Fluorine in PDB 8p4h: Crystal Structure of Human Methionine Adenosyltransferase 2A (MAT2A) in Complex with Sam and Allosteric Compound Ideaya Cmpd A
Enzymatic activity of Crystal Structure of Human Methionine Adenosyltransferase 2A (MAT2A) in Complex with Sam and Allosteric Compound Ideaya Cmpd A
All present enzymatic activity of Crystal Structure of Human Methionine Adenosyltransferase 2A (MAT2A) in Complex with Sam and Allosteric Compound Ideaya Cmpd A:
2.5.1.6;
Protein crystallography data
The structure of Crystal Structure of Human Methionine Adenosyltransferase 2A (MAT2A) in Complex with Sam and Allosteric Compound Ideaya Cmpd A, PDB code: 8p4h
was solved by
M.Thomsen,
G.Thieulin-Pardo,
L.Neumann,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
78.30 /
1.71
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
67.898,
106.742,
114.996,
90,
93.18,
90
|
R / Rfree (%)
|
15.3 /
18.4
|
Other elements in 8p4h:
The structure of Crystal Structure of Human Methionine Adenosyltransferase 2A (MAT2A) in Complex with Sam and Allosteric Compound Ideaya Cmpd A also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Crystal Structure of Human Methionine Adenosyltransferase 2A (MAT2A) in Complex with Sam and Allosteric Compound Ideaya Cmpd A
(pdb code 8p4h). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 5 binding sites of Fluorine where determined in the
Crystal Structure of Human Methionine Adenosyltransferase 2A (MAT2A) in Complex with Sam and Allosteric Compound Ideaya Cmpd A, PDB code: 8p4h:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
Fluorine binding site 1 out
of 5 in 8p4h
Go back to
Fluorine Binding Sites List in 8p4h
Fluorine binding site 1 out
of 5 in the Crystal Structure of Human Methionine Adenosyltransferase 2A (MAT2A) in Complex with Sam and Allosteric Compound Ideaya Cmpd A
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 Human Methionine Adenosyltransferase 2A (MAT2A) in Complex with Sam and Allosteric Compound Ideaya Cmpd A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F401
b:24.8
occ:0.60
|
F16
|
A:UM6401
|
0.0
|
24.8
|
0.6
|
C17
|
A:UM6401
|
1.0
|
29.8
|
0.4
|
C15
|
A:UM6401
|
1.4
|
19.8
|
0.6
|
C15
|
A:UM6401
|
2.0
|
26.0
|
0.4
|
C18
|
A:UM6401
|
2.3
|
28.0
|
0.4
|
C14
|
A:UM6401
|
2.4
|
24.7
|
0.6
|
C17
|
A:UM6401
|
2.4
|
23.4
|
0.6
|
C14
|
A:UM6401
|
2.7
|
31.3
|
0.4
|
C18
|
A:UM6401
|
2.8
|
29.0
|
0.6
|
CB
|
A:GLN190
|
2.9
|
33.1
|
0.5
|
CE1
|
A:PHE18
|
2.9
|
29.9
|
1.0
|
N13
|
A:UM6401
|
3.0
|
25.4
|
1.0
|
F16
|
A:UM6401
|
3.2
|
30.9
|
0.4
|
