Fluorine in PDB 6pm9: Crystal Structure of the Core Catalytic Domain of Human O-Glcnacase Bound to Mk-8719
Enzymatic activity of Crystal Structure of the Core Catalytic Domain of Human O-Glcnacase Bound to Mk-8719
All present enzymatic activity of Crystal Structure of the Core Catalytic Domain of Human O-Glcnacase Bound to Mk-8719:
3.2.1.169;
Protein crystallography data
The structure of Crystal Structure of the Core Catalytic Domain of Human O-Glcnacase Bound to Mk-8719, PDB code: 6pm9
was solved by
D.J.Klein,
H.G.Selnick,
J.L.Duffy,
E.J.Mceachern,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
40.69 /
2.86
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
89.920,
91.460,
94.610,
77.27,
62.61,
62.86
|
R / Rfree (%)
|
23.9 /
30.9
|
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Crystal Structure of the Core Catalytic Domain of Human O-Glcnacase Bound to Mk-8719
(pdb code 6pm9). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the
Crystal Structure of the Core Catalytic Domain of Human O-Glcnacase Bound to Mk-8719, PDB code: 6pm9:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Fluorine binding site 1 out
of 8 in 6pm9
Go back to
Fluorine Binding Sites List in 6pm9
Fluorine binding site 1 out
of 8 in the Crystal Structure of the Core Catalytic Domain of Human O-Glcnacase Bound to Mk-8719
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 the Core Catalytic Domain of Human O-Glcnacase Bound to Mk-8719 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F501
b:58.5
occ:1.00
|
F
|
A:OQ1501
|
0.0
|
58.5
|
1.0
|
C5
|
A:OQ1501
|
1.4
|
59.2
|
1.0
|
F1
|
A:OQ1501
|
2.3
|
59.0
|
1.0
|
C
|
A:OQ1501
|
2.4
|
58.5
|
1.0
|
CB
|
A:ALA283
|
3.0
|
37.8
|
1.0
|
CG
|
A:ASN280
|
3.3
|
45.2
|
1.0
|
CB
|
A:ASN280
|
3.3
|
40.2
|
1.0
|
C1
|
A:OQ1501
|
3.4
|
58.8
|
1.0
|
O7
|
A:OQ1501
|
3.4
|
58.9
|
1.0
|
O
|
A:OQ1501
|
3.4
|
55.9
|
1.0
|
OD1
|
A:ASN280
|
3.6
|
44.1
|
1.0
|
ND2
|
A:ASN280
|
3.7
|
47.6
|
1.0
|
CE2
|
A:TYR286
|
3.9
|
40.0
|
1.0
|
CD2
|
A:TYR286
|
3.9
|
37.3
|
1.0
|
OD1
|
A:ASP285
|
3.9
|
41.5
|
1.0
|
CG2
|
A:VAL255
|
4.0
|
38.7
|
1.0
|
CG1
|
A:VAL254
|
4.2
|
39.4
|
1.0
|
O
|
A:ASN280
|
4.4
|
41.7
|
1.0
|
CA
|
A:ALA283
|
4.4
|
37.5
|
1.0
|
ND2
|
A:ASN313
|
4.4
|
41.4
|
1.0
|
CA
|
A:ASN280
|
4.5
|
45.6
|
1.0
|
C4
|
A:OQ1501
|
4.6
|
54.8
|
1.0
|
C2
|
A:OQ1501
|
4.7
|
56.1
|
1.0
|
C
|
A:ALA283
|
4.8
|
37.3
|
1.0
|
CG
|
A:ASP285
|
4.8
|
43.3
|
1.0
|
O
|
A:ALA283
|
4.9
|
40.7
|
1.0
|
C
|
