sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.400 Å
X-ray
2006-03-20
| Name: | Phosphatidyl-myo-inositol mannosyltransferase |
|---|---|
| ID: | PIMA_MYCS2 |
| AC: | A0QWG6 |
| Organism: | Mycobacterium smegmatis 155) |
| Reign: | Bacteria |
| TaxID: | 246196 |
| EC Number: | 2.4.1.57 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 36.566 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 29 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.177 | 1208.250 |
| % Hydrophobic | % Polar |
|---|---|
| 45.81 | 54.19 |
| According to VolSite | |
| HET Code: | GDP |
|---|---|
| Formula: | C10H12N5O11P2 |
| Molecular weight: | 440.177 g/mol |
| DrugBank ID: | DB04315 |
| Buried Surface Area: | 52.76 % |
| Polar Surface area: | 276.39 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 14 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 3 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| -0.342643 | 46.1793 | 29.4593 |
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 |
| C1' | CB | PRO- 14 | 4.43 | 0 | Hydrophobic |
| O3B | N | GLY- 16 | 3.27 | 161.78 | H-Bond (Protein Donor) |
| C2' | CD1 | LEU- 194 | 4.25 | 0 | Hydrophobic |
| O2B | NZ | LYS- 202 | 2.76 | 153.92 | H-Bond (Protein Donor) |
| O2B | NZ | LYS- 202 | 2.76 | 0 | Ionic (Protein Cationic) |
| O2A | NZ | LYS- 202 | 3.71 | 0 | Ionic (Protein Cationic) |
| N1 | O | VAL- 251 | 2.9 | 150.03 | H-Bond (Ligand Donor) |
| N2 | O | VAL- 251 | 3.09 | 138.19 | H-Bond (Ligand Donor) |
| N2 | O | ASP- 252 | 3.38 | 126.74 | H-Bond (Ligand Donor) |
| C2' | CD | LYS- 256 | 4.38 | 0 | Hydrophobic |
| O2' | NZ | LYS- 256 | 2.81 | 162.63 | H-Bond (Protein Donor) |
| C3' | CG2 | ILE- 278 | 3.66 | 0 | Hydrophobic |
| C2' | CG2 | VAL- 279 | 3.85 | 0 | Hydrophobic |
| O3' | OE2 | GLU- 282 | 2.74 | 167.99 | H-Bond (Ligand Donor) |
| O2' | OE2 | GLU- 282 | 2.99 | 134.45 | H-Bond (Ligand Donor) |
| O2' | OE1 | GLU- 282 | 2.57 | 146.42 | H-Bond (Ligand Donor) |
