sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.570 Å
X-ray
1994-07-19
| Name: | Phospholipase A2, membrane associated |
|---|---|
| ID: | PA2GA_HUMAN |
| AC: | P14555 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| C | 5 % |
| E | 95 % |
| B-Factor: | 15.964 |
|---|---|
| Number of residues: | 37 |
| Including | |
| Standard Amino Acids: | 36 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | CA |
| Ligandability | Volume (Å3) |
|---|---|
| 1.003 | 999.000 |
| % Hydrophobic | % Polar |
|---|---|
| 46.62 | 53.38 |
| According to VolSite | |
| HET Code: | INB |
|---|---|
| Formula: | C26H53NO6PS |
| Molecular weight: | 538.741 g/mol |
| DrugBank ID: | DB04112 |
| Buried Surface Area: | 60.93 % |
| Polar Surface area: | 132.03 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 1 |
| Rings: | 0 |
| Aromatic rings: | 0 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 27 |
| X | Y | Z |
|---|---|---|
| -23.5736 | 35.4427 | 79.101 |
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' | CD2 | LEU- 2 | 4.26 | 0 | Hydrophobic |
| C11 | CB | LEU- 2 | 4.02 | 0 | Hydrophobic |
| C13 | CB | LEU- 2 | 4.1 | 0 | Hydrophobic |
| C1 | CD2 | LEU- 2 | 4.01 | 0 | Hydrophobic |
| C14 | CD2 | PHE- 5 | 4.35 | 0 | Hydrophobic |
| C16 | CE2 | PHE- 5 | 3.63 | 0 | Hydrophobic |
| C13 | CB | HIS- 6 | 3.76 | 0 | Hydrophobic |
| C14 | CD1 | ILE- 9 | 4.37 | 0 | Hydrophobic |
| C16 | CD1 | ILE- 9 | 4.42 | 0 | Hydrophobic |
| C18 | CD1 | ILE- 9 | 4.35 | 0 | Hydrophobic |
| C14 | CB | ALA- 17 | 3.9 | 0 | Hydrophobic |
| C12 | CB | ALA- 18 | 3.96 | 0 | Hydrophobic |
| C7 | CB | ALA- 18 | 3.77 | 0 | Hydrophobic |
| C9 | CB | ALA- 18 | 3.29 | 0 | Hydrophobic |
| C18 | CB | TYR- 21 | 3.64 | 0 | Hydrophobic |
| C6 | CZ | PHE- 23 | 4.28 | 0 | Hydrophobic |
| O' | N | GLY- 29 | 3.11 | 131.79 | H-Bond (Protein Donor) |
| C2 | CG2 | VAL- 30 | 3.82 | 0 | Hydrophobic |
| O2P | N | GLY- 31 | 2.88 | 124.61 | H-Bond (Protein Donor) |
| CM' | CB | CYS- 44 | 3.53 | 0 | Hydrophobic |
| N2' | ND1 | HIS- 47 | 2.79 | 153.7 | H-Bond (Ligand Donor) |
| CM' | CB | HIS- 47 | 3.99 | 0 | Hydrophobic |
| C2B | CB | ASP- 48 | 4.45 | 0 | Hydrophobic |
| CMB | CB | ASP- 48 | 4.06 | 0 | Hydrophobic |
| C1' | CE2 | TYR- 51 | 3.96 | 0 | Hydrophobic |
| C3' | CD2 | TYR- 51 | 3.7 | 0 | Hydrophobic |
| C1B | CB | TYR- 51 | 3.63 | 0 | Hydrophobic |
| CMB | CB | LYS- 52 | 4.19 | 0 | Hydrophobic |
| C2B | CB | LYS- 52 | 3.81 | 0 | Hydrophobic |
| O1P | NZ | LYS- 62 | 3.4 | 156.37 | H-Bond (Protein Donor) |
| O1P | NZ | LYS- 62 | 3.4 | 0 | Ionic (Protein Cationic) |
| C18 | CE2 | PHE- 98 | 3.93 | 0 | Hydrophobic |
| S | CB | LYS- 115 | 4.47 | 0 | Hydrophobic |
| O' | CA | CA- 309 | 2.49 | 0 | Metal Acceptor |
| O2P | CA | CA- 309 | 2.31 | 0 | Metal Acceptor |