NE2
|
A:GLN190
|
3.3
|
45.6
|
0.5
|
CB
|
A:GLN190
|
3.4
|
39.7
|
0.5
|
CZ
|
A:PHE18
|
3.4
|
29.6
|
1.0
|
CD
|
A:GLN190
|
3.5
|
35.5
|
0.5
|
CD
|
A:GLN190
|
3.6
|
43.1
|
0.5
|
NE2
|
A:GLN190
|
3.6
|
35.0
|
0.5
|
CG
|
A:GLN190
|
3.7
|
42.4
|
0.5
|
CG
|
A:GLN190
|
3.7
|
34.1
|
0.5
|
OE1
|
A:GLN190
|
3.8
|
33.8
|
0.5
|
CD1
|
A:PHE18
|
3.8
|
28.6
|
1.0
|
CG1
|
A:VAL195
|
3.9
|
29.4
|
1.0
|
CA
|
A:GLN190
|
4.0
|
37.5
|
0.5
|
CA
|
A:GLN190
|
4.1
|
34.2
|
0.5
|
O
|
A:HOH700
|
4.3
|
41.0
|
1.0
|
C9
|
A:UM6401
|
4.3
|
22.9
|
1.0
|
OE1
|
A:GLN190
|
4.4
|
45.7
|
0.5
|
N
|
A:GLN190
|
4.5
|
36.1
|
0.5
|
N
|
A:GLN190
|
4.5
|
34.4
|
0.5
|
CE2
|
A:PHE18
|
4.5
|
24.6
|
1.0
|
O
|
A:ALA194
|
4.7
|
33.2
|
1.0
|
CG
|
A:PHE18
|
4.8
|
23.8
|
1.0
|
N8
|
A:UM6401
|
4.8
|
21.4
|
1.0
|
O
|
B:HOH785
|
4.9
|
29.7
|
1.0
|
C
|
A:MET189
|
4.9
|
31.8
|
1.0
|
CB
|
A:VAL195
|
4.9
|
32.4
|
1.0
|
O
|
A:MET189
|
4.9
|
35.4
|
1.0
|
|
Fluorine binding site 2 out
of 5 in 8p4h
Go back to
Fluorine Binding Sites List in 8p4h
Fluorine binding site 2 out
of 5 in the Crystal Structure of Human Methionine Adenosyltransferase 2A (MAT2A) in Complex with Sam and Allosteric Compound Ideaya Cmpd A
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 Human Methionine Adenosyltransferase 2A (MAT2A) in Complex with Sam and Allosteric Compound Ideaya Cmpd A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F401
b:30.9
occ:0.40
|
F16
|
A:UM6401
|
0.0
|
30.9
|
0.4
|
C17
|
A:UM6401
|
1.1
|
23.4
|
0.6
|
C15
|
A:UM6401
|
1.4
|
26.0
|
0.4
|
C15
|
A:UM6401
|
2.0
|
19.8
|
0.6
|
C18
|
A:UM6401
|
2.4
|
29.0
|
0.6
|
C14
|
A:UM6401
|
2.4
|
31.3
|
0.4
|
C17
|
A:UM6401
|
2.4
|
29.8
|
0.4
|
C14
|
A:UM6401
|
2.7
|
24.7
|
0.6
|
C18
|
A:UM6401
|
2.8
|
28.0
|
0.4
|
N13
|
A:UM6401
|
2.9
|
25.4
|
1.0
|
O
|
B:HOH695
|
3.2
|
50.3
|
1.0
|
F16
|
A:UM6401
|
3.2
|
24.8
|
0.6
|
CE1
|
B:PHE333
|
3.3
|
33.1
|
1.0
|
NE2
|
A:GLN190
|
3.4
|
45.6
|
0.5
|
NE2
|
A:GLN190
|
3.4
|
35.0
|
0.5
|
CD1
|
B:PHE333
|
3.5
|
29.8
|
1.0
|
OE1
|
B:GLU342
|
3.6
|
40.6
|
0.8
|
O
|
B:HOH763
|
3.8
|
56.2
|
1.0
|
OE2
|
B:GLU342
|
3.9
|
29.5
|
0.8
|
CD
|
A:GLN190
|
4.0
|
43.1
|
0.5
|
C9
|
A:UM6401
|
4.1
|
22.9
|
1.0
|
CD
|
A:GLN190
|
4.1
|
35.5
|
0.5
|
CD
|
B:GLU342
|
4.2
|
34.7
|
0.8
|
OE1
|
A:GLN190
|
4.2
|
45.7
|
0.5
|
OE1
|
A:GLN190
|
4.2
|
33.8
|
0.5
|
O
|
A:HOH732
|
4.5
|
33.2
|
1.0
|
O
|
B:HOH785
|
4.5
|
29.7
|
1.0
|
CZ
|
B:PHE333
|
4.5
|
33.4
|
1.0
|
N8
|
A:UM6401
|
4.7
|
21.4
|
1.0
|
O
|
A:HOH700
|
4.7
|
41.0
|
1.0
|
C10
|
A:UM6401
|
4.9
|
21.6
|
1.0
|
CG
|
B:PHE333
|
4.9
|
28.7
|
1.0
