henry, D.P.Lane, T.K.Sawyer, C.S.Verma, P.W.Partridge. Macrocyclization of An All-D Linear Peptide Improves Target Affinity and Imparts Cellular Activity: A Novel Stapled Alpha-Helical Peptide Modality To Be Published.
Page generated: Thu Aug 1 21:54:30 2024

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