Chlorine 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:
Chlorine Binding Sites:
The binding sites of Chlorine 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 Chlorine atom.
In total 6 binding sites of Chlorine 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 Chlorine binding site number:
1;
2;
3;
4;
5;
6;
Chlorine binding site 1 out
of 6 in 8p4h
Go back to
Chlorine Binding Sites List in 8p4h
Chlorine binding site 1 out
of 6 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 Chlorine with other atoms in the Cl 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:Cl401
b:25.7
occ:1.00
|
CL1
|
A:UM6401
|
0.0
|
25.7
|
1.0
|
C2
|
A:UM6401
|
1.7
|
26.8
|
1.0
|
C3
|
A:UM6401
|
2.7
|
23.3
|
1.0
|
C12
|
A:UM6401
|
2.7
|
27.3
|
1.0
|
O
|
B:SER331
|
3.7
|
25.5
|
1.0
|
N
|
B:GLN317
|
3.7
|
22.3
|
1.0
|
CB
|
B:GLN317
|
3.8
|
24.7
|
1.0
|
C
|
B:SER331
|
3.8
|
27.5
|
1.0
|
CB
|
B:SER331
|
3.9
|
27.5
|
1.0
|
C11
|
A:UM6401
|
3.9
|
22.0
|
1.0
|
C4
|
A:UM6401
|
4.0
|
21.7
|
1.0
|
O
|
B:LEU315
|
4.1
|
23.7
|
1.0
|
N
|
B:ILE332
|
4.1
|
24.5
|
1.0
|
CD2
|
B:LEU315
|
4.1
|
21.8
|
1.0
|
N
|
B:PHE333
|
4.2
|
25.1
|
1.0
|
CG
|
B:LEU315
|
4.2
|
21.2
|
1.0
|
C
|
B:ILE332
|
4.2
|
24.7
|
1.0
|
CB
|
B:PHE333
|
4.3
|
24.2
|
1.0
|
C
|
B:VAL316
|
4.3
|
23.2
|
1.0
|
CA
|
B:GLN317
|
4.3
|
22.6
|
1.0
|
CE1
|
B:PHE139
|
4.4
|
24.7
|
1.0
|
C
|
B:LEU315
|
4.4
|
22.9
|
1.0
|
CA
|
B:ILE332
|
4.4
|
26.3
|
1.0
|
CE2
|
A:PHE20
|
4.5
|
23.7
|
1.0
|
CA
|
B:SER331
|
4.5
|
26.4
|
1.0
|
C10
|
A:UM6401
|
4.5
|
21.6
|
1.0
|
CD1
|
B:PHE139
|
4.6
|
22.5
|
1.0
|
CA
|
B:VAL316
|
4.6
|
22.7
|
1.0
|
N
|
B:VAL316
|
4.7
|
21.5
|
1.0
|
CB
|
B:LEU315
|
4.7
|
21.5
|
1.0
|
O
|
B:ILE332
|
4.8
|
25.0
|
1.0
|
CD2
|
A:PHE20
|
4.8
|
24.0
|
1.0
|
CA
|
B:PHE333
|
4.9
|
26.4
|
1.0
|
|
Chlorine binding site 2 out
of 6 in 8p4h
Go back to
Chlorine Binding Sites List in 8p4h
Chlorine binding site 2 out
of 6 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 Chlorine with other atoms in the Cl 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
|
B:Cl503
b:25.6
occ:1.00
|
CL1
|
B:UM6503
|
0.0
|
25.6
|
1.0
|
C2
|
B:UM6503
|
1.7
