Atomistry » Fluorine » PDB 3ohh-3oyj » 3ovx
Atomistry »
  Fluorine »
    PDB 3ohh-3oyj »
      3ovx »

Fluorine in PDB 3ovx: Cathepsin S in Complex with A Covalent Inhibitor with An Aldehyde Warhead

Enzymatic activity of Cathepsin S in Complex with A Covalent Inhibitor with An Aldehyde Warhead

All present enzymatic activity of Cathepsin S in Complex with A Covalent Inhibitor with An Aldehyde Warhead:
3.4.22.27;

Protein crystallography data

The structure of Cathepsin S in Complex with A Covalent Inhibitor with An Aldehyde Warhead, PDB code: 3ovx was solved by X.Fradera, M.Van Zeeland, J.C.M.Uitdehaag, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 74.38 / 1.49
Space group P 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 85.545, 85.545, 150.571, 90.00, 90.00, 90.00
R / Rfree (%) 20 / 22.6

Other elements in 3ovx:

The structure of Cathepsin S in Complex with A Covalent Inhibitor with An Aldehyde Warhead also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Cathepsin S in Complex with A Covalent Inhibitor with An Aldehyde Warhead (pdb code 3ovx). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Cathepsin S in Complex with A Covalent Inhibitor with An Aldehyde Warhead, PDB code: 3ovx:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 3ovx

Go back to Fluorine Binding Sites List in 3ovx
Fluorine binding site 1 out of 6 in the Cathepsin S in Complex with A Covalent Inhibitor with An Aldehyde Warhead


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Cathepsin S in Complex with A Covalent Inhibitor with An Aldehyde Warhead within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F218

b:23.1
occ:0.50
 F17 A:O64218 0.0 23.1 0.5
C16 A:O64218 1.3 22.3 0.5
F18 A:O64218 2.1 22.2 0.5
F19 A:O64218 2.2 24.5 0.5
C1 A:O64218 2.3 22.1 0.5
CL7 A:O64218 2.9 23.7 0.5
C6 A:O64218 2.9 21.5 0.5
C2 A:O64218 3.4 22.4 0.5
CA A:GLY137 3.5 13.8 1.0
CG2 A:VAL162 4.0 17.9 1.0
C A:HIS164 4.1 14.8 1.0
O A:HIS164 4.1 15.7 1.0
N A:GLY165 4.2 13.8 1.0
C5 A:O64218 4.2 21.3 0.5
N A:HIS164 4.2 15.9 1.0
N A:GLY137 4.3 13.6 1.0
CE A:MET71 4.3 18.5 1.0
CA A:GLY165 4.3 13.2 1.0
SD A:MET71 4.4 17.2 1.0
CB A:VAL162 4.6 18.0 1.0
C3 A:O64218 4.6 21.6 0.5
C A:GLY137 4.7 14.8 1.0
C A:ASN163 4.7 16.6 1.0
N A:ASN163 4.7 16.7 1.0
CA A:HIS164 4.7 15.6 1.0
C A:VAL162 4.8 17.3 1.0
CA A:ASN163 4.9 16.7 1.0
O A:VAL136 4.9 13.1 1.0
C4 A:O64218 4.9 22.1 0.5
C A:VAL136 4.9 12.9 1.0
N A:VAL138 4.9 14.1 1.0
O A:VAL162 4.9 16.9 1.0

Fluorine binding site 2 out of 6 in 3ovx

Go back to Fluorine Binding Sites List in 3ovx
Fluorine binding site 2 out of 6 in the Cathepsin S in Complex with A Covalent Inhibitor with An Aldehyde Warhead


