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Fluorine in PDB 3kwb: Structure of Catk Covalently Bound to A Dioxo-Triazine Inhibitor

Enzymatic activity of Structure of Catk Covalently Bound to A Dioxo-Triazine Inhibitor

All present enzymatic activity of Structure of Catk Covalently Bound to A Dioxo-Triazine Inhibitor:
3.4.22.38;

Protein crystallography data

The structure of Structure of Catk Covalently Bound to A Dioxo-Triazine Inhibitor, PDB code: 3kwb 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) 27.47 / 2.02
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 31.452, 69.338, 90.850, 90.00, 98.83, 90.00
R / Rfree (%) 19.4 / 26.3

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of Catk Covalently Bound to A Dioxo-Triazine Inhibitor (pdb code 3kwb). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Structure of Catk Covalently Bound to A Dioxo-Triazine Inhibitor, PDB code: 3kwb:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 3kwb

Go back to Fluorine Binding Sites List in 3kwb
Fluorine binding site 1 out of 6 in the Structure of Catk Covalently Bound to A Dioxo-Triazine Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of Catk Covalently Bound to A Dioxo-Triazine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
X:F1216

b:33.4
occ:1.00
F1 X:ORH1216 0.0 33.4 1.0
C13 X:ORH1216 1.3 31.3 1.0
F2 X:ORH1216 2.1 32.9 1.0
F3 X:ORH1216 2.1 32.4 1.0
C8 X:ORH1216 2.3 29.1 1.0
C10 X:ORH1216 2.8 30.1 1.0
CD1 X:TYR1067 3.3 19.0 1.0
C7 X:ORH1216 3.4 27.1 1.0
O X:GLY1066 3.5 15.1 1.0
CE1 X:TYR1067 3.6 19.5 1.0
CD2 X:LEU1209 3.6 19.7 1.0
C12 X:ORH1216 4.2 30.6 1.0
SD X:MET1068 4.2 11.9 1.0
CG X:TYR1067 4.2 15.5 1.0
CA X:TYR1067 4.3 14.1 1.0
CB X:ALA1134 4.4 11.2 1.0
C X:GLY1066 4.5 16.7 1.0
C9 X:ORH1216 4.6 26.7 1.0
CE X:MET1068 4.6 13.8 1.0
O X:HOH50 4.6 31.1 1.0
CB X:TYR1067 4.7 15.5 1.0
CZ X:TYR1067 4.7 19.5 1.0
N X:TYR1067 4.9 14.5 1.0
O X:HOH22 4.9 14.4 1.0
C11 X:ORH1216 4.9 28.1 1.0
CB X:ALA1163 4.9 13.7 1.0
CG X:LEU1209 4.9 16.8 1.0

Fluorine binding site 2 out of 6 in 3kwb

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Fluorine binding site 2 out of 6 in the Structure of Catk Covalently Bound to A Dioxo-Triazine Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of Catk Covalently Bound to A Dioxo-Triazine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
X:F1216

b:32.9
occ:1.00
F2 X:ORH1216 0.0 32.9 1.0
C13 X:ORH1216 1.3 31.3 1.0
F1 X:ORH1216 2.1 33.4 1.0
F3 X:ORH1216 2.2 32.4 1.0
C8 X:ORH1216 2.2 29.1 1.0
C10 X:ORH1216 2.8 30.1 1.0
CB X:ALA1134 3.2 11.2 1.0
C7 X:ORH1216 3.4 27.1 1.0
CD2 X:LEU1209 3.4 19.7 1.0
CB X:LEU1160 3.6 20.7 1.0
O X:LEU1160 3.8 20.8 1.0
C12 X:ORH1216 4.1 30.6 1.0
C X:LEU1160 4.2 20.0 1.0
O X:HOH60 4.3 34.9 1.0
CE1 X:TYR1067 4.3 19.5 1.0
O X:HOH117 4.3 31.3 1.0
CD1 X:LEU1160 4.5 20.9 1.0
CA X:LEU1160 4.5 20.2 1.0
CD1 X:TYR1067 4.5 19.0 1.0
C9 X:ORH1216 4.6 26.7 1.0
CA X:ALA1134 4.6 12.0 1.0
CG X:LEU1160 4.7 22.9 1.0
CG X:LEU1209 4.7 16.8 1.0
O X:HIS1162 4.8 13.1 1.0
C11 X:ORH1216 4.9 28.1 1.0
CB X:LEU1209 4.9 16.2 1.0

