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Fluorine in PDB 5tdi: Crystal Structure of Cathepsin K with A Covalently-Linked Inhibitor at 1.4 Angstrom Resolution.

Enzymatic activity of Crystal Structure of Cathepsin K with A Covalently-Linked Inhibitor at 1.4 Angstrom Resolution.

All present enzymatic activity of Crystal Structure of Cathepsin K with A Covalently-Linked Inhibitor at 1.4 Angstrom Resolution.:
3.4.22.38;

Protein crystallography data

The structure of Crystal Structure of Cathepsin K with A Covalently-Linked Inhibitor at 1.4 Angstrom Resolution., PDB code: 5tdi was solved by S.Law, A.Aguda, N.Nguyen, G.Brayer, D.Bromme, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.16 / 1.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.249, 54.620, 80.300, 90.00, 90.00, 90.00
R / Rfree (%) 14.3 / 17.1

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Cathepsin K with A Covalently-Linked Inhibitor at 1.4 Angstrom Resolution. (pdb code 5tdi). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of Cathepsin K with A Covalently-Linked Inhibitor at 1.4 Angstrom Resolution., PDB code: 5tdi:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 5tdi

Go back to Fluorine Binding Sites List in 5tdi
Fluorine binding site 1 out of 4 in the Crystal Structure of Cathepsin K with A Covalently-Linked Inhibitor at 1.4 Angstrom Resolution.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Cathepsin K with A Covalently-Linked Inhibitor at 1.4 Angstrom Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:11.5
occ:1.00
 F33 A:7AS301 0.0 11.5 1.0
C32 A:7AS301 1.3 10.6 1.0
F34 A:7AS301 2.2 10.7 1.0
F35 A:7AS301 2.2 12.8 1.0
C15 A:7AS301 2.3 7.8 1.0
C16 A:7AS301 2.8 9.8 1.0
C21 A:7AS301 3.2 9.2 1.0
O A:HOH620 3.6 32.2 1.0
N14 A:7AS301 3.6 6.8 1.0
C17 A:7AS301 3.6 8.2 1.0
O A:HOH618 3.9 26.5 1.0
C20 A:7AS301 4.2 9.4 1.0
O A:HOH622 4.4 38.0 1.0
O A:HOH558 4.4 25.0 1.0
C05 A:7AS301 4.5 6.9 1.0
C18 A:7AS301 4.6 7.1 1.0
O A:LEU160 4.8 12.1 1.0
C19 A:7AS301 4.8 7.8 1.0

Fluorine binding site 2 out of 4 in 5tdi

Go back to Fluorine Binding Sites List in 5tdi
Fluorine binding site 2 out of 4 in the Crystal Structure of Cathepsin K with A Covalently-Linked Inhibitor at 1.4 Angstrom Resolution.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Cathepsin K with A Covalently-Linked Inhibitor at 1.4 Angstrom Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:10.7
occ:1.00
 F34 A:7AS301 0.0 10.7 1.0
C32 A:7AS301 1.3 10.6 1.0
F35 A:7AS301 2.2 12.8 1.0
F33 A:7AS301 2.2 11.5 1.0
C15 A:7AS301 2.3 7.8 1.0
N14 A:7AS301 2.9 6.8 1.0
O A:LEU160 3.0 12.1 1.0
C05 A:7AS301 3.2 6.9 1.0
O A:HOH620 3.3 32.2 1.0
C01 A:7AS301 3.5 9.4 1.0
O A:HOH618 3.5 26.5 1.0
O A:HOH558 3.6 25.0 1.0
C16 A:7AS301 3.6 9.8 1.0
CA A:ASN161 3.9 5.7 1.0
C A:LEU160 4.0 9.2 1.0
C06 A:7AS301 4.2 6.9 1.0
C04 A:7AS301 4.2 5.8 1.0
C02 A:7AS301 4.3 6.1 1.0
N A:ASN161 4.4 7.2 1.0
C17 A:7AS301 4.4 8.2 1.0
C A:ASN161 4.4 6.4 1.0
C21 A:7AS301 4.5 9.2 1.0
N08 A:7AS301 4.6 7.6 1.0
O A:ASN161 4.6 8.3 1.0
C03 A:7AS301 4.7 8.2 1.0
CB A:ASN161 4.8 8.5 1.0
O A:HOH437 4.9 28.3 1.0
O A:HOH622 4.9 38.0 1.0

Fluorine binding site 3 out of 4 in 5tdi

Go back to Fluorine Binding Sites List in 5tdi
Fluorine binding site 3 out of 4 in the Crystal Structure of Cathepsin K with A Covalently-Linked Inhibitor at 1.4 Angstrom Resolution.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Cathepsin K with A Covalently-Linked Inhibitor at 1.4 Angstrom Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:12.8
occ:1.00
 F35 A:7AS301 0.0 12.8 1.0
C32 A:7AS301 1.4 10.6 1.0
F34 A:7AS301 2.2 10.7 1.0
F33 A:7AS301 2.2 11.5 1.0
C15 A:7AS301 2.3 7.8 1.0
N14 A:7AS301 2.8 6.8 1.0
C16 A:7AS301 2.9 9.8 1.0
C17 A:7AS301 3.0 8.2 1.0
OH A:TYR67 3.6 15.6 1.0
O A:HOH558 3.6 25.0 1.0
O A:HOH437 3.6 28.3 1.0
CE1 A:TYR67 3.8 12.4 1.0
CZ A:TYR67 3.8 12.4 1.0
C05 A:7AS301 3.9 6.9 1.0
C21 A:7AS301 4.1 9.2 1.0
C01 A:7AS301 4.2 9.4 1.0
C18 A:7AS301 4.2 7.1 1.0
C03 A:7AS301 4.3 8.2 1.0
O A:LEU160 4.6 12.1 1.0
CD1 A:TYR67 4.6 9.8 1.0
C02 A:7AS301 4.7 6.1 1.0
CE2 A:TYR67 4.7 12.0 1.0
C04 A:7AS301 4.8 5.8 1.0
O A:HOH620 5.0 32.2 1.0

Fluorine binding site 4 out of 4 in 5tdi

Go back to Fluorine Binding Sites List in 5tdi
Fluorine binding site 4 out of 4 in the Crystal Structure of Cathepsin K with A Covalently-Linked Inhibitor at 1.4 Angstrom Resolution.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Cathepsin K with A Covalently-Linked Inhibitor at 1.4 Angstrom Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:7.0
occ:1.00
 F36 A:7AS301 0.0 7.0 1.0
C02 A:7AS301 1.4 6.1 1.0
C04 A:7AS301 2.3 5.8 1.0
C03 A:7AS301 2.3 8.2 1.0
C01 A:7AS301 2.4 9.4 1.0
CB A:ALA134 3.2 9.4 1.0
CB A:ALA163 3.3 7.2 1.0
CA A:ALA163 3.5 6.1 1.0
O A:HIS162 3.5 8.1 1.0
N A:ALA163 3.6 5.6 1.0
C A:HIS162 3.6 4.8 1.0
CE A:MET68 3.7 8.3 1.0
C05 A:7AS301 3.7 6.9 1.0
CA A:ALA134 3.8 6.2 1.0
SD A:MET68 3.8 6.5 1.0
N14 A:7AS301 4.4 6.8 1.0
N A:HIS162 4.4 5.7 1.0
CA A:HIS162 4.5 6.1 1.0
O A:VAL133 4.6 6.0 1.0
N A:ALA134 4.6 5.8 1.0
C06 A:7AS301 4.8 6.9 1.0
O A:GLY66 4.9 6.4 1.0
C A:ALA134 4.9 7.1 1.0
C A:VAL133 4.9 6.8 1.0
C A:ALA163 5.0 4.7 1.0

Reference:

S.Law, P.M.Andrault, A.H.Aguda, N.T.Nguyen, N.Kruglyak, G.D.Brayer, D.Bromme. Identification of Mouse Cathepsin K Structural Elements That Regulate the Potency of Odanacatib. Biochem. J. V. 474 851 2017.
ISSN: ESSN 1470-8728
PubMed: 28049758
DOI: 10.1042/BCJ20160985
Page generated: Thu Aug 1 15:10:04 2024

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