sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.100 Å
X-ray
2015-09-02
| Name: | NPH1-2 |
|---|---|
| ID: | O49004_AVESA |
| AC: | O49004 |
| Organism: | Avena sativa |
| Reign: | Eukaryota |
| TaxID: | 4498 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 8 % |
| C | 92 % |
| B-Factor: | 31.441 |
|---|---|
| Number of residues: | 39 |
| Including | |
| Standard Amino Acids: | 36 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 1 |
| Cofactors: | FMN |
| Metals: | CL |
| Ligandability | Volume (Å3) |
|---|---|
| 0.590 | 1009.125 |
| % Hydrophobic | % Polar |
|---|---|
| 38.13 | 61.87 |
| According to VolSite | |
| HET Code: | FMN |
|---|---|
| Formula: | C17H19N4O9P |
| Molecular weight: | 454.328 g/mol |
| DrugBank ID: | DB03247 |
| Buried Surface Area: | 76.44 % |
| Polar Surface area: | 217.05 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 12 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| -18.1954 | -10.9279 | -12.3531 |
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 |
| C6 | CG2 | VAL- 416 | 3.37 | 0 | Hydrophobic |
| C7M | CG2 | THR- 418 | 3.58 | 0 | Hydrophobic |
| O2' | OD1 | ASN- 449 | 2.89 | 164.75 | H-Bond (Ligand Donor) |
| C6 | CB | ALA- 450 | 4.03 | 0 | Hydrophobic |
| C2' | CB | ALA- 450 | 4.36 | 0 | Hydrophobic |
| C9A | CB | ALA- 450 | 3.55 | 0 | Hydrophobic |
| C2' | CB | ARG- 451 | 4.3 | 0 | Hydrophobic |
| O1P | CZ | ARG- 451 | 3.9 | 0 | Ionic (Protein Cationic) |
| O3P | CZ | ARG- 451 | 3.59 | 0 | Ionic (Protein Cationic) |
| O1P | NH2 | ARG- 451 | 3.04 | 155.14 | H-Bond (Protein Donor) |
| O3P | NE | ARG- 451 | 2.8 | 174.3 | H-Bond (Protein Donor) |
| N1 | NE2 | GLN- 454 | 3.17 | 141.26 | H-Bond (Protein Donor) |
| O2 | NE2 | GLN- 454 | 2.84 | 152.34 | H-Bond (Protein Donor) |
| O4' | NE2 | GLN- 454 | 3.01 | 175.55 | H-Bond (Protein Donor) |
| C5' | CG1 | VAL- 463 | 3.98 | 0 | Hydrophobic |
| C1' | CG2 | ILE- 466 | 3.63 | 0 | Hydrophobic |
| C4' | CG2 | ILE- 466 | 4.14 | 0 | Hydrophobic |
| C5' | CB | ARG- 467 | 3.52 | 0 | Hydrophobic |
| C8M | CD1 | ILE- 470 | 3.72 | 0 | Hydrophobic |
| O2 | ND2 | ASN- 482 | 3.17 | 159.21 | H-Bond (Protein Donor) |
| N3 | OD1 | ASN- 482 | 2.89 | 165.32 | H-Bond (Ligand Donor) |
| O4 | ND2 | ASN- 492 | 3.2 | 121.82 | H-Bond (Protein Donor) |
| C8M | CD1 | LEU- 496 | 4.04 | 0 | Hydrophobic |
| C7M | CB | PHE- 509 | 4.19 | 0 | Hydrophobic |
| C8M | CB | PHE- 509 | 3.84 | 0 | Hydrophobic |
| O4 | NE2 | GLN- 513 | 3.01 | 146.39 | H-Bond (Protein Donor) |
| O3P | O | HOH- 715 | 2.75 | 154.97 | H-Bond (Protein Donor) |