|
|
Fluorine binding site 3 out
of 5 in 8p4h
Go back to
Fluorine Binding Sites List in 8p4h
Fluorine binding site 3 out
of 5 in the Crystal Structure of Human Methionine Adenosyltransferase 2A (MAT2A) in Complex with Sam and Allosteric Compound Ideaya Cmpd A
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 Human Methionine Adenosyltransferase 2A (MAT2A) in Complex with Sam and Allosteric Compound Ideaya Cmpd A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F503
b:33.4
occ:1.00
|
F16
|
B:UM6503
|
0.0
|
33.4
|
1.0
|
C15
|
B:UM6503
|
1.4
|
23.2
|
1.0
|
C14
|
B:UM6503
|
2.3
|
27.9
|
1.0
|
C17
|
B:UM6503
|
2.3
|
23.0
|
1.0
|
C18
|
B:UM6503
|
2.8
|
27.2
|
1.0
|
N13
|
B:UM6503
|
3.0
|
26.8
|
1.0
|
CB
|
B:GLN190
|
3.0
|
32.6
|
0.5
|
CE1
|
B:PHE18
|
3.1
|
30.4
|
1.0
|
NE2
|
B:GLN190
|
3.1
|
33.7
|
0.5
|
CB
|
B:GLN190
|
3.3
|
34.5
|
0.5
|
CD
|
B:GLN190
|
3.4
|
39.0
|
0.5
|
CZ
|
B:PHE18
|
3.6
|
31.4
|
1.0
|
CG
|
B:GLN190
|
3.6
|
35.5
|
0.5
|
NE2
|
B:GLN190
|
3.6
|
30.9
|
0.5
|
CD
|
B:GLN190
|
3.6
|
34.1
|
0.5
|
CG
|
B:GLN190
|
3.8
|
32.7
|
0.5
|
CD1
|
B:PHE18
|
3.9
|
28.0
|
1.0
|
O
|
B:HOH676
|
3.9
|
32.6
|
1.0
|
CG1
|
B:VAL195
|
4.0
|
33.2
|
1.0
|
OE1
|
B:GLN190
|
4.0
|
28.6
|
0.5
|
OE1
|
B:GLN190
|
4.1
|
41.1
|
0.5
|
CA
|
B:GLN190
|
4.2
|
33.0
|
0.5
|
CA
|
B:GLN190
|
4.2
|
31.9
|
0.5
|
C9
|
B:UM6503
|
4.3
|
26.1
|
1.0
|
CE2
|
B:PHE18
|
4.6
|
26.4
|
1.0
|
N
|
B:GLN190
|
4.7
|
31.2
|
0.5
|
N
|
B:GLN190
|
4.7
|
31.5
|
0.5
|
O
|
B:MET189
|
4.8
|
33.0
|
1.0
|
O
|
A:HOH607
|
4.9
|
25.9
|
1.0
|
N8
|
B:UM6503
|
4.9
|
23.2
|
1.0
|
O
|
B:ALA194
|
4.9
|
30.9
|
1.0
|
CG
|
B:PHE18
|
4.9
|
25.6
|
1.0
|
O
|
B:HOH610
|
5.0
|
47.6
|
1.0
|
C
|
B:MET189
|
5.0
|
31.7
|
1.0
|
|
Fluorine binding site 4 out
of 5 in 8p4h
Go back to
Fluorine Binding Sites List in 8p4h
Fluorine binding site 4 out
of 5 in the Crystal Structure of Human Methionine Adenosyltransferase 2A (MAT2A) in Complex with Sam and Allosteric Compound Ideaya Cmpd A
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 Human Methionine Adenosyltransferase 2A (MAT2A) in Complex with Sam and Allosteric Compound Ideaya Cmpd A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:F401
b:34.6
occ:1.00
|
F16
|
C:UM6401
|
0.0
|
34.6
|
1.0
|
C15
|
C:UM6401
|
1.4
|
24.8
|
1.0
|
C14
|
C:UM6401
|
2.3
|
26.9
|
1.0
|
C17
|
C:UM6401
|
2.4
|
23.4
|
1.0
|
C18
|
C:UM6401
|
2.8
|
30.2
|
1.0
|
N13
|
C:UM6401
|
3.0
|
27.2
|
1.0
|
CE1
|
C:PHE18
|
3.1
|
33.8
|
1.0
|
CB
|
C:GLN190
|
3.2
|
41.0
|
1.0
|
CG
|
C:GLN190
|
3.2
|
50.7
|
1.0
|
NE2
|
C:GLN190
|
3.4
|
36.5
|
