Fluorine in PDB 3qc4: PDK1 in Complex with Dfg-Out Inhibitor Xxx

All present enzymatic activity of PDK1 in Complex with Dfg-Out Inhibitor Xxx:
2.7.11.1;

The structure of PDK1 in Complex with Dfg-Out Inhibitor Xxx, PDB code: 3qc4 was solved by J.W.Arndt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.49 / 1.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	183.147, 57.336, 83.694, 90.00, 114.13, 90.00
R / Rfree (%)	17.2 / 21.3

The binding sites of Fluorine atom in the PDK1 in Complex with Dfg-Out Inhibitor Xxx (pdb code 3qc4). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the PDK1 in Complex with Dfg-Out Inhibitor Xxx, PDB code: 3qc4:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the PDK1 in Complex with Dfg-Out Inhibitor Xxx


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of PDK1 in Complex with Dfg-Out Inhibitor Xxx within 5.0Å range: probe atom residue distance (Å) B Occ A:F1 b:36.0 occ:1.00 F A:MP71 0.0 36.0 1.0 C10 A:MP71 1.3 32.3 1.0 C9 A:MP71 2.3 30.8 1.0 C11 A:MP71 2.4 32.0 1.0 F12 A:MP71 2.7 32.0 1.0 CD2 A:HIS203 3.2 25.6 1.0 CG2 A:ILE221 3.4 26.2 1.0 CE1 A:PHE142 3.4 25.0 1.0 CD1 A:PHE142 3.4 29.9 1.0 C6 A:MP71 3.6 32.2 1.0 C8 A:MP71 3.6 34.0 1.0 NE2 A:HIS203 3.9 27.5 1.0 CD2 A:LEU196 3.9 28.2 1.0 C7 A:MP71 4.1 32.5 1.0 CG A:HIS203 4.3 26.0 1.0 CD1 A:LEU196 4.3 27.8 1.0 CB A:ILE221 4.4 28.3 1.0 O A:ILE221 4.5 27.1 1.0 O A:THR222 4.5 27.5 1.0 C A:THR222 4.5 28.9 1.0 N A:ASP223 4.5 30.5 1.0 C A:ILE221 4.6 28.2 1.0 CB A:ASP223 4.7 32.6 1.0 CZ A:PHE142 4.7 33.4 1.0 CG A:PHE142 4.8 25.5 1.0 CD2 A:LEU137 4.8 36.6 1.0 CG A:LEU196 4.8 28.5 1.0 C5 A:MP71 4.8 35.9 1.0 CB A:HIS203 4.8 21.2 1.0 CA A:ASP223 4.9 31.7 1.0 N A:THR222 4.9 26.0 1.0

Fluorine binding site 2 out of 4 in the PDK1 in Complex with Dfg-Out Inhibitor Xxx


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of PDK1 in Complex with Dfg-Out Inhibitor Xxx within 5.0Å range: probe atom residue distance (Å) B Occ A:F1 b:32.0 occ:1.00 F12 A:MP71 0.0 32.0 1.0 C9 A:MP71 1.3 30.8 1.0 C10 A:MP71 2.3 32.3 1.0 C8 A:MP71 2.3 34.0 1.0 F A:MP71 2.7 36.0 1.0 CB A:ALA227 3.0 26.4 1.0 CD1 A:LEU196 3.5 27.8 1.0 C11 A:MP71 3.6 32.0 1.0 C7 A:MP71 3.6 32.5 1.0 CG2 A:ILE201 3.7 28.3 1.0 CD2 A:LEU196 3.7 28.2 1.0 C6 A:MP71 4.0 32.2 1.0 CD2 A:HIS203 4.1 25.6 1.0 CG A:LEU196 4.2 28.5 1.0 CB A:ASP223 4.5 32.6 1.0 CA A:ALA227 4.5 28.7 1.0 CA A:HIS203 4.6 24.9 1.0 CG A:HIS203 4.6 26.0 1.0 CB A:HIS203 4.7 21.2 1.0 O A:ILE202 4.7 28.7 1.0 CG A:ASP223 4.8 33.4 1.0 CD2 A:LEU137 4.9 36.6 1.0 CB A:ILE201 4.9 31.7 1.0 N A:HIS203 5.0 24.7 1.0 CG A:MET134 5.0 52.0 1.0

Fluorine binding site 3 out of 4 in the PDK1 in Complex with Dfg-Out Inhibitor Xxx


