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Fluorine in PDB 2op3: The Structure of Cathepsin S with A Novel 2- Arylphenoxyacetaldehyde Inhibitor Derived By the Substrate Activity Screening (Sas) Method

Enzymatic activity of The Structure of Cathepsin S with A Novel 2- Arylphenoxyacetaldehyde Inhibitor Derived By the Substrate Activity Screening (Sas) Method

All present enzymatic activity of The Structure of Cathepsin S with A Novel 2- Arylphenoxyacetaldehyde Inhibitor Derived By the Substrate Activity Screening (Sas) Method:
3.4.22.27;

Protein crystallography data

The structure of The Structure of Cathepsin S with A Novel 2- Arylphenoxyacetaldehyde Inhibitor Derived By the Substrate Activity Screening (Sas) Method, PDB code: 2op3 was solved by G.Spraggon, H.Inagaki, H.Tsuruoka, M.Hornsby, S.A.Lesley, J.A.Ellman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.40 / 1.60
Space group P 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 85.384, 85.384, 151.200, 90.00, 90.00, 90.00
R / Rfree (%) 15.8 / 18.1

Fluorine Binding Sites:

The binding sites of Fluorine atom in the The Structure of Cathepsin S with A Novel 2- Arylphenoxyacetaldehyde Inhibitor Derived By the Substrate Activity Screening (Sas) Method (pdb code 2op3). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the The Structure of Cathepsin S with A Novel 2- Arylphenoxyacetaldehyde Inhibitor Derived By the Substrate Activity Screening (Sas) Method, PDB code: 2op3:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 2op3

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Fluorine binding site 1 out of 6 in the The Structure of Cathepsin S with A Novel 2- Arylphenoxyacetaldehyde Inhibitor Derived By the Substrate Activity Screening (Sas) Method


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of The Structure of Cathepsin S with A Novel 2- Arylphenoxyacetaldehyde Inhibitor Derived By the Substrate Activity Screening (Sas) Method within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:26.8
occ:1.00
F13 A:TF5501 0.0 26.8 1.0
C8 A:TF5501 1.3 25.5 1.0
C9 A:TF5501 2.3 27.7 1.0
C7 A:TF5501 2.4 26.9 1.0
F14 A:TF5501 2.7 29.0 1.0
F A:TF5501 2.9 28.6 1.0
CB A:TRP26 3.3 12.1 1.0
N A:GLY165 3.3 11.3 1.0
CA A:GLY165 3.3 11.1 1.0
SD A:MET71 3.4 13.5 1.0
C10 A:TF5501 3.6 26.9 1.0
O A:GLY69 3.6 13.6 1.0
CA A:TRP26 3.6 11.6 1.0
C6 A:TF5501 3.6 27.0 1.0
N A:TRP26 3.9 12.8 1.0
SG A:CYS25 3.9 17.8 1.0
C11 A:TF5501 4.1 26.6 1.0
C A:HIS164 4.1 12.7 1.0
CE A:MET71 4.3 15.9 1.0
CG A:TRP26 4.5 11.7 1.0
O A:TF5501 4.6 28.4 1.0
C A:GLY69 4.7 13.3 1.0
C A:CYS25 4.7 13.0 1.0
C A:GLY165 4.7 11.1 1.0
CA A:HIS164 4.8 13.0 1.0
O A:HIS164 4.9 13.9 1.0
C2 A:TF5501 4.9 27.9 1.0
CD1 A:TRP26 4.9 12.2 1.0

Fluorine binding site 2 out of 6 in 2op3

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Fluorine binding site 2 out of 6 in the The Structure of Cathepsin S with A Novel 2- Arylphenoxyacetaldehyde Inhibitor Derived By the Substrate Activity Screening (Sas) Method


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of The Structure of Cathepsin S with A Novel 2- Arylphenoxyacetaldehyde Inhibitor Derived By the Substrate Activity Screening (Sas) Method within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:28.6
occ:1.00
F A:TF5501 0.0 28.6 1.0
C7 A:TF5501 1.4 26.9 1.0
C6 A:TF5501 2.3 27.0 1.0
C8 A:TF5501 2.4 25.5 1.0
O A:TF5501 2.4 28.4 1.0
C2 A:TF5501 2.7 27.9 1.0
C3 A:TF5501 2.8 27.5 1.0
F13 A:TF5501 2.9 26.8 1.0
O A:GLY69 3.3 13.6 1.0
SG A:CYS25 3.3 17.8 1.0
N A:GLY69 3.4 13.9 1.0
CD1 A:TRP26 3.4 12.2 1.0
CB A:TRP26 3.6 12.1 1.0
C11 A:TF5501 3.6 26.6 1.0
C16 A:TF5501 3.7 29.6 1.0
C9 A:TF5501 3.7 27.7 1.0
CA A:GLY68 3.7 13.8 1.0
CG A:TRP26 3.8 11.7 1.0
C1 A:TF5501 3.9 28.1 1.0
C17 A:TF5501 3.9 27.6 1.0
C4 A:TF5501 4.0 28.0 1.0
C A:GLY68 4.1 13.8 1.0
N A:TRP26 4.1 12.8 1.0
C10 A:TF5501 4.1 26.9 1.0
C A:GLY69 4.2 13.3 1.0
CA A:GLY69 4.4 12.8 1.0
CA A:TRP26 4.4 11.6 1.0
O A:GLY23 4.5 18.0 1.0
NE1 A:TRP26 4.6 12.9 1.0
O20 A:TF5501 4.7 28.9 1.0
C A:TF5501 4.8 28.0 1.0
C5 A:TF5501 4.8 27.9 1.0
F14 A:TF5501 4.8 29.0 1.0
N A:GLY165 4.9 11.3 1.0
N A:GLY68 5.0 14.8 1.0
CB A:CYS25 5.0 14.5 1.0

Fluorine binding site 3 out of 6 in 2op3

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Fluorine binding site 3 out of 6 in the The Structure of Cathepsin S with A Novel 2- Arylphenoxyacetaldehyde Inhibitor Derived By the Substrate Activity Screening (Sas) Method


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of The Structure of Cathepsin S with A Novel 2- Arylphenoxyacetaldehyde Inhibitor Derived By the Substrate Activity Screening (Sas) Method within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F501

b:29.0
occ:1.00
F14 A:TF5501 0.0 29.0 1.0
C9 A:TF5501 1.4 27.7 1.0
C8 A:TF5501 2.4 25.5 1.0
C10 A:TF5501 2.4 26.9 1.0
F13 A:TF5501 2.7 26.8 1.0
N A:GLY165 3.6 11.3 1.0
CA A:GLY137 3.6 11.5 1.0
C11 A:TF5501 3.7 26.6 1.0
C7 A:TF5501 3.7 26.9 1.0
C A:HIS164 3.7 12.7 1.0
CA A:GLY165 3.8 11.1 1.0
O A:HIS164 3.8 13.9 1.0
N A:HIS164 4.0 13.7 1.0
C6 A:TF5501 4.1 27.0 1.0
CE A:MET71 4.2 15.9 1.0
CG2 A:VAL162 4.3 16.5 1.0
CA A:HIS164 4.3 13.0 1.0
SD A:MET71 4.4 13.5 1.0
N A:GLY137 4.4 10.7 1.0
C A:ASN163 4.6 15.1 1.0
O A:VAL136 4.7 10.8 1.0
F A:TF5501 4.8 28.6 1.0
C A:GLY137 4.8 11.8 1.0
CB A:VAL162 4.9 15.1 1.0
C A:VAL136 5.0 10.5 1.0
N A:ASN163 5.0 13.8 1.0

Fluorine binding site 4 out of 6 in 2op3

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Fluorine binding site 4 out of 6 in the The Structure of Cathepsin S with A Novel 2- Arylphenoxyacetaldehyde Inhibitor Derived By the Substrate Activity Screening (Sas) Method


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of The Structure of Cathepsin S with A Novel 2- Arylphenoxyacetaldehyde Inhibitor Derived By the Substrate Activity Screening (Sas) Method within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F502

b:36.1
occ:1.00
F13 B:TF5502 0.0 36.1 1.0
C8 B:TF5502 1.3 35.1 1.0
C9 B:TF5502 2.3 36.0 1.0
C7 B:TF5502 2.4 36.2 1.0
F14 B:TF5502 2.7 36.4 1.0
F B:TF5502 2.8 35.4 1.0
CB B:TRP26 3.2 12.1 1.0
N B:GLY165 3.3 13.8 1.0
CA B:GLY165 3.3 12.7 1.0
SD B:MET71 3.3 13.5 1.0
O B:GLY69 3.5 15.0 1.0
CA B:TRP26 3.5 12.3 1.0
C10 B:TF5502 3.6 35.8 1.0
C6 B:TF5502 3.6 35.3 1.0
N B:TRP26 3.8 13.9 1.0
SG B:CYS25 3.9 21.3 1.0
O B:HOH648 4.0 31.8 1.0
C11 B:TF5502 4.1 36.5 1.0
C B:HIS164 4.1 14.6 1.0
CE B:MET71 4.3 14.6 1.0
CG B:TRP26 4.3 11.8 1.0
C B:GLY69 4.6 13.2 1.0
C B:GLY165 4.7 12.7 1.0
C B:CYS25 4.7 14.8 1.0
CA B:HIS164 4.7 14.5 1.0
O B:TF5502 4.7 34.8 1.0
CD1 B:TRP26 4.8 13.7 1.0
O B:HIS164 4.9 15.4 1.0
C2 B:TF5502 4.9 35.7 1.0
C B:TRP26 5.0 11.9 1.0
CG B:MET71 5.0 12.5 1.0
N B:HIS164 5.0 15.8 1.0

