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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:

Magnesium (Mg) 2 atoms
Fluorine (F) 5 atoms

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

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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: Sun Jul 13 13:02:32 2025

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