Chlorine 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:

Fluorine (F) 6 atoms
Calcium (Ca) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 2 binding sites of Chlorine 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 Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 6qbs

Go back to Chlorine Binding Sites List in 6qbs
Chlorine binding site 1 out of 2 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 Chlorine with other atoms in the Cl 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:Cl303

b:37.4
occ:1.00
 HZ3 A:LYS176 2.3 2.0 0.0
HZ2 A:LYS122 2.3 2.0 0.0
HH12 A:ARG198 2.4 2.0 0.0
H2 A:HOH640 2.4 2.0 0.0
HD21 A:ASN199 2.5 2.0 0.0
H2 A:HOH457 2.7 2.0 0.0
HD22 A:ASN199 3.1 2.0 0.0
ND2 A:ASN199 3.2 25.9 1.0
NH1 A:ARG198 3.2 13.5 1.0
NZ A:LYS176 3.3 40.2 1.0
NZ A:LYS122 3.3 27.4 1.0
O A:HOH640 3.3 19.4 1.0
H1 A:HOH481 3.3 2.0 0.0
H1 A:HOH640 3.4 2.0 0.0
HH11 A:ARG198 3.4 2.0 0.0
HZ3 A:LYS122 3.4 2.0 0.0
H1 A:HOH629 3.5 2.0 0.0
O A:HOH457 3.6 27.6 1.0
HZ2 A:LYS176 3.6 2.0 0.0
HZ1 A:LYS176 3.6 2.0 0.0
H1 A:HOH603 3.8 2.0 0.0
H2 A:HOH481 3.8 2.0 0.0
H1 A:HOH457 3.9 2.0 0.0
HZ1 A:LYS122 3.9 2.0 0.0
H2 A:HOH629 3.9 2.0 0.0
CD A:LYS122 4.1 10.4 1.0
O A:HOH481 4.1 16.2 1.0
HH22 A:ARG198 4.1 2.0 0.0
H1 A:HOH587 4.1 2.0 0.0
H2 A:HOH587 4.1 2.0 0.0
CE A:LYS122 4.2 22.7 1.0
O A:HOH629 4.2 40.1 1.0
H2 A:HOH416 4.2 2.0 0.0
CE A:LYS176 4.3 28.6 1.0
CZ A:ARG198 4.3 18.7 1.0
CD A:LYS176 4.3 21.7 1.0
H2 A:HOH603 4.4 2.0 0.0
H1 A:HOH416 4.4 2.0 0.0
CG A:ASN199 4.4 22.1 1.0
O A:HOH603 4.6 34.1 1.0
NH2 A:ARG198 4.6 16.9 1.0
O A:HOH587 4.6 34.9 1.0
O A:HOH416 4.8 34.5 1.0
OD1 A:ASN199 4.9 28.0 1.0
H1 A:HOH706 5.0 2.0 0.0

Chlorine binding site 2 out of 2 in 6qbs

Go back to Chlorine Binding Sites List in 6qbs
Chlorine binding site 2 out of 2 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 Chlorine with other atoms in the Cl 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
B:Cl502

b:24.3
occ:1.00
 H2 B:HOH709 2.1 2.0 0.0
HZ3 B:LYS391 2.2 2.0 0.0
HZ2 B:LYS337 2.3 2.0 0.0
HH12 B:ARG413 2.4 2.0 0.0
H1 B:HOH665 2.5 2.0 0.0
H1 B:HOH852 2.6 2.0 0.0
H1 B:HOH709 2.7 2.0 0.0
HD21 B:ASN414 2.8 2.0 0.0
O B:HOH709 2.8 34.6 1.0
H1 B:HOH839 3.2 2.0 0.0
NZ B:LYS391 3.2 23.1 1.0
NH1 B:ARG413 3.2 13.2 1.0
O B:HOH665 3.4 17.3 1.0
NZ B:LYS337 3.4 15.3 1.0
ND2 B:ASN414 3.4 16.1 1.0
HD22 B:ASN414 3.5 2.0 0.0
H2 B:HOH665 3.5 2.0 0.0
HZ2 B:LYS391 3.5 2.0 0.0
HH11 B:ARG413 3.5 2.0 0.0
O B:HOH852 3.6 25.8 1.0
H1 B:HOH685 3.6 2.0 0.0
H2 B:HOH717 3.7 2.0 0.0
HZ1 B:LYS391 3.8 2.0 0.0
H2 B:HOH852 3.8 2.0 0.0
HZ3 B:LYS337 3.8 2.0 0.0
HZ1 B:LYS337 3.9 2.0 0.0
H2 B:HOH839 4.0 2.0 0.0
O B:HOH839 4.0 26.1 1.0
HH22 B:ARG413 4.0 2.0 0.0
CE B:LYS391 4.0 17.6 1.0
H2 B:HOH685 4.1 2.0 0.0
CD B:LYS391 4.1 14.4 1.0
CD B:LYS337 4.2 9.8 1.0
CE B:LYS337 4.2 19.0 1.0
H1 B:HOH717 4.2 2.0 0.0
O B:HOH685 4.3 13.6 1.0
CZ B:ARG413 4.3 12.4 1.0
O B:HOH717 4.5 24.1 1.0
H1 B:HOH667 4.5 2.0 0.0
NH2 B:ARG413 4.6 10.0 1.0
CG B:ASN414 4.7 20.1 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: Sat Dec 12 13:33:16 2020

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