sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.800 Å
X-ray
1995-05-26
| Name: | Snake venom metalloproteinase atrolysin-D |
|---|---|
| ID: | VM1AD_CROAT |
| AC: | P15167 |
| Organism: | Crotalus atrox |
| Reign: | Eukaryota |
| TaxID: | 8730 |
| EC Number: | 3.4.24.42 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 19.387 |
|---|---|
| Number of residues: | 27 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.153 | 300.375 |
| % Hydrophobic | % Polar |
|---|---|
| 41.57 | 58.43 |
| According to VolSite | |
| HET Code: | 0QI |
|---|---|
| Formula: | C17H24NO4S |
| Molecular weight: | 338.442 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 56.54 % |
| Polar Surface area: | 117.26 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 2 |
| Rings: | 1 |
| Aromatic rings: | 1 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| 2.20704 | 24.0433 | 2.40452 |
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 | N | LEU- 108 | 2.76 | 173.62 | H-Bond (Protein Donor) |
| CH | CG | LEU- 108 | 4.31 | 0 | Hydrophobic |
| S | CD1 | LEU- 108 | 3.7 | 0 | Hydrophobic |
| CB | CB | LEU- 108 | 4.33 | 0 | Hydrophobic |
| CD2 | CG2 | THR- 139 | 4.25 | 0 | Hydrophobic |
| DuAr | DuAr | HIS- 142 | 3.78 | 0 | Aromatic Face/Face |
| CE2 | CB | HIS- 142 | 4.21 | 0 | Hydrophobic |
| C6 | CB | ARG- 167 | 3.75 | 0 | Hydrophobic |
| N | O | PRO- 168 | 3.43 | 141.61 | H-Bond (Ligand Donor) |
| S | CB | LEU- 170 | 4.16 | 0 | Hydrophobic |
| C6 | CD1 | LEU- 170 | 4.24 | 0 | Hydrophobic |
| CZ | CB | LEU- 170 | 3.7 | 0 | Hydrophobic |
| O | ZN | ZN- 401 | 2.17 | 0 | Metal Acceptor |
| OXT | ZN | ZN- 401 | 2.14 | 0 | Metal Acceptor |
