Chlorine in PDB 2xu3: 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: 2xu3 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)	44.53 / 0.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	44.441, 49.394, 46.129, 90.00, 105.13, 90.00
R / Rfree (%)	14.183 / 15.473

The binding sites of Chlorine atom in the Cathepsin L with A Nitrile Inhibitor (pdb code 2xu3). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Cathepsin L with A Nitrile Inhibitor, PDB code: 2xu3:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in the Cathepsin L with A Nitrile Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Cathepsin L with A Nitrile Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1221 b:12.8 occ:0.75 CL2 A:XU31221 0.0 12.8 0.8 CL2 A:XU31221 0.3 4.7 0.2 C11 A:XU31221 1.7 7.9 0.8 C11 A:XU31221 1.8 4.5 0.2 H3 A:XU31221 2.6 6.8 0.8 C12 A:XU31221 2.6 8.1 0.8 C8 A:XU31221 2.7 4.5 0.2 H12 A:XU31221 2.7 8.4 0.8 O9 A:XU31221 2.7 4.7 0.2 C8 A:XU31221 2.7 7.5 0.8 H3 A:XU31221 2.8 4.3 0.2 C12 A:XU31221 2.9 4.6 0.2 S6 A:XU31221 3.0 4.3 0.2 H12 A:XU31221 3.1 4.5 0.2 O9 A:XU31221 3.1 7.0 0.8 O A:HOH2146 3.3 7.7 1.0 S6 A:XU31221 3.3 6.5 0.8 C3 A:XU31221 3.3 6.8 0.8 CE A:MET70 3.4 6.3 1.0 C3 A:XU31221 3.4 4.3 0.2 CD2 A:LEU69 3.5 8.2 1.0 H A:MET70 3.6 5.0 1.0 HA A:LEU69 3.6 5.4 1.0 SD A:MET70 3.7 5.2 1.0 C13 A:XU31221 3.9 8.4 0.8 CB A:ALA135 3.9 5.6 1.0 C15 A:XU31221 4.0 8.2 0.8 C15 A:XU31221 4.0 4.9 0.2 O A:HOH2354 4.1 10.6 1.0 C13 A:XU31221 4.2 4.6 0.2 HB3 A:LEU69 4.2 6.1 1.0 C2 A:XU31221 4.4 6.7 0.8 N A:MET70 4.4 4.8 1.0 O10 A:XU31221 4.4 4.3 0.2 H2 A:XU31221 4.4 7.0 0.8 O A:HOH2147 4.4 13.4 1.0 C14 A:XU31221 4.4 8.6 0.8 HB2 A:MET70 4.5 4.8 1.0 C2 A:XU31221 4.5 4.2 0.2 C4 A:XU31221 4.5 6.5 0.8 CA A:LEU69 4.5 5.3 1.0 H4A A:XU31221 4.5 6.2 0.8 H2 A:XU31221 4.5 4.2 0.2 HA A:ALA135 4.6 4.7 1.0 H2A A:XU31221 4.6 4.3 0.2 H2A A:XU31221 4.6 6.8 0.8 C4 A:XU31221 4.6 4.3 0.2 C14 A:XU31221 4.6 4.7 0.2 CB A:ALA214 4.6 7.3 1.0 CB A:LEU69 4.6 6.1 1.0 O A:ALA214 4.7 6.8 1.0 CG A:LEU69 4.7 7.0 1.0 H4A A:XU31221 4.7 4.3 0.2 O10 A:XU31221 4.7 6.7 0.8 H13 A:XU31221 4.7 8.0 0.8 CA A:ALA135 4.7 4.5 1.0 H4 A:XU31221 4.8 6.4 0.8 H15 A:XU31221 4.8 4.7 0.2 H15 A:XU31221 4.9 7.9 0.8 H4 A:XU31221 4.9 4.3 0.2 N A:ALA135 4.9 4.1 1.0 H A:ALA135 5.0 4.2 1.0 C A:LEU69 5.0 5.2 1.0

Chlorine binding site 2 out of 5 in the Cathepsin L with A Nitrile Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Cathepsin L with A Nitrile Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1221 b:13.1 occ:0.75 CL3 A:XU31221 0.0 13.1 0.8 CL3 A:XU31221 1.1 8.1 0.2 C30 A:XU31221 1.4 4.8 0.2 C30 A:XU31221 1.7 10.6 0.8 C29 A:XU31221 2.0 4.9 0.2 H29 A:XU31221 2.1 5.3 0.2 C29 A:XU31221 2.8 10.0 0.8 HA3 A:GLY68 2.8 5.4 1.0 S31 A:XU31221 3.0 10.7 0.8 S31 A:XU31221 3.0 4.8 0.2 H29 A:XU31221 3.0 9.9 0.8 O A:GLY61 3.1 8.1 1.0 HG2 A:GLU63 3.1 7.5 0.4 C28 A:XU31221 3.3 5.0 0.2 HE2 A:TYR72 3.4 7.7 1.0 HA A:ASN62 3.4 6.2 1.0 HG3 A:GLU63 3.5 7.8 0.4 O A:HOH2135 3.5 14.2 1.0 CA A:GLY68 3.7 5.4 1.0 HG A:LEU69 3.7 7.8 1.0 C27 A:XU31221 3.7 4.5 0.2 CG A:GLU63 3.8 7.1 0.4 HG3 A:GLU63 3.8 9.7 0.6 HD2 A:TYR72 3.9 6.8 1.0 C28 A:XU31221 4.0 9.6 0.8 N A:GLY68 4.1 5.3 1.0 H28 A:XU31221 4.1 5.2 0.2 O A:HOH2138 4.1 15.0 1.0 C27 A:XU31221 4.2 10.2 0.8 CE2 A:TYR72 4.2 8.5 1.0 C A:GLY61 4.2 7.1 1.0 C A:GLY68 4.2 5.3 1.0 HB2 A:GLU63 4.3 6.8 0.4 H A:GLU63 4.3 6.6 0.6 H A:GLU63 4.3 6.2 0.4 H A:LEU69 4.3 5.5 1.0 CA A:ASN62 4.3 6.1 1.0 HA2 A:GLY68 4.3 5.3 1.0 HB2 A:GLU63 4.4 8.6 0.6 O A:GLY67 4.4 6.1 1.0 C A:GLY67 4.4 5.6 1.0 CD2 A:TYR72 4.4 6.9 1.0 H A:GLY68 4.4 5.4 1.0 N A:LEU69 4.5 5.5 1.0 OD1 A:ASN62 4.5 6.1 1.0 N A:GLU63 4.6 6.2 0.4 N A:GLU63 4.6 6.6 0.6 CB A:GLU63 4.6 6.6 0.4 CG A:GLU63 4.6 9.7 0.6 CG A:LEU69 4.7 7.0 1.0 C A:ASN62 4.7 6.6 1.0 N A:ASN62 4.8 6.3 1.0 O A:GLY68 4.8 5.7 1.0 H2A A:XU31221 4.9 6.8 0.8 H28 A:XU31221 4.9 10.3 0.8 CD A:GLU63 4.9 8.8 0.4 CB A:GLU63 5.0 8.5 0.6 H2A A:XU31221 5.0 4.3 0.2

Chlorine binding site 3 out of 5 in the Cathepsin L with A Nitrile Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Cathepsin L with A Nitrile Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1221 b:4.7 occ:0.25 CL2 A:XU31221 0.0 4.7 0.2 CL2 A:XU31221 0.3 12.8 0.8 C11 A:XU31221 1.6 7.9 0.8 C11 A:XU31221 1.7 4.5 0.2 C12 A:XU31221 2.4 8.1 0.8 H12 A:XU31221 2.5 8.4 0.8 C8 A:XU31221 2.7 4.5 0.2 C8 A:XU31221 2.7 7.5 0.8 C12 A:XU31221 2.7 4.6 0.2 O9 A:XU31221 2.8 4.7 0.2 H3 A:XU31221 2.8 6.8 0.8 H12 A:XU31221 2.9 4.5 0.2 H3 