Fluorine in PDB 3dv3: MEK1 with Pf-04622664 Bound

All present enzymatic activity of MEK1 with Pf-04622664 Bound:
2.7.12.2;

The structure of MEK1 with Pf-04622664 Bound, PDB code: 3dv3 was solved by S.L.Kazmirski, M.Kothe, Y.-H.Ding, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.83 / 2.30
Space group	P 62
Cell size a, b, c (Å), α, β, γ (°)	81.596, 81.596, 129.966, 90.00, 90.00, 120.00
R / Rfree (%)	18.2 / 22.1

The structure of MEK1 with Pf-04622664 Bound also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Iodine	(I)	1 atom

The binding sites of Fluorine atom in the MEK1 with Pf-04622664 Bound (pdb code 3dv3). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the MEK1 with Pf-04622664 Bound, PDB code: 3dv3:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the MEK1 with Pf-04622664 Bound


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of MEK1 with Pf-04622664 Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:F9001 b:44.8 occ:1.00 F3 A:MEK9001 0.0 44.8 1.0 C10 A:MEK9001 1.3 42.8 1.0 C9 A:MEK9001 2.3 44.5 1.0 C11 A:MEK9001 2.3 42.4 1.0 C16 A:MEK9001 2.7 46.4 1.0 F2 A:MEK9001 2.7 45.0 1.0 O A:PHE209 3.2 52.5 1.0 N A:VAL211 3.3 54.4 1.0 N A:SER212 3.4 54.0 1.0 C8 A:MEK9001 3.5 41.6 1.0 C12 A:MEK9001 3.6 43.4 1.0 CD2 A:LEU215 3.6 48.9 1.0 CA A:GLY210 3.8 52.8 1.0 CG2 A:VAL211 3.8 56.2 1.0 C A:GLY210 3.9 53.7 1.0 O4 A:MEK9001 3.9 51.1 1.0 C17 A:MEK9001 4.0 50.2 1.0 C7 A:MEK9001 4.0 44.3 1.0 CB A:SER212 4.0 53.9 1.0 O A:SER212 4.0 53.0 1.0 CB A:LEU215 4.1 54.0 1.0 CG A:LEU215 4.1 53.2 1.0 CA A:SER212 4.1 54.1 1.0 C A:PHE209 4.2 53.1 1.0 CA A:VAL211 4.2 54.9 1.0 C A:VAL211 4.3 54.7 1.0 N A:GLY210 4.4 52.2 1.0 CB A:VAL211 4.5 56.2 1.0 C A:SER212 4.6 53.2 1.0 CD2 A:LEU115 4.6 50.0 1.0 N2 A:MEK9001 4.7 46.5 1.0 CG1 A:ILE216 4.9 50.4 1.0 O A:GLY210 4.9 53.7 1.0 N A:ILE216 5.0 53.4 1.0 C2 A:MEK9001 5.0 46.1 1.0

Fluorine binding site 2 out of 3 in the MEK1 with Pf-04622664 Bound


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of MEK1 with Pf-04622664 Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:F9001 b:45.0 occ:1.00 F2 A:MEK9001 0.0 45.0 1.0 C11 A:MEK9001 1.3 42.4 1.0 C10 A:MEK9001 2.3 42.8 1.0 C12 A:MEK9001 2.3 43.4 1.0 F3 A:MEK9001 2.7 44.8 1.0 C2 A:MEK9001 2.7 46.1 1.0 N2 A:MEK9001 2.8 46.5 1.0 C1 A:MEK9001 3.0 46.2 1.0 CG2 A:VAL211 3.1 56.2 1.0 O A:PHE209 3.4 52.5 1.0 CD2 A:LEU115 3.5 50.0 1.0 C9 A:MEK9001 3.5 44.5 1.0 C7 A:MEK9001 3.6 44.3 1.0 C3 A:MEK9001 3.8 39.4 1.0 C8 A:MEK9001 4.0 41.6 1.0 CD2 A:LEU215 4.1 48.9 1.0 C6 A:MEK9001 4.2 47.3 1.0 CD1 A:ILE141 4.3 54.2 1.0 CD1 A:LEU118 4.3 52.2 1.0 N A:VAL211 4.4 54.4 1.0 CB A:VAL211 4.5 56.2 1.0 C A:PHE209 4.6 53.1 1.0 C16 A:MEK9001 4.7 46.4 1.0 C13 A:MEK9001 4.8 46.8 1.0 C4 A:MEK9001 4.8 47.9 1.0 F1 A:MEK9001 5.0 43.9 1.0 C5 A:MEK9001 5.0 41.0 1.0 CA A:VAL211 5.0 54.9 1.0

Fluorine binding site 3 out of 3 in the MEK1 with Pf-04622664 Bound


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of MEK1 with Pf-04622664 Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:F9001 b:43.9 occ:1.00 F1 A:MEK9001 0.0 43.9 1.0 C6 A:MEK9001 1.3 47.3 1.0 C1 A:MEK9001 2.3 46.2 1.0 C5 A:MEK9001 2.3 41.0 1.0 N2 A:MEK9001 2.6 46.5 1.0 OD1 A:ASP208 3.2 53.2 1.0 CE A:LYS97 3.3 53.9 1.0 C2 A:MEK9001 3.5 46.1 1.0 CE A:MET143 3.6 51.9 1.0 O1 A:MEK9001 3.6 46.8 1.0 C4 A:MEK9001 3.6 47.9 1.0 CD1 A:ILE141 3.7 54.2 1.0 CG2 A:ILE141 3.9 53.9 1.0 C12 A:MEK9001 4.0 43.4 1.0 NZ A:LYS97 4.0 55.0 1.0 C3 A:MEK9001 4.0 39.4 1.0 CB A:ILE141 4.1 54.3 1.0 SD A:MET143 4.1 54.9 1.0 CD A:LYS97 4.3 56.3 1.0 C13 A:MEK9001 4.4 46.8 1.0 CG A:LYS97 4.4 56.1 1.0 CG A:ASP208 4.4 54.2 1.0 CB A:LYS97 4.5 51.8 1.0 CG1 A:ILE141 4.5 53.0 1.0 O A:HOH9079 4.6 49.3 1.0 C7 A:MEK9001 4.6 44.3 1.0 N A:ASP208 4.7 53.4 1.0 CA A:ASP208 4.8 54.5 1.0 C11 A:MEK9001 4.9 42.4 1.0 F2 A:MEK9001 5.0 45.0 1.0

H.Tecle, J.Shao, Y.Li, M.Kothe, S.Kazmirski, J.Penzotti, Y.H.Ding, J.Ohren, D.Moshinsky, R.Coli, N.Jhawar, E.Bora, S.Jacques-O'hagan, J.Wu. Beyond the Mek-Pocket: Can Current Mek Kinase Inhibitors Be Utilized to Synthesize Novel Type III Nckis? Does the Mek-Pocket Exist in Kinases Other Than Mek? Bioorg.Med.Chem.Lett. V. 19 226 2009.
ISSN: ISSN 0960-894X
PubMed: 19019675
DOI: 10.1016/J.BMCL.2008.10.108