Fluorine binding site 3 out of 6 in 3kwb

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Fluorine binding site 3 out of 6 in the Structure of Catk Covalently Bound to A Dioxo-Triazine Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of Catk Covalently Bound to A Dioxo-Triazine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
X:F1216

b:32.4
occ:1.00
F3 X:ORH1216 0.0 32.4 1.0
C13 X:ORH1216 1.3 31.3 1.0
F1 X:ORH1216 2.1 33.4 1.0
F2 X:ORH1216 2.2 32.9 1.0
C8 X:ORH1216 2.3 29.1 1.0
C7 X:ORH1216 2.7 27.1 1.0
CB X:ALA1134 3.5 11.2 1.0
CB X:ALA1163 3.5 13.7 1.0
O X:HIS1162 3.6 13.1 1.0
C10 X:ORH1216 3.6 30.1 1.0
C X:HIS1162 3.6 14.4 1.0
N X:ALA1163 3.8 12.9 1.0
CA X:ALA1163 3.8 12.6 1.0
C9 X:ORH1216 4.2 26.7 1.0
N X:HIS1162 4.3 15.8 1.0
CA X:ALA1134 4.3 12.0 1.0
SD X:MET1068 4.4 11.9 1.0
CA X:HIS1162 4.4 14.7 1.0
CE X:MET1068 4.5 13.8 1.0
O X:HOH50 4.6 31.1 1.0
O X:GLY1066 4.7 15.1 1.0
N4 X:ORH1216 4.8 20.9 1.0
CD2 X:LEU1209 4.8 19.7 1.0
C12 X:ORH1216 4.8 30.6 1.0
O X:LEU1160 4.8 20.8 1.0

Fluorine binding site 4 out of 6 in 3kwb

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Fluorine binding site 4 out of 6 in the Structure of Catk Covalently Bound to A Dioxo-Triazine Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structure of Catk Covalently Bound to A Dioxo-Triazine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:F2216

b:28.9
occ:1.00
F1 Y:ORH2216 0.0 28.9 1.0
C13 Y:ORH2216 1.3 28.7 1.0
F2 Y:ORH2216 2.1 31.6 1.0
F3 Y:ORH2216 2.1 30.7 1.0
C8 Y:ORH2216 2.2 28.2 1.0
C10 Y:ORH2216 2.9 28.6 1.0
C7 Y:ORH2216 3.3 26.7 1.0
CD1 Y:TYR2067 3.6 20.3 1.0
O Y:GLY2066 3.7 15.7 1.0
CD2 Y:LEU2209 3.8 16.6 1.0
SD Y:MET2068 4.0 13.6 1.0
CE1 Y:TYR2067 4.0 20.6 1.0
CB Y:ALA2134 4.2 9.3 1.0
C12 Y:ORH2216 4.2 30.0 1.0
CE Y:MET2068 4.4 12.9 1.0
CA Y:TYR2067 4.5 14.8 1.0
C9 Y:ORH2216 4.5 27.0 1.0
CG Y:TYR2067 4.6 19.2 1.0
CB Y:ALA2163 4.7 10.0 1.0
C Y:GLY2066 4.7 16.6 1.0
C11 Y:ORH2216 4.9 29.1 1.0
CB Y:TYR2067 4.9 17.3 1.0

