Fluorine in PDB 3b2w: Crystal Structure of Pyrimidine Amide 11 Bound to Lck

All present enzymatic activity of Crystal Structure of Pyrimidine Amide 11 Bound to Lck:
2.7.10.2;

The structure of Crystal Structure of Pyrimidine Amide 11 Bound to Lck, PDB code: 3b2w was solved by X.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	45.180, 75.190, 47.110, 90.00, 112.35, 90.00
R / Rfree (%)	23 / 30.8

The binding sites of Fluorine atom in the Crystal Structure of Pyrimidine Amide 11 Bound to Lck (pdb code 3b2w). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of Pyrimidine Amide 11 Bound to Lck, PDB code: 3b2w:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Crystal Structure of Pyrimidine Amide 11 Bound to Lck


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 Pyrimidine Amide 11 Bound to Lck within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:27.5 occ:1.00 F1 A:9NH601 0.0 27.5 1.0 C14 A:9NH601 1.3 25.5 1.0 F3 A:9NH601 2.1 27.9 1.0 F2 A:9NH601 2.2 27.4 1.0 C10 A:9NH601 2.4 24.1 1.0 C9 A:9NH601 2.8 22.3 1.0 CZ A:PHE383 3.2 21.8 1.0 CE1 A:PHE383 3.3 18.8 1.0 CD2 A:LEU300 3.3 9.9 1.0 C11 A:9NH601 3.7 21.3 1.0 CE2 A:PHE383 4.0 18.8 1.0 CD2 A:LEU295 4.0 20.7 1.0 CD1 A:PHE383 4.0 19.1 1.0 CG A:LEU300 4.2 11.9 1.0 F4 A:9NH601 4.2 20.2 1.0 C8 A:9NH601 4.2 22.1 1.0 CB A:LEU295 4.2 21.9 1.0 CG A:LEU295 4.5 21.0 1.0 CD2 A:PHE383 4.6 18.2 1.0 CG A:PHE383 4.6 19.1 1.0 CB A:LEU300 4.8 12.7 1.0 C26 A:9NH601 4.9 20.9 1.0 O A:LEU295 4.9 24.4 1.0 CD1 A:ILE355 5.0 11.8 1.0

Fluorine binding site 2 out of 4 in the Crystal Structure of Pyrimidine Amide 11 Bound to Lck


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 Pyrimidine Amide 11 Bound to Lck within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:27.9 occ:1.00 F3 A:9NH601 0.0 27.9 1.0 C14 A:9NH601 1.3 25.5 1.0 F1 A:9NH601 2.1 27.5 1.0 F2 A:9NH601 2.2 27.4 1.0 C10 A:9NH601 2.3 24.1 1.0 F4 A:9NH601 2.9 20.2 1.0 C11 A:9NH601 3.0 21.3 1.0 C9 A:9NH601 3.5 22.3 1.0 O A:VAL301 3.6 15.1 1.0 CD2 A:LEU300 3.8 9.9 1.0 CG A:MET292 3.9 24.2 1.0 CA A:MET292 4.1 22.8 1.0 C26 A:9NH601 4.3 20.9 1.0 CB A:MET292 4.4 24.2 1.0 CB A:LEU300 4.4 12.7 1.0 CB A:LEU295 4.4 21.9 1.0 O A:LEU295 4.4 24.4 1.0 CG A:LEU300 4.4 11.9 1.0 C A:VAL301 4.7 15.4 1.0 N A:VAL301 4.7 16.1 1.0 C8 A:9NH601 4.7 22.1 1.0 O A:MET292 4.8 25.6 1.0 N A:MET292 4.9 21.9 1.0 C A:MET292 5.0 23.5 1.0

Fluorine binding site 3 out of 4 in the Crystal Structure of Pyrimidine Amide 11 Bound to Lck


