sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.900 Å
X-ray
2013-03-15
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 5.290 | 5.290 | 5.290 | 0.000 | 5.290 | 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: | 31.130 |
|---|---|
| Number of residues: | 36 |
| Including | |
| Standard Amino Acids: | 29 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 6 |
| Cofactors: | NAI |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.779 | 826.875 |
| % Hydrophobic | % Polar |
|---|---|
| 41.22 | 58.78 |
| According to VolSite | |
| HET Code: | ZHK |
|---|---|
| Formula: | C20H15Cl2N5O4S2 |
| Molecular weight: | 524.400 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 62 % |
| Polar Surface area: | 188.19 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| -4.43906 | 4.96627 | 22.7455 |
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 |
| CL1 | CB | ARG- 105 | 3.68 | 0 | Hydrophobic |
| CL1 | CD1 | LEU- 108 | 3.49 | 0 | Hydrophobic |
| CL1 | CG2 | VAL- 109 | 4.3 | 0 | Hydrophobic |
| CL2 | CG2 | VAL- 109 | 3.65 | 0 | Hydrophobic |
| C26 | CB | ASN- 137 | 4.18 | 0 | Hydrophobic |
| CL2 | CB | PRO- 138 | 4.03 | 0 | Hydrophobic |
| C9 | CB | PRO- 138 | 3.88 | 0 | Hydrophobic |
| C27 | CB | PRO- 138 | 3.78 | 0 | Hydrophobic |
| O14 | N | ASP- 140 | 3.03 | 132.19 | H-Bond (Protein Donor) |
| N15 | OD2 | ASP- 140 | 2.76 | 136.22 | H-Bond (Ligand Donor) |
| O14 | N | ILE- 141 | 3.43 | 160.04 | H-Bond (Protein Donor) |
| N15 | OE2 | GLU- 191 | 3.01 | 158.66 | H-Bond (Ligand Donor) |
| C10 | CB | HIS- 192 | 4.38 | 0 | Hydrophobic |
| C1 | CB | ALA- 237 | 4.02 | 0 | Hydrophobic |
| S16 | CE2 | TYR- 238 | 4.18 | 0 | Hydrophobic |
| C1 | CZ | TYR- 238 | 3.47 | 0 | Hydrophobic |
| S16 | CD1 | ILE- 241 | 3.91 | 0 | Hydrophobic |
| O21 | O2D | NAI- 801 | 2.86 | 150.02 | H-Bond (Protein Donor) |
| O4 | O | HOH- 1010 | 2.84 | 156.25 | H-Bond (Protein Donor) |
| N5 | O | HOH- 1159 | 2.9 | 137.48 | H-Bond (Ligand Donor) |
