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Fluorine in PDB 5qc4: Crystal Structure of Human Cathepsin-S with Bound Ligand

Enzymatic activity of Crystal Structure of Human Cathepsin-S with Bound Ligand

All present enzymatic activity of Crystal Structure of Human Cathepsin-S with Bound Ligand:
3.4.22.27;

Protein crystallography data

The structure of Crystal Structure of Human Cathepsin-S with Bound Ligand, PDB code: 5qc4 was solved by S.D.Bembenek, M.K.Ameriks, T.Mirzadegan, H.Yang, C.Shao, S.K.Burley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.10 / 2.00
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 37.020, 52.970, 58.580, 70.75, 71.79, 73.21
R / Rfree (%) 15.2 / 21

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Human Cathepsin-S with Bound Ligand (pdb code 5qc4). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of Human Cathepsin-S with Bound Ligand, PDB code: 5qc4:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 5qc4

Go back to Fluorine Binding Sites List in 5qc4
Fluorine binding site 1 out of 6 in the Crystal Structure of Human Cathepsin-S with Bound Ligand


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Human Cathepsin-S with Bound Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:17.4
occ:1.00
 F39 A:BC7901 0.0 17.4 1.0
C38 A:BC7901 1.3 16.2 1.0
F40 A:BC7901 2.1 14.1 1.0
F41 A:BC7901 2.1 19.4 1.0
C26 A:BC7901 2.4 15.7 1.0
N A:HIS164 2.9 13.1 1.0
C A:HIS164 2.9 13.6 1.0
N A:GLY165 3.0 14.0 1.0
C27 A:BC7901 3.0 19.9 1.0
S29 A:BC7901 3.1 18.0 1.0
CA A:HIS164 3.3 14.9 1.0
O A:HIS164 3.4 14.6 1.0
C A:ASN163 3.4 15.7 1.0
C25 A:BC7901 3.4 18.0 1.0
CA A:GLY165 3.6 12.6 1.0
CA A:ASN163 3.9 12.5 1.0
O A:ASN163 4.0 14.2 1.0
CA A:GLY137 4.0 10.9 1.0
N A:ASN163 4.0 15.9 1.0
O A:HOH1182 4.2 19.8 1.0
C28 A:BC7901 4.3 18.1 1.0
C A:VAL162 4.6 19.4 1.0
CG2 A:VAL162 4.6 13.8 1.0
C24 A:BC7901 4.6 20.8 1.0
CB A:VAL162 4.8 16.0 1.0
C30 A:BC7901 4.8 23.6 0.5
N A:VAL138 4.8 12.9 1.0
CB A:HIS164 4.8 14.4 1.0
C A:GLY137 5.0 12.1 1.0
O A:VAL162 5.0 19.8 1.0
O A:VAL138 5.0 14.4 1.0
C23 A:BC7901 5.0 19.9 1.0

Fluorine binding site 2 out of 6 in 5qc4

Go back to Fluorine Binding Sites List in 5qc4
Fluorine binding site 2 out of 6 in the Crystal Structure of Human Cathepsin-S with Bound Ligand


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Human Cathepsin-S with Bound Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:14.1
occ:1.00
 F40 A:BC7901 0.0 14.1 1.0
C38 A:BC7901 1.3 16.2 1.0
F41 A:BC7901 2.1 19.4 1.0
F39 A:BC7901 2.1 17.4 1.0
C26 A:BC7901 2.3 15.7 1.0
C25 A:BC7901 2.7 18.0 1.0
CA A:GLY165 3.0 12.6 1.0
SD A:MET71 3.1 15.9 1.0
CE A:MET71 3.3 13.8 1.0
N A:GLY165 3.3 14.0 1.0
CA A:GLY137 3.5 10.9 1.0
C27 A:BC7901 3.6 19.9 1.0
C A:HIS164 3.7 13.6 1.0
O A:HIS164 3.9 14.6 1.0
O A:VAL136 3.9 12.5 1.0
N A:GLY137 4.0 11.4 1.0
C24 A:BC7901 4.1 20.8 1.0
C A:VAL136 4.2 12.9 1.0
C A:GLY165 4.4 14.8 1.0
S29 A:BC7901 4.4 18.0 1.0
N A:HIS164 4.7 13.1 1.0
CA A:HIS164 4.7 14.9 1.0
C28 A:BC7901 4.8 18.1 1.0
C A:GLY137 4.8 12.1 1.0
N A:VAL166 4.9 16.4 1.0
CG A:MET71 4.9 13.3 1.0
C23 A:BC7901 4.9 19.9 1.0
CB A:TRP26 4.9 12.2 1.0
CA A:TRP26 4.9 12.7 1.0
O A:GLY69 5.0 15.5 1.0

