sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.300 Å
X-ray
2012-12-30
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 6.680 | 6.680 | 6.680 | 0.000 | 6.680 | 1 |
| Name: | 1-deoxy-D-xylulose 5-phosphate reductoisomerase |
|---|---|
| ID: | DXR_MYCTU |
| AC: | P9WNS1 |
| Organism: | Mycobacterium tuberculosis |
| Reign: | Bacteria |
| TaxID: | 83332 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 46.361 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 0 |
| Cofactors: | NDP |
| Metals: | MN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.483 | 435.375 |
| % Hydrophobic | % Polar |
|---|---|
| 31.78 | 68.22 |
| According to VolSite | |
| HET Code: | FM6 |
|---|---|
| Formula: | C16H14Cl2NO5P |
| Molecular weight: | 402.166 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 52.44 % |
| Polar Surface area: | 113.54 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 1 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 26.4745 | 43.435 | 24.8002 |
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 |
| O1 | OG | SER- 152 | 3.16 | 166.68 | H-Bond (Protein Donor) |
| C15 | CB | SER- 152 | 3.85 | 0 | Hydrophobic |
| OP3 | N | SER- 177 | 2.92 | 164.55 | H-Bond (Protein Donor) |
| OP2 | OG | SER- 177 | 2.55 | 161.98 | H-Bond (Protein Donor) |
| C7 | CB | SER- 177 | 4.02 | 0 | Hydrophobic |
| OP2 | OG | SER- 213 | 3.04 | 167.78 | H-Bond (Protein Donor) |
| C3 | CB | SER- 213 | 4.27 | 0 | Hydrophobic |
| OP1 | ND2 | ASN- 218 | 2.79 | 161.67 | H-Bond (Protein Donor) |
| O2 | ND2 | ASN- 218 | 3.12 | 143.82 | H-Bond (Protein Donor) |
| OP1 | NZ | LYS- 219 | 3.36 | 122.69 | H-Bond (Protein Donor) |
| OP3 | NZ | LYS- 219 | 2.76 | 150.13 | H-Bond (Protein Donor) |
| OP1 | NZ | LYS- 219 | 3.36 | 0 | Ionic (Protein Cationic) |
| OP3 | NZ | LYS- 219 | 2.76 | 0 | Ionic (Protein Cationic) |
| CL2 | CB | SER- 245 | 3.42 | 0 | Hydrophobic |
| C10 | CB | SER- 245 | 3.5 | 0 | Hydrophobic |
| CL2 | CB | PRO- 265 | 3.73 | 0 | Hydrophobic |
| C16 | CB | PRO- 265 | 4.04 | 0 | Hydrophobic |
| C12 | CG | MET- 267 | 3.77 | 0 | Hydrophobic |
| C14 | SD | MET- 267 | 3.81 | 0 | Hydrophobic |
| O2 | MN | MN- 401 | 2.15 | 0 | Metal Acceptor |
| O1 | MN | MN- 401 | 2.19 | 0 | Metal Acceptor |
| C13 | C4N | NDP- 601 | 3.65 | 0 | Hydrophobic |
