Fluorine in PDB 4eh9: Human P38 Map Kinase in Complex with Np-F11 and RL87

All present enzymatic activity of Human P38 Map Kinase in Complex with Np-F11 and RL87:
2.7.11.24;

The structure of Human P38 Map Kinase in Complex with Np-F11 and RL87, PDB code: 4eh9 was solved by B.Over, C.Gruetter, H.Waldmann, D.Rauh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.74 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	65.620, 74.920, 78.190, 90.00, 90.00, 90.00
R / Rfree (%)	22.9 / 28

The binding sites of Fluorine atom in the Human P38 Map Kinase in Complex with Np-F11 and RL87 (pdb code 4eh9). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Human P38 Map Kinase in Complex with Np-F11 and RL87, PDB code: 4eh9:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Human P38 Map Kinase in Complex with Np-F11 and RL87


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Human P38 Map Kinase in Complex with Np-F11 and RL87 within 5.0Å range: probe atom residue distance (Å) B Occ A:F402 b:53.2 occ:0.90 FAD A:0OQ402 0.0 53.2 0.9 CAZ A:0OQ402 1.4 52.3 0.9 FAC A:0OQ402 2.2 51.8 0.9 FAE A:0OQ402 2.3 53.9 0.9 CAS A:0OQ402 2.3 51.0 0.9 CAJ A:0OQ402 2.8 49.4 0.9 CAK A:0OQ402 3.5 50.7 0.9 CG A:MET78 3.6 33.1 1.0 SD A:MET78 3.9 35.7 1.0 CAH A:0OQ402 4.1 48.1 0.9 CB A:LEU74 4.2 26.9 1.0 CG1 A:VAL83 4.4 28.5 1.0 CAI A:0OQ402 4.6 48.4 0.9 O A:LEU74 4.6 27.1 1.0 C A:LEU74 4.7 27.2 1.0 CG2 A:ILE84 4.8 31.7 1.0 CB A:MET78 4.9 32.2 1.0 CAR A:0OQ402 4.9 48.1 0.9 CD2 A:LEU75 5.0 31.8 1.0

Fluorine binding site 2 out of 3 in the Human P38 Map Kinase in Complex with Np-F11 and RL87


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Human P38 Map Kinase in Complex with Np-F11 and RL87 within 5.0Å range: probe atom residue distance (Å) B Occ A:F402 b:53.9 occ:0.90 FAE A:0OQ402 0.0 53.9 0.9 CAZ A:0OQ402 1.4 52.3 0.9 FAC A:0OQ402 2.2 51.8 0.9 FAD A:0OQ402 2.3 53.2 0.9 CAS A:0OQ402 2.3 51.0 0.9 N A:ASP168 3.0 43.6 1.0 CAJ A:0OQ402 3.0 49.4 0.9 CA A:ASP168 3.1 47.0 1.0 C A:LEU167 3.3 40.0 1.0 CG2 A:ILE84 3.4 31.7 1.0 CAK A:0OQ402 3.4 50.7 0.9 CB A:ASP168 3.5 47.5 1.0 O A:LEU167 3.6 38.9 1.0 CA A:LEU167 4.2 37.7 1.0 CAH A:0OQ402 4.3 48.1 0.9 O A:ILE166 4.3 31.8 1.0 C A:ASP168 4.5 48.7 1.0 CD2 A:LEU75 4.5 31.8 1.0 CG A:ASP168 4.5 50.2 1.0 CAI A:0OQ402 4.6 48.4 0.9 CG1 A:VAL83 4.8 28.5 1.0 C A:ILE166 4.9 32.4 1.0 CB A:ILE84 4.9 31.9 1.0 N A:LEU167 4.9 34.4 1.0 CE1 A:HIS148 4.9 31.0 1.0 O A:ASP168 4.9 48.5 1.0 OD1 A:ASP168 4.9 51.6 1.0 CAR A:0OQ402 5.0 48.1 0.9

Fluorine binding site 3 out of 3 in the Human P38 Map Kinase in Complex with Np-F11 and RL87


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Human P38 Map Kinase in Complex with Np-F11 and RL87 within 5.0Å range: probe atom residue distance (Å) B Occ A:F402 b:51.8 occ:0.90 FAC A:0OQ402 0.0 51.8 0.9 CAZ A:0OQ402 1.3 52.3 0.9 FAE A:0OQ402 2.2 53.9 0.9 FAD A:0OQ402 2.2 53.2 0.9 CAS A:0OQ402 2.2 51.0 0.9 CAK A:0OQ402 2.7 50.7 0.9 CD2 A:LEU75 3.2 31.8 1.0 CB A:ASP168 3.4 47.5 1.0 CAJ A:0OQ402 3.5 49.4 0.9 CG A:LEU75 3.6 29.9 1.0 CA A:ASP168 3.9 47.0 1.0 CAI A:0OQ402 4.1 48.4 0.9 CB A:LEU74 4.1 26.9 1.0 CG2 A:ILE84 4.2 31.7 1.0 N A:LEU75 4.2 26.8 1.0 N A:ASP168 4.3 43.6 1.0 OE1 A:GLU71 4.4 42.1 1.0 CA A:LEU75 4.4 28.0 1.0 C A:LEU74 4.5 27.2 1.0 CG A:ASP168 4.5 50.2 1.0 CB A:LEU75 4.6 27.1 1.0 CAH A:0OQ402 4.7 48.1 0.9 CG A:MET78 4.7 33.1 1.0 CD1 A:LEU75 4.7 31.7 1.0 O A:LEU74 4.8 27.1 1.0 OD2 A:ASP168 4.9 54.3 1.0 CAR A:0OQ402 4.9 48.1 0.9 CA A:LEU74 5.0 27.0 1.0 O A:GLU71 5.0 27.8 1.0

B.Over, S.Wetzel, C.Grutter, Y.Nakai, S.Renner, D.Rauh, H.Waldmann. Natural-Product-Derived Fragments For Fragment-Based Ligand Discovery. Nat Chem V. 5 21 2012.
ISSN: ISSN 1755-4349
PubMed: 23247173
DOI: 10.1038/NCHEM.1506