Fluorine binding site 3 out of 6 in 5qc4

Go back to Fluorine Binding Sites List in 5qc4
Fluorine binding site 3 out of 6 in the Crystal Structure of Human Cathepsin-S with Bound Ligand


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Human Cathepsin-S with Bound Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:19.4
occ:1.00
 F41 A:BC7901 0.0 19.4 1.0
C38 A:BC7901 1.3 16.2 1.0
F40 A:BC7901 2.1 14.1 1.0
F39 A:BC7901 2.1 17.4 1.0
C26 A:BC7901 2.4 15.7 1.0
O A:HOH1182 3.0 19.8 1.0
C27 A:BC7901 3.0 19.9 1.0
S29 A:BC7901 3.2 18.0 1.0
O A:GLY69 3.2 15.5 1.0
C25 A:BC7901 3.4 18.0 1.0
N A:GLY165 3.7 14.0 1.0
CB A:TRP26 3.7 12.2 1.0
SD A:MET71 3.9 15.9 1.0
CA A:GLY165 3.9 12.6 1.0
CA A:TRP26 4.1 12.7 1.0
C30 A:BC7901 4.2 23.6 0.5
C A:HIS164 4.3 13.6 1.0
C28 A:BC7901 4.3 18.1 1.0
C A:GLY69 4.4 19.2 1.0
N A:TRP26 4.5 16.4 1.0
C24 A:BC7901 4.6 20.8 1.0
N A:HIS164 4.7 13.1 1.0
CA A:HIS164 4.8 14.9 1.0
CG A:TRP26 4.8 14.8 1.0
OG A:SER25 4.8 15.8 1.0
CE A:MET71 4.8 13.8 1.0
O A:HIS164 4.9 14.6 1.0
C23 A:BC7901 5.0 19.9 1.0
C A:ASN163 5.0 15.7 1.0
CA A:PHE70 5.0 16.8 1.0

Fluorine binding site 4 out of 6 in 5qc4

Go back to Fluorine Binding Sites List in 5qc4
Fluorine binding site 4 out of 6 in the Crystal Structure of Human Cathepsin-S with Bound Ligand


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Human Cathepsin-S with Bound Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F901

b:17.5
occ:1.00
 F39 B:BC7901 0.0 17.5 1.0
C38 B:BC7901 1.4 18.3 1.0
F40 B:BC7901 2.1 17.9 1.0
F41 B:BC7901 2.2 18.7 1.0
C26 B:BC7901 2.4 17.3 1.0
N B:HIS164 2.8 17.6 1.0
C27 B:BC7901 2.9 21.9 1.0
S29 B:BC7901 3.0 20.5 1.0
C B:HIS164 3.1 13.9 1.0
C B:ASN163 3.3 18.0 1.0
N B:GLY165 3.3 14.8 1.0
O B:HIS164 3.4 16.6 1.0
CA B:HIS164 3.4 15.8 1.0
C25 B:BC7901 3.5 21.3 1.0
CA B:ASN163 3.7 15.8 1.0
N B:ASN163 3.8 16.3 1.0
CA B:GLY165 3.9 14.6 1.0
O B:ASN163 4.0 19.7 1.0
CA B:GLY137 4.1 16.0 1.0
C28 B:BC7901 4.3 20.5 1.0
C B:VAL162 4.3 17.4 1.0
O B:HOH1156 4.4 23.5 1.0
CG2 B:VAL162 4.5 19.2 1.0
C30 B:BC7901 4.5 24.4 0.5
CB B:VAL162 4.6 18.0 1.0
C24 B:BC7901 4.7 19.9 1.0
O B:VAL162 4.7 14.0 1.0
O B:HOH1098 4.8 22.3 1.0
CB B:HIS164 4.8 13.7 1.0
N B:VAL138 4.9 15.2 1.0
O B:VAL138 5.0 18.7 1.0
C23 B:BC7901 5.0 19.7 1.0