|
25.0
|
1.0
|
C3
|
B:UM6503
|
2.7
|
21.2
|
1.0
|
C12
|
B:UM6503
|
2.7
|
25.0
|
1.0
|
O
|
A:SER331
|
3.8
|
24.6
|
1.0
|
N
|
A:GLN317
|
3.8
|
22.4
|
1.0
|
CB
|
A:GLN317
|
3.8
|
23.3
|
1.0
|
CB
|
A:SER331
|
3.9
|
28.6
|
1.0
|
C
|
A:SER331
|
3.9
|
24.0
|
1.0
|
C11
|
B:UM6503
|
3.9
|
23.1
|
1.0
|
C4
|
B:UM6503
|
4.0
|
19.2
|
1.0
|
O
|
A:LEU315
|
4.1
|
23.9
|
1.0
|
N
|
A:ILE332
|
4.1
|
22.8
|
1.0
|
CD2
|
A:LEU315
|
4.2
|
25.2
|
1.0
|
CG
|
A:LEU315
|
4.2
|
22.5
|
1.0
|
N
|
A:PHE333
|
4.2
|
24.3
|
1.0
|
C
|
A:ILE332
|
4.3
|
26.2
|
1.0
|
CB
|
A:PHE333
|
4.3
|
23.8
|
1.0
|
CE2
|
A:PHE139
|
4.3
|
24.3
|
1.0
|
C
|
A:VAL316
|
4.3
|
22.2
|
1.0
|
CA
|
A:GLN317
|
4.4
|
21.4
|
1.0
|
CA
|
A:ILE332
|
4.4
|
27.0
|
1.0
|
C
|
A:LEU315
|
4.5
|
24.2
|
1.0
|
CE2
|
B:PHE20
|
4.5
|
27.9
|
1.0
|
C10
|
B:UM6503
|
4.5
|
22.0
|
1.0
|
CA
|
A:SER331
|
4.5
|
24.9
|
1.0
|
CD2
|
A:PHE139
|
4.6
|
20.7
|
1.0
|
CA
|
A:VAL316
|
4.6
|
21.3
|
1.0
|
N
|
A:VAL316
|
4.7
|
21.8
|
1.0
|
CD2
|
B:PHE20
|
4.7
|
25.3
|
1.0
|
CB
|
A:LEU315
|
4.8
|
22.2
|
1.0
|
O
|
A:ILE332
|
4.8
|
25.3
|
1.0
|
CA
|
A:PHE333
|
4.9
|
25.2
|
1.0
|
|
Chlorine binding site 3 out
of 6 in 8p4h
Go back to
Chlorine Binding Sites List in 8p4h
Chlorine binding site 3 out
of 6 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 Chlorine with other atoms in the Cl 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:Cl504
b:35.2
occ:1.00
|
NE2
|
B:HIS29
|
3.1
|
26.0
|
1.0
|
O
|
A:HOH776
|
3.2
|
42.7
|
1.0
|
NZ
|
B:LYS181
|
3.2
|
25.1
|
1.0
|
NZ
|
B:LYS265
|
3.3
|
30.1
|
1.0
|
O
|
A:HOH508
|
3.6
|
41.2
|
1.0
|
C5'
|
B:SAM502
|
3.6
|
32.5
|
1.0
|
CE1
|
B:HIS29
|
3.6
|
26.5
|
1.0
|
CE
|
B:LYS265
|
3.7
|
31.2
|
1.0
|
OD2
|
A:ASP134
|
3.7
|
32.5
|
1.0
|
O
|
B:HOH603
|
3.8
|
34.0
|
1.0
|
C4'
|
B:SAM502
|
3.9
|
28.5
|
1.0
|
O
|
A:HOH509
|
3.9
|
48.9
|
1.0
|
O
|
B:HOH645
|
4.0
|
35.9
|
1.0
|
CE
|
B:LYS181
|
4.1
|
25.6
|
1.0
|
OD2
|
B:ASP31
|
4.1
|
27.3
|
1.0
|
OD2
|
B:ASP258
|
4.1
|
39.5
|
0.8
|
O3'
|
B:SAM502
|
4.3
|
30.5
|
1.0
|
O
|
B:HOH792
|
4.3
|
46.3
|
1.0
|
CD2
|
B:HIS29
|
4.4
|
26.3
|
1.0
|
CD
|
B:LYS181
|
4.6
|
28.2
|
1.0
|
O
|
B:HOH609
|
4.6
|
27.8
|
1.0