A:ASN280
|
4.9
|
41.2
|
1.0
|
OD2
|
A:ASP285
|
4.9
|
43.5
|
1.0
|
|
Fluorine binding site 2 out
of 8 in 6pm9
Go back to
Fluorine Binding Sites List in 6pm9
Fluorine binding site 2 out
of 8 in the Crystal Structure of the Core Catalytic Domain of Human O-Glcnacase Bound to Mk-8719
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 the Core Catalytic Domain of Human O-Glcnacase Bound to Mk-8719 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F501
b:59.0
occ:1.00
|
F1
|
A:OQ1501
|
0.0
|
59.0
|
1.0
|
C5
|
A:OQ1501
|
1.4
|
59.2
|
1.0
|
F
|
A:OQ1501
|
2.3
|
58.5
|
1.0
|
C
|
A:OQ1501
|
2.4
|
58.5
|
1.0
|
OD1
|
A:ASP285
|
2.7
|
41.5
|
1.0
|
C1
|
A:OQ1501
|
2.9
|
58.8
|
1.0
|
O
|
A:OQ1501
|
2.9
|
55.9
|
1.0
|
CD2
|
A:TYR286
|
3.2
|
37.3
|
1.0
|
O7
|
A:OQ1501
|
3.3
|
58.9
|
1.0
|
CG
|
A:ASP285
|
3.6
|
43.3
|
1.0
|
OD2
|
A:ASP285
|
3.8
|
43.5
|
1.0
|
CE2
|
A:TYR286
|
4.0
|
40.0
|
1.0
|
CG
|
A:TYR286
|
4.2
|
41.9
|
1.0
|
CB
|
A:TYR286
|
4.2
|
40.5
|
1.0
|
C4
|
A:OQ1501
|
4.3
|
54.8
|
1.0
|
C2
|
A:OQ1501
|
4.3
|
56.1
|
1.0
|
CZ3
|
G:TRP679
|
4.3
|
60.2
|
1.0
|
N
|
A:TYR286
|
4.5
|
38.7
|
1.0
|
CG1
|
A:VAL254
|
4.6
|
39.4
|
1.0
|
CB
|
A:ALA283
|
4.6
|
37.8
|
1.0
|
C3
|
A:OQ1501
|
4.8
|
55.9
|
1.0
|
CH2
|
G:TRP679
|
4.8
|
57.8
|
1.0
|
CA
|
A:TYR286
|
4.9
|
39.2
|
1.0
|
|
Fluorine binding site 3 out
of 8 in 6pm9
Go back to
Fluorine Binding Sites List in 6pm9
Fluorine binding site 3 out
of 8 in the Crystal Structure of the Core Catalytic Domain of Human O-Glcnacase Bound to Mk-8719
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 the Core Catalytic Domain of Human O-Glcnacase Bound to Mk-8719 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F501
b:54.8
occ:1.00
|
F
|
B:OQ1501
|
0.0
|
54.8
|
1.0
|
C5
|
B:OQ1501
|
1.4
|
55.5
|
1.0
|
F1
|
B:OQ1501
|
2.2
|
57.2
|
1.0
|
C
|
B:OQ1501
|
2.4
|
52.5
|
1.0
|
O
|
B:OQ1501
|
2.7
|
47.8
|
1.0
|
CG2
|
B:VAL255
|
3.5
|
35.2
|
1.0
|
CB
|
B:ASN280
|
3.5
|
39.5
|
1.0
|
CG1
|
B:VAL254
|
3.5
|
39.7
|
1.0
|
CG
|
B:ASN280
|
3.5
|
43.8
|
1.0
|
C1
|
B:OQ1501
|
3.8
|
52.7
|
1.0
|
ND2
|
B:ASN280
|
3.8
|
44.6
|
1.0
|
CD2
|
B:TYR286
|
3.8
|
43.9
|
1.0
|
CE2
|
B:TYR286
|
3.9
|
44.0
|
1.0
|
OD1
|
B:ASN280
|
4.0
|
45.9
|
1.0
|
CB
|
B:ALA283
|
4.0
|
41.2
|
1.0
|
C4
|
B:OQ1501
|
4.1
|
44.9
|
1.0
|
O7
|
B:OQ1501
|
4.3
|
54.4
|
1.0
|
OD1
|
B:ASP285
|
4.3
|
36.4
|
1.0
|
S
|
B:OQ1501
|
4.7
|
40.9
|
1.0
|
CB
|
B:VAL254
|
4.7
|
47.3
|
1.0
|
CA
|
B:ASN280
|
4.8
|
43.6
|
1.0
|
CB
|
B:VAL255
|