A:XU31221 3.1 4.3 0.2 S6 A:XU31221 3.1 4.3 0.2 O9 A:XU31221 3.2 7.0 0.8 O A:HOH2146 3.3 7.7 1.0 S6 A:XU31221 3.4 6.5 0.8 CE A:MET70 3.5 6.3 1.0 C3 A:XU31221 3.5 6.8 0.8 C3 A:XU31221 3.6 4.3 0.2 CD2 A:LEU69 3.7 8.2 1.0 C13 A:XU31221 3.7 8.4 0.8 CB A:ALA135 3.8 5.6 1.0 H A:MET70 3.8 5.0 1.0 SD A:MET70 3.9 5.2 1.0 HA A:LEU69 3.9 5.4 1.0 C15 A:XU31221 3.9 8.2 0.8 C15 A:XU31221 4.0 4.9 0.2 O A:HOH2354 4.0 10.6 1.0 C13 A:XU31221 4.0 4.6 0.2 C14 A:XU31221 4.3 8.6 0.8 CB A:ALA214 4.3 7.3 1.0 O A:HOH2147 4.4 13.4 1.0 HB3 A:LEU69 4.4 6.1 1.0 O10 A:XU31221 4.4 4.3 0.2 O A:ALA214 4.4 6.8 1.0 HA A:ALA135 4.5 4.7 1.0 C14 A:XU31221 4.5 4.7 0.2 H2 A:XU31221 4.5 7.0 0.8 H13 A:XU31221 4.5 8.0 0.8 HB2 A:MET70 4.5 4.8 1.0 C2 A:XU31221 4.6 6.7 0.8 N A:MET70 4.6 4.8 1.0 CA A:ALA135 4.6 4.5 1.0 C2 A:XU31221 4.6 4.2 0.2 H2 A:XU31221 4.6 4.2 0.2 C4 A:XU31221 4.7 6.5 0.8 H4A A:XU31221 4.7 6.2 0.8 CA A:LEU69 4.7 5.3 1.0 O10 A:XU31221 4.7 6.7 0.8 H2A A:XU31221 4.8 4.3 0.2 N A:ALA135 4.8 4.1 1.0 H A:ALA135 4.8 4.2 1.0 H15 A:XU31221 4.8 4.7 0.2 H2A A:XU31221 4.8 6.8 0.8 H15 A:XU31221 4.8 7.9 0.8 C4 A:XU31221 4.8 4.3 0.2 CB A:LEU69 4.8 6.1 1.0 CG A:LEU69 4.8 7.0 1.0 H4A A:XU31221 4.9 4.3 0.2 H13 A:XU31221 4.9 4.5 0.2

Chlorine binding site 4 out of 5 in the Cathepsin L with A Nitrile Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Cathepsin L with A Nitrile Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1221 b:8.1 occ:0.25 CL3 A:XU31221 0.0 8.1 0.2 CL3 A:XU31221 1.1 13.1 0.8 C30 A:XU31221 1.7 4.8 0.2 HG2 A:GLU63 2.1 7.5 0.4 HG3 A:GLU63 2.4 7.8 0.4 C30 A:XU31221 2.4 10.6 0.8 CG A:GLU63 2.7 7.1 0.4 C29 A:XU31221 2.8 4.9 0.2 HG3 A:GLU63 2.8 9.7 0.6 S31 A:XU31221 3.0 4.8 0.2 O A:GLY61 3.0 8.1 1.0 H29 A:XU31221 3.0 5.3 0.2 HA3 A:GLY68 3.1 5.4 1.0 S31 A:XU31221 3.3 10.7 0.8 HB2 A:GLU63 3.3 6.8 0.4 HA A:ASN62 3.3 6.2 1.0 HB2 A:GLU63 3.3 8.6 0.6 CB A:GLU63 3.5 6.6 0.4 O A:HOH2135 3.5 14.2 1.0 CG A:GLU63 3.6 9.7 0.6 C29 A:XU31221 3.6 10.0 0.8 H A:GLU63 3.6 6.6 0.6 O A:HOH2138 3.7 15.0 1.0 H A:GLU63 3.7 6.2 0.4 N A:GLU63 3.8 6.2 0.4 N A:GLU63 3.9 6.6 0.6 CD A:GLU63 3.9 8.8 0.4 O A:GLY67 3.9 6.1 1.0 CB A:GLU63 3.9 8.5 0.6 C28 A:XU31221 3.9 5.0 0.2 CA A:GLY68 3.9 5.4 1.0 H29 A:XU31221 4.0 9.9 0.8 CD A:GLU63 