|
C3'
|
B:SAM502
|
4.7
|
28.6
|
1.0
|
CG
|
A:ASP134
|
4.8
|
31.6
|
1.0
|
ND1
|
B:HIS29
|
4.9
|
25.3
|
1.0
|
O4'
|
B:SAM502
|
5.0
|
27.7
|
1.0
|
|
Chlorine binding site 4 out
of 6 in 8p4h
Go back to
Chlorine Binding Sites List in 8p4h
Chlorine binding site 4 out
of 6 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 Chlorine with other atoms in the Cl 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:Cl401
b:27.6
occ:1.00
|
CL1
|
C:UM6401
|
0.0
|
27.6
|
1.0
|
C2
|
C:UM6401
|
1.7
|
27.0
|
1.0
|
C12
|
C:UM6401
|
2.7
|
29.0
|
1.0
|
C3
|
C:UM6401
|
2.7
|
26.0
|
1.0
|
O
|
D:SER331
|
3.7
|
27.5
|
1.0
|
N
|
D:GLN317
|
3.8
|
25.8
|
1.0
|
CB
|
D:GLN317
|
3.8
|
26.0
|
1.0
|
CB
|
D:SER331
|
3.9
|
31.5
|
1.0
|
C
|
D:SER331
|
3.9
|
28.0
|
1.0
|
C11
|
C:UM6401
|
3.9
|
28.2
|
1.0
|
C4
|
C:UM6401
|
4.0
|
22.1
|
1.0
|
O
|
D:LEU315
|
4.1
|
26.5
|
1.0
|
CG
|
D:LEU315
|
4.2
|
26.3
|
1.0
|
N
|
D:PHE333
|
4.2
|
29.8
|
1.0
|
N
|
D:ILE332
|
4.2
|
28.1
|
1.0
|
CD2
|
D:LEU315
|
4.2
|
26.3
|
1.0
|
C
|
D:ILE332
|
4.3
|
29.6
|
1.0
|
CB
|
D:PHE333
|
4.3
|
32.9
|
1.0
|
C
|
D:VAL316
|
4.4
|
27.1
|
1.0
|
CE2
|
D:PHE139
|
4.4
|
25.7
|
1.0
|
CA
|
D:GLN317
|
4.4
|
25.1
|
1.0
|
CA
|
D:ILE332
|
4.4
|
31.5
|
1.0
|
CE2
|
C:PHE20
|
4.5
|
30.9
|
1.0
|
C
|
D:LEU315
|
4.5
|
25.0
|
1.0
|
C10
|
C:UM6401
|
4.5
|
29.8
|
1.0
|
CA
|
D:SER331
|
4.5
|
28.0
|
1.0
|
CD2
|
D:PHE139
|
4.6
|
26.4
|
1.0
|
CA
|
D:VAL316
|
4.6
|
26.8
|
1.0
|
N
|
D:VAL316
|
4.7
|
25.9
|
1.0
|
CD2
|
C:PHE20
|
4.7
|
28.4
|
1.0
|
CB
|
D:LEU315
|
4.7
|
27.3
|
1.0
|
O
|
D:ILE332
|
4.8
|
31.8
|
1.0
|
CA
|
D:PHE333
|
4.9
|
28.5
|
1.0
|
|
Chlorine binding site 5 out
of 6 in 8p4h
Go back to
Chlorine Binding Sites List in 8p4h
Chlorine binding site 5 out
of 6 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 Chlorine with other atoms in the Cl 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:Cl403
b:26.2
occ:1.00
|
CL1
|
D:UM6403
|
0.0
|
26.2
|
1.0
|
C2
|
D:UM6403
|
1.7
|
22.3
|
1.0
|
C12
|
D:UM6403
|
2.7
|
25.2
|
1.0
|
C3
|
D:UM6403
|
2.7
|
20.4
|
1.0
|
O
|
C:SER331
|
3.7
|
26.0
|
1.0
|
N
|
C:GLN317
|
3.7
|
24.6
|
1.0
|
CB
|
C:GLN317
|
3.8
|
26.7
|
