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Calcium 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
Chlorine (Cl) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total only one binding site of Calcium was determined in the The Alkyne Moiety As A Latent Electrophile in Irreversible Covalent Small Molecule Inhibitors of Cathepsin K, PDB code: 6qbs:

Calcium binding site 1 out of 1 in 6qbs

Go back to Calcium Binding Sites List in 6qbs
Calcium binding site 1 out of 1 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 Calcium with other atoms in the Ca 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:Ca302

b:6.2
occ:1.00
 OE1 B:GLN288 2.2 8.4 1.0
OE1 A:GLN73 2.2 8.4 1.0
OD1 A:ASN70 2.4 9.3 1.0
OD1 B:ASN285 2.4 8.3 1.0
OE2 B:GLU274 2.5 9.5 1.0
OE2 A:GLU59 2.5 9.6 1.0
OE1 A:GLU59 2.6 9.3 1.0
OE1 B:GLU274 2.7 7.6 1.0
CD A:GLU59 2.9 10.0 1.0
CD B:GLU274 2.9 10.7 1.0
HE22 B:GLN288 3.2 2.0 0.0
CD B:GLN288 3.2 6.0 1.0
CD A:GLN73 3.3 8.2 1.0
HE22 A:GLN73 3.3 2.0 0.0
NE2 B:GLN288 3.6 7.7 1.0
CG A:ASN70 3.6 8.6 1.0
CG B:ASN285 3.6 8.3 1.0
NE2 A:GLN73 3.7 7.9 1.0
CA B:ASN285 4.2 9.4 1.0
CA A:ASN70 4.2 6.6 1.0
HD21 A:ASN70 4.3 2.0 0.0
HD21 B:ASN285 4.4 2.0 0.0
CG A:GLU59 4.4 11.3 1.0
CG B:GLU274 4.4 9.5 1.0
O B:HOH770 4.4 25.2 1.0
ND2 A:ASN70 4.4 8.5 1.0
CB A:ASN70 4.4 6.5 1.0
O A:HOH619 4.5 18.0 1.0
HG1 B:THR284 4.5 2.0 0.0
CB B:ASN285 4.5 9.4 1.0
ND2 B:ASN285 4.5 8.7 1.0
HE21 B:GLN288 4.6 2.0 0.0
CG A:GLN73 4.6 8.8 1.0
CG B:GLN288 4.6 8.7 1.0
N A:ASN70 4.6 7.6 1.0
HE21 A:GLN73 4.6 2.0 0.0
N B:ASN285 4.7 6.7 1.0
H2 A:HOH619 4.8 2.0 0.0
H A:ASN70 4.8 2.0 0.0
CB A:GLU59 4.9 9.6 1.0
H B:ASN285 4.9 2.0 0.0
CB B:GLU274 4.9 9.6 1.0
OG1 B:THR284 4.9 11.2 1.0
OG1 A:THR69 4.9 13.1 1.0
CB A:GLN73 4.9 8.7 1.0
O A:HOH426 5.0 8.5 1.0
O B:HOH615 5.0 8.9 1.0
H2 B:HOH770 5.0 2.0 0.0
CB B:GLN288 5.0 9.0 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: Tue Jul 16 13:44:56 2024

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