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Fluorine in PDB 6qbs: The Alkyne Moiety As A Latent Electrophile in Irreversible Covalent Small Molecule Inhibitors of Cathepsin K

Enzymatic activity of The Alkyne Moiety As A Latent Electrophile in Irreversible Covalent Small Molecule Inhibitors of Cathepsin K

All present enzymatic activity of The Alkyne Moiety As A Latent Electrophile in Irreversible Covalent Small Molecule Inhibitors of Cathepsin K:
3.4.22.38;

Protein crystallography data

The structure of The Alkyne Moiety As A Latent Electrophile in Irreversible Covalent Small Molecule Inhibitors of Cathepsin K, PDB code: 6qbs was solved by E.Mons, I.D.C.Jansen, J.Loboda, B.R.Van Doodewaerd, M.Verdoes, C.A.A.Vanboeckel, P.A.Van Veelen, B.Turk, D.Turk, J.Hermans, H.Ovaa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.09 / 1.70
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 75.350, 75.350, 340.200, 90.00, 90.00, 120.00
R / Rfree (%) 20.4 / 21

Other elements in 6qbs:

The structure of The Alkyne Moiety As A Latent Electrophile in Irreversible Covalent Small Molecule Inhibitors of Cathepsin K also contains other interesting chemical elements:

Calcium (Ca) 1 atom
Chlorine (Cl) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the The Alkyne Moiety As A Latent Electrophile in Irreversible Covalent Small Molecule Inhibitors of Cathepsin K (pdb code 6qbs). 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 Alkyne Moiety As A Latent Electrophile in Irreversible Covalent Small Molecule Inhibitors of Cathepsin K, PDB code: 6qbs:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 6qbs

Go back to Fluorine Binding Sites List in 6qbs
Fluorine binding site 1 out of 6 in the The Alkyne Moiety As A Latent Electrophile in Irreversible Covalent Small Molecule Inhibitors of Cathepsin K


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of The Alkyne Moiety As A Latent Electrophile in Irreversible Covalent Small Molecule Inhibitors of Cathepsin K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:19.3
occ:1.00
 F15 A:HVW301 0.0 19.3 1.0
C14 A:HVW301 1.3 17.4 1.0
F16 A:HVW301 2.1 17.6 1.0
F17 A:HVW301 2.1 21.3 1.0
C13 A:HVW301 2.4 9.1 1.0
H43 A:HVW301 2.4 2.0 0.0
N12 A:HVW301 2.9 8.9 1.0
H1 A:HOH523 2.9 2.0 0.0
C18 A:HVW301 2.9 9.7 1.0
H40 A:HVW301 3.0 2.0 0.0
O A:HOH523 3.2 34.2 1.0
H42 A:HVW301 3.2 2.0 0.0
C19 A:HVW301 3.2 9.8 1.0
H1 A:HOH722 3.3 2.0 0.0
HH A:TYR67 3.4 2.0 0.0
H51 A:HVW301 3.5 2.0 0.0
OH A:TYR67 3.7 26.4 1.0
H44 A:HVW301 3.8 2.0 0.0
O A:HOH722 3.9 56.6 1.0
H47 A:HVW301 3.9 2.0 0.0
C22 A:HVW301 3.9 20.4 1.0
C7 A:HVW301 3.9 11.2 1.0
CZ A:TYR67 4.0 21.0 1.0
H2 A:HOH722 4.1 2.0 0.0
H2 A:HOH523 4.1 2.0 0.0
H1 A:HOH573 4.1 2.0 0.0
CE1 A:TYR67 4.1 13.6 1.0
H1 B:HOH726 4.2 2.0 0.0
H39 A:HVW301 4.2 2.0 0.0
C11 A:HVW301 4.2 10.6 1.0
O A:LEU160 4.3 14.2 1.0
O A:HOH573 4.3 24.6 1.0
C20 A:HVW301 4.3 13.3 1.0
H53 A:HVW301 4.4 2.0 0.0
C9 A:HVW301 4.5 13.2 1.0
H2 A:HOH725 4.7 2.0 0.0
H2 B:HOH726 4.8 2.0 0.0
C8 A:HVW301 4.8 9.1 1.0
H41 A:HVW301 4.9 2.0 0.0
C23 A:HVW301 4.9 14.0 1.0
CE2 A:TYR67 4.9 11.5 1.0
H2 A:HOH573 4.9 2.0 0.0
O B:HOH726 4.9 42.5 1.0

Fluorine binding site 2 out of 6 in 6qbs

Go back to Fluorine Binding Sites List in 6qbs
Fluorine binding site 2 out of 6 in the The Alkyne Moiety As A Latent Electrophile in Irreversible Covalent Small Molecule Inhibitors of Cathepsin K


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of The Alkyne Moiety As A Latent Electrophile in Irreversible Covalent Small Molecule Inhibitors of Cathepsin K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:17.6
occ:1.00
 F16 A:HVW301 0.0 17.6 1.0
C14 A:HVW301 1.3 17.4 1.0
F15 A:HVW301 2.1 19.3 1.0
F17 A:HVW301 2.1 21.3 1.0
C13 A:HVW301 2.4 9.1 1.0
H44 A:HVW301 2.5 2.0 0.0
H1 A:HOH573 2.6 2.0 0.0
H42 A:HVW301 2.6 2.0 0.0
H51 A:HVW301 2.8 2.0 0.0
H43 A:HVW301 2.8 2.0 0.0
N12 A:HVW301 2.8 8.9 1.0
H1 A:HOH523 3.0 2.0 0.0
C7 A:HVW301 3.1 11.2 1.0
O A:HOH573 3.1 24.6 1.0
O A:LEU160 3.3 14.2 1.0
CA A:ASN161 3.6 9.8 1.0
C18 A:HVW301 3.7 9.7 1.0
C11 A:HVW301 3.7 10.6 1.0
H2 A:HOH721 3.7 2.0 0.0
O A:HOH523 3.8 34.2 1.0
H1 A:HOH722 3.8 2.0 0.0
O A:HOH422 3.8 25.1 1.0
H2 A:HOH573 3.8 2.0 0.0
O A:HOH721 3.8 35.5 1.0
H1 A:HOH422 3.9 2.0 0.0
H47 A:HVW301 4.1 2.0 0.0
O A:ASN161 4.1 10.3 1.0
H54 A:HVW301 4.1 2.0 0.0
C A:ASN161 4.1 10.8 1.0
C A:LEU160 4.2 11.6 1.0
C5 A:HVW301 4.2 10.2 1.0
C8 A:HVW301 4.2 9.1 1.0
H53 A:HVW301 4.2 2.0 0.0
H2 A:HOH422 4.2 2.0 0.0
H52 A:HVW301 4.2 2.0 0.0
C9 A:HVW301 4.2 13.2 1.0
CB A:ASN161 4.3 13.2 1.0
N A:ASN161 4.3 9.8 1.0
H39 A:HVW301 4.4 2.0 0.0
H1 A:HOH721 4.4 2.0 0.0
H40 A:HVW301 4.4 2.0 0.0
N4 A:HVW301 4.5 11.0 1.0
C22 A:HVW301 4.5 20.4 1.0
C19 A:HVW301 4.5 9.8 1.0
H2 A:HOH523 4.5 2.0 0.0
H46 A:HVW301 4.6 2.0 0.0
O A:HOH722 4.7 56.6 1.0
O A:HOH600 4.8 28.6 1.0
H45 A:HVW301 4.9 2.0 0.0
H2 A:HOH722 5.0 2.0 0.0

Fluorine binding site 3 out of 6 in 6qbs

Go back to Fluorine Binding Sites List in 6qbs
Fluorine binding site 3 out of 6 in the The Alkyne Moiety As A Latent Electrophile in Irreversible Covalent Small Molecule Inhibitors of Cathepsin K


