sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.050 Å
X-ray
2013-08-06
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 5.300 | 5.300 | 5.300 | 0.000 | 5.300 | 1 |
| Name: | L-lactate dehydrogenase A chain |
|---|---|
| ID: | LDHA_HUMAN |
| AC: | P00338 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 1.1.1.27 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| C | 100 % |
| B-Factor: | 60.985 |
|---|---|
| Number of residues: | 21 |
| Including | |
| Standard Amino Acids: | 20 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | NAI |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.500 | 830.250 |
| % Hydrophobic | % Polar |
|---|---|
| 35.77 | 64.23 |
| According to VolSite | |
| HET Code: | 22Y |
|---|---|
| Formula: | C19H16ClN4O2 |
| Molecular weight: | 367.809 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 52.99 % |
| Polar Surface area: | 103.96 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| -0.755962 | 3.38708 | 17.4348 |
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 | CD | ARG- 98 | 3.36 | 0 | Hydrophobic |
| C2 | CG | ARG- 98 | 4.28 | 0 | Hydrophobic |
| O26 | NE2 | HIS- 192 | 2.84 | 141.68 | H-Bond (Protein Donor) |
| C19 | CB | ALA- 237 | 3.87 | 0 | Hydrophobic |
| C9 | CD1 | ILE- 241 | 4.28 | 0 | Hydrophobic |
| CL1 | CD1 | ILE- 241 | 3.43 | 0 | Hydrophobic |
| C8 | CG2 | ILE- 241 | 3.6 | 0 | Hydrophobic |
| C22 | CD1 | ILE- 241 | 3.9 | 0 | Hydrophobic |
| C9 | CB | TYR- 246 | 4.39 | 0 | Hydrophobic |
| N13 | N | THR- 247 | 3.45 | 135.56 | H-Bond (Protein Donor) |
| N27 | O | THR- 247 | 2.92 | 170.7 | H-Bond (Ligand Donor) |
| N10 | O2N | NAI- 801 | 2.94 | 158 | H-Bond (Ligand Donor) |
| N27 | O2N | NAI- 801 | 2.73 | 136.24 | H-Bond (Ligand Donor) |
| C18 | C4N | NAI- 801 | 4.48 | 0 | Hydrophobic |