4.8
|
41.4
|
1.0
|
N
|
B:VAL255
|
4.9
|
39.2
|
1.0
|
O
|
B:ASN280
|
4.9
|
42.9
|
1.0
|
C2
|
B:OQ1501
|
4.9
|
47.9
|
1.0
|
|
Fluorine binding site 4 out
of 8 in 6pm9
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Fluorine Binding Sites List in 6pm9
Fluorine binding site 4 out
of 8 in the Crystal Structure of the Core Catalytic Domain of Human O-Glcnacase Bound to Mk-8719
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 the Core Catalytic Domain of Human O-Glcnacase Bound to Mk-8719 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F501
b:57.2
occ:1.00
|
F1
|
B:OQ1501
|
0.0
|
57.2
|
1.0
|
C5
|
B:OQ1501
|
1.4
|
55.5
|
1.0
|
F
|
B:OQ1501
|
2.2
|
54.8
|
1.0
|
C
|
B:OQ1501
|
2.3
|
52.5
|
1.0
|
O
|
B:OQ1501
|
2.5
|
47.8
|
1.0
|
OD1
|
B:ASP285
|
2.9
|
36.4
|
1.0
|
C1
|
B:OQ1501
|
3.0
|
52.7
|
1.0
|
CD2
|
B:TYR286
|
3.5
|
43.9
|
1.0
|
O7
|
B:OQ1501
|
3.7
|
54.4
|
1.0
|
C4
|
B:OQ1501
|
3.8
|
44.9
|
1.0
|
CG
|
B:ASP285
|
3.9
|
43.5
|
1.0
|
OD2
|
B:ASP285
|
4.1
|
43.6
|
1.0
|
C2
|
B:OQ1501
|
4.3
|
47.9
|
1.0
|
CE2
|
B:TYR286
|
4.3
|
44.0
|
1.0
|
CB
|
B:TYR286
|
4.4
|
41.1
|
1.0
|
CG
|
B:TYR286
|
4.4
|
46.7
|
1.0
|
C3
|
B:OQ1501
|
4.5
|
46.0
|
1.0
|
CG1
|
B:VAL254
|
4.5
|
39.7
|
1.0
|
N
|
B:TYR286
|
4.8
|
39.9
|
1.0
|
CB
|
B:ALA283
|
5.0
|
41.2
|
1.0
|
|
Fluorine binding site 5 out
of 8 in 6pm9
Go back to
Fluorine Binding Sites List in 6pm9
Fluorine binding site 5 out
of 8 in the Crystal Structure of the Core Catalytic Domain of Human O-Glcnacase Bound to Mk-8719
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 5 of Crystal Structure of the Core Catalytic Domain of Human O-Glcnacase Bound to Mk-8719 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:F501
b:55.5
occ:1.00
|
F
|
C:OQ1501
|
0.0
|
55.5
|
1.0
|
C5
|
C:OQ1501
|
1.4
|
55.3
|
1.0
|
F1
|
C:OQ1501
|
2.1
|
57.5
|
1.0
|
C
|
C:OQ1501
|
2.3
|
52.8
|
1.0
|
O
|
C:OQ1501
|
2.6
|
50.9
|
1.0
|
CG2
|
C:VAL255
|
3.4
|
46.9
|
1.0
|
CG1
|
C:VAL254
|
3.4
|
29.6
|
1.0
|
CZ3
|
E:TRP679
|
3.6
|
60.3
|
1.0
|
C1
|
C:OQ1501
|
3.7
|
53.5
|
1.0
|
CD2
|
C:TYR286
|
3.7
|
59.9
|
1.0
|
C4
|
C:OQ1501
|
3.9
|
53.6
|
1.0
|
CE2
|
C:TYR286
|
4.0
|
62.5
|
1.0
|
CG
|
C:ASN280
|
4.2
|
42.3
|
1.0
|
CB
|
C:ASN280
|
4.3
|
41.4
|
1.0
|
O7
|
C:OQ1501
|
4.3
|
54.1
|
1.0
|
CH2
|
E:TRP679
|
4.4
|
55.7
|
1.0
|
CE3
|
E:TRP679
|
4.4
|
71.4
|
1.0
|
OD1
|
C:ASP285
|
4.5
|
63.5
|
1.0
|
OD1
|
C:ASN280
|
4.5
|
39.2
|
1.0
|
ND2
|
C:ASN280
|
4.5
|
40.6
|
1.0
|
CB
|
C:ALA283
|
4.6
|
53.0