Fluorine binding site 5 out of 6 in 3kwb

Go back to Fluorine Binding Sites List in 3kwb
Fluorine binding site 5 out of 6 in the Structure of Catk Covalently Bound to A Dioxo-Triazine Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Structure of Catk Covalently Bound to A Dioxo-Triazine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:F2216

b:31.6
occ:1.00
F2 Y:ORH2216 0.0 31.6 1.0
C13 Y:ORH2216 1.3 28.7 1.0
F1 Y:ORH2216 2.1 28.9 1.0
F3 Y:ORH2216 2.2 30.7 1.0
C8 Y:ORH2216 2.2 28.2 1.0
C10 Y:ORH2216 2.8 28.6 1.0
C7 Y:ORH2216 3.4 26.7 1.0
CB Y:ALA2134 3.4 9.3 1.0
CD2 Y:LEU2209 3.6 16.6 1.0
CB Y:LEU2160 3.6 18.4 1.0
O Y:LEU2160 3.7 20.9 1.0
O Y:HOH77 4.0 35.8 1.0
C12 Y:ORH2216 4.1 30.0 1.0
C Y:LEU2160 4.1 19.0 1.0
CE1 Y:TYR2067 4.3 20.6 1.0
CD1 Y:TYR2067 4.5 20.3 1.0
CA Y:LEU2160 4.5 17.8 1.0
C9 Y:ORH2216 4.5 27.0 1.0
CD1 Y:LEU2160 4.6 20.1 1.0
CA Y:ALA2134 4.7 10.9 1.0
O Y:HOH174 4.7 20.0 1.0
CG Y:LEU2160 4.7 17.9 1.0
O Y:HIS2162 4.8 13.5 1.0
C11 Y:ORH2216 4.8 29.1 1.0
N Y:ASN2161 4.9 17.1 1.0
CG Y:LEU2209 5.0 15.9 1.0

Fluorine binding site 6 out of 6 in 3kwb

Go back to Fluorine Binding Sites List in 3kwb
Fluorine binding site 6 out of 6 in the Structure of Catk Covalently Bound to A Dioxo-Triazine Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Structure of Catk Covalently Bound to A Dioxo-Triazine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:F2216

b:30.7
occ:1.00
F3 Y:ORH2216 0.0 30.7 1.0
C13 Y:ORH2216 1.3 28.7 1.0
F1 Y:ORH2216 2.1 28.9 1.0
F2 Y:ORH2216 2.2 31.6 1.0
C8 Y:ORH2216 2.3 28.2 1.0
C7 Y:ORH2216 2.7 26.7 1.0
O Y:HIS2162 3.1 13.5 1.0
CB Y:ALA2134 3.3 9.3 1.0
C Y:HIS2162 3.3 13.4 1.0
C10 Y:ORH2216 3.6 28.6 1.0
N Y:ALA2163 3.6 12.3 1.0
CB Y:ALA2163 3.8 10.0 1.0
CA Y:ALA2163 3.8 10.5 1.0
N Y:HIS2162 3.9 14.0 1.0
CA Y:ALA2134 4.0 10.9 1.0
CA Y:HIS2162 4.1 13.6 1.0
C9 Y:ORH2216 4.2 27.0 1.0
O Y:LEU2160 4.6 20.9 1.0
C Y:ASN2161 4.6 14.1 1.0
SD Y:MET2068 4.7 13.6 1.0
C Y:LEU2160 4.7 19.0 1.0
CE Y:MET2068 4.7 12.9 1.0
CB Y:LEU2160 4.8 18.4 1.0
C12 Y:ORH2216 4.8 30.0 1.0
N Y:ASN2161 4.9 17.1 1.0
N4 Y:ORH2216 4.9 23.4 1.0
N Y:ILE2135 5.0 12.7 1.0
CD2 Y:LEU2209 5.0 16.6 1.0

Reference:

Z.Rankovic, J.Cai, X.Fradera, M.Dempster, A.Mistry, A.Mitchell, C.Long, E.Hamilton, A.King, S.Boucharens, C.Jamieson, J.Gillespie, I.Cumming, J.Uitdehaag, M.Van Zeeland. Dioxo-Triazines As A Novel Series of Cathepsin K Inhibitors Bioorg.Med.Chem.Lett. V. 20 1488 2010.
ISSN: ISSN 0960-894X
PubMed: 20153187
DOI: 10.1016/J.BMCL.2010.01.116
Page generated: Sun Dec 13 11:49:52 2020

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