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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

Go back to 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

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