Atomistry » Chlorine » PDB 6q96-6qig » 6qbs
Atomistry »
  Chlorine »
    PDB 6q96-6qig »
      6qbs »

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: Mon Jul 29 13:54:35 2024

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy