Fluorine in PDB 2yj9: Cathepsin L with A Nitrile Inhibitor

All present enzymatic activity of Cathepsin L with A Nitrile Inhibitor:
3.4.22.15;

The structure of Cathepsin L with A Nitrile Inhibitor, PDB code: 2yj9 was solved by D.W.Banner, J.M.Benz, W.Haap, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.43 / 1.35
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.992, 57.153, 76.589, 90.00, 90.00, 90.00
R / Rfree (%)	15.033 / 20.091

The structure of Cathepsin L with A Nitrile Inhibitor also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Fluorine atom in the Cathepsin L with A Nitrile Inhibitor (pdb code 2yj9). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Cathepsin L with A Nitrile Inhibitor, PDB code: 2yj9:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Cathepsin L with A Nitrile Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Cathepsin L with A Nitrile Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F1221 b:31.2 occ:1.00 F36 A:YJ91221 0.0 31.2 1.0 C35 A:YJ91221 1.3 22.5 1.0 F37 A:YJ91221 2.1 29.0 1.0 F38 A:YJ91221 2.1 31.1 1.0 C30 A:YJ91221 2.4 20.9 1.0 H31 A:YJ91221 2.4 18.6 1.0 HG3 A:GLU63 2.6 17.7 1.0 HA2 A:GLY68 2.7 12.9 1.0 C31 A:YJ91221 2.8 19.2 1.0 HB2 A:GLU63 3.1 17.4 1.0 HA A:ASN62 3.3 13.3 1.0 CG A:GLU63 3.3 17.5 1.0 O A:GLY61 3.4 16.9 1.0 H A:GLU63 3.4 14.1 1.0 O A:GLY67 3.5 14.2 1.0 CA A:GLY68 3.6 12.9 1.0 CD A:GLU63 3.6 26.2 1.0 C29 A:YJ91221 3.7 18.6 1.0 CB A:GLU63 3.7 17.4 1.0 N A:GLY68 3.7 14.1 1.0 C A:GLY67 3.7 14.4 1.0 N A:GLU63 3.7 14.3 1.0 OE2 A:GLU63 3.9 32.6 1.0 H29 A:YJ91221 4.0 19.0 1.0 HA3 A:GLY68 4.1 12.8 1.0 O A:HOH2101 4.1 36.6 1.0 C32 A:YJ91221 4.2 17.2 1.0 HG2 A:GLU63 4.2 18.5 1.0 CA A:ASN62 4.2 13.4 1.0 H A:GLY68 4.2 13.3 1.0 OE1 A:GLU63 4.2 32.4 1.0 C A:ASN62 4.2 13.4 1.0 CA A:GLU63 4.4 16.1 1.0 C A:GLY61 4.5 14.5 1.0 HB3 A:GLU63 4.5 17.8 1.0 HA3 A:GLY67 4.5 15.7 1.0 HE2 A:TYR72 4.5 17.6 1.0 C A:GLY68 4.6 11.7 1.0 CA A:GLY67 4.7 14.9 1.0 HD2 A:TYR72 4.7 17.1 1.0 H32 A:YJ91221 4.8 17.1 1.0 HG A:LEU69 4.8 15.7 1.0 C34 A:YJ91221 4.8 18.7 1.0 OD1 A:ASN62 4.9 13.9 1.0 N A:ASN62 4.9 15.8 1.0 H A:LEU69 4.9 12.2 1.0 HA A:GLU63 5.0 15.8 1.0

