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Fluorine in PDB 5lvo: Human PDK1 Kinase Domain in Complex with Allosteric Compound PSE10 Bound to the Pif-Pocket

Enzymatic activity of Human PDK1 Kinase Domain in Complex with Allosteric Compound PSE10 Bound to the Pif-Pocket

All present enzymatic activity of Human PDK1 Kinase Domain in Complex with Allosteric Compound PSE10 Bound to the Pif-Pocket:
2.7.11.1;

Protein crystallography data

The structure of Human PDK1 Kinase Domain in Complex with Allosteric Compound PSE10 Bound to the Pif-Pocket, PDB code: 5lvo was solved by J.O.Schulze, G.Saladino, K.Busschots, S.Neimanis, E.Suess, D.Odadzic, S.Zeuzem, V.Hindie, A.K.Herbrand, M.N.Lisa, P.M.Alzari, F.L.Gervasio, R.M.Biondi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 72.54 / 1.09
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 148.220, 44.420, 47.870, 90.00, 101.81, 90.00
R / Rfree (%) 13.5 / 15.7

Other elements in 5lvo:

The structure of Human PDK1 Kinase Domain in Complex with Allosteric Compound PSE10 Bound to the Pif-Pocket also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Human PDK1 Kinase Domain in Complex with Allosteric Compound PSE10 Bound to the Pif-Pocket (pdb code 5lvo). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total only one binding site of Fluorine was determined in the Human PDK1 Kinase Domain in Complex with Allosteric Compound PSE10 Bound to the Pif-Pocket, PDB code: 5lvo:

Fluorine binding site 1 out of 1 in 5lvo

Go back to Fluorine Binding Sites List in 5lvo
Fluorine binding site 1 out of 1 in the Human PDK1 Kinase Domain in Complex with Allosteric Compound PSE10 Bound to the Pif-Pocket


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Human PDK1 Kinase Domain in Complex with Allosteric Compound PSE10 Bound to the Pif-Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F402

b:28.2
occ:1.00
 F1 A:78W402 0.0 28.2 1.0
C13 A:78W402 1.3 23.9 1.0
C12 A:78W402 2.4 25.8 1.0
C14 A:78W402 2.4 22.1 1.0
C11 A:78W402 2.8 32.1 1.0
O20 A:78W402 2.8 36.5 1.0
HB3 A:GLN150 2.8 27.5 1.0
HG2 A:GLN150 3.4 30.7 1.0
O A:PHE149 3.4 15.5 1.0
HB A:THR148 3.4 19.7 1.0
C A:PHE149 3.5 15.2 1.0
HE21 A:GLN150 3.5 36.2 1.0
HD22 A:LEU155 3.6 26.2 1.0
CB A:GLN150 3.6 22.9 1.0
HA A:PHE149 3.6 18.4 1.0
C17 A:78W402 3.7 26.7 1.0
HD23 A:LEU155 3.7 26.2 1.0
C15 A:78W402 3.7 22.6 1.0
N10 A:78W402 3.7 35.3 1.0
CG A:GLN150 3.8 25.6 1.0
NE2 A:GLN150 3.9 30.1 1.0
N A:GLN150 3.9 19.0 1.0
CA A:PHE149 3.9 15.3 1.0
H A:PHE149 4.0 17.6 1.0
N A:PHE149 4.0 14.6 1.0
CD A:GLN150 4.0 27.8 1.0
CD2 A:LEU155 4.1 21.8 1.0
HG1 A:THR148 4.2 25.1 1.0
C16 A:78W402 4.2 24.7 1.0
CB A:THR148 4.3 16.4 1.0
H A:TYR156 4.3 15.1 1.0
CA A:GLN150 4.3 19.9 1.0
HA A:LEU155 4.3 18.1 1.0
OG1 A:THR148 4.3 20.9 1.0
HE22 A:GLN150 4.3 36.2 1.0
H A:GLN150 4.4 22.8 1.0
HB3 A:LEU155 4.4 21.1 1.0
HB2 A:GLN150 4.4 27.5 1.0
HA A:GLN150 4.5 23.9 1.0
C A:THR148 4.5 15.3 1.0
HD21 A:LEU155 4.6 26.2 1.0
C9 A:78W402 4.7 39.6 1.0
HD2 A:ARG131 4.7 23.2 0.6
HG3 A:GLN150 4.8 30.7 1.0
OE1 A:GLN150 4.9 29.7 1.0
C22 A:78W402 4.9 45.4 1.0
HD3 A:ARG131 4.9 22.7 0.4
O A:TYR156 5.0 12.7 1.0

Reference:

J.O.Schulze, G.Saladino, K.Busschots, S.Neimanis, E.Su, D.Odadzic, S.Zeuzem, V.Hindie, A.K.Herbrand, M.N.Lisa, P.M.Alzari, F.L.Gervasio, R.M.Biondi. Bidirectional Allosteric Communication Between the Atp-Binding Site and the Regulatory Pif Pocket in PDK1 Protein Kinase. Cell Chem Biol V. 23 1193 2016.
ISSN: ESSN 2451-9456
PubMed: 27693059
DOI: 10.1016/J.CHEMBIOL.2016.06.017
Page generated: Thu Aug 1 11:29:21 2024

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