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of The Alkyne Moiety As A Latent Electrophile in Irreversible Covalent Small Molecule Inhibitors of Cathepsin K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:21.3
occ:1.00
 F17 A:HVW301 0.0 21.3 1.0
C14 A:HVW301 1.3 17.4 1.0
F15 A:HVW301 2.1 19.3 1.0
F16 A:HVW301 2.1 17.6 1.0
C13 A:HVW301 2.3 9.1 1.0
H42 A:HVW301 2.6 2.0 0.0
H1 A:HOH722 2.6 2.0 0.0
C18 A:HVW301 2.8 9.7 1.0
H39 A:HVW301 2.9 2.0 0.0
C22 A:HVW301 3.1 20.4 1.0
H2 A:HOH725 3.2 2.0 0.0
O A:HOH722 3.3 56.6 1.0
H1 A:HOH573 3.3 2.0 0.0
O A:HOH573 3.6 24.6 1.0
N12 A:HVW301 3.6 8.9 1.0
H1 A:HOH725 3.7 2.0 0.0
H43 A:HVW301 3.7 2.0 0.0
O A:HOH721 3.7 35.5 1.0
O A:HOH725 3.8 46.7 1.0
C19 A:HVW301 3.8 9.8 1.0
H2 A:HOH573 3.9 2.0 0.0
H1 A:HOH721 3.9 2.0 0.0
H1 A:HOH523 3.9 2.0 0.0
H2 A:HOH722 3.9 2.0 0.0
H2 A:HOH721 4.0 2.0 0.0
H44 A:HVW301 4.1 2.0 0.0
H40 A:HVW301 4.1 2.0 0.0
C23 A:HVW301 4.2 14.0 1.0
H1 A:HOH422 4.3 2.0 0.0
O A:HOH600 4.3 28.6 1.0
H1 A:HOH600 4.4 2.0 0.0
C7 A:HVW301 4.4 11.2 1.0
O A:HOH523 4.5 34.2 1.0
O A:HOH422 4.6 25.1 1.0
H51 A:HVW301 4.7 2.0 0.0
H38 A:HVW301 4.7 2.0 0.0
C20 A:HVW301 4.8 13.3 1.0
H1 B:HOH885 4.9 2.0 0.0
O A:LEU160 4.9 14.2 1.0
C21 A:HVW301 5.0 10.3 1.0

Fluorine binding site 4 out of 6 in 6qbs

Go back to Fluorine Binding Sites List in 6qbs
Fluorine binding site 4 out of 6 in the The Alkyne Moiety As A Latent Electrophile in Irreversible Covalent Small Molecule Inhibitors of Cathepsin K


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of The Alkyne Moiety As A Latent Electrophile in Irreversible Covalent Small Molecule Inhibitors of Cathepsin K within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F501

b:17.0
occ:1.00
 F15 B:HVW501 0.0 17.0 1.0
C14 B:HVW501 1.4 14.3 1.0
F16 B:HVW501 2.1 15.8 1.0
F17 B:HVW501 2.2 12.6 1.0
C13 B:HVW501 2.4 11.9 1.0
H42 B:HVW501 2.6 2.0 0.0
C18 B:HVW501 2.8 9.9 1.0
H40 B:HVW501 3.2 2.0 0.0
C19 B:HVW501 3.3 11.9 1.0
N12 B:HVW501 3.7 11.2 1.0
H43 B:HVW501 3.7 2.0 0.0
C22 B:HVW501 3.7 9.1 1.0
H1 B:HOH742 3.8 2.0 0.0
H39 B:HVW501 4.0 2.0 0.0
H2 B:HOH915 4.0 2.0 0.0
O B:HOH915 4.0 26.0 1.0
H1 B:HOH915 4.0 2.0 0.0
H44 B:HVW501 4.1 2.0 0.0
O B:HOH742 4.3 27.8 1.0
C20 B:HVW501 4.4 16.2 1.0
C7 B:HVW501 4.4 10.7 1.0
H51 B:HVW501 4.6 2.0 0.0
C23 B:HVW501 4.7 18.2 1.0
O B:HOH885 4.8 54.8 1.0
H41 B:HVW501 4.9 2.0 0.0

Fluorine binding site 5 out of 6 in 6qbs

Go back to Fluorine Binding Sites List in 6qbs
Fluorine binding site 5 out of 6 in the The Alkyne Moiety As A Latent Electrophile in Irreversible Covalent Small Molecule Inhibitors of Cathepsin K


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of The Alkyne Moiety As A Latent Electrophile in Irreversible Covalent Small Molecule Inhibitors of Cathepsin K within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F501

