sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Å
NMR
1999-02-01
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 7.480 | 7.480 | 7.480 | 0.000 | 7.480 | 8 |
| Name: | Interstitial collagenase |
|---|---|
| ID: | MMP1_HUMAN |
| AC: | P03956 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 3.4.24.7 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 0.000 |
|---|---|
| Number of residues: | 24 |
| Including | |
| Standard Amino Acids: | 23 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.158 | 334.125 |
| % Hydrophobic | % Polar |
|---|---|
| 47.47 | 52.53 |
| According to VolSite | |
| HET Code: | CGS |
|---|---|
| Formula: | C18H23N3O5S |
| Molecular weight: | 393.457 g/mol |
| DrugBank ID: | DB07556 |
| Buried Surface Area: | 50.02 % |
| Polar Surface area: | 117.21 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 2 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| 3.58711 | -4.33641 | -0.647222 |
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 |
| CD | CB | ASN- 80 | 4.3 | 0 | Hydrophobic |
| CG1 | CB | ASN- 80 | 3.58 | 0 | Hydrophobic |
| O32 | N | LEU- 81 | 3.45 | 153.29 | H-Bond (Protein Donor) |
| O33 | N | LEU- 81 | 2.66 | 139.43 | H-Bond (Protein Donor) |
| O33 | N | ALA- 82 | 2.95 | 144.67 | H-Bond (Protein Donor) |
| CG2 | CB | HIS- 83 | 3.71 | 0 | Hydrophobic |
| COM | CG | ARG- 114 | 3.84 | 0 | Hydrophobic |
| COM | CG2 | VAL- 115 | 4.25 | 0 | Hydrophobic |
| COM | CB | HIS- 118 | 3.56 | 0 | Hydrophobic |
| CD1 | CB | HIS- 118 | 3.8 | 0 | Hydrophobic |
| CE2 | CB | TYR- 140 | 4.13 | 0 | Hydrophobic |
| O47 | ZN | ZN- 170 | 2.09 | 0 | Metal Acceptor |
| O48 | ZN | ZN- 170 | 2.07 | 0 | Metal Acceptor |