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 Pyrimidine Amide 11 Bound to Lck within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:27.4 occ:1.00 F2 A:9NH601 0.0 27.4 1.0 C14 A:9NH601 1.4 25.5 1.0 F1 A:9NH601 2.2 27.5 1.0 F3 A:9NH601 2.2 27.9 1.0 C10 A:9NH601 2.4 24.1 1.0 F4 A:9NH601 3.0 20.2 1.0 C11 A:9NH601 3.0 21.3 1.0 O A:ILE380 3.3 15.6 1.0 CD2 A:LEU300 3.5 9.9 1.0 C9 A:9NH601 3.5 22.3 1.0 CG A:LEU300 3.5 11.9 1.0 CB A:LEU300 3.8 12.7 1.0 N A:VAL301 4.0 16.1 1.0 CE1 A:PHE383 4.1 18.8 1.0 C A:ILE380 4.2 14.7 1.0 O A:VAL301 4.3 15.1 1.0 C26 A:9NH601 4.4 20.9 1.0 CA A:LEU300 4.4 13.5 1.0 CA A:ALA381 4.5 14.7 1.0 CB A:VAL301 4.6 15.6 1.0 C A:LEU300 4.6 15.5 1.0 CD1 A:PHE383 4.6 19.1 1.0 CZ A:PHE383 4.7 21.8 1.0 C8 A:9NH601 4.7 22.1 1.0 N A:ALA381 4.7 14.2 1.0 CA A:VAL301 4.7 16.0 1.0 O2 A:9NH601 4.9 18.1 1.0 C A:ALA381 4.9 16.2 1.0 CD1 A:LEU300 4.9 10.9 1.0

Fluorine binding site 4 out of 4 in the Crystal Structure of Pyrimidine Amide 11 Bound to Lck


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Pyrimidine Amide 11 Bound to Lck within 5.0Å range: probe atom residue distance (Å) B Occ A:F601 b:20.2 occ:1.00 F4 A:9NH601 0.0 20.2 1.0 C11 A:9NH601 1.3 21.3 1.0 C26 A:9NH601 2.3 20.9 1.0 C10 A:9NH601 2.4 24.1 1.0 N3 A:9NH601 2.8 18.9 1.0 O2 A:9NH601 2.9 18.1 1.0 C14 A:9NH601 2.9 25.5 1.0 F3 A:9NH601 2.9 27.9 1.0 C25 A:9NH601 3.0 18.5 1.0 F2 A:9NH601 3.0 27.4 1.0 CB A:VAL301 3.4 15.6 1.0 O A:VAL301 3.6 15.1 1.0 C7 A:9NH601 3.6 19.8 1.0 C9 A:9NH601 3.7 22.3 1.0 CG1 A:VAL301 3.8 15.9 1.0 CG A:MET292 3.8 24.2 1.0 SD A:MET292 4.0 26.6 1.0 CE A:MET292 4.0 23.0 1.0 C24 A:9NH601 4.1 19.7 1.0 C8 A:9NH601 4.2 22.1 1.0 F1 A:9NH601 4.2 27.5 1.0 CA A:VAL301 4.3 16.0 1.0 C A:VAL301 4.3 15.4 1.0 CG2 A:VAL301 4.4 16.3 1.0 N A:VAL301 4.4 16.1 1.0 O A:ILE380 4.6 15.6 1.0 N A:ASP382 4.6 18.0 1.0 CA A:ALA381 4.7 14.7 1.0 C23 A:9NH601 4.8 17.8 1.0 CB A:MET292 4.9 24.2 1.0 C12 A:9NH601 4.9 17.4 1.0

H.L.Deak, J.R.Newcomb, J.J.Nunes, C.Boucher, A.C.Cheng, E.F.Dimauro, L.F.Epstein, P.Gallant, B.L.Hodous, X.Huang, J.H.Lee, V.F.Patel, S.Schneider, S.M.Turci, X.Zhu. N-(3-(Phenylcarbamoyl)Arylpyrimidine)-5- Carboxamides As Potent and Selective Inhibitors of Lck: Structure, Synthesis and Sar. Bioorg.Med.Chem.Lett. V. 18 1172 2008.
ISSN: ISSN 0960-894X
PubMed: 18083554
DOI: 10.1016/J.BMCL.2007.11.123