1.0
|
CD
|
C:GLN190
|
3.4
|
47.0
|
1.0
|
CZ
|
C:PHE18
|
3.5
|
34.1
|
1.0
|
O
|
C:HOH525
|
3.8
|
34.7
|
1.0
|
CG1
|
C:VAL195
|
3.9
|
34.6
|
1.0
|
CD1
|
C:PHE18
|
4.0
|
32.1
|
1.0
|
CA
|
C:GLN190
|
4.1
|
38.2
|
1.0
|
OE1
|
C:GLN190
|
4.1
|
45.6
|
1.0
|
C9
|
C:UM6401
|
4.3
|
26.2
|
1.0
|
CE2
|
C:PHE18
|
4.6
|
30.5
|
1.0
|
O
|
C:ALA194
|
4.7
|
32.4
|
1.0
|
N
|
C:GLN190
|
4.7
|
35.3
|
1.0
|
O
|
C:MET189
|
4.8
|
33.0
|
0.5
|
N8
|
C:UM6401
|
4.9
|
24.3
|
1.0
|
O
|
C:MET189
|
4.9
|
35.4
|
0.5
|
O
|
D:HOH550
|
4.9
|
26.4
|
1.0
|
O
|
C:HOH672
|
4.9
|
51.6
|
1.0
|
CG
|
C:PHE18
|
5.0
|
29.9
|
1.0
|
|
Fluorine binding site 5 out
of 5 in 8p4h
Go back to
Fluorine Binding Sites List in 8p4h
Fluorine binding site 5 out
of 5 in the Crystal Structure of Human Methionine Adenosyltransferase 2A (MAT2A) in Complex with Sam and Allosteric Compound Ideaya Cmpd A
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 Human Methionine Adenosyltransferase 2A (MAT2A) in Complex with Sam and Allosteric Compound Ideaya Cmpd A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:F403
b:36.7
occ:1.00
|
F16
|
D:UM6403
|
0.0
|
36.7
|
1.0
|
C15
|
D:UM6403
|
1.4
|
26.0
|
1.0
|
C14
|
D:UM6403
|
2.3
|
29.9
|
1.0
|
C17
|
D:UM6403
|
2.4
|
26.0
|
1.0
|
C18
|
D:UM6403
|
2.9
|
30.5
|
1.0
|
N13
|
D:UM6403
|
3.0
|
27.7
|
1.0
|
CE1
|
D:PHE18
|
3.1
|
30.2
|
1.0
|
CB
|
D:GLN190
|
3.3
|
46.4
|
1.0
|
CG
|
D:GLN190
|
3.5
|
50.8
|
1.0
|
NE2
|
D:GLN190
|
3.5
|
43.3
|
1.0
|
CZ
|
D:PHE18
|
3.6
|
33.1
|
1.0
|
CD
|
D:GLN190
|
3.6
|
42.9
|
1.0
|
CG1
|
D:VAL195
|
3.7
|
37.2
|
1.0
|
CA
|
D:GLN190
|
3.9
|
43.3
|
1.0
|
CD1
|
D:PHE18
|
4.0
|
29.1
|
1.0
|
OE1
|
D:GLN190
|
4.3
|
60.4
|
1.0
|
C9
|
D:UM6403
|
4.3
|
26.9
|
1.0
|
N
|
D:GLN190
|
4.3
|
36.2
|
1.0
|
O
|
D:HOH704
|
4.4
|
44.5
|
1.0
|
O
|
D:ALA194
|
4.6
|
38.0
|
1.0
|
CE2
|
D:PHE18
|
4.7
|
29.7
|
1.0
|
O
|
D:HOH575
|
4.8
|
53.0
|
1.0
|
N8
|
D:UM6403
|
4.8
|
23.3
|
1.0
|
CB
|
D:VAL195
|
4.9
|
36.8
|
1.0
|
C
|
D:MET189
|
4.9
|
38.1
|
1.0
|
O
|
C:HOH647
|
4.9
|
31.8
|
1.0
|
CG
|
D:PHE18
|
5.0
|
28.1
|
1.0
|
O
|
D:MET189
|
5.0
|
39.2
|
1.0
|
|
Reference:
T.Kalliokoski,
H.Kettunen,
E.Kumpulainen,
E.Kettunen,
G.Thieulin-Pardo,
L.Neumann,
M.Thomsen,
R.Paul,
A.Malyutina,
M.Georgiadou.
Discovery of Novel Methionine Adenosyltransferase 2A (MAT2A) Allosteric Inhibitors By Structure-Based Virtual Screening. Bioorg.Med.Chem.Lett. V. 94 29450 2023.
ISSN: ESSN 1464-3405
PubMed: 37591318
DOI: 10.1016/J.BMCL.2023.129450
Page generated: Fri Aug 2 21:43:46 2024
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