sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.400 Å
X-ray
2014-10-08
| Name: | Malate dehydrogenase, mitochondrial |
|---|---|
| ID: | MDHM_HUMAN |
| AC: | P40926 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 1.1.1.37 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 98 % |
| D | 2 % |
| B-Factor: | 35.479 |
|---|---|
| Number of residues: | 46 |
| Including | |
| Standard Amino Acids: | 46 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.407 | 941.625 |
| % Hydrophobic | % Polar |
|---|---|
| 58.42 | 41.58 |
| According to VolSite | |
| HET Code: | NAD |
|---|---|
| Formula: | C21H26N7O14P2 |
| Molecular weight: | 662.417 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 64.29 % |
| Polar Surface area: | 343.54 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 18 |
| H-Bond Donors: | 6 |
| Rings: | 5 |
| Aromatic rings: | 3 |
| Anionic atoms: | 2 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 3 |
| Rotatable Bonds: | 11 |
| X | Y | Z |
|---|---|---|
| -16.802 | -1.37068 | 20.014 |
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 |
| O2A | N | GLY- 35 | 2.8 | 156.95 | H-Bond (Protein Donor) |
| O2N | N | ILE- 36 | 3.02 | 168.88 | H-Bond (Protein Donor) |
| C5N | CD1 | ILE- 36 | 4.05 | 0 | Hydrophobic |
| C5D | CD1 | ILE- 36 | 4 | 0 | Hydrophobic |
| O3B | OD2 | ASP- 57 | 2.76 | 154.83 | H-Bond (Ligand Donor) |
| O2B | OD1 | ASP- 57 | 2.58 | 153.17 | H-Bond (Ligand Donor) |
| C1B | CB | ALA- 100 | 4.48 | 0 | Hydrophobic |
| O4B | N | GLY- 101 | 3.34 | 161.77 | H-Bond (Protein Donor) |
| O3D | O | VAL- 102 | 3.22 | 147.3 | H-Bond (Ligand Donor) |
| C2D | CB | PRO- 103 | 4.39 | 0 | Hydrophobic |
| C3N | CG2 | ILE- 140 | 4.02 | 0 | Hydrophobic |
| N7N | O | ILE- 140 | 3.11 | 154.35 | H-Bond (Ligand Donor) |
| O3D | N | ASN- 142 | 3.48 | 160.65 | H-Bond (Protein Donor) |
| O2D | ND2 | ASN- 142 | 3.43 | 147.59 | H-Bond (Protein Donor) |
| C2D | CB | ASN- 142 | 4.42 | 0 | Hydrophobic |
| N7N | O | VAL- 169 | 3.2 | 159.22 | H-Bond (Ligand Donor) |
| C4N | CD2 | LEU- 172 | 4.25 | 0 | Hydrophobic |
| C5N | CG | MET- 251 | 3.98 | 0 | Hydrophobic |
| C4N | SD | MET- 251 | 3.44 | 0 | Hydrophobic |
