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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:

Chlorine (Cl) 6 atoms
Magnesium (Mg) 2 atoms

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: Thu Dec 28 04:42:00 2023

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