sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.500 Å
X-ray
2012-12-05
| Name: | L-lactate dehydrogenase A chain |
|---|---|
| ID: | LDHA_RABIT |
| AC: | P13491 |
| Organism: | Oryctolagus cuniculus |
| Reign: | Eukaryota |
| TaxID: | 9986 |
| EC Number: | 1.1.1.27 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| C | 100 % |
| B-Factor: | 32.744 |
|---|---|
| Number of residues: | 20 |
| Including | |
| Standard Amino Acids: | 20 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.895 | 951.750 |
| % Hydrophobic | % Polar |
|---|---|
| 50.71 | 49.29 |
| According to VolSite | |
| HET Code: | 1E7 |
|---|---|
| Formula: | C15H12ClN2O4S |
| Molecular weight: | 351.785 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 54.93 % |
| Polar Surface area: | 116.65 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 1 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 19.6283 | 41.933 | 48.9625 |
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 |
| CL3 | CG1 | VAL- 25 | 3.53 | 0 | Hydrophobic |
| CL3 | CB | ASP- 51 | 3.98 | 0 | Hydrophobic |
| C6 | CG1 | VAL- 52 | 3.95 | 0 | Hydrophobic |
| C23 | CG1 | VAL- 52 | 3.71 | 0 | Hydrophobic |
| C24 | CG2 | VAL- 52 | 4.38 | 0 | Hydrophobic |
| C27 | CG2 | VAL- 52 | 3.94 | 0 | Hydrophobic |
| CL3 | CB | ALA- 95 | 3.66 | 0 | Hydrophobic |
| C25 | CB | ALA- 95 | 3.42 | 0 | Hydrophobic |
| C33 | CB | ALA- 97 | 4.43 | 0 | Hydrophobic |
| O20 | NH1 | ARG- 111 | 2.88 | 152.14 | H-Bond (Protein Donor) |
| O21 | NH1 | ARG- 111 | 3.02 | 129.36 | H-Bond (Protein Donor) |
| O21 | NE | ARG- 111 | 2.66 | 146.58 | H-Bond (Protein Donor) |
| O20 | CZ | ARG- 111 | 3.9 | 0 | Ionic (Protein Cationic) |
| O21 | CZ | ARG- 111 | 3.24 | 0 | Ionic (Protein Cationic) |
| C11 | CB | ASN- 114 | 3.96 | 0 | Hydrophobic |
| C23 | CG2 | ILE- 115 | 4.34 | 0 | Hydrophobic |
| C27 | CD1 | ILE- 115 | 3.97 | 0 | Hydrophobic |
| C33 | CD1 | ILE- 115 | 3.7 | 0 | Hydrophobic |
| C11 | CG1 | ILE- 115 | 3.69 | 0 | Hydrophobic |
| C6 | CD2 | PHE- 118 | 3.94 | 0 | Hydrophobic |
| S7 | CB | PHE- 118 | 3.74 | 0 | Hydrophobic |
| CL3 | CD1 | ILE- 119 | 3.91 | 0 | Hydrophobic |
| C23 | CD1 | ILE- 119 | 3.58 | 0 | Hydrophobic |
