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Chlorine in PDB 8xb0: Structure-Based Design and Optimization of Methionine Adenosyltransferase 2A (MAT2A) Inhibitors with Sam and Compound 292

Enzymatic activity of Structure-Based Design and Optimization of Methionine Adenosyltransferase 2A (MAT2A) Inhibitors with Sam and Compound 292

All present enzymatic activity of Structure-Based Design and Optimization of Methionine Adenosyltransferase 2A (MAT2A) Inhibitors with Sam and Compound 292:
2.5.1.6;

Protein crystallography data

The structure of Structure-Based Design and Optimization of Methionine Adenosyltransferase 2A (MAT2A) Inhibitors with Sam and Compound 292, PDB code: 8xb0 was solved by S.L.Tong, G.P.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 58.57 / 1.12
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 68.276, 94.105, 117.011, 90, 90, 90
R / Rfree (%) 12.4 / 13.9

Other elements in 8xb0:

The structure of Structure-Based Design and Optimization of Methionine Adenosyltransferase 2A (MAT2A) Inhibitors with Sam and Compound 292 also contains other interesting chemical elements:

Sodium (Na) 1 atom
Fluorine (F) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Structure-Based Design and Optimization of Methionine Adenosyltransferase 2A (MAT2A) Inhibitors with Sam and Compound 292 (pdb code 8xb0). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Structure-Based Design and Optimization of Methionine Adenosyltransferase 2A (MAT2A) Inhibitors with Sam and Compound 292, PDB code: 8xb0:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 8xb0

Go back to Chlorine Binding Sites List in 8xb0
Chlorine binding site 1 out of 6 in the Structure-Based Design and Optimization of Methionine Adenosyltransferase 2A (MAT2A) Inhibitors with Sam and Compound 292


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure-Based Design and Optimization of Methionine Adenosyltransferase 2A (MAT2A) Inhibitors with Sam and Compound 292 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl404

b:17.2
occ:0.85
 CL1 A:YN8404 0.0 17.2 0.8
C16 A:YN8404 1.7 14.8 0.8
C17 A:YN8404 2.7 15.1 0.8
C15 A:YN8404 2.7 13.4 0.8
F1 A:YN8404 2.9 17.4 0.8
C18 A:YN8404 3.9 14.2 0.8
C14 A:YN8404 4.0 13.0 0.8
C19 A:YN8404 4.5 13.7 0.8
CE2 A:PHE20 4.7 11.1 1.0
CD2 A:PHE20 5.0 10.4 1.0

Chlorine binding site 2 out of 6 in 8xb0

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Chlorine binding site 2 out of 6 in the Structure-Based Design and Optimization of Methionine Adenosyltransferase 2A (MAT2A) Inhibitors with Sam and Compound 292


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure-Based Design and Optimization of Methionine Adenosyltransferase 2A (MAT2A) Inhibitors with Sam and Compound 292 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl406

b:32.4
occ:0.70
 O A:HOH587 2.7 28.2 0.5
O A:HOH954 2.9 47.9 1.0
N A:GLU147 3.0 14.4 0.4
O A:HOH711 3.0 36.5 1.0
N A:GLU147 3.0 14.7 0.6
CA A:THR146 3.5 12.9 1.0
CG A:GLU147 3.6 19.8 0.6
O A:HOH587 3.7 31.8 0.5
CB A:GLU147 3.7 16.8 0.4
C A:THR146 3.7 13.4 1.0
CB A:THR146 3.8 12.9 1.0
CB A:GLU147 3.8 18.0 0.6
CA A:GLU147 3.9 15.5 0.4
CA A:GLU147 4.0 16.3 0.6
OE1 A:GLU148 4.0 20.4 1.0
CG2 A:THR146 4.3 13.2 1.0
O A:HOH680 4.5 31.8 1.0
CD A:GLU147 4.8 22.1 0.6
N A:THR146 4.8 12.5 1.0
O A:GLU145 4.8 13.8 1.0
OE2 A:GLU147 4.9 24.6 0.6
O A:THR146 4.9 13.4 1.0
O A:HOH661 5.0 32.1 1.0

Chlorine binding site 3 out of 6 in 8xb0

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Chlorine binding site 3 out of 6 in the Structure-Based Design and Optimization of Methionine Adenosyltransferase 2A (MAT2A) Inhibitors with Sam and Compound 292


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structure-Based Design and Optimization of Methionine Adenosyltransferase 2A (MAT2A) Inhibitors with Sam and Compound 292 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl407

b:37.2
occ:0.60
 O A:HOH760 2.5 28.5 0.6
OD2 A:ASP49 2.7 14.3 1.0
O A:HOH912 3.0 31.6 1.0
NE A:ARG74 3.5 24.8 1.0
CG A:ASP49 3.6 12.9 1.0
OD1 A:ASP49 3.8 13.0 1.0
CG A:ARG74 3.9 18.3 1.0
NH2 A:ARG74 4.0 28.3 1.0
CZ A:ARG74 4.0 27.6 1.0
N A:ARG74 4.0 12.8 1.0
CD A:ARG74 4.2 21.2 1.0
O A:ASP51 4.2 11.8 1.0
CA A:SER73 4.2 11.8 1.0
O A:THR72 4.4 11.4 1.0
C A:SER73 4.4 12.3 1.0
C A:ASP51 4.4 11.3 1.0
O A:HOH941 4.5 45.4 1.0
O A:HOH922 4.6 32.5 1.0
O A:HOH972 4.6 43.7 1.0
CB A:ARG74 4.7 15.8 1.0
N A:SER73 4.7 10.9 1.0
N A:ALA52 4.7 11.0 1.0
CA A:ALA52 4.8 10.9 1.0
CB A:ASP51 4.8 13.7 1.0
C A:THR72 4.8 10.8 1.0
CA A:ARG74 4.9 14.0 1.0
NH1 A:ARG74 5.0 30.2 1.0
CB A:ASP49 5.0 12.1 1.0

