Fluorine in PDB 3roc: Crystal Structure of Human P38 Alpha Complexed with A Pyrimidinone Compound

All present enzymatic activity of Crystal Structure of Human P38 Alpha Complexed with A Pyrimidinone Compound:
2.7.11.24;

The structure of Crystal Structure of Human P38 Alpha Complexed with A Pyrimidinone Compound, PDB code: 3roc was solved by H.-S.Shieh, L.Xing, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	65.311, 74.609, 77.752, 90.00, 90.00, 90.00
R / Rfree (%)	23.9 / 27.6

The structure of Crystal Structure of Human P38 Alpha Complexed with A Pyrimidinone Compound also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Fluorine atom in the Crystal Structure of Human P38 Alpha Complexed with A Pyrimidinone Compound (pdb code 3roc). 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 Human P38 Alpha Complexed with A Pyrimidinone Compound, PDB code: 3roc:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Crystal Structure of Human P38 Alpha Complexed with A Pyrimidinone Compound


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 Human P38 Alpha Complexed with A Pyrimidinone Compound within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:24.6 occ:1.00 F21 A:29A401 0.0 24.6 1.0 C2 A:29A401 1.3 19.6 1.0 C3 A:29A401 2.4 20.6 1.0 C1 A:29A401 2.4 20.9 1.0 C7 A:29A401 2.8 22.2 1.0 O A:ALA51 3.1 18.0 1.0 C A:ALA51 3.2 16.4 1.0 CB A:ALA51 3.3 21.5 1.0 O8 A:29A401 3.3 22.5 1.0 N A:LYS53 3.5 19.4 1.0 N A:VAL52 3.5 18.6 1.0 CB A:LYS53 3.5 21.5 1.0 C A:VAL52 3.6 16.8 1.0 C4 A:29A401 3.6 22.1 1.0 C6 A:29A401 3.6 20.3 1.0 CA A:ALA51 3.8 19.8 1.0 CA A:VAL52 3.8 19.2 1.0 CG1 A:VAL38 4.0 22.4 1.0 CA A:LYS53 4.0 19.0 1.0 CG2 A:THR106 4.0 16.4 1.0 O A:VAL52 4.1 20.0 1.0 C5 A:29A401 4.1 22.0 1.0 O A:LEU104 4.1 17.1 1.0 C9 A:29A401 4.2 20.4 1.0 CG2 A:VAL38 4.5 23.9 1.0 CG A:LYS53 4.7 24.2 1.0 N14 A:29A401 4.7 20.5 1.0 N A:THR106 4.7 18.2 1.0 F22 A:29A401 4.7 27.9 1.0 CB A:VAL38 4.9 25.4 1.0 N A:ALA51 4.9 20.1 1.0 CD A:LYS53 4.9 26.2 1.0

Fluorine binding site 2 out of 3 in the Crystal Structure of Human P38 Alpha Complexed with A Pyrimidinone Compound


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 Human P38 Alpha Complexed with A Pyrimidinone Compound within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:27.9 occ:1.00 F22 A:29A401 0.0 27.9 1.0 C4 A:29A401 1.3 22.1 1.0 C5 A:29A401 2.4 22.0 1.0 C3 A:29A401 2.4 20.6 1.0 CB A:LEU104 3.1 18.1 1.0 CD2 A:LEU86 3.2 24.3 1.0 C2 A:29A401 3.6 19.6 1.0 C6 A:29A401 3.6 20.3 1.0 CD1 A:LEU75 3.7 20.0 1.0 C A:LEU104 3.7 14.9 1.0 N A:VAL105 3.8 17.0 1.0 C A:VAL105 4.0 13.7 1.0 CA A:LEU104 4.0 15.3 1.0 O A:VAL105 4.0 15.8 1.0 C1 A:29A401 4.1 20.9 1.0 O A:LEU104 4.1 17.1 1.0 CB A:THR106 4.2 16.3 1.0 CG A:LEU104 4.2 15.2 1.0 CA A:VAL105 4.2 17.4 1.0 CD2 A:LEU75 4.3 22.2 1.0 N A:THR106 4.3 18.2 1.0 CD1 A:LEU104 4.3 18.3 1.0 O A:GLY85 4.4 18.1 1.0 CG A:LEU86 4.5 26.3 1.0 CG A:LEU75 4.5 17.7 1.0 CG2 A:THR106 4.6 16.4 1.0 CD2 A:LEU104 4.7 17.8 1.0 F21 A:29A401 4.7 24.6 1.0 CA A:THR106 4.8 18.5 1.0 CG2 A:ILE84 4.9 20.7 1.0

Fluorine binding site 3 out of 3 in the Crystal Structure of Human P38 Alpha Complexed with A Pyrimidinone Compound


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 Human P38 Alpha Complexed with A Pyrimidinone Compound within 5.0Å range: probe atom residue distance (Å) B Occ A:F402 b:26.1 occ:1.00 F18 A:29B402 0.0 26.1 1.0 C2 A:29B402 1.4 22.8 1.0 C3 A:29B402 2.4 19.4 1.0 C1 A:29B402 2.4 21.7 1.0 CD1 A:ILE259 3.2 32.7 1.0 CG1 A:ILE259 3.3 29.1 1.0 C4 A:29B402 3.6 19.9 1.0 C6 A:29B402 3.6 19.6 1.0 CG2 A:ILE259 4.0 28.4 1.0 CG A:PRO242 4.0 20.7 1.0 CD2 A:LEU232 4.0 33.0 1.0 CG A:LEU195 4.0 32.9 1.0 C5 A:29B402 4.2 16.1 1.0 CD1 A:LEU232 4.2 32.5 1.0 CD1 A:LEU195 4.2 30.4 1.0 CD2 A:LEU236 4.3 28.5 1.0 CB A:ILE259 4.3 29.1 1.0 CD A:PRO242 4.5 23.1 1.0 CD2 A:LEU195 4.5 29.6 1.0 CD1 A:LEU236 4.6 26.8 1.0 CG A:LEU232 4.7 34.3 1.0 CG A:LEU236 4.9 29.4 1.0

B.Devadas, S.R.Selness, L.Xing, H.M.Madsen, L.D.Marrufo, H.Shieh, D.M.Messing, J.Z.Yang, H.M.Morgan, G.D.Anderson, E.G.Webb, J.Zhang, R.V.Devraj, J.B.Monahan. Substituted N-Aryl-6-Pyrimidinones: A New Class of Potent, Selective, and Orally Active P38 Map Kinase Inhibitors. Bioorg.Med.Chem.Lett. V. 21 3856 2011.
ISSN: ISSN 0960-894X
PubMed: 21620699
DOI: 10.1016/J.BMCL.2011.05.006