|
1.0
|
CB
|
C:VAL254
|
4.7
|
45.0
|
1.0
|
CB
|
C:VAL255
|
4.8
|
46.8
|
1.0
|
C2
|
C:OQ1501
|
4.8
|
53.5
|
1.0
|
C
|
C:VAL254
|
4.9
|
40.4
|
1.0
|
C3
|
C:OQ1501
|
5.0
|
52.0
|
1.0
|
CG
|
C:TYR286
|
5.0
|
62.1
|
1.0
|
N
|
C:VAL255
|
5.0
|
44.6
|
1.0
|
O
|
C:VAL254
|
5.0
|
46.9
|
1.0
|
|
Fluorine binding site 6 out
of 8 in 6pm9
Go back to
Fluorine Binding Sites List in 6pm9
Fluorine binding site 6 out
of 8 in the Crystal Structure of the Core Catalytic Domain of Human O-Glcnacase Bound to Mk-8719
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 6 of Crystal Structure of the Core Catalytic Domain of Human O-Glcnacase Bound to Mk-8719 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:F501
b:57.5
occ:1.00
|
F1
|
C:OQ1501
|
0.0
|
57.5
|
1.0
|
C5
|
C:OQ1501
|
1.4
|
55.3
|
1.0
|
F
|
C:OQ1501
|
2.1
|
55.5
|
1.0
|
C
|
C:OQ1501
|
2.4
|
52.8
|
1.0
|
OD1
|
C:ASP285
|
2.7
|
63.5
|
1.0
|
O7
|
C:OQ1501
|
3.1
|
54.1
|
1.0
|
C1
|
C:OQ1501
|
3.1
|
53.5
|
1.0
|
CB
|
C:ALA283
|
3.2
|
53.0
|
1.0
|
CD2
|
C:TYR286
|
3.3
|
59.9
|
1.0
|
O
|
C:OQ1501
|
3.5
|
50.9
|
1.0
|
CG
|
C:ASP285
|
3.7
|
66.0
|
1.0
|
CE2
|
C:TYR286
|
3.7
|
62.5
|
1.0
|
OD2
|
C:ASP285
|
4.0
|
66.5
|
1.0
|
O
|
C:ALA283
|
4.3
|
58.8
|
1.0
|
C
|
C:ALA283
|
4.4
|
56.5
|
1.0
|
CA
|
C:ALA283
|
4.4
|
52.6
|
1.0
|
CG
|
C:TYR286
|
4.5
|
62.1
|
1.0
|
C2
|
C:OQ1501
|
4.5
|
53.5
|
1.0
|
N
|
C:ASP285
|
4.6
|
57.4
|
1.0
|
CG2
|
C:VAL255
|
4.7
|
46.9
|
1.0
|
C4
|
C:OQ1501
|
4.8
|
53.6
|
1.0
|
OD1
|
C:ASN280
|
4.8
|
39.2
|
1.0
|
N
|
C:TYR286
|
4.8
|
56.9
|
1.0
|
CB
|
C:TYR286
|
4.9
|
56.2
|
1.0
|
CB
|
C:ASP285
|
5.0
|
59.4
|
1.0
|
CG
|
C:ASN280
|
5.0
|
42.3
|
1.0
|
N
|
C:ASN284
|
5.0
|
55.1
|
1.0
|
CB
|
C:ASN280
|
5.0
|
41.4
|
1.0
|
|
Fluorine binding site 7 out
of 8 in 6pm9
Go back to
Fluorine Binding Sites List in 6pm9
Fluorine binding site 7 out
of 8 in the Crystal Structure of the Core Catalytic Domain of Human O-Glcnacase Bound to Mk-8719
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 7 of Crystal Structure of the Core Catalytic Domain of Human O-Glcnacase Bound to Mk-8719 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:F501
b:58.8
occ:1.00
|
F
|
D:OQ1501
|
0.0
|
58.8
|
1.0
|
C5
|
D:OQ1501
|
1.4
|
56.5
|
1.0
|
F1
|
D:OQ1501
|
2.2
|
58.6
|
1.0
|
C
|
D:OQ1501
|
2.3
|
52.2
|
1.0
|
O
|
D:OQ1501
|
2.4
|
53.8
|
1.0
|
CG2
|
D:VAL255
|
3.5
|
56.4
|
1.0
|
CZ3
|
H:TRP679
|
3.5
|
46.3
|
1.0
|
CG1
|
D:VAL254
|
3.5
|
55.9
|
1.0
|
C1
|
D:OQ1501
|
3.6
|
49.8