Fluorine binding site 5 out of 6 in 5qc4

Go back to Fluorine Binding Sites List in 5qc4
Fluorine binding site 5 out of 6 in the Crystal Structure of Human Cathepsin-S with Bound Ligand


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of Human Cathepsin-S with Bound Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F901

b:17.9
occ:1.00
 F40 B:BC7901 0.0 17.9 1.0
C38 B:BC7901 1.3 18.3 1.0
F41 B:BC7901 2.1 18.7 1.0
F39 B:BC7901 2.1 17.5 1.0
C26 B:BC7901 2.4 17.3 1.0
C25 B:BC7901 2.8 21.3 1.0
CA B:GLY165 3.1 14.6 1.0
SD B:MET71 3.2 15.9 1.0
CE B:MET71 3.3 14.1 1.0
CA B:GLY137 3.4 16.0 1.0
N B:GLY165 3.4 14.8 1.0
C27 B:BC7901 3.7 21.9 1.0
C B:HIS164 3.7 13.9 1.0
O B:HIS164 3.7 16.6 1.0
N B:GLY137 3.9 18.4 1.0
O B:VAL136 3.9 17.6 1.0
C24 B:BC7901 4.1 19.9 1.0
C B:VAL136 4.2 16.5 1.0
S29 B:BC7901 4.4 20.5 1.0
C B:GLY165 4.5 16.4 1.0
N B:HIS164 4.6 17.6 1.0
CA B:HIS164 4.7 15.8 1.0
C B:GLY137 4.8 16.9 1.0
C28 B:BC7901 4.8 20.5 1.0
N B:VAL166 4.9 15.2 1.0
C23 B:BC7901 5.0 19.7 1.0
CG B:MET71 5.0 13.8 1.0

Fluorine binding site 6 out of 6 in 5qc4

Go back to Fluorine Binding Sites List in 5qc4
Fluorine binding site 6 out of 6 in the Crystal Structure of Human Cathepsin-S with Bound Ligand


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of Human Cathepsin-S with Bound Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F901

b:18.7
occ:1.00
 F41 B:BC7901 0.0 18.7 1.0
C38 B:BC7901 1.3 18.3 1.0
F40 B:BC7901 2.1 17.9 1.0
F39 B:BC7901 2.2 17.5 1.0
C26 B:BC7901 2.4 17.3 1.0
C27 B:BC7901 3.1 21.9 1.0
O B:HOH1156 3.2 23.5 1.0
O B:GLY69 3.2 19.5 1.0
S29 B:BC7901 3.2 20.5 1.0
C25 B:BC7901 3.4 21.3 1.0
CB B:TRP26 3.7 14.7 1.0
N B:GLY165 3.8 14.8 1.0
SD B:MET71 3.9 15.9 1.0
CA B:GLY165 4.0 14.6 1.0
C30 B:BC7901 4.0 24.4 0.5
CA B:TRP26 4.2 14.8 1.0
C B:HIS164 4.3 13.9 1.0
C28 B:BC7901 4.3 20.5 1.0
C B:GLY69 4.4 16.4 1.0
N B:TRP26 4.6 18.3 1.0
C24 B:BC7901 4.6 19.9 1.0
N B:HIS164 4.7 17.6 1.0
CE B:MET71 4.7 14.1 1.0
CG B:TRP26 4.8 17.1 1.0
CA B:HIS164 4.8 15.8 1.0
O B:HOH1098 4.8 22.3 1.0
O B:HIS164 4.8 16.6 1.0
OG B:SER25 4.8 13.4 1.0
CA B:PHE70 4.9 16.3 1.0
C B:ASN163 4.9 18.0 1.0
C23 B:BC7901 5.0 19.7 1.0

Reference:

D.K.Wiener, A.Lee-Dutra, S.Bembenek, S.Nguyen, R.L.Thurmond, S.Sun, L.Karlsson, C.A.Grice, T.K.Jones, J.P.Edwards. Thioether Acetamides As P3 Binding Elements For Tetrahydropyrido-Pyrazole Cathepsin S Inhibitors. Bioorg.Med.Chem.Lett. V. 20 2379 2010.
ISSN: ISSN 0960-894X
PubMed: 20188543
DOI: 10.1016/J.BMCL.2010.01.103
Page generated: Thu Aug 1 13:01:21 2024

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