Atomistry » Fluorine » PDB 5tbo-5tvj » 5tdi
Atomistry »
  Fluorine »
    PDB 5tbo-5tvj »
      5tdi »

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: Tue Jul 15 07:53:09 2025

Last articles

Mg in 1KK3
Mg in 1KK2
Mg in 1KJY
Mg in 1KK1
Mg in 1KJJ
Mg in 1KJQ
Mg in 1KJI
Mg in 1KJ9
Mg in 1KJ8
Mg in 1KIZ
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy