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Fluorine in PDB 3kw9: X-Ray Structure of Cathepsin K Covalently Bound to A Triazine Ligand

Enzymatic activity of X-Ray Structure of Cathepsin K Covalently Bound to A Triazine Ligand

All present enzymatic activity of X-Ray Structure of Cathepsin K Covalently Bound to A Triazine Ligand:
3.4.22.38;

Protein crystallography data

The structure of X-Ray Structure of Cathepsin K Covalently Bound to A Triazine Ligand, PDB code: 3kw9 was solved by J.C.M.Uitdehaag, M.Van Zeeland, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.80
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 55.391, 55.391, 128.719, 90.00, 90.00, 90.00
R / Rfree (%) 23 / 25.9

Fluorine Binding Sites:

The binding sites of Fluorine atom in the X-Ray Structure of Cathepsin K Covalently Bound to A Triazine Ligand (pdb code 3kw9). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the X-Ray Structure of Cathepsin K Covalently Bound to A Triazine Ligand, PDB code: 3kw9:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 3kw9

Go back to Fluorine Binding Sites List in 3kw9
Fluorine binding site 1 out of 3 in the X-Ray Structure of Cathepsin K Covalently Bound to A Triazine Ligand


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of X-Ray Structure of Cathepsin K Covalently Bound to A Triazine Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F217

b:42.2
occ:1.00
F1 A:TFA217 0.0 42.2 1.0
C2 A:TFA217 1.2 43.7 1.0
F2 A:TFA217 1.9 45.5 1.0
F3 A:TFA217 2.0 43.0 1.0
C1 A:TFA217 2.2 45.6 1.0
O A:TFA217 2.5 48.2 1.0
O A:HOH287 2.9 53.5 1.0
N15 A:ORG216 3.2 25.1 1.0
NE2 A:GLN19 3.3 24.7 1.0
OXT A:TFA217 3.4 46.4 1.0
NE1 A:TRP184 3.4 16.1 1.0
ND1 A:HIS162 3.4 22.9 1.0
CE1 A:HIS162 3.4 21.4 1.0
CZ2 A:TRP184 3.8 18.1 1.0
CE2 A:TRP184 3.9 18.0 1.0
C9 A:ORG216 4.1 24.3 1.0
CD A:GLN19 4.1 23.7 1.0
OE1 A:GLN19 4.4 22.3 1.0
CD1 A:TRP184 4.6 17.8 1.0
NE2 A:HIS162 4.6 21.3 1.0
CG A:HIS162 4.6 22.6 1.0
N5 A:ORG216 4.7 25.5 1.0
C6 A:ORG216 4.8 26.2 1.0

Fluorine binding site 2 out of 3 in 3kw9

Go back to Fluorine Binding Sites List in 3kw9
Fluorine binding site 2 out of 3 in the X-Ray Structure of Cathepsin K Covalently Bound to A Triazine Ligand


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of X-Ray Structure of Cathepsin K Covalently Bound to A Triazine Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F217

b:45.5
occ:1.00
F2 A:TFA217 0.0 45.5 1.0
C2 A:TFA217 1.2 43.7 1.0
F1 A:TFA217 1.9 42.2 1.0
F3 A:TFA217 1.9 43.0 1.0
C1 A:TFA217 2.2 45.6 1.0
OXT A:TFA217 2.7 46.4 1.0
O A:TFA217 3.2 48.2 1.0
NE2 A:GLN19 3.3 24.7 1.0
NE1 A:TRP184 3.8 16.1 1.0
CD A:GLN19 4.3 23.7 1.0
N15 A:ORG216 4.4 25.1 1.0
CE2 A:TRP184 4.5 18.0 1.0
CZ2 A:TRP184 4.7 18.1 1.0
CD1 A:TRP184 4.7 17.8 1.0
O A:HOH287 4.7 53.5 1.0
O A:GLY20 4.9 29.6 1.0
O A:CYS22 5.0 24.7 1.0

Fluorine binding site 3 out of 3 in 3kw9

Go back to Fluorine Binding Sites List in 3kw9
Fluorine binding site 3 out of 3 in the X-Ray Structure of Cathepsin K Covalently Bound to A Triazine Ligand


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of X-Ray Structure of Cathepsin K Covalently Bound to A Triazine Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F217

b:43.0
occ:1.00
F3 A:TFA217 0.0 43.0 1.0
C2 A:TFA217 1.2 43.7 1.0
F2 A:TFA217 1.9 45.5 1.0
F1 A:TFA217 2.0 42.2 1.0
C1 A:TFA217 2.1 45.6 1.0
OXT A:TFA217 2.7 46.4 1.0
N15 A:ORG216 3.1 25.1 1.0
O A:TFA217 3.1 48.2 1.0
NE2 A:GLN19 3.3 24.7 1.0
CA A:GLY23 3.8 24.9 1.0
N5 A:ORG216 3.8 25.5 1.0
O A:HOH287 3.8 53.5 1.0
C14 A:ORG216 3.9 32.5 1.0
C9 A:ORG216 4.0 24.3 1.0
C13 A:ORG216 4.2 33.8 1.0
C6 A:ORG216 4.3 26.2 1.0
O A:CYS22 4.5 24.7 1.0
CD A:GLN19 4.5 23.7 1.0
N A:GLY23 4.6 25.4 1.0
C A:GLY23 4.8 23.1 1.0
C4 A:ORG216 4.8 28.3 1.0
N8 A:ORG216 4.9 31.8 1.0
C A:CYS22 4.9 26.5 1.0
ND1 A:HIS162 5.0 22.9 1.0
NE1 A:TRP184 5.0 16.1 1.0

Reference:

Z.Rankovic, J.Cai, J.Kerr, X.Fradera, J.Robinson, A.Mistry, E.Hamilton, G.Mcgarry, F.Andrews, W.Caulfield, I.Cumming, M.Dempster, J.Waller, P.Scullion, I.Martin, A.Mitchell, C.Long, M.Baugh, P.Westwood, E.Kinghorn, J.Bruin, W.Hamilton, J.Uitdehaag, M.Van Zeeland, D.Potin, L.Saniere, A.Fouquet, F.Chevallier, H.Deronzier, C.Dorleans, E.Nicolai. Design and Optimization of A Series of Novel 2-Cyano-Pyrimidines As Cathepsin K Inhibitors. Bioorg.Med.Chem.Lett. V. 20 1524 2010.
ISSN: ISSN 0960-894X
PubMed: 20149657
DOI: 10.1016/J.BMCL.2010.01.100
Page generated: Mon Jul 14 17:38:16 2025

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