sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.350 Å
X-ray
2013-05-20
| Name: | Cytochrome P450 |
|---|---|
| ID: | I6YD01_MYCTU |
| AC: | I6YD01 |
| Organism: | Mycobacterium tuberculosis |
| Reign: | Bacteria |
| TaxID: | 83332 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 8.733 |
|---|---|
| Number of residues: | 27 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.228 | 1535.625 |
| % Hydrophobic | % Polar |
|---|---|
| 54.07 | 45.93 |
| According to VolSite | |
| HET Code: | 1TM |
|---|---|
| Formula: | C15H13N3O2 |
| Molecular weight: | 267.283 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 60.12 % |
| Polar Surface area: | 95.16 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| -11.9512 | 17.3751 | 3.19775 |
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 |
| CAO | CG1 | VAL- 78 | 4.23 | 0 | Hydrophobic |
| CAD | CG1 | VAL- 78 | 3.48 | 0 | Hydrophobic |
| CAP | CG1 | VAL- 82 | 4.23 | 0 | Hydrophobic |
| CAQ | CB | ASN- 85 | 4.39 | 0 | Hydrophobic |
| OAT | ND2 | ASN- 85 | 3.07 | 154.62 | H-Bond (Protein Donor) |
| NAA | O | ALA- 167 | 2.99 | 153.6 | H-Bond (Ligand Donor) |
| CAE | CB | ALA- 167 | 3.41 | 0 | Hydrophobic |
| CAF | CG1 | VAL- 228 | 3.84 | 0 | Hydrophobic |
| CAR | CB | THR- 229 | 3.82 | 0 | Hydrophobic |
| CAR | CB | ALA- 233 | 4.04 | 0 | Hydrophobic |
| NAM | OE1 | GLN- 385 | 3.44 | 123.85 | H-Bond (Ligand Donor) |
| NAL | NE2 | GLN- 385 | 2.98 | 166.66 | H-Bond (Protein Donor) |