Fluorine binding site 2 out of 3 in the Cathepsin L with A Nitrile Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Cathepsin L with A Nitrile Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F1221 b:29.0 occ:1.00 F37 A:YJ91221 0.0 29.0 1.0 C35 A:YJ91221 1.3 22.5 1.0 F36 A:YJ91221 2.1 31.2 1.0 F38 A:YJ91221 2.1 31.1 1.0 C30 A:YJ91221 2.4 20.9 1.0 HE2 A:TYR72 2.7 17.6 1.0 H29 A:YJ91221 2.7 19.0 1.0 HA2 A:GLY68 2.9 12.9 1.0 C29 A:YJ91221 2.9 18.6 1.0 HG A:LEU69 3.1 15.7 1.0 O A:GLY61 3.2 16.9 1.0 HD2 A:TYR72 3.3 17.1 1.0 CE2 A:TYR72 3.4 18.0 1.0 C31 A:YJ91221 3.6 19.2 1.0 HA A:ASN62 3.6 13.3 1.0 O A:HOH2101 3.7 36.6 1.0 CD2 A:TYR72 3.7 17.7 1.0 CA A:GLY68 3.8 12.9 1.0 H31 A:YJ91221 3.8 18.6 1.0 CG A:LEU69 4.1 15.9 1.0 H A:LEU69 4.1 12.2 1.0 C A:GLY61 4.1 14.5 1.0 HG3 A:GLU63 4.1 17.7 1.0 C A:GLY68 4.2 11.7 1.0 N A:LEU69 4.3 13.5 1.0 C34 A:YJ91221 4.3 18.7 1.0 OD1 A:ASN62 4.4 13.9 1.0 HA3 A:GLY68 4.4 12.8 1.0 CD1 A:LEU69 4.5 19.3 1.0 CA A:ASN62 4.5 13.4 1.0 N A:GLY68 4.5 14.1 1.0 CZ A:TYR72 4.6 17.6 1.0 HB2 A:LEU69 4.6 13.8 1.0 N A:ASN62 4.7 15.8 1.0 C32 A:YJ91221 4.7 17.2 1.0 HA3 A:GLY61 4.8 16.4 1.0 CB A:LEU69 4.8 12.7 1.0 H A:GLU63 4.8 14.1 1.0 H A:GLY68 4.8 13.3 1.0 CD2 A:LEU69 4.9 18.5 1.0 O A:GLY68 4.9 12.1 1.0 OH A:TYR72 4.9 22.9 1.0 H34 A:YJ91221 5.0 18.9 1.0

Fluorine binding site 3 out of 3 in the Cathepsin L with A Nitrile Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Cathepsin L with A Nitrile Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:F1221 b:31.1 occ:1.00 F38 A:YJ91221 0.0 31.1 1.0 C35 A:YJ91221 1.3 22.5 1.0 F36 A:YJ91221 2.1 31.2 1.0 F37 A:YJ91221 2.1 29.0 1.0 C30 A:YJ91221 2.4 20.9 1.0 O A:HOH2101 3.1 36.6 1.0 C29 A:YJ91221 3.2 18.6 1.0 H29 A:YJ91221 3.2 19.0 1.0 C31 A:YJ91221 3.3 19.2 1.0 H31 A:YJ91221 3.4 18.6 1.0 OE2 A:GLU63 3.6 32.6 1.0 HG3 A:GLU63 3.6 17.7 1.0 O A:GLY61 3.8 16.9 1.0 CD A:GLU63 3.9 26.2 1.0 HE2 A:TYR72 4.1 17.6 1.0 CG A:GLU63 4.2 17.5 1.0 HA2 A:GLY68 4.4 12.9 1.0 C34 A:YJ91221 4.4 18.7 1.0 C32 A:YJ91221 4.5 17.2 1.0 OE1 A:GLU63 4.5 32.4 1.0 HB2 A:GLU63 4.7 17.4 1.0 HA A:ASN62 4.9 13.3 1.0 HG A:LEU69 4.9 15.7 1.0 CE2 A:TYR72 4.9 18.0 1.0 HG2 A:GLU63 5.0 18.5 1.0 C33 A:YJ91221 5.0 18.0 1.0

L.A.Hardegger, B.Kuhn, B.Spinnler, L.Anselm, R.Ecabert, M.Stihle, B.Gsell, R.Thoma, J.Diez, J.M.Benz, J.Plancher, G.Hartmann, Y.Isshiki, K.Morikami, N.Shimma, W.Haap, D.W.Banner, F.Diederich. Halogen Bonding at the Active Sites of Human Cathepsin L and MEK1 Kinase: Efficient Interactions in Different Environments. Chemmedchem V. 6 2048 2011.
ISSN: ISSN 1860-7179
PubMed: 21898833
DOI: 10.1002/CMDC.201100353