Fluorine in PDB 5ls6: Structure of Human Polycomb Repressive Complex 2 (PRC2) with Inhibitor
Enzymatic activity of Structure of Human Polycomb Repressive Complex 2 (PRC2) with Inhibitor
All present enzymatic activity of Structure of Human Polycomb Repressive Complex 2 (PRC2) with Inhibitor:
2.1.1.43;
Protein crystallography data
The structure of Structure of Human Polycomb Repressive Complex 2 (PRC2) with Inhibitor, PDB code: 5ls6
was solved by
Y.Zhang,
N.Justin,
S.Chen,
J.Wilson,
S.Gamblin,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
68.84 /
3.47
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
131.310,
170.270,
275.540,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
22.9 /
29.9
|
Other elements in 5ls6:
The structure of Structure of Human Polycomb Repressive Complex 2 (PRC2) with Inhibitor also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Structure of Human Polycomb Repressive Complex 2 (PRC2) with Inhibitor
(pdb code 5ls6). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the
Structure of Human Polycomb Repressive Complex 2 (PRC2) with Inhibitor, PDB code: 5ls6:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Fluorine binding site 1 out
of 8 in 5ls6
Go back to
Fluorine Binding Sites List in 5ls6
Fluorine binding site 1 out
of 8 in the Structure of Human Polycomb Repressive Complex 2 (PRC2) with 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 Human Polycomb Repressive Complex 2 (PRC2) with Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F809
b:91.0
occ:1.00
|
FBI
|
A:74D809
|
0.0
|
91.0
|
1.0
|
CBH
|
A:74D809
|
1.3
|
81.7
|
1.0
|
FBJ
|
A:74D809
|
2.1
|
82.0
|
1.0
|
CBG
|
A:74D809
|
2.3
|
75.5
|
1.0
|
CBK
|
A:74D809
|
2.3
|
82.7
|
1.0
|
NBD
|
A:74D809
|
3.5
|
70.0
|
1.0
|
OD2
|
B:ASP237
|
3.6
|
79.5
|
1.0
|
CG
|
B:ASP237
|
4.0
|
85.8
|
1.0
|
CBC
|
A:74D809
|
4.1
|
69.6
|
1.0
|
ND2
|
A:ASN130
|
4.2
|
86.7
|
1.0
|
OD1
|
B:ASP237
|
4.3
|
83.4
|
1.0
|
CB
|
A:PRO132
|
4.4
|
71.3
|
1.0
|
OH
|
A:TYR661
|
4.5
|
86.8
|
1.0
|
CBE
|
A:74D809
|
4.6
|
70.1
|
1.0
|
CG
|
A:PRO132
|
4.6
|
70.7
|
1.0
|
CB
|
B:ASP237
|
4.7
|
87.2
|
1.0
|
O
|
B:ARG236
|
4.9
|
85.6
|
1.0
|
CA
|
A:PRO132
|
5.0
|
75.9
|
1.0
|
|
Fluorine binding site 2 out
of 8 in 5ls6
Go back to
Fluorine Binding Sites List in 5ls6
Fluorine binding site 2 out
of 8 in the Structure of Human Polycomb Repressive Complex 2 (PRC2) with 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 Human Polycomb Repressive Complex 2 (PRC2) with Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F809
b:82.0
occ:1.00
|
FBJ
|
A:74D809
|
0.0
|
82.0
|
1.0
|
CBH
|
A:74D809
|
1.3
|
81.7
|
1.0
|
FBI
|
A:74D809
|
2.1
|
91.0
|
1.0
|
CBG
|
A:74D809
|
2.3
|
75.5
|
1.0
|
CBK
|
A:74D809
|
2.3
|
82.7
|
1.0
|
NBD
|
A:74D809
|
2.5
|
70.0
|
1.0
|
CBC
|
A:74D809
|
2.7
|
69.6
|
1.0
|
CBB
|
A:74D809
|
3.7
|
68.1
|
1.0
|
CG1
|
A:VAL657
|
3.8
|
71.4
|
1.0
|
CBE
|
A:74D809
|
4.0
|
70.1
|
1.0
|
CE1
|
A:TYR658
|
4.7
|
63.5
|
1.0
|
CE1
|
A:TYR661
|
4.7
|
82.4
|
1.0
|
CBF
|
A:74D809
|
4.8
|
68.2
|
1.0
|
CG2
|
A:VAL657
|
4.8
|
64.8
|
1.0
|
CBA
|
A:74D809
|
4.9
|
63.9
|
1.0
|
OH
|
A:TYR661
|
4.9
|
86.8
|
1.0
|
CB
|
A:VAL657
|
4.9
|
66.7
|
1.0
|
CD1
|
A:TYR658
|
5.0
|
63.9
|
1.0
|
|
Fluorine binding site 3 out
of 8 in 5ls6
Go back to
Fluorine Binding Sites List in 5ls6
Fluorine binding site 3 out
of 8 in the Structure of Human Polycomb Repressive Complex 2 (PRC2) with 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 Human Polycomb Repressive Complex 2 (PRC2) with Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:F809
b:68.4
occ:1.00
|
FBI
|
D:74D809
|
0.0
|
68.4
|
1.0
|
CBH
|
D:74D809
|
1.3
|
67.0
|
1.0
|
FBJ
|
D:74D809
|
2.1
|
66.7
|
1.0
|
CBG
|
D:74D809
|
2.2
|
65.0
|
1.0
|
CBK
|
D:74D809
|
2.3
|
69.4
|
1.0
|
OD2
|
E:ASP237
|
2.9
|
82.8
|
1.0
|
CG
|
E:ASP237
|
3.5
|
79.5
|
1.0
|
NBD
|
D:74D809
|
3.5
|
63.8
|
1.0
|
OD1
|
E:ASP237
|
3.9
|
76.0
|
1.0
|
CBE
|
D:74D809
|
4.1
|
64.7
|
1.0
|
ND2
|
D:ASN130
|
4.1
|
94.3
|
1.0
|
CBC
|
D:74D809
|
4.2
|
64.2
|
1.0
|
OH
|
D:TYR661
|
4.2
|
84.8
|
1.0
|
CB
|
D:PRO132
|
4.3
|
67.5
|
1.0
|
CB
|
E:ASP237
|
4.4
|
78.0
|
1.0
|
O
|
E:ARG236
|
4.6
|
71.5
|
1.0
|
CG
|
D:PRO132
|
4.7
|
66.8
|
1.0
|
CA
|
D:PRO132
|
4.8
|
70.6
|
1.0
|
|
Fluorine binding site 4 out
of 8 in 5ls6
Go back to
Fluorine Binding Sites List in 5ls6
Fluorine binding site 4 out
of 8 in the Structure of Human Polycomb Repressive Complex 2 (PRC2) with 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 Human Polycomb Repressive Complex 2 (PRC2) with Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:F809
b:66.7
occ:1.00
|
FBJ
|
D:74D809
|
0.0
|
66.7
|
1.0
|
CBH
|
D:74D809
|
1.4
|
67.0
|
1.0
|
FBI
|
D:74D809
|
2.1
|
68.4
|
1.0
|
CBG
|
D:74D809
|
2.4
|
65.0
|
1.0
|
CBK
|
D:74D809
|
2.4
|
69.4
|
1.0
|
NBD
|
D:74D809
|
2.7
|
63.8
|
1.0
|
CBC
|
D:74D809
|
2.9
|
64.2
|
1.0
|
CBE
|
D:74D809
|
3.0
|
64.7
|
1.0
|
CBB
|
D:74D809
|
3.6
|
62.5
|
1.0
|
CE1
|
D:TYR661
|
3.8
|
81.9
|
1.0
|
OH
|
D:TYR661
|
3.8
|
84.8
|