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Cathepsin S in Complex with A Covalent Inhibitor with An Aldehyde Warhead within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F218

b:22.2
occ:0.50
 F18 A:O64218 0.0 22.2 0.5
C16 A:O64218 1.3 22.3 0.5
F19 A:O64218 2.1 24.5 0.5
F17 A:O64218 2.1 23.1 0.5
C1 A:O64218 2.3 22.1 0.5
C6 A:O64218 2.9 21.5 0.5
CL7 A:O64218 3.0 23.7 0.5
C2 A:O64218 3.4 22.4 0.5
O A:GLY69 3.5 14.4 1.0
SD A:MET71 4.0 17.2 1.0
CD2 A:PHE70 4.1 21.3 1.0
CA A:PHE70 4.2 14.6 1.0
O A:HOH244 4.2 25.8 1.0
C5 A:O64218 4.2 21.3 0.5
CE A:MET71 4.3 18.5 1.0
C A:GLY69 4.5 14.6 1.0
C3 A:O64218 4.6 21.6 0.5
N A:MET71 4.7 13.2 1.0
CE2 A:PHE70 4.7 21.4 1.0
CG A:PHE70 4.8 16.9 1.0
N A:PHE70 4.8 14.2 1.0
CB A:PHE70 4.8 16.6 1.0
C4 A:O64218 4.9 22.1 0.5

Fluorine binding site 3 out of 6 in 3ovx

Go back to Fluorine Binding Sites List in 3ovx
Fluorine binding site 3 out of 6 in the Cathepsin S in Complex with A Covalent Inhibitor with An Aldehyde Warhead


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Cathepsin S in Complex with A Covalent Inhibitor with An Aldehyde Warhead within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F218

b:24.5
occ:0.50
 F19 A:O64218 0.0 24.5 0.5
C16 A:O64218 1.3 22.3 0.5
F18 A:O64218 2.1 22.2 0.5
F17 A:O64218 2.2 23.1 0.5
C1 A:O64218 2.3 22.1 0.5
C2 A:O64218 2.7 22.4 0.5
CG2 A:VAL162 3.3 17.9 1.0
C6 A:O64218 3.6 21.5 0.5
C3 A:O64218 4.1 21.6 0.5
O A:VAL162 4.2 16.9 1.0
CL7 A:O64218 4.3 23.7 0.5
CB A:VAL162 4.5 18.0 1.0
C A:VAL162 4.6 17.3 1.0
C5 A:O64218 4.7 21.3 0.5
CD2 A:PHE70 4.8 21.3 1.0
CA A:GLY137 4.8 13.8 1.0
C4 A:O64218 4.9 22.1 0.5
CE2 A:PHE70 4.9 21.4 1.0

Fluorine binding site 4 out of 6 in 3ovx

Go back to Fluorine Binding Sites List in 3ovx
Fluorine binding site 4 out of 6 in the Cathepsin S in Complex with A Covalent Inhibitor with An Aldehyde Warhead


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Cathepsin S in Complex with A Covalent Inhibitor with An Aldehyde Warhead within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F218

b:30.4
occ:0.75
 F17 B:O64218 0.0 30.4 0.8
C16 B:O64218 1.3 30.2 0.8
F19 B:O64218 2.1 32.5 0.8
F18 B:O64218 2.2 32.9 0.8
C1 B:O64218 2.3 29.5 0.8
C6 B:O64218 2.8 28.9 0.8
CL7 B:O64218 2.8 30.7 0.8
C2 B:O64218 3.4 29.4 0.8
CA B:GLY137 3.4 13.6 1.0
N B:GLY165 4.0 13.6 1.0
CA B:GLY165 4.0 13.1 1.0
C B:HIS164 4.1 13.7 1.0
O B:HIS164 4.1 13.9 1.0
C5 B:O64218 4.1 28.3 0.8
CG2 B:VAL162 4.2 17.4 1.0
CE B:MET71 4.2 16.2 1.0
N B:GLY137 4.2 13.3 1.0
SD B:MET71 4.2 17.0 1.0
N B:HIS164 4.4 14.1 1.0
C3 B:O64218 4.5 29.2 0.8
O B:VAL136 4.6 12.8 1.0
C B:GLY137 4.7 14.4 1.0
C B:VAL136 4.7 13.5 1.0
CA B:HIS164 4.8 13.8 1.0
C4 B:O64218 4.8 29.4 0.8
CB B:VAL162 4.9 17.4 1.0
C B:ASN163 4.9 14.7 1.0