Fluorine binding site 5 out of 6 in 2op3

Go back to Fluorine Binding Sites List in 2op3
Fluorine binding site 5 out of 6 in the The Structure of Cathepsin S with A Novel 2- Arylphenoxyacetaldehyde Inhibitor Derived By the Substrate Activity Screening (Sas) Method


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of The Structure of Cathepsin S with A Novel 2- Arylphenoxyacetaldehyde Inhibitor Derived By the Substrate Activity Screening (Sas) Method within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F502

b:35.4
occ:1.00
F B:TF5502 0.0 35.4 1.0
C7 B:TF5502 1.4 36.2 1.0
C6 B:TF5502 2.3 35.3 1.0
C8 B:TF5502 2.4 35.1 1.0
O B:TF5502 2.6 34.8 1.0
C2 B:TF5502 2.8 35.7 1.0
F13 B:TF5502 2.8 36.1 1.0
C3 B:TF5502 2.9 35.2 1.0
C16 B:TF5502 3.2 34.2 1.0
SG B:CYS25 3.2 21.3 1.0
O B:GLY69 3.3 15.0 1.0
CD1 B:TRP26 3.4 13.7 1.0
N B:GLY69 3.4 13.2 1.0
CB B:TRP26 3.6 12.1 1.0
C11 B:TF5502 3.6 36.5 1.0
C17 B:TF5502 3.7 33.0 1.0
C9 B:TF5502 3.7 36.0 1.0
CA B:GLY68 3.7 14.6 1.0
CG B:TRP26 3.8 11.8 1.0
C1 B:TF5502 3.9 35.5 1.0
C4 B:TF5502 4.1 35.1 1.0
N B:TRP26 4.1 13.9 1.0
C B:GLY68 4.1 13.9 1.0
C10 B:TF5502 4.1 35.8 1.0
C B:GLY69 4.2 13.2 1.0
CA B:TRP26 4.4 12.3 1.0
CA B:GLY69 4.4 13.0 1.0
NE1 B:TRP26 4.5 12.8 1.0
O B:GLY23 4.6 20.0 1.0
O20 B:TF5502 4.7 30.1 1.0
O B:ASN163 4.8 19.3 1.0
F14 B:TF5502 4.8 36.4 1.0
N B:GLY165 4.8 13.8 1.0
C B:TF5502 4.8 35.3 1.0
C5 B:TF5502 4.9 34.9 1.0
CB B:CYS25 4.9 16.9 1.0
OCJ A:PEU601 5.0 58.7 1.0
N B:GLY68 5.0 15.8 1.0

Fluorine binding site 6 out of 6 in 2op3

Go back to Fluorine Binding Sites List in 2op3
Fluorine binding site 6 out of 6 in the The Structure of Cathepsin S with A Novel 2- Arylphenoxyacetaldehyde Inhibitor Derived By the Substrate Activity Screening (Sas) Method


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of The Structure of Cathepsin S with A Novel 2- Arylphenoxyacetaldehyde Inhibitor Derived By the Substrate Activity Screening (Sas) Method within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F502

b:36.4
occ:1.00
F14 B:TF5502 0.0 36.4 1.0
C9 B:TF5502 1.4 36.0 1.0
C8 B:TF5502 2.4 35.1 1.0
C10 B:TF5502 2.4 35.8 1.0
F13 B:TF5502 2.7 36.1 1.0
O B:HOH648 3.3 31.8 1.0
CA B:GLY137 3.6 12.4 1.0
C7 B:TF5502 3.7 36.2 1.0
C11 B:TF5502 3.7 36.5 1.0
N B:GLY165 3.7 13.8 1.0
CA B:GLY165 3.8 12.7 1.0
C B:HIS164 3.8 14.6 1.0
O B:HIS164 4.0 15.4 1.0
CE B:MET71 4.0 14.6 1.0
N B:HIS164 4.0 15.8 1.0
C6 B:TF5502 4.1 35.3 1.0
SD B:MET71 4.2 13.5 1.0
N B:GLY137 4.4 12.6 1.0
CG2 B:VAL162 4.4 19.4 1.0
CA B:HIS164 4.5 14.5 1.0
C B:ASN163 4.6 17.2 1.0
O B:VAL136 4.7 11.4 1.0
F B:TF5502 4.8 35.4 1.0
C B:GLY137 4.8 12.9 1.0
C B:VAL136 4.9 11.1 1.0
CCN A:PEU601 4.9 56.8 1.0
CB B:VAL162 4.9 18.0 1.0
N B:ASN163 5.0 16.3 1.0
O B:GLY69 5.0 15.0 1.0

Reference:

H.Inagaki, H.Tsuruoka, M.Hornsby, S.A.Lesley, G.Spraggon, J.A.Ellman. Characterization and Optimization of Selective, Nonpeptidic Inhibitors of Cathepsin S with An Unprecedented Binding Mode. J.Med.Chem. V. 50 2693 2007.
ISSN: ISSN 0022-2623
PubMed: 17469812
DOI: 10.1021/JM070111+
Page generated: Sun Dec 13 11:38:34 2020

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