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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

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