1.0
|
CG2
|
D:VAL657
|
4.1
|
67.1
|
1.0
|
CZ
|
D:TYR661
|
4.1
|
80.1
|
1.0
|
CG1
|
D:VAL657
|
4.4
|
72.7
|
1.0
|
CBF
|
D:74D809
|
4.4
|
64.6
|
1.0
|
CB
|
D:PRO132
|
4.6
|
67.5
|
1.0
|
CBA
|
D:74D809
|
4.6
|
61.5
|
1.0
|
CG
|
D:PRO132
|
4.7
|
66.8
|
1.0
|
CD1
|
D:TYR661
|
4.7
|
82.9
|
1.0
|
CE1
|
D:TYR658
|
4.9
|
64.7
|
1.0
|
CB
|
D:VAL657
|
4.9
|
67.9
|
1.0
|
OD2
|
E:ASP237
|
5.0
|
82.8
|
1.0
|
|
Fluorine binding site 5 out
of 8 in 5ls6
Go back to
Fluorine Binding Sites List in 5ls6
Fluorine binding site 5 out
of 8 in the Structure of Human Polycomb Repressive Complex 2 (PRC2) with 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 Human Polycomb Repressive Complex 2 (PRC2) with Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:F809
b:61.1
occ:1.00
|
FBI
|
G:74D809
|
0.0
|
61.1
|
1.0
|
CBH
|
G:74D809
|
1.3
|
67.5
|
1.0
|
CBG
|
G:74D809
|
2.3
|
70.7
|
1.0
|
FBJ
|
G:74D809
|
2.3
|
63.8
|
1.0
|
CBK
|
G:74D809
|
2.3
|
69.4
|
1.0
|
NBD
|
G:74D809
|
3.5
|
76.4
|
1.0
|
CB
|
G:PRO132
|
3.7
|
82.2
|
1.0
|
CG
|
G:PRO132
|
4.0
|
79.8
|
1.0
|
CBE
|
G:74D809
|
4.0
|
77.1
|
1.0
|
OD2
|
H:ASP237
|
4.2
|
65.3
|
1.0
|
OH
|
G:TYR661
|
4.3
|
0.8
|
1.0
|
CA
|
G:PRO132
|
4.3
|
80.9
|
1.0
|
CG2
|
G:VAL657
|
4.3
|
62.9
|
1.0
|
CBC
|
G:74D809
|
4.4
|
76.4
|
1.0
|
CG
|
H:ASP237
|
4.4
|
71.2
|
1.0
|
OD1
|
H:ASP237
|
4.5
|
79.0
|
1.0
|
ND2
|
G:ASN130
|
4.7
|
97.1
|
1.0
|
CE1
|
G:TYR661
|
4.8
|
87.6
|
1.0
|
CBF
|
G:74D809
|
4.8
|
72.9
|
1.0
|
CZ
|
G:TYR661
|
4.9
|
89.1
|
1.0
|
|
Fluorine binding site 6 out
of 8 in 5ls6
Go back to
Fluorine Binding Sites List in 5ls6
Fluorine binding site 6 out
of 8 in the Structure of Human Polycomb Repressive Complex 2 (PRC2) with 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 Human Polycomb Repressive Complex 2 (PRC2) with Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:F809
b:63.8
occ:1.00
|
FBJ
|
G:74D809
|
0.0
|
63.8
|
1.0
|
CBH
|
G:74D809
|
1.4
|
67.5
|
1.0
|
FBI
|
G:74D809
|
2.3
|
61.1
|
1.0
|
CBG
|
G:74D809
|
2.4
|
70.7
|
1.0
|
CBK
|
G:74D809
|
2.4
|
69.4
|
1.0
|
NBD
|
G:74D809
|
2.7
|
76.4
|
1.0
|
CBE
|
G:74D809
|
3.0
|
77.1
|
1.0
|
CBC
|
G:74D809
|
3.1
|
76.4
|
1.0
|
CBB
|
G:74D809
|
3.2
|
74.2
|
1.0
|
CBF
|
G:74D809
|
3.2
|
72.9
|
1.0
|
CG2
|
G:VAL657
|
3.6
|
62.9
|
1.0
|
CBA
|
G:74D809
|
3.9
|
69.5
|
1.0
|
CE1
|
G:TYR661
|
3.9
|
87.6
|
1.0
|
CG1
|
G:VAL657
|
4.2
|
66.4
|
1.0
|
CZ
|
G:TYR661
|
4.5
|
89.1
|
1.0
|
CD1
|
G:TYR661
|
4.5
|
87.7
|
1.0
|
OH
|
G:TYR661
|
4.5
|
0.8
|
1.0
|
CB
|
G:VAL657
|