Fluorine binding site 5 out of 6 in 3ovx

Go back to Fluorine Binding Sites List in 3ovx
Fluorine binding site 5 out of 6 in the Cathepsin S in Complex with A Covalent Inhibitor with An Aldehyde Warhead


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Cathepsin S in Complex with A Covalent Inhibitor with An Aldehyde Warhead within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F218

b:32.9
occ:0.75
 F18 B:O64218 0.0 32.9 0.8
C16 B:O64218 1.3 30.2 0.8
F19 B:O64218 2.1 32.5 0.8
F17 B:O64218 2.2 30.4 0.8
C1 B:O64218 2.3 29.5 0.8
C6 B:O64218 2.9 28.9 0.8
CL7 B:O64218 3.0 30.7 0.8
C2 B:O64218 3.4 29.4 0.8
O B:GLY69 3.8 16.1 1.0
SD B:MET71 3.8 17.0 1.0
O B:HOH240 4.2 22.5 1.0
C5 B:O64218 4.2 28.3 0.8
CE B:MET71 4.2 16.2 1.0
CA B:PHE70 4.3 15.7 1.0
CD2 B:PHE70 4.5 23.1 1.0
C3 B:O64218 4.6 29.2 0.8
N B:MET71 4.7 14.1 1.0
C B:GLY69 4.8 15.9 1.0
C4 B:O64218 4.9 29.4 0.8
CB B:PHE70 4.9 18.0 1.0

Fluorine binding site 6 out of 6 in 3ovx

Go back to Fluorine Binding Sites List in 3ovx
Fluorine binding site 6 out of 6 in the Cathepsin S in Complex with A Covalent Inhibitor with An Aldehyde Warhead


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Cathepsin S in Complex with A Covalent Inhibitor with An Aldehyde Warhead within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F218

b:32.5
occ:0.75
 F19 B:O64218 0.0 32.5 0.8
C16 B:O64218 1.3 30.2 0.8
F18 B:O64218 2.1 32.9 0.8
F17 B:O64218 2.1 30.4 0.8
C1 B:O64218 2.4 29.5 0.8
C2 B:O64218 2.7 29.4 0.8
CG2 B:VAL162 3.4 17.4 1.0
C6 B:O64218 3.6 28.9 0.8
C3 B:O64218 4.1 29.2 0.8
CL7 B:O64218 4.3 30.7 0.8
CA B:GLY137 4.6 13.6 1.0
CB B:VAL162 4.7 17.4 1.0
O B:VAL162 4.8 16.9 1.0
C5 B:O64218 4.8 28.3 0.8
CD2 B:PHE211 4.8 16.9 1.0
C4 B:O64218 5.0 29.4 0.8
CB B:PHE211 5.0 15.9 1.0

Reference:

J.Cai, J.Robinson, S.Belshaw, K.Everett, X.Fradera, M.Van Zeeland, L.Van Berkom, P.Van Rijnsbergen, L.Popplestone, M.Baugh, M.Dempster, J.Bruin, W.Hamilton, E.Kinghorn, P.Westwood, J.Kerr, Z.Rankovic, W.Arbuckle, D.J.Bennett, P.S.Jones, C.Long, I.Martin, J.C.Uitdehaag, T.Meulemans. Trifluoromethylphenyl As P2 For Ketoamide-Based Cathepsin S Inhibitors. Bioorg.Med.Chem.Lett. V. 20 6890 2010.
ISSN: ISSN 0960-894X
PubMed: 21030256
DOI: 10.1016/J.BMCL.2010.10.012
Page generated: Mon Jul 14 18:29:53 2025

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy