sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.500 Å
X-ray
2011-01-28
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 7.370 | 7.370 | 7.370 | 0.000 | 7.370 | 1 |
| Name: | 3-dehydroquinate dehydratase |
|---|---|
| ID: | AROQ_MYCTU |
| AC: | P9WPX7 |
| Organism: | Mycobacterium tuberculosis |
| Reign: | Bacteria |
| TaxID: | 83332 |
| EC Number: | 4.2.1.10 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 14.736 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.161 | 239.625 |
| % Hydrophobic | % Polar |
|---|---|
| 53.52 | 46.48 |
| According to VolSite | |
| HET Code: | CB6 |
|---|---|
| Formula: | C17H17O6S |
| Molecular weight: | 349.378 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 62.55 % |
| Polar Surface area: | 138.29 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 7.30708 | -29.3106 | -47.1364 |
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 |
| SAO | CB | ASN- 12 | 3.6 | 0 | Hydrophobic |
| CAL | CB | ASN- 12 | 4.47 | 0 | Hydrophobic |
| CAU | CB | ASN- 12 | 3.77 | 0 | Hydrophobic |
| CAL | CD2 | LEU- 13 | 3.98 | 0 | Hydrophobic |
| CAA | CB | ARG- 15 | 3.51 | 0 | Hydrophobic |
| CAH | CB | ARG- 15 | 3.68 | 0 | Hydrophobic |
| SAO | CE2 | TYR- 24 | 3.64 | 0 | Hydrophobic |
| CAL | CZ | TYR- 24 | 3.8 | 0 | Hydrophobic |
| CAW | CZ | TYR- 24 | 4.47 | 0 | Hydrophobic |
| CAX | CE1 | TYR- 24 | 4.16 | 0 | Hydrophobic |
| OAB | ND2 | ASN- 75 | 2.88 | 154.53 | H-Bond (Protein Donor) |
| OAF | OD1 | ASN- 75 | 2.74 | 144.42 | H-Bond (Ligand Donor) |
| OAD | NE2 | HIS- 81 | 2.76 | 173.27 | H-Bond (Ligand Donor) |
| CAX | CB | HIS- 101 | 4.39 | 0 | Hydrophobic |
| OAB | N | ILE- 102 | 2.8 | 156.91 | H-Bond (Protein Donor) |
| OAC | N | SER- 103 | 2.83 | 157.19 | H-Bond (Protein Donor) |
| OAC | OG | SER- 103 | 2.68 | 168.32 | H-Bond (Protein Donor) |
| CAM | CG1 | VAL- 105 | 3.72 | 0 | Hydrophobic |
| OAD | NH1 | ARG- 112 | 2.91 | 159.07 | H-Bond (Protein Donor) |