Chlorine binding site 4 out of 6 in 8xb0

Go back to Chlorine Binding Sites List in 8xb0
Chlorine binding site 4 out of 6 in the Structure-Based Design and Optimization of Methionine Adenosyltransferase 2A (MAT2A) Inhibitors with Sam and Compound 292


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Structure-Based Design and Optimization of Methionine Adenosyltransferase 2A (MAT2A) Inhibitors with Sam and Compound 292 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl408

b:22.3
occ:0.60
 N A:SAM405 3.1 14.3 1.0
CB A:SAM405 3.4 15.0 1.0
NA A:NA411 3.8 23.9 1.0
CG A:SAM405 3.8 15.6 1.0
CA A:SAM405 3.8 13.7 1.0
C A:SAM405 4.5 12.3 1.0
OD1 A:ASP258 4.5 15.0 1.0
O A:HOH505 4.6 12.2 1.0
O A:SAM405 5.0 12.2 1.0
OXT A:SAM405 5.0 12.2 1.0

Chlorine binding site 5 out of 6 in 8xb0

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Chlorine binding site 5 out of 6 in the Structure-Based Design and Optimization of Methionine Adenosyltransferase 2A (MAT2A) Inhibitors with Sam and Compound 292


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Structure-Based Design and Optimization of Methionine Adenosyltransferase 2A (MAT2A) Inhibitors with Sam and Compound 292 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl409

b:42.7
occ:0.70
 OE1 A:GLU147 2.9 21.1 0.4
O A:HOH871 3.0 39.1 1.0
O A:HOH964 3.1 45.3 1.0
CD A:GLU147 3.1 20.3 0.4
CG A:GLU147 3.6 18.4 0.4
OE2 A:GLU147 3.6 22.2 0.4
CG A:GLU147 4.0 19.8 0.6
CB A:GLU147 4.4 18.0 0.6
CB A:GLU147 4.4 16.8 0.4
OE1 A:GLU147 4.6 24.0 0.6
CD A:GLU147 4.6 22.1 0.6
O A:HOH881 4.8 33.5 1.0

Chlorine binding site 6 out of 6 in 8xb0

Go back to Chlorine Binding Sites List in 8xb0
Chlorine binding site 6 out of 6 in the Structure-Based Design and Optimization of Methionine Adenosyltransferase 2A (MAT2A) Inhibitors with Sam and Compound 292


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Structure-Based Design and Optimization of Methionine Adenosyltransferase 2A (MAT2A) Inhibitors with Sam and Compound 292 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl410

b:19.0
occ:1.00
 NZ A:LYS181 3.1 10.7 1.0
NE2 A:HIS29 3.2 10.2 1.0
NZ A:LYS265 3.3 13.4 1.0
NA A:NA411 3.3 23.9 1.0
O A:HOH676 3.5 7.1 0.5
C5' A:SAM405 3.5 12.4 1.0
CE1 A:HIS29 3.7 10.4 1.0
CE A:LYS265 3.7 12.9 1.0
C4' A:SAM405 3.8 10.5 1.0
O A:HOH535 3.9 23.2 1.0
CE A:LYS181 4.0 10.4 1.0
O A:HOH676 4.1 11.5 0.5
OD2 A:ASP31 4.2 10.8 1.0
OD2 A:ASP258 4.2 15.0 1.0
O3' A:SAM405 4.3 11.3 1.0
CD2 A:HIS29 4.4 9.8 1.0
O A:HOH592 4.5 12.2 1.0
CD A:LYS181 4.6 10.0 1.0
C3' A:SAM405 4.7 10.3 1.0
O A:HOH836 4.9 10.9 0.5
ND1 A:HIS29 4.9 10.4 1.0
O4' A:SAM405 4.9 10.0 1.0

Reference:

J.Zheng, T.Zhang, S.Tong, T.Liu, J.Cui, H.Xu, D.Hu, Y.Shen, Y.Yin, D.Zhao, C.Tan, X.Dong, J.Chen, F.Ji, C.Tong, J.J.Li, J.Li, G.Zhang. Structure-Based Design and Optimization of Methionine Adenosyltransferase 2A (MAT2A) Inhibitors with High Selectivity, Brain Penetration, and in Vivo Efficacy. J.Med.Chem. V. 67 9431 2024.
ISSN: ISSN 0022-2623
PubMed: 38818879
DOI: 10.1021/ACS.JMEDCHEM.4C00552
Page generated: Tue Jul 30 13:54:56 2024

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