sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.310 Å
X-ray
2013-06-12
| Name: | 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase |
|---|---|
| ID: | METE_CANAL |
| AC: | P82610 |
| Organism: | Candida albicans |
| Reign: | Eukaryota |
| TaxID: | 237561 |
| EC Number: | 2.1.1.14 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 53.831 |
|---|---|
| Number of residues: | 25 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.386 | 519.750 |
| % Hydrophobic | % Polar |
|---|---|
| 39.61 | 60.39 |
| According to VolSite | |
| HET Code: | C2F |
|---|---|
| Formula: | C20H23N7O6 |
| Molecular weight: | 457.440 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 41.84 % |
| Polar Surface area: | 204.14 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 11 |
| H-Bond Donors: | 5 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| -18.6348 | 6.37361 | -22.6118 |
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 |
| O1 | NZ | LYS- 19 | 2.67 | 152.12 | H-Bond (Protein Donor) |
| O2 | NZ | LYS- 19 | 3.03 | 141.26 | H-Bond (Protein Donor) |
| O1 | NZ | LYS- 19 | 2.67 | 0 | Ionic (Protein Cationic) |
| O2 | NZ | LYS- 19 | 3.03 | 0 | Ionic (Protein Cationic) |
| N1 | ND2 | ASN- 126 | 3.01 | 163.48 | H-Bond (Protein Donor) |
| N8 | OD1 | ASN- 126 | 3.13 | 171.68 | H-Bond (Ligand Donor) |
| NA2 | OD1 | ASP- 504 | 3.28 | 134.98 | H-Bond (Ligand Donor) |
| N3 | OD1 | ASP- 504 | 2.97 | 150.98 | H-Bond (Ligand Donor) |
| N3 | OD2 | ASP- 504 | 3.43 | 146.52 | H-Bond (Ligand Donor) |
| CB | CZ3 | TRP- 523 | 4.09 | 0 | Hydrophobic |
| C16 | CB | SER- 526 | 4.18 | 0 | Hydrophobic |
| C9 | CE2 | TYR- 527 | 4.16 | 0 | Hydrophobic |
| O1 | CZ | ARG- 530 | 3.89 | 0 | Ionic (Protein Cationic) |
| C12 | CD | ARG- 530 | 3.29 | 0 | Hydrophobic |
| C17 | CG | ARG- 530 | 3.78 | 0 | Hydrophobic |
| N | O | TYR- 531 | 3.1 | 147.89 | H-Bond (Ligand Donor) |
| O2 | N | TYR- 531 | 2.91 | 170.71 | H-Bond (Protein Donor) |
| C17 | CG1 | VAL- 532 | 3.65 | 0 | Hydrophobic |
| C7 | CZ2 | TRP- 576 | 3.62 | 0 | Hydrophobic |
| C11 | CH2 | TRP- 576 | 3.96 | 0 | Hydrophobic |
