Chlorine in PDB 6f06: Cathepsin L in Complex with (3S,14E)-8-(Azetidin-3-Yl)-19-Chloro-N-(1- Cyanocyclopropyl)-5-Oxo-12,17-Dioxa-4-Azatricyclo[16.2.2.06, 11]Docosa-1(21),6,8,10,14,18(22),19-Heptaene-3-Carboxamide

Enzymatic activity of Cathepsin L in Complex with (3S,14E)-8-(Azetidin-3-Yl)-19-Chloro-N-(1- Cyanocyclopropyl)-5-Oxo-12,17-Dioxa-4-Azatricyclo[16.2.2.06, 11]Docosa-1(21),6,8,10,14,18(22),19-Heptaene-3-Carboxamide

All present enzymatic activity of Cathepsin L in Complex with (3S,14E)-8-(Azetidin-3-Yl)-19-Chloro-N-(1- Cyanocyclopropyl)-5-Oxo-12,17-Dioxa-4-Azatricyclo[16.2.2.06, 11]Docosa-1(21),6,8,10,14,18(22),19-Heptaene-3-Carboxamide:
3.4.22.15;

Protein crystallography data

The structure of Cathepsin L in Complex with (3S,14E)-8-(Azetidin-3-Yl)-19-Chloro-N-(1- Cyanocyclopropyl)-5-Oxo-12,17-Dioxa-4-Azatricyclo[16.2.2.06, 11]Docosa-1(21),6,8,10,14,18(22),19-Heptaene-3-Carboxamide, PDB code: 6f06 was solved by A.Kuglstatter, M.Stihle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.48 / 2.02
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 43.040, 50.791, 84.911, 90.00, 91.53, 90.00
R / Rfree (%) 20.1 / 27.4

Other elements in 6f06:

The structure of Cathepsin L in Complex with (3S,14E)-8-(Azetidin-3-Yl)-19-Chloro-N-(1- Cyanocyclopropyl)-5-Oxo-12,17-Dioxa-4-Azatricyclo[16.2.2.06, 11]Docosa-1(21),6,8,10,14,18(22),19-Heptaene-3-Carboxamide also contains other interesting chemical elements:

Zinc (Zn) 14 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Cathepsin L in Complex with (3S,14E)-8-(Azetidin-3-Yl)-19-Chloro-N-(1- Cyanocyclopropyl)-5-Oxo-12,17-Dioxa-4-Azatricyclo[16.2.2.06, 11]Docosa-1(21),6,8,10,14,18(22),19-Heptaene-3-Carboxamide (pdb code 6f06). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Cathepsin L in Complex with (3S,14E)-8-(Azetidin-3-Yl)-19-Chloro-N-(1- Cyanocyclopropyl)-5-Oxo-12,17-Dioxa-4-Azatricyclo[16.2.2.06, 11]Docosa-1(21),6,8,10,14,18(22),19-Heptaene-3-Carboxamide, PDB code: 6f06:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 6f06

Go back to Chlorine Binding Sites List in 6f06
Chlorine binding site 1 out of 4 in the Cathepsin L in Complex with (3S,14E)-8-(Azetidin-3-Yl)-19-Chloro-N-(1- Cyanocyclopropyl)-5-Oxo-12,17-Dioxa-4-Azatricyclo[16.2.2.06, 11]Docosa-1(21),6,8,10,14,18(22),19-Heptaene-3-Carboxamide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Cathepsin L in Complex with (3S,14E)-8-(Azetidin-3-Yl)-19-Chloro-N-(1- Cyanocyclopropyl)-5-Oxo-12,17-Dioxa-4-Azatricyclo[16.2.2.06, 11]Docosa-1(21),6,8,10,14,18(22),19-Heptaene-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl301

b:38.0
occ:1.00
 CL A:C7T301 0.0 38.0 1.0
C6 A:C7T301 1.7 35.4 1.0
C7 A:C7T301 2.7 35.2 1.0
C5 A:C7T301 2.8 33.8 1.0
O A:HOH444 3.0 23.0 1.0
O11 A:C7T301 3.1 37.0 1.0
CD2 A:LEU69 3.3 24.7 1.0
CE A:MET70 3.5 20.7 1.0
SD A:MET70 3.9 20.1 1.0
C18 A:C7T301 4.0 36.6 1.0
C8 A:C7T301 4.0 36.8 1.0
C4 A:C7T301 4.1 33.6 1.0
CB A:ALA135 4.1 28.2 1.0
O A:HOH446 4.1 33.8 1.0
N A:MET70 4.3 26.2 1.0
CB A:ALA214 4.4 24.8 1.0
CA A:LEU69 4.5 26.6 1.0
CG A:LEU69 4.5 25.9 1.0
C9 A:C7T301 4.5 34.1 1.0
CB A:LEU69 4.6 25.7 1.0
O A:ALA214 4.6 28.7 1.0
C27 A:C7T301 4.8 40.5 1.0
C28 A:C7T301 4.8 41.0 1.0

Chlorine binding site 2 out of 4 in 6f06

Go back to Chlorine Binding Sites List in 6f06
Chlorine binding site 2 out of 4 in the Cathepsin L in Complex with (3S,14E)-8-(Azetidin-3-Yl)-19-Chloro-N-(1- Cyanocyclopropyl)-5-Oxo-12,17-Dioxa-4-Azatricyclo[16.2.2.06, 11]Docosa-1(21),6,8,10,14,18(22),19-Heptaene-3-Carboxamide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Cathepsin L in Complex with (3S,14E)-8-(Azetidin-3-Yl)-19-Chloro-N-(1- Cyanocyclopropyl)-5-Oxo-12,17-Dioxa-4-Azatricyclo[16.2.2.06, 11]Docosa-1(21),6,8,10,14,18(22),19-Heptaene-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl308

b:37.1
occ:1.00
 ZN A:ZN302 2.3 29.5 1.0
NE2 A:GLN19 3.0 28.2 1.0
ND1 A:HIS163 3.2 24.0 1.0
N30 A:C7T301 3.3 36.6 1.0
CE1 A:HIS163 3.3 24.4 1.0
OE1 A:GLN19 3.5 26.3 1.0
O A:HOH402 3.6 23.6 1.0
CD A:GLN19 3.6 28.4 1.0
NE1 A:TRP189 3.7 30.4 1.0
CB A:CYS25 3.8 27.7 1.0
C29 A:C7T301 3.9 35.6 1.0
SG A:CYS25 3.9 32.2 1.0
CZ2 A:TRP189 4.3 34.3 1.0
CE2 A:TRP189 4.4 32.9 1.0
CG A:HIS163 4.5 23.9 1.0
NE2 A:HIS163 4.5 24.1 1.0
N A:CYS25 4.6 27.9 1.0
CA A:CYS25 4.8 27.2 1.0
CD1 A:TRP189 4.9 29.8 1.0
CG A:GLN19 4.9 28.3 1.0
C2 A:C7T301 5.0 36.0 1.0

Chlorine binding site 3 out of 4 in 6f06

Go back to Chlorine Binding Sites List in 6f06
Chlorine binding site 3 out of 4 in the Cathepsin L in Complex with (3S,14E)-8-(Azetidin-3-Yl)-19-Chloro-N-(1- Cyanocyclopropyl)-5-Oxo-12,17-Dioxa-4-Azatricyclo[16.2.2.06, 11]Docosa-1(21),6,8,10,14,18(22),19-Heptaene-3-Carboxamide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Cathepsin L in Complex with (3S,14E)-8-(Azetidin-3-Yl)-19-Chloro-N-(1- Cyanocyclopropyl)-5-Oxo-12,17-Dioxa-4-Azatricyclo[16.2.2.06, 11]Docosa-1(21),6,8,10,14,18(22),19-Heptaene-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl301

