2.260 Å
X-ray
2014-04-07
Name: | Dimethylglycine dehydrogenase, mitochondrial |
---|---|
ID: | M2GD_RAT |
AC: | Q63342 |
Organism: | Rattus norvegicus |
Reign: | Eukaryota |
TaxID: | 10116 |
EC Number: | 1.5.8.4 |
Chain Name: | Percentage of Residues within binding site |
---|---|
A | 100 % |
B-Factor: | 20.587 |
---|---|
Number of residues: | 35 |
Including | |
Standard Amino Acids: | 34 |
Non Standard Amino Acids: | 0 |
Water Molecules: | 1 |
Cofactors: | |
Metals: |
Ligandability | Volume (Å3) |
---|---|
0.753 | 1731.375 |
% Hydrophobic | % Polar |
---|---|
51.46 | 48.54 |
According to VolSite |
HET Code: | THG |
---|---|
Formula: | C19H21N7O6 |
Molecular weight: | 443.413 g/mol |
DrugBank ID: | DB02031 |
Buried Surface Area: | 59.33 % |
Polar Surface area: | 212.92 Å2 |
Number of | |
---|---|
H-Bond Acceptors: | 11 |
H-Bond Donors: | 6 |
Rings: | 3 |
Aromatic rings: | 1 |
Anionic atoms: | 2 |
Cationic atoms: | 0 |
Rule of Five Violation: | 2 |
Rotatable Bonds: | 9 |
X | Y | Z |
---|---|---|
-37.5249 | -0.355062 | 43.0069 |
Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand
Ligand | Protein | Interaction | |||
---|---|---|---|---|---|
Atom | Atom | Residue | Distance (Å) | Angle (°) | Type |
CG | CD1 | ILE- 560 | 4.32 | 0 | Hydrophobic |
C6' | CG1 | ILE- 560 | 3.47 | 0 | Hydrophobic |
N10 | OE2 | GLU- 573 | 2.75 | 136.25 | H-Bond (Ligand Donor) |
N1 | OG1 | THR- 575 | 2.7 | 170.85 | H-Bond (Protein Donor) |
C3' | CG2 | THR- 575 | 4.49 | 0 | Hydrophobic |
N2 | OG1 | THR- 575 | 3.12 | 128.48 | H-Bond (Ligand Donor) |
N8 | O | ILE- 587 | 3.26 | 155.22 | H-Bond (Ligand Donor) |
CB | CZ | PHE- 649 | 3.7 | 0 | Hydrophobic |
C2' | CD1 | ILE- 667 | 4.13 | 0 | Hydrophobic |
C9 | CE1 | TYR- 669 | 3.57 | 0 | Hydrophobic |
N3 | OE1 | GLU- 676 | 3.28 | 129.04 | H-Bond (Ligand Donor) |
N3 | OE2 | GLU- 676 | 2.86 | 160.33 | H-Bond (Ligand Donor) |
N2 | OE1 | GLU- 676 | 2.82 | 143.46 | H-Bond (Ligand Donor) |
CG | CE2 | TYR- 737 | 4.32 | 0 | Hydrophobic |
OE2 | OH | TYR- 737 | 3.13 | 129.34 | H-Bond (Protein Donor) |
CG | CE1 | PHE- 738 | 3.87 | 0 | Hydrophobic |