4.0 12.9 0.6 CA A:ASN62 4.1 6.1 1.0 C27 A:XU31221 4.1 4.5 0.2 C A:GLY67 4.1 5.6 1.0 N A:GLY68 4.1 5.3 1.0 C A:ASN62 4.1 6.6 1.0 C A:GLY61 4.2 7.1 1.0 HE2 A:TYR72 4.2 7.7 1.0 OE2 A:GLU63 4.2 12.0 0.4 OE2 A:GLU63 4.3 16.7 0.6 HB3 A:GLU63 4.3 6.5 0.4 CA A:GLU63 4.3 6.3 0.4 HG2 A:GLU63 4.4 10.2 0.6 HA2 A:GLY68 4.5 5.3 1.0 CA A:GLU63 4.5 7.3 0.6 OE1 A:GLU63 4.5 13.3 0.6 HD2 A:TYR72 4.6 6.8 1.0 H A:GLY68 4.6 5.4 1.0 N A:ASN62 4.7 6.3 1.0 C27 A:XU31221 4.7 10.2 0.8 C28 A:XU31221 4.7 9.6 0.8 HB3 A:GLU63 4.7 8.3 0.6 HG A:LEU69 4.8 7.8 1.0 C A:GLY68 4.8 5.3 1.0 HA A:GLU63 4.8 6.6 0.4 OE1 A:GLU63 4.8 11.9 0.4 HA2 A:GLY67 4.9 6.0 1.0 OD1 A:ASN62 4.9 6.1 1.0 H28 A:XU31221 4.9 5.2 0.2 O A:ASN62 4.9 7.9 1.0 CE2 A:TYR72 5.0 8.5 1.0

Chlorine binding site 5 out of 5 in the Cathepsin L with A Nitrile Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Cathepsin L with A Nitrile Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1223 b:8.1 occ:1.00 HA3 A:GLY23 2.8 5.9 1.0 H22 A:XU31221 2.8 4.9 0.2 H22 A:XU31221 2.8 5.5 0.8 H82 A:BTB1222 2.9 11.2 1.0 O A:HOH2057 3.1 12.4 1.0 O A:HOH2319 3.2 10.8 1.0 N20 A:XU31221 3.4 5.0 0.8 NE2 A:GLN19 3.5 6.3 1.0 N20 A:XU31221 3.6 5.2 0.2 CA A:GLY23 3.6 6.1 1.0 HA2 A:GLY23 3.7 5.9 1.0 C22 A:XU31221 3.8 5.7 0.8 C22 A:XU31221 3.9 5.0 0.2 H21 A:XU31221 3.9 5.3 0.8 C8 A:BTB1222 4.0 11.9 1.0 O A:CYS22 4.0 6.4 1.0 N A:GLY23 4.2 6.0 1.0 C19 A:XU31221 4.3 5.2 0.8 H21 A:XU31221 4.3 5.1 0.2 C21 A:XU31221 4.4 5.4 0.8 C A:CYS22 4.4 6.2 1.0 C19 A:XU31221 4.4 4.6 0.2 O8 A:BTB1222 4.4 15.2 1.0 H81 A:BTB1222 4.5 9.9 1.0 H72 A:BTB1222 4.5 10.4 1.0 H22A A:XU31221 4.6 5.1 0.2 C18 A:XU31221 4.6 5.0 0.8 H22A A:XU31221 4.6 5.4 0.8 CD A:GLN19 4.6 5.2 1.0 C18 A:XU31221 4.6 4.9 0.2 C21 A:XU31221 4.7 4.9 0.2 C A:GLY23 4.7 5.2 1.0 H A:GLY23 4.8 6.2 1.0 H A:SER24 4.8 5.1 1.0 C7 A:BTB1222 4.9 10.8 1.0 HE1 A:TRP189 4.9 6.1 1.0 HG3 A:GLN19 5.0 5.3 1.0

L.A.Hardegger, B.Kuhn, B.Spinnler, L.Anselm, R.Ecabert, M.Stihle, B.Gsell, R.Thoma, J.Diez, J.Benz, J.M.Plancher, G.Hartmann, D.W.Banner, W.Haap, F.Diederich. Systematic Investigation of Halogen Bonding in Protein-Ligand Interactions. Angew.Chem.Int.Ed.Engl. V. 50 314 2011.
ISSN: ISSN 1433-7851
PubMed: 21184410
DOI: 10.1002/ANIE.201006781