|
1.0
|
C4
|
D:OQ1501
|
3.9
|
55.8
|
1.0
|
CH2
|
H:TRP679
|
3.9
|
43.9
|
1.0
|
O7
|
D:OQ1501
|
4.2
|
49.5
|
1.0
|
CD2
|
D:TYR286
|
4.3
|
57.6
|
1.0
|
CB
|
D:VAL254
|
4.3
|
62.6
|
1.0
|
CB
|
D:ASN280
|
4.3
|
50.7
|
1.0
|
CG
|
D:ASN280
|
4.4
|
52.9
|
1.0
|
OD1
|
D:ASP285
|
4.5
|
61.5
|
1.0
|
ND2
|
D:ASN280
|
4.6
|
54.9
|
1.0
|
O
|
D:VAL254
|
4.6
|
54.8
|
1.0
|
CE2
|
D:TYR286
|
4.6
|
61.2
|
1.0
|
CE3
|
H:TRP679
|
4.6
|
57.0
|
1.0
|
C
|
D:VAL254
|
4.6
|
51.7
|
1.0
|
C2
|
D:OQ1501
|
4.7
|
50.0
|
1.0
|
OD1
|
D:ASN280
|
4.7
|
53.9
|
1.0
|
CB
|
D:VAL255
|
4.8
|
57.3
|
1.0
|
C3
|
D:OQ1501
|
4.9
|
54.1
|
1.0
|
S
|
D:OQ1501
|
4.9
|
57.5
|
1.0
|
N
|
D:VAL255
|
4.9
|
51.2
|
1.0
|
CB
|
D:ALA283
|
5.0
|
53.7
|
1.0
|
|
Fluorine binding site 8 out
of 8 in 6pm9
Go back to
Fluorine Binding Sites List in 6pm9
Fluorine binding site 8 out
of 8 in the Crystal Structure of the Core Catalytic Domain of Human O-Glcnacase Bound to Mk-8719
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 8 of Crystal Structure of the Core Catalytic Domain of Human O-Glcnacase Bound to Mk-8719 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:F501
b:58.6
occ:1.00
|
F1
|
D:OQ1501
|
0.0
|
58.6
|
1.0
|
C5
|
D:OQ1501
|
1.3
|
56.5
|
1.0
|
F
|
D:OQ1501
|
2.2
|
58.8
|
1.0
|
C
|
D:OQ1501
|
2.3
|
52.2
|
1.0
|
OD1
|
D:ASP285
|
2.7
|
61.5
|
1.0
|
O7
|
D:OQ1501
|
2.9
|
49.5
|
1.0
|
C1
|
D:OQ1501
|
3.1
|
49.8
|
1.0
|
CB
|
D:ALA283
|
3.2
|
53.7
|
1.0
|
O
|
D:OQ1501
|
3.4
|
53.8
|
1.0
|
CG
|
D:ASP285
|
3.8
|
66.7
|
1.0
|
CD2
|
D:TYR286
|
3.9
|
57.6
|
1.0
|
OD2
|
D:ASP285
|
4.2
|
64.4
|
1.0
|
CE2
|
D:TYR286
|
4.2
|
61.2
|
1.0
|
CG2
|
D:VAL255
|
4.2
|
56.4
|
1.0
|
OD1
|
D:ASN280
|
4.2
|
53.9
|
1.0
|
CB
|
D:ASN280
|
4.3
|
50.7
|
1.0
|
CG
|
D:ASN280
|
4.4
|
52.9
|
1.0
|
ND2
|
D:ASN313
|
4.4
|
45.0
|
1.0
|
C2
|
D:OQ1501
|
4.4
|
50.0
|
1.0
|
CA
|
D:ALA283
|
4.5
|
53.3
|
1.0
|
C
|
D:ALA283
|
4.6
|
58.0
|
1.0
|
C4
|
D:OQ1501
|
4.7
|
55.8
|
1.0
|
O
|
D:ALA283
|
4.7
|
61.0
|
1.0
|
CZ3
|
H:TRP679
|
4.9
|
46.3
|
1.0
|
|
Reference:
H.Selnick,
J.F.Hess,
C.Tang,
K.Liu,
J.Schachter,
J.E.Ballard,
J.N.Marcus,
D.J.Klein,
X.Wang,
M.Pearson,
M.J.Savage,
R.Kaul,
T.Li,
D.J.Vocadlo,
Y.Zhou,
Y.Zhu,
C.Mu,
Y.Wang,
Z.Wei,
C.Bai,
J.L.Duffy,
E.J.Mceachern.
Discovery of Mk-8719, A Potent O-Glcnacase Inhibitor As A Potential Treatment For Tauopathies. J.Med.Chem. 2019.
ISSN: ISSN 0022-2623
PubMed: 31487175
DOI: 10.1021/ACS.JMEDCHEM.9B01090
Page generated: Fri Aug 2 00:27:27 2024
|