sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.950 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: | 11.056 |
|---|---|
| Number of residues: | 34 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.167 | 1542.375 |
| % Hydrophobic | % Polar |
|---|---|
| 55.14 | 44.86 |
| According to VolSite | |
| HET Code: | 1CQ |
|---|---|
| Formula: | C21H17N3O3 |
| Molecular weight: | 359.378 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 58.37 % |
| Polar Surface area: | 101.4 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 5 |
| Rings: | 4 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| -10.4999 | 16.9811 | 3.01848 |
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 | 4.12 | 0 | Hydrophobic |
| CAT | CG1 | VAL- 78 | 3.56 | 0 | Hydrophobic |
| CAJ | CG2 | VAL- 78 | 4.24 | 0 | Hydrophobic |
| CAP | CG1 | VAL- 82 | 3.9 | 0 | Hydrophobic |
| CAK | CG2 | VAL- 83 | 3.98 | 0 | Hydrophobic |
| OAY | ND2 | ASN- 85 | 2.98 | 159.99 | H-Bond (Protein Donor) |
| NAD | O | ALA- 167 | 2.97 | 150.15 | H-Bond (Ligand Donor) |
| CAU | CB | ALA- 167 | 3.38 | 0 | Hydrophobic |
| CAX | CZ | PHE- 168 | 3.4 | 0 | Hydrophobic |
| DuAr | DuAr | PHE- 168 | 3.89 | 0 | Aromatic Face/Face |
| CAV | CG1 | VAL- 228 | 3.75 | 0 | Hydrophobic |
| CAQ | CB | THR- 229 | 4.11 | 0 | Hydrophobic |
| CAP | CG2 | THR- 229 | 3.64 | 0 | Hydrophobic |
| CAR | CB | ALA- 233 | 4.04 | 0 | Hydrophobic |
| NAE | NE2 | GLN- 385 | 3.06 | 156.12 | H-Bond (Protein Donor) |
| NAH | OE1 | GLN- 385 | 3.11 | 132.53 | H-Bond (Ligand Donor) |