4.6
|
63.7
|
1.0
|
CE1
|
G:TYR658
|
4.8
|
57.6
|
1.0
|
CD1
|
G:TYR658
|
4.9
|
55.3
|
1.0
|
|
Fluorine binding site 7 out
of 8 in 5ls6
Go back to
Fluorine Binding Sites List in 5ls6
Fluorine binding site 7 out
of 8 in the Structure of Human Polycomb Repressive Complex 2 (PRC2) with Inhibitor
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 7 of Structure of Human Polycomb Repressive Complex 2 (PRC2) with Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:F809
b:89.7
occ:1.00
|
FBI
|
J:74D809
|
0.0
|
89.7
|
1.0
|
CBH
|
J:74D809
|
1.4
|
84.6
|
1.0
|
FBJ
|
J:74D809
|
2.2
|
90.0
|
1.0
|
CBG
|
J:74D809
|
2.4
|
81.4
|
1.0
|
CBK
|
J:74D809
|
2.4
|
83.0
|
1.0
|
NBD
|
J:74D809
|
3.3
|
79.4
|
1.0
|
CBC
|
J:74D809
|
3.7
|
76.8
|
1.0
|
O
|
K:ARG236
|
3.9
|
66.7
|
1.0
|
CBE
|
J:74D809
|
4.6
|
79.5
|
1.0
|
CBB
|
J:74D809
|
4.9
|
74.3
|
1.0
|
|
Fluorine binding site 8 out
of 8 in 5ls6
Go back to
Fluorine Binding Sites List in 5ls6
Fluorine binding site 8 out
of 8 in the Structure of Human Polycomb Repressive Complex 2 (PRC2) with Inhibitor
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 8 of Structure of Human Polycomb Repressive Complex 2 (PRC2) with Inhibitor within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:F809
b:90.0
occ:1.00
|
FBJ
|
J:74D809
|
0.0
|
90.0
|
1.0
|
CBH
|
J:74D809
|
1.4
|
84.6
|
1.0
|
FBI
|
J:74D809
|
2.2
|
89.7
|
1.0
|
CBG
|
J:74D809
|
2.3
|
81.4
|
1.0
|
CBK
|
J:74D809
|
2.4
|
83.0
|
1.0
|
NBD
|
J:74D809
|
2.4
|
79.4
|
1.0
|
CBC
|
J:74D809
|
3.2
|
76.8
|
1.0
|
CBE
|
J:74D809
|
3.6
|
79.5
|
1.0
|
OD1
|
K:ASP237
|
3.7
|
67.1
|
1.0
|
CE1
|
K:HIS213
|
3.8
|
58.4
|
1.0
|
CBB
|
J:74D809
|
3.9
|
74.3
|
1.0
|
O
|
K:ARG236
|
4.0
|
66.7
|
1.0
|
CG
|
K:ASP237
|
4.0
|
66.0
|
1.0
|
NE2
|
K:HIS213
|
4.1
|
58.0
|
1.0
|
CBF
|
J:74D809
|
4.3
|
78.4
|
1.0
|
OD2
|
K:ASP237
|
4.4
|
61.7
|
1.0
|
CB
|
K:ASP237
|
4.7
|
67.2
|
1.0
|
CBA
|
J:74D809
|
4.7
|
74.1
|
1.0
|
CA
|
K:ASP237
|
4.8
|
69.4
|
1.0
|
ND1
|
K:HIS213
|
5.0
|
58.9
|
1.0
|
OH
|
J:TYR661
|
5.0
|
78.3
|
1.0
|
|
Reference:
R.G.Vaswani,
V.S.Gehling,
L.A.Dakin,
A.S.Cook,
C.G.Nasveschuk,
M.Duplessis,
P.Iyer,
S.Balasubramanian,
F.Zhao,
A.C.Good,
R.Campbell,
C.Lee,
N.Cantone,
R.T.Cummings,
E.Normant,
S.F.Bellon,
B.K.Albrecht,
J.C.Harmange,
P.Trojer,
J.E.Audia,
Y.Zhang,
N.Justin,
S.Chen,
J.R.Wilson,
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ISSN: ISSN 1520-4804
PubMed: 27739677
DOI: 10.1021/ACS.JMEDCHEM.6B01315
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