b:15.8
occ:1.00
 F16 B:HVW501 0.0 15.8 1.0
C14 B:HVW501 1.3 14.3 1.0
F15 B:HVW501 2.1 17.0 1.0
F17 B:HVW501 2.1 12.6 1.0
H43 B:HVW501 2.4 2.0 0.0
C13 B:HVW501 2.4 11.9 1.0
H39 B:HVW501 2.8 2.0 0.0
N12 B:HVW501 2.9 11.2 1.0
C18 B:HVW501 2.9 9.9 1.0
C22 B:HVW501 3.1 9.1 1.0
H42 B:HVW501 3.2 2.0 0.0
H51 B:HVW501 3.3 2.0 0.0
H2 B:HOH780 3.3 2.0 0.0
HH B:TYR282 3.6 2.0 0.0
OH B:TYR282 3.7 23.6 1.0
H44 B:HVW501 3.7 2.0 0.0
O B:HOH780 3.8 40.8 1.0
C7 B:HVW501 3.9 10.7 1.0
H47 B:HVW501 3.9 2.0 0.0
C19 B:HVW501 4.0 11.9 1.0
H1 B:HOH780 4.1 2.0 0.0
C11 B:HVW501 4.1 8.8 1.0
H2 B:HOH831 4.2 2.0 0.0
O B:HOH915 4.2 26.0 1.0
CZ B:TYR282 4.2 15.6 1.0
C23 B:HVW501 4.3 18.2 1.0
O B:LEU375 4.3 25.7 1.0
H40 B:HVW501 4.4 2.0 0.0
H1 B:HOH915 4.4 2.0 0.0
H53 B:HVW501 4.4 2.0 0.0
O B:HOH885 4.4 54.8 1.0
C9 B:HVW501 4.5 8.9 1.0
H2 B:HOH885 4.5 2.0 0.0
CE1 B:TYR282 4.5 16.1 1.0
H2 B:HOH915 4.6 2.0 0.0
H38 B:HVW501 4.7 2.0 0.0
C8 B:HVW501 4.8 8.2 1.0
H52 B:HVW501 4.9 2.0 0.0
C20 B:HVW501 5.0 16.2 1.0

Fluorine binding site 6 out of 6 in 6qbs

Go back to Fluorine Binding Sites List in 6qbs
Fluorine binding site 6 out of 6 in the The Alkyne Moiety As A Latent Electrophile in Irreversible Covalent Small Molecule Inhibitors of Cathepsin K


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of The Alkyne Moiety As A Latent Electrophile in Irreversible Covalent Small Molecule Inhibitors of Cathepsin K within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F501

b:12.6
occ:1.00
 F17 B:HVW501 0.0 12.6 1.0
C14 B:HVW501 1.3 14.3 1.0
F16 B:HVW501 2.1 15.8 1.0
F15 B:HVW501 2.2 17.0 1.0
C13 B:HVW501 2.3 11.9 1.0
H44 B:HVW501 2.4 2.0 0.0
H42 B:HVW501 2.6 2.0 0.0
H43 B:HVW501 2.7 2.0 0.0
H51 B:HVW501 2.8 2.0 0.0
N12 B:HVW501 2.8 11.2 1.0
C7 B:HVW501 3.1 10.7 1.0
H1 B:HOH742 3.1 2.0 0.0
CA B:ASN376 3.4 18.1 1.0
O B:LEU375 3.5 25.7 1.0
O B:HOH742 3.6 27.8 1.0
C18 B:HVW501 3.7 9.9 1.0
C11 B:HVW501 3.7 8.8 1.0
O B:ASN376 3.8 14.7 1.0
C B:ASN376 3.9 13.6 1.0
C5 B:HVW501 4.0 9.8 1.0
CB B:ASN376 4.0 16.6 1.0
H52 B:HVW501 4.0 2.0 0.0
H54 B:HVW501 4.1 2.0 0.0
C8 B:HVW501 4.2 8.2 1.0
H47 B:HVW501 4.2 2.0 0.0
C9 B:HVW501 4.3 8.9 1.0
H39 B:HVW501 4.3 2.0 0.0
H53 B:HVW501 4.3 2.0 0.0
C B:LEU375 4.3 16.6 1.0
N4 B:HVW501 4.3 11.9 1.0
N B:ASN376 4.3 14.0 1.0
H2 B:HOH742 4.4 2.0 0.0
C22 B:HVW501 4.4 9.1 1.0
H40 B:HVW501 4.5 2.0 0.0
C19 B:HVW501 4.6 11.9 1.0
H46 B:HVW501 4.6 2.0 0.0
O6 B:HVW501 4.9 10.3 1.0
H2 B:HOH780 4.9 2.0 0.0
H45 B:HVW501 4.9 2.0 0.0
O B:HOH780 5.0 40.8 1.0
N B:HIS377 5.0 13.0 1.0

Reference:

E.Mons, I.D.C.Jansen, J.Loboda, B.R.Van Doodewaerd, J.Hermans, M.Verdoes, C.A.A.Van Boeckel, P.A.Van Veelen, B.Turk, D.Turk, H.Ovaa. The Alkyne Moiety As A Latent Electrophile in Irreversible Covalent Small Molecule Inhibitors of Cathepsin K. J. Am. Chem. Soc. V. 141 3507 2019.
ISSN: ESSN 1520-5126
PubMed: 30689386
DOI: 10.1021/JACS.8B11027
Page generated: Fri Aug 2 00:46:27 2024

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