Chlorine in PDB 8xam: Co-Crystal Structure of Compound 7 in Complex with MAT2A

Enzymatic activity of Co-Crystal Structure of Compound 7 in Complex with MAT2A

All present enzymatic activity of Co-Crystal Structure of Compound 7 in Complex with MAT2A:
2.5.1.6;

Protein crystallography data

The structure of Co-Crystal Structure of Compound 7 in Complex with MAT2A, PDB code: 8xam was solved by F.Gao, X.Ding, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.12 / 1.30
Space group I 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 67.968, 94.043, 116.892, 90, 90, 90
R / Rfree (%) 12.1 / 14.3

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Co-Crystal Structure of Compound 7 in Complex with MAT2A (pdb code 8xam). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Co-Crystal Structure of Compound 7 in Complex with MAT2A, PDB code: 8xam:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 8xam

Go back to Chlorine Binding Sites List in 8xam
Chlorine binding site 1 out of 4 in the Co-Crystal Structure of Compound 7 in Complex with MAT2A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Co-Crystal Structure of Compound 7 in Complex with MAT2A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl401

b:11.7
occ:0.50
 CL B:XRH401 0.0 11.7 0.5
CL1 B:XRH401 0.0 11.8 0.5
C7 B:XRH401 1.8 11.2 0.5
C25 B:XRH401 1.8 11.5 0.5
C8 B:XRH401 2.7 11.4 0.5
C24 B:XRH401 2.7 11.5 0.5
C6 B:XRH401 2.7 12.4 0.5
C26 B:XRH401 2.7 13.0 0.5
O B:SER331 3.5 8.2 1.0
N B:GLN317 3.7 7.3 1.0
CB B:SER331 3.7 8.6 1.0
C B:SER331 3.7 8.5 1.0
CB B:GLN317 3.8 7.2 1.0
N B:ILE332 3.9 9.3 1.0
O B:LEU315 4.0 9.2 1.0
C9 B:XRH401 4.0 11.8 0.5
C23 B:XRH401 4.0 12.1 0.5
C5 B:XRH401 4.0 12.8 0.5
C27 B:XRH401 4.0 13.8 0.5
N B:PHE333 4.1 9.6 1.0
C B:ILE332 4.2 10.3 1.0
CB B:PHE333 4.2 11.8 1.0
CA B:ILE332 4.2 9.9 1.0
C B:VAL316 4.3 7.9 1.0
CA B:SER331 4.3 8.2 1.0
CA B:GLN317 4.3 7.0 1.0
CD2 B:LEU315 4.3 10.5 1.0
CG B:LEU315 4.4 9.0 1.0
C B:LEU315 4.4 8.8 1.0
C4 B:XRH401 4.5 12.6 0.5
C22 B:XRH401 4.5 12.6 0.5
CE2 B:PHE139 4.5 7.8 1.0
CA B:VAL316 4.6 8.2 1.0
N B:VAL316 4.7 7.8 1.0
O B:ILE332 4.8 10.5 1.0
CD2 B:PHE139 4.8 7.6 1.0
CA B:PHE333 4.8 9.6 1.0
CB B:LEU315 4.8 9.4 1.0
OG B:SER331 4.9 9.7 1.0
CD2 A:PHE20 5.0 11.1 1.0

Chlorine binding site 2 out of 4 in 8xam

Go back to Chlorine Binding Sites List in 8xam
Chlorine binding site 2 out of 4 in the Co-Crystal Structure of Compound 7 in Complex with MAT2A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Co-Crystal Structure of Compound 7 in Complex with MAT2A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl401

b:11.8
occ:0.50
 CL B:XRH401 0.0 11.8 0.5
CL1 B:XRH401 0.0 11.9 0.5
C7 B:XRH401 1.8 11.4 0.5
C25 B:XRH401 1.8 11.7 0.5
C8 B:XRH401 2.7 11.3 0.5
C24 B:XRH401 2.7 11.4 0.5
C6 B:XRH401 2.7 12.1 0.5
C26 B:XRH401 2.7 12.8 0.5
O A:SER331 3.5 8.5 1.0
N A:GLN317 3.7 7.2 1.0
C A:SER331 3.7 8.3 1.0
CB A:SER331 3.7 9.1 1.0
CB A:GLN317 3.8 7.5 1.0
N A:ILE332 3.9 9.1 1.0
O A:LEU315 4.0 9.5 1.0
C9 B:XRH401 4.0 12.0 0.5
C23 B:XRH401 4.0 12.1 0.5
C5 B:XRH401 4.0 13.2 0.5
C27 B:XRH401 4.1 14.3 0.5
N A:PHE333 4.1 9.3 1.0
C A:ILE332 4.2 10.1 1.0
CB A:PHE333 4.2 11.7 1.0
CA A:ILE332 4.2 9.6 1.0
C A:VAL316 4.3 8.0 1.0
CA A:SER331 4.3 8.4 1.0
CD2 A:LEU315 4.3 10.8 1.0
CG A:LEU315 4.3 9.3 1.0
CA A:GLN317 4.3 7.1 1.0
C A:LEU315 4.4 8.7 1.0
C4 B:XRH401 4.5 12.8 0.5
C22 B:XRH401 4.5 12.8 0.5
CE2 A:PHE139 4.6 7.8 1.0
CA A:VAL316 4.6 8.1 1.0
N A:VAL316 4.7 8.0 1.0
O A:ILE332 4.7 10.3 1.0
CD2 A:PHE139 4.8 7.6 1.0
CB A:LEU315 4.8 9.8 1.0
CA A:PHE333 4.8 10.2 1.0
OG A:SER331 4.9 9.6 1.0
CD2 B:PHE20 5.0 11.0 1.0

Chlorine binding site 3 out of 4 in 8xam

Go back to Chlorine Binding Sites List in 8xam
Chlorine binding site 3 out of 4 in the Co-Crystal Structure of Compound 7 in Complex with MAT2A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Co-Crystal Structure of Compound 7 in Complex with MAT2A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl401

b:11.9
occ:0.50
 CL1 B:XRH401 0.0 11.9 0.5
CL B:XRH401 0.0 11.8 0.5
C7 B:XRH401 1.8 11.4 0.5
C25 B:XRH401 1.8 11.7 0.5
C8 B:XRH401 2.7 11.3 0.5
C24 B:XRH401 2.7 11.4 0.5
C6 B:XRH401 2.7 12.1 0.5
C26 B:XRH401 2.7 12.8 0.5
O A:SER331 3.5 8.5 1.0
CB A:SER331 3.7 9.1 1.0
C A:SER331 3.7 8.3 1.0
N A:GLN317 3.7 7.2 1.0
CB A:GLN317 3.8 7.5 1.0
N A:ILE332 3.9 9.1 1.0
C9 B:XRH401 4.0 12.0 0.5
C23 B:XRH401 4.0 12.1 0.5
O A:LEU315 4.0 9.5 1.0
C5 B:XRH401 4.0 13.2 0.5
C27 B:XRH401 4.0 14.3 0.5
N A:PHE333 4.1 9.3 1.0
C A:ILE332 4.2 10.1 1.0
CB A:PHE333 4.2 11.7 1.0
CA A:ILE332 4.2 9.6 1.0
C A:VAL316 4.3 8.0 1.0
CA A:SER331 4.3 8.4 1.0
CA A:GLN317 4.3 7.1 1.0
CD2 A:LEU315 4.4 10.8 1.0
CG A:LEU315 4.4 9.3 1.0
C A:LEU315 4.4 8.7 1.0
C4 B:XRH401 4.5 12.8 0.5
C22 B:XRH401 4.5 12.8 0.5
CE2 A:PHE139 4.6 7.8 1.0
CA A:VAL316 4.6 8.1 1.0
N A:VAL316 4.7 8.0 1.0
O A:ILE332 4.7 10.3 1.0
CD2 A:PHE139 4.8 7.6 1.0
CA A:PHE333 4.8 10.2 1.0
OG A:SER331 4.8 9.6 1.0
CB A:LEU315 4.8 9.8 1.0
CD2 B:PHE20 5.0 11.0 1.0

Chlorine binding site 4 out of 4 in 8xam

Go back to Chlorine Binding Sites List in 8xam
Chlorine binding site 4 out of 4 in the Co-Crystal Structure of Compound 7 in Complex with MAT2A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Co-Crystal Structure of Compound 7 in Complex with MAT2A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl401

b:11.8
occ:0.50
 CL1 B:XRH401 0.0 11.8 0.5
CL B:XRH401 0.0 11.7 0.5
C7 B:XRH401 1.8 11.2 0.5
C25 B:XRH401 1.8 11.5 0.5
C6 B:XRH401 2.7 12.4 0.5
C8 B:XRH401 2.7 11.4 0.5
C26 B:XRH401 2.7 13.0 0.5
C24 B:XRH401 2.7 11.5 0.5
O B:SER331 3.5 8.2 1.0
CB B:SER331 3.7 8.6 1.0
C B:SER331 3.7 8.5 1.0
N B:GLN317 3.7 7.3 1.0
CB B:GLN317 3.8 7.2 1.0
N B:ILE332 3.9 9.3 1.0
C9 B:XRH401 4.0 11.8 0.5
C23 B:XRH401 4.0 12.1 0.5
O B:LEU315 4.0 9.2 1.0
C5 B:XRH401 4.0 12.8 0.5
C27 B:XRH401 4.0 13.8 0.5
N B:PHE333 4.1 9.6 1.0
C B:ILE332 4.2 10.3 1.0
CB B:PHE333 4.2 11.8 1.0
CA B:ILE332 4.2 9.9 1.0
C B:VAL316 4.3 7.9 1.0
CA B:SER331 4.3 8.2 1.0
CA B:GLN317 4.3 7.0 1.0
CD2 B:LEU315 4.4 10.5 1.0
CG B:LEU315 4.4 9.0 1.0
C B:LEU315 4.5 8.8 1.0
C4 B:XRH401 4.5 12.6 0.5
C22 B:XRH401 4.5 12.6 0.5
CE2 B:PHE139 4.5 7.8 1.0
CA B:VAL316 4.6 8.2 1.0
N B:VAL316 4.7 7.8 1.0
O B:ILE332 4.8 10.5 1.0
CD2 B:PHE139 4.8 7.6 1.0
CA B:PHE333 4.8 9.6 1.0
OG B:SER331 4.8 9.7 1.0
CB B:LEU315 4.9 9.4 1.0
CD2 A:PHE20 5.0 11.1 1.0

Reference:

F.Gao, X.Ding, Z.Cao, W.Zhu, Y.Fan, B.Steurer, H.Wang, X.Cai, M.Zhang, A.Aliper, F.Ren, X.Ding, A.Zhavoronkov. Discovery of Novel MAT2A Inhibitors By An Allosteric Site-Compatible Fragment Growing Approach. Bioorg.Med.Chem. V. 100 17633 2024.
ISSN: ESSN 1464-3391
PubMed: 38342078
DOI: 10.1016/J.BMC.2024.117633
Page generated: Tue Jul 30 13:54:16 2024

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