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of PDK1 in Complex with Dfg-Out Inhibitor Xxx within 5.0Å range: probe atom residue distance (Å) B Occ B:F2 b:36.9 occ:1.00 F B:MP72 0.0 36.9 1.0 C10 B:MP72 1.4 30.2 1.0 C9 B:MP72 2.3 29.9 1.0 C11 B:MP72 2.4 24.9 1.0 F12 B:MP72 2.5 29.9 1.0 CD2 B:HIS203 3.1 23.4 1.0 CE1 B:PHE142 3.4 24.2 1.0 C6 B:MP72 3.6 27.5 1.0 CD1 B:PHE142 3.6 22.8 1.0 C8 B:MP72 3.6 30.8 1.0 NE2 B:HIS203 3.7 25.6 1.0 CG2 B:ILE221 3.7 20.3 1.0 CD2 B:LEU196 4.0 21.0 1.0 C7 B:MP72 4.1 27.8 1.0 CG B:HIS203 4.1 19.9 1.0 CD1 B:LEU196 4.2 22.7 1.0 O B:THR222 4.4 22.4 1.0 N B:ASP223 4.4 24.1 1.0 C B:THR222 4.4 24.5 1.0 CB B:ASP223 4.5 26.7 1.0 CZ B:PHE142 4.6 22.4 1.0 CA B:ASP223 4.7 26.9 1.0 CB B:ILE221 4.7 20.0 1.0 CB B:HIS203 4.7 17.8 1.0 CG B:LEU196 4.7 20.3 1.0 C5 B:MP72 4.8 25.3 1.0 O B:ILE221 4.8 21.3 1.0 CE1 B:HIS203 4.9 23.6 1.0 CG B:PHE142 4.9 22.8 1.0 C B:ILE221 4.9 20.5 1.0 CB B:ALA227 5.0 25.2 1.0 CD2 B:LEU137 5.0 33.1 1.0

Fluorine binding site 4 out of 4 in the PDK1 in Complex with Dfg-Out Inhibitor Xxx


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of PDK1 in Complex with Dfg-Out Inhibitor Xxx within 5.0Å range: probe atom residue distance (Å) B Occ B:F2 b:29.9 occ:1.00 F12 B:MP72 0.0 29.9 1.0 C9 B:MP72 1.3 29.9 1.0 C10 B:MP72 2.3 30.2 1.0 C8 B:MP72 2.4 30.8 1.0 F B:MP72 2.5 36.9 1.0 CB B:ALA227 3.1 25.2 1.0 CD1 B:LEU196 3.3 22.7 1.0 CG2 B:ILE201 3.5 21.0 1.0 C11 B:MP72 3.6 24.9 1.0 C7 B:MP72 3.6 27.8 1.0 CD2 B:LEU196 3.7 21.0 1.0 C6 B:MP72 4.1 27.5 1.0 CG B:LEU196 4.1 20.3 1.0 CD2 B:HIS203 4.2 23.4 1.0 CB B:ASP223 4.5 26.7 1.0 CA B:ALA227 4.6 24.4 1.0 CA B:HIS203 4.6 19.3 1.0 CG B:HIS203 4.7 19.9 1.0 CB B:ILE201 4.8 24.1 1.0 CB B:HIS203 4.8 17.8 1.0 O B:ILE202 4.8 23.7 1.0 CD2 B:LEU137 4.9 33.1 1.0 CG B:ASP223 5.0 27.6 1.0 N B:HIS203 5.0 19.9 1.0

D.A.Erlanson, J.W.Arndt, M.T.Cancilla, K.Cao, R.A.Elling, N.English, J.Friedman, S.K.Hansen, C.Hession, I.Joseph, G.Kumaravel, W.C.Lee, K.E.Lind, R.S.Mcdowell, K.Miatkowski, C.Nguyen, T.B.Nguyen, S.Park, N.Pathan, D.M.Penny, M.J.Romanowski, D.Scott, L.Silvian, R.L.Simmons, B.T.Tangonan, W.Yang, L.Sun. Discovery of A Potent and Highly Selective PDK1 Inhibitor Via Fragment-Based Drug Discovery. Bioorg.Med.Chem.Lett. V. 21 3078 2011.
ISSN: ISSN 0960-894X
PubMed: 21459573
DOI: 10.1016/J.BMCL.2011.03.032