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
Go back to
Fluorine Binding Sites List in 3kwb
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
Go back to
Fluorine Binding Sites List in 3kwb
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
Go back to
Fluorine Binding Sites List in 3kwb
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
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