sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.600 Å
X-ray
2011-07-19
| Name: | Endopeptidase, peptidase family M13 |
|---|---|
| ID: | O53649_MYCTO |
| AC: | O53649 |
| Organism: | Mycobacterium tuberculosis |
| Reign: | Bacteria |
| TaxID: | 83331 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 17.816 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.981 | 945.000 |
| % Hydrophobic | % Polar |
|---|---|
| 50.71 | 49.29 |
| According to VolSite | |
| HET Code: | RDF |
|---|---|
| Formula: | C23H32N3O10P |
| Molecular weight: | 541.488 g/mol |
| DrugBank ID: | DB02557 |
| Buried Surface Area: | 47.51 % |
| Polar Surface area: | 226.14 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 10 |
| H-Bond Donors: | 6 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 3 |
| Rotatable Bonds: | 11 |
| X | Y | Z |
|---|---|---|
| 95.2692 | 92.9196 | 34.5561 |
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 |
| CG | CZ | PHE- 48 | 4.34 | 0 | Hydrophobic |
| CD1 | CE2 | PHE- 48 | 3.72 | 0 | Hydrophobic |
| CB1 | CZ | PHE- 48 | 4.15 | 0 | Hydrophobic |
| CZ2 | CB | PHE- 48 | 3.91 | 0 | Hydrophobic |
| C2 | CE | MET- 446 | 3.88 | 0 | Hydrophobic |
| O2 | ND2 | ASN- 452 | 3.46 | 131.62 | H-Bond (Protein Donor) |
| O6 | ND2 | ASN- 452 | 3.23 | 146.55 | H-Bond (Protein Donor) |
| N1 | OD1 | ASN- 452 | 3.38 | 149.52 | H-Bond (Ligand Donor) |
| N | O | ALA- 453 | 2.95 | 147.9 | H-Bond (Ligand Donor) |
| CB | CB | ALA- 453 | 4.29 | 0 | Hydrophobic |
| CD1 | CD1 | ILE- 468 | 3.7 | 0 | Hydrophobic |
| CD1 | CE1 | PHE- 473 | 4.22 | 0 | Hydrophobic |
| CD1 | CG2 | VAL- 490 | 3.86 | 0 | Hydrophobic |
| O2P | OE1 | GLU- 494 | 2.51 | 160.26 | H-Bond (Protein Donor) |
| CD2 | CH2 | TRP- 604 | 4.06 | 0 | Hydrophobic |
| C6 | CG | PRO- 621 | 3.87 | 0 | Hydrophobic |
| O1P | NE2 | HIS- 622 | 2.83 | 174.93 | H-Bond (Protein Donor) |
| O | NH1 | ARG- 628 | 2.86 | 155.51 | H-Bond (Protein Donor) |
| O | NH2 | ARG- 628 | 3.13 | 140.01 | H-Bond (Protein Donor) |
| O1P | ZN | ZN- 1664 | 1.96 | 0 | Metal Acceptor |
