Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Promising
SASA cached
Promising and worth follow-up
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
2.7 kcal/mol
Protein clashes
0
Internal clashes
3
Native overlap
contact recall 0.79, Jaccard 0.73, H-bond role recall 0.44
Reason: no major geometry red flags detected
3 intramolecular clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Low conformational strain (2.7 kcal/mol)
✓ Excellent LE (-1.882 kcal/mol/HA)
✓ Good fit quality (FQ -12.97)
✓ Strong H-bond network (9 bonds)
✓ Deep burial (90% SASA buried)
✓ Lipophilic contacts well-matched (84%)
✗ Geometry warnings
Score
-24.470
kcal/mol
LE
-1.882
kcal/mol/HA
Fit Quality
-12.97
FQ (Leeson)
HAC
13
heavy atoms
MW
176
Da
LogP
1.37
cLogP
Interaction summary
HB 9
HY 4
PI 2
CLASH 0
Interaction summary
HB 9
HY 4
PI 2
CLASH 0
HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
HY · Hydrophobic contacts
CLASH · Clashes
No clash · clashes detected for this pose.
| Final rank | 0.563 | Score | -24.470 |
|---|---|---|---|
| Inter norm | -2.100 | Intra norm | 0.218 |
| Top1000 | no | Excluded | no |
| Contacts | 12 | H-bonds | 9 |
| Artifact reason | geometry warning; 3 clashes; 1 protein clash | ||
| Residues |
ARG137
ARG141
ASN103
HIS102
HIS138
CYS69
GLY70
GLY72
GLY74
ILE73
SER71
TYR46
| ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 3K7O | Contacts | 14 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ARG137
ARG141
ASN103
HIS102
HIS138
ASP10
CYS69
GLY70
GLY74
HIS11
ILE73
PRO12
SER71
TYR46
| ||
| Current overlap | 11 | Native recall | 0.79 |
| Jaccard | 0.73 | RMSD | - |
| HB strict | 5 | Strict recall | 0.42 |
| HB same residue+role | 4 | HB role recall | 0.44 |
| HB same residue | 5 | HB residue recall | 0.62 |
Protein summary
305 residues
| Protein target | T21 | Atoms | 4646 |
|---|---|---|---|
| Residues | 305 | Chains | 2 |
| Residue summary | ARG:576; ILE:532; VAL:512; GLU:420; ALA:360; PHE:240; HIS:238; LYS:220; THR:210; LEU:190; PRO:168; TYR:168; GLY:154; SER:154; ASP:144; ASN:112 | ||
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 656 | 0.5625139505195538 | -2.10042 | -24.4699 | 9 | 12 | 11 | 0.79 | 0.44 | - | no | Current |
| 653 | 1.0488076881999107 | -1.9466 | -19.9302 | 10 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-24.470kcal/mol
Ligand efficiency (LE)
-1.8823kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-12.974
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
13HA
Physicochemical properties
Molecular weight
176.2Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.37
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
2.71kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
29.65kcal/mol
Minimised FF energy
26.95kcal/mol
SASA & burial
✓ computed
SASA (unbound)
381.4Ų
Total solvent-accessible surface area of free ligand
BSA total
344.6Ų
Buried surface area upon binding
BSA apolar
289.7Ų
Hydrophobic contacts buried
BSA polar
54.8Ų
Polar contacts buried
Fraction buried
90.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
84.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2072.4Ų
SASA_nonpolar(complex) − SASA_nonpolar(receptor) − SASA_nonpolar(ligand free). Negative = non-polar surface buried upon binding. Requires full polarity-decomposed SASA computation.
Receptor non-polar SASA
2482.0Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
735.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)