b:45.0
occ:1.00
 CL B:C7T301 0.0 45.0 1.0
C6 B:C7T301 1.7 33.4 1.0
C7 B:C7T301 2.7 29.7 1.0
C5 B:C7T301 2.7 34.9 1.0
O11 B:C7T301 3.0 35.6 1.0
CE B:MET70 3.3 29.0 1.0
CB B:ALA135 3.7 22.8 1.0
SD B:MET70 3.8 29.7 1.0
C18 B:C7T301 3.8 31.7 1.0
C4 B:C7T301 4.0 33.8 1.0
C8 B:C7T301 4.0 29.9 1.0
CD2 B:LEU69 4.1 29.4 1.0
CB B:ALA214 4.2 24.6 1.0
N B:MET70 4.4 25.8 1.0
C9 B:C7T301 4.4 31.2 1.0
O B:ALA214 4.6 24.4 1.0
CA B:LEU69 4.7 27.7 1.0
CB B:LEU69 4.7 29.7 1.0
C28 B:C7T301 4.7 30.5 1.0
CB B:MET70 4.8 26.8 1.0
C27 B:C7T301 4.9 30.2 1.0
CG B:LEU69 4.9 30.3 1.0
CA B:ALA135 5.0 22.0 1.0

Chlorine binding site 4 out of 4 in 6f06

Go back to Chlorine Binding Sites List in 6f06
Chlorine binding site 4 out of 4 in the Cathepsin L in Complex with (3S,14E)-8-(Azetidin-3-Yl)-19-Chloro-N-(1- Cyanocyclopropyl)-5-Oxo-12,17-Dioxa-4-Azatricyclo[16.2.2.06, 11]Docosa-1(21),6,8,10,14,18(22),19-Heptaene-3-Carboxamide


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Cathepsin L in Complex with (3S,14E)-8-(Azetidin-3-Yl)-19-Chloro-N-(1- Cyanocyclopropyl)-5-Oxo-12,17-Dioxa-4-Azatricyclo[16.2.2.06, 11]Docosa-1(21),6,8,10,14,18(22),19-Heptaene-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl310

b:33.4
occ:1.00
 ZN B:ZN302 2.2 28.9 1.0
O B:HOH408 3.2 35.0 1.0
NE2 B:GLN19 3.2 21.9 1.0
ND1 B:HIS163 3.3 26.2 1.0
N30 B:C7T301 3.5 32.8 1.0
CE1 B:HIS163 3.5 23.9 1.0
NE1 B:TRP189 3.6 27.2 1.0
SG B:CYS25 3.9 25.7 1.0
CZ2 B:TRP189 3.9 27.5 1.0
OE1 B:GLN19 3.9 22.6 1.0
CD B:GLN19 3.9 23.9 1.0
CB B:CYS25 4.0 24.7 1.0
CE2 B:TRP189 4.1 27.4 1.0
C29 B:C7T301 4.2 33.1 1.0
CG B:HIS163 4.5 26.1 1.0
N B:CYS25 4.7 24.7 1.0
NE2 B:HIS163 4.8 25.2 1.0
CD1 B:TRP189 4.9 27.4 1.0
CA B:CYS25 4.9 24.3 1.0

Reference:

M.Giroud, U.Dietzel, L.Anselm, D.Banner, A.Kuglstatter, J.Benz, J.B.Blanc, D.Gaufreteau, H.Liu, X.Lin, A.Stich, B.Kuhn, F.Schuler, M.Kaiser, R.Brun, T.Schirmeister, C.Kisker, F.Diederich, W.Haap. Repurposing A Library of Human Cathepsin L Ligands: Identification of Macrocyclic Lactams As Potent Rhodesain and Trypanosoma Brucei Inhibitors. J. Med. Chem. V. 61 3350 2018.
ISSN: ISSN 1520-4804
PubMed: 29590750
DOI: 10.1021/ACS.JMEDCHEM.7B01869
Page generated: Sat Dec 12 12:56:54 2020

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