sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.000 Å
X-ray
1996-02-12
| 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 |
|---|---|
| B | 100 % |
| B-Factor: | 20.943 |
|---|---|
| Number of residues: | 34 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.037 | 307.125 |
| % Hydrophobic | % Polar |
|---|---|
| 41.76 | 58.24 |
| According to VolSite | |
| HET Code: | BAT |
|---|---|
| Formula: | C23H31N3O4S2 |
| Molecular weight: | 477.640 g/mol |
| DrugBank ID: | DB03880 |
| Buried Surface Area: | 68.17 % |
| Polar Surface area: | 161.07 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 4 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 12 |
| X | Y | Z |
|---|---|---|
| -2.18066 | 24.0765 | 45.1422 |
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 |
| C17 | CG2 | THR- 107 | 3.7 | 0 | Hydrophobic |
| C10 | CB | LEU- 108 | 3.58 | 0 | Hydrophobic |
| C11 | CD2 | LEU- 108 | 3.33 | 0 | Hydrophobic |
| C12 | CD1 | LEU- 108 | 3.7 | 0 | Hydrophobic |
| N3 | O | GLY- 109 | 2.83 | 139.92 | H-Bond (Ligand Donor) |
| C3 | CB | HIS- 142 | 4.34 | 0 | Hydrophobic |
| O2 | OE2 | GLU- 143 | 3.25 | 139.1 | H-Bond (Ligand Donor) |
| S2 | CB | ARG- 167 | 3.84 | 0 | Hydrophobic |
| N2 | O | PRO- 168 | 2.65 | 168.74 | H-Bond (Ligand Donor) |
| S1 | CD1 | LEU- 170 | 3.55 | 0 | Hydrophobic |
| S2 | CD1 | LEU- 170 | 3.53 | 0 | Hydrophobic |
| C11 | CB | LEU- 170 | 3.29 | 0 | Hydrophobic |
| S2 | CB | THR- 171 | 4.42 | 0 | Hydrophobic |
| O4 | ZN | ZN- 902 | 1.99 | 0 | Metal Acceptor |