1.0
|
C
|
C:SER331
|
3.9
|
26.6
|
1.0
|
CB
|
C:SER331
|
3.9
|
27.6
|
1.0
|
C11
|
D:UM6403
|
3.9
|
25.2
|
1.0
|
C4
|
D:UM6403
|
4.0
|
19.7
|
1.0
|
O
|
C:LEU315
|
4.1
|
25.2
|
1.0
|
CG
|
C:LEU315
|
4.1
|
25.1
|
1.0
|
CD2
|
C:LEU315
|
4.2
|
26.0
|
1.0
|
N
|
C:PHE333
|
4.2
|
26.4
|
1.0
|
N
|
C:ILE332
|
4.2
|
25.0
|
1.0
|
C
|
C:ILE332
|
4.3
|
26.2
|
1.0
|
CB
|
C:PHE333
|
4.3
|
28.7
|
1.0
|
C
|
C:VAL316
|
4.3
|
25.1
|
1.0
|
CA
|
C:GLN317
|
4.4
|
25.1
|
1.0
|
CE1
|
C:PHE139
|
4.4
|
23.2
|
1.0
|
C
|
C:LEU315
|
4.4
|
27.5
|
1.0
|
CA
|
C:ILE332
|
4.5
|
28.3
|
1.0
|
CE2
|
D:PHE20
|
4.5
|
29.0
|
1.0
|
C10
|
D:UM6403
|
4.5
|
25.9
|
1.0
|
CA
|
C:SER331
|
4.5
|
25.7
|
1.0
|
CD1
|
C:PHE139
|
4.6
|
22.9
|
1.0
|
CA
|
C:VAL316
|
4.6
|
23.5
|
1.0
|
CB
|
C:LEU315
|
4.7
|
24.6
|
1.0
|
N
|
C:VAL316
|
4.7
|
22.6
|
1.0
|
CD2
|
D:PHE20
|
4.7
|
25.4
|
1.0
|
O
|
C:ILE332
|
4.8
|
26.4
|
1.0
|
CA
|
C:PHE333
|
4.9
|
27.9
|
1.0
|
|
Chlorine binding site 6 out
of 6 in 8p4h
Go back to
Chlorine Binding Sites List in 8p4h
Chlorine binding site 6 out
of 6 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 Chlorine with other atoms in the Cl binding
site number 6 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:Cl405
b:60.1
occ:1.00
|
O
|
C:HOH757
|
2.9
|
57.5
|
1.0
|
NZ
|
D:LYS265
|
3.2
|
29.4
|
1.0
|
NE2
|
D:HIS29
|
3.3
|
29.6
|
1.0
|
O
|
C:HOH502
|
3.4
|
53.2
|
1.0
|
NZ
|
D:LYS181
|
3.5
|
37.3
|
1.0
|
C5'
|
D:SAM401
|
3.6
|
37.9
|
0.5
|
CE1
|
D:HIS29
|
3.7
|
30.4
|
1.0
|
CE
|
D:LYS265
|
3.7
|
30.2
|
1.0
|
O
|
D:HOH509
|
3.8
|
45.0
|
1.0
|
OD2
|
C:ASP134
|
3.8
|
44.9
|
1.0
|
O
|
D:HOH611
|
4.0
|
59.7
|
1.0
|
C4'
|
D:SAM401
|
4.1
|
37.1
|
0.5
|
CE
|
D:LYS181
|
4.1
|
40.3
|
1.0
|
OD2
|
D:ASP31
|
4.1
|
27.6
|
1.0
|
O
|
D:HOH510
|
4.2
|
32.6
|
1.0
|
O
|
D:HOH564
|
4.2
|
31.4
|
1.0
|
OD2
|
D:ASP258
|
4.3
|
49.3
|
0.8
|
O
|
D:HOH712
|
4.4
|
43.0
|
1.0
|
CD2
|
D:HIS29
|
4.6
|
30.6
|
1.0
|
O3'
|
D:SAM401
|
4.7
|
33.2
|
0.5
|
ND1
|
D:HIS29
|
5.0
|
26.4
|
1.0
|
O
|
C:HOH546
|
5.0
|
36.0
|
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: Tue Jul 30 11:25:28 2024
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