sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.030 Å
X-ray
2009-01-19
| Name: | Transcriptional repressor CcpN |
|---|---|
| ID: | CCPN_BACSU |
| AC: | O34994 |
| Organism: | Bacillus subtilis |
| Reign: | Bacteria |
| TaxID: | 224308 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 21 % |
| B | 79 % |
| B-Factor: | 29.233 |
|---|---|
| Number of residues: | 34 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.700 | 1066.500 |
| % Hydrophobic | % Polar |
|---|---|
| 32.59 | 67.41 |
| According to VolSite | |
| HET Code: | ANP |
|---|---|
| Formula: | C10H13N6O12P3 |
| Molecular weight: | 502.164 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 63.58 % |
| Polar Surface area: | 322.68 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 16 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 4 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| 10.0386 | 49.9594 | 41.92 |
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 |
| C1' | CG2 | VAL- 123 | 4.29 | 0 | Hydrophobic |
| O1B | OG | SER- 125 | 2.66 | 177.13 | H-Bond (Protein Donor) |
| C2' | CB | SER- 125 | 3.8 | 0 | Hydrophobic |
| O2B | CZ | ARG- 126 | 3.75 | 0 | Ionic (Protein Cationic) |
| O2B | NH1 | ARG- 126 | 2.7 | 133.75 | H-Bond (Protein Donor) |
| O1G | NZ | LYS- 127 | 3.46 | 0 | Ionic (Protein Cationic) |
| O2B | N | LYS- 127 | 3.23 | 157.82 | H-Bond (Protein Donor) |
| O3' | OD1 | ASP- 128 | 2.57 | 170.33 | H-Bond (Ligand Donor) |
| O3' | OD2 | ASP- 128 | 3.42 | 120.05 | H-Bond (Ligand Donor) |
| O2' | OD2 | ASP- 128 | 2.53 | 174.46 | H-Bond (Ligand Donor) |
| O2' | OG1 | THR- 149 | 2.67 | 152.95 | H-Bond (Protein Donor) |
| N6 | O | THR- 155 | 3.03 | 172.41 | H-Bond (Ligand Donor) |
| N1 | N | THR- 155 | 2.84 | 161.61 | H-Bond (Protein Donor) |
| C5' | CG2 | ILE- 175 | 4.36 | 0 | Hydrophobic |
| C1' | CG2 | ILE- 175 | 4.35 | 0 | Hydrophobic |
| O2A | N | ASP- 176 | 3.03 | 165.41 | H-Bond (Protein Donor) |
| N6 | O | ALA- 177 | 2.95 | 150.13 | H-Bond (Ligand Donor) |
| O2B | MG | MG- 223 | 2.6 | 0 | Metal Acceptor |
