sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.650 Å
X-ray
2004-07-16
| Name: | 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase 1 |
|---|---|
| ID: | METE1_ARATH |
| AC: | O50008 |
| Organism: | Arabidopsis thaliana |
| Reign: | Eukaryota |
| TaxID: | 3702 |
| EC Number: | 2.1.1.14 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 48.163 |
|---|---|
| Number of residues: | 24 |
| Including | |
| Standard Amino Acids: | 23 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.720 | 1026.000 |
| % Hydrophobic | % Polar |
|---|---|
| 36.84 | 63.16 |
| According to VolSite | |
| HET Code: | THG |
|---|---|
| Formula: | C19H21N7O6 |
| Molecular weight: | 443.413 g/mol |
| DrugBank ID: | DB02031 |
| Buried Surface Area: | 42.33 % |
| 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 |
|---|---|---|
| -51.7228 | 41.0498 | -70.5187 |
Image generated by PoseView
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 |
| OX2 | NZ | LYS- 18 | 2.72 | 156.89 | H-Bond (Protein Donor) |
| OX2 | NZ | LYS- 18 | 2.72 | 0 | Ionic (Protein Cationic) |
| OX1 | NZ | LYS- 18 | 3.73 | 0 | Ionic (Protein Cationic) |
| N3 | OD1 | ASP- 495 | 2.66 | 138.5 | H-Bond (Ligand Donor) |
| CB | CZ3 | TRP- 514 | 4.38 | 0 | Hydrophobic |
| C5' | CB | SER- 517 | 3.55 | 0 | Hydrophobic |
| C1' | CG | ARG- 521 | 4.17 | 0 | Hydrophobic |
| C6' | CB | ARG- 521 | 3.52 | 0 | Hydrophobic |
| O11 | NH1 | ARG- 521 | 3.23 | 128.27 | H-Bond (Protein Donor) |
| N | O | CYS- 522 | 3.09 | 154.87 | H-Bond (Ligand Donor) |
| OX1 | N | CYS- 522 | 2.82 | 145.31 | H-Bond (Protein Donor) |
| C4' | CG1 | VAL- 523 | 4.05 | 0 | Hydrophobic |
| C9 | CZ2 | TRP- 567 | 4.46 | 0 | Hydrophobic |
| DuAr | DuAr | TRP- 567 | 3.88 | 0 | Aromatic Face/Face |
