Human papain-like cysteine protease target
Isosurface of electrostatic potential.
The electrostatic potential isosurface corresponds to the electrostatic potential in space at a fixed value. It allows identification of protein surface patches corresponding to positive electrostatic potential, which may be attractive for negatively charged GAGs. The PBSA method is applied for electrostatic potential calculations: solute atoms containing point charges produce an electrostatic field in the solute and solvent regions, which can be computed by solving the Poisson–Boltzmann equation.
Electrostatic potential levels: None and None kcal/mol·e−1
Cartoon representation of the selected cathepsin input structure.
| Glycosaminoglycan (GAG) | AA MD dp2 | AA MD dp4 | AA MD dp6 | RS-REMD dp16 | CG MD dp6 |
|---|---|---|---|---|---|
| Chondroitin 4-sulfate (CS4) | Yes | Yes | Yes | Yes | No |
| Chondroitin 6-sulfate (CS6) | Yes | Yes | Yes | Yes | No |
| Dermatan sulfate (DS) | Yes | Yes | Yes | Yes | No |
| Hyaluronic acid (HA) | Yes | Yes | Yes | Yes | No |
| Heparin (HP) | Yes | Yes | Yes | Yes | No |
| Desulfated Heparan sulfate (deHS) | Yes | Yes | Yes | Yes | No |
Note: Coarse-grained (CG) MD coverage is heparin-specific due to SUGRES force-field constraints.
| Complex Identifier / Name | Glycosaminoglycan | No. of binding poses | Actions |
|---|---|---|---|
| CATB002 — Cathepsin B - CS4, dp2 | Chondroitin 4-sulfate (dp2) | 3 | View Record |
| CATB102 — Cathepsin B - CS6, dp2 | Chondroitin 6-sulfate (dp2) | 3 | View Record |
| CATB202 — Cathepsin B - DS, dp2 | Dermatan sulfate (dp2) | 3 | View Record |
| CATB302 — Cathepsin B - HA, dp2 | Hyaluronic acid (dp2) | 3 | View Record |
| CATB402 — Cathepsin B - HP, dp2 | Heparin (dp2) | 3 | View Record |
| CATB502 — Cathepsin B - deHS, dp2 | Desulfated heparan sulfate (dp2) | 3 | View Record |