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
Weak
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
37.4 kcal/mol
Protein clashes
6
Internal clashes
6
Native overlap
contact recall 0.69, Jaccard 0.50
Reason: 6 internal clashes
6 protein-contact clashes
6 intramolecular clashes
43% of hydrophobic surface appears solvent-exposed (9/21 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
EcoTox / ADMET
In-silico prediction only
Fish LC₅₀
Cat. 3 — Harmful (10–100 mg/L)
Daphnia EC₅₀
Cat. 2 — Toxic (1–10 mg/L)
Algae IC₅₀
Cat. 2 — Toxic (1–10 mg/L)
Bioaccum.
Not B (BCF≤2000)
Persistent
No
ADMET alerts (in-silico)
hERG Medium
Ames Clear
DILI Low
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.629 kcal/mol/HA)
✓ Good fit quality (FQ -5.94)
✓ Good H-bonds (4 bonds)
✓ Deep burial (70% SASA buried)
✓ Lipophilic contacts well-matched (72%)
✗ Very high strain energy (37.4 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (10)
Score
-17.610
kcal/mol
LE
-0.629
kcal/mol/HA
Fit Quality
-5.94
FQ (Leeson)
HAC
28
heavy atoms
MW
401
Da
LogP
3.56
cLogP
Final rank
3.8276
rank score
Inter norm
-0.836
normalised
Contacts
14
H-bonds 8
Interaction summary
HBD 1
HBA 3
HY 4
PI 0
CLASH 6
Interaction summary
HBD 1
HBA 3
HY 4
PI 0
CLASH 6
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 4.
PI · π–π interactions
No pi · π–π interactions detected for this pose.
HY · Hydrophobic contacts
CLASH · Clashes
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 9IFF | Contacts | 13 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA209
ARG74
ASN208
GLY214
GLY215
GLY85
LEU73
LYS211
MET70
PHE83
PRO212
PRO213
VAL88
| ||
| Current overlap | 9 | Native recall | 0.69 |
| Jaccard | 0.50 | RMSD | - |
| HB strict | 0 | Strict recall | - |
| HB same residue+role | 0 | HB role recall | - |
| HB same residue | 0 | HB residue recall | - |
Protein summary
489 residues
| Protein target | T15 | Atoms | 7420 |
|---|---|---|---|
| Residues | 489 | Chains | 1 |
| Residue summary | VAL:768; LYS:704; LEU:703; ILE:532; GLU:450; THR:434; ARG:408; PHE:400; ALA:390; ASN:350; PRO:350; GLY:336; SER:319; TYR:294; ASP:264; MET:204 | ||
All stored poses for this docking hit
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-17.610kcal/mol
Ligand efficiency (LE)
-0.6289kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.937
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
28HA
Physicochemical properties
Molecular weight
401.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.56
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
37.38kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
18.92kcal/mol
Minimised FF energy
-18.46kcal/mol
SASA & burial
✓ computed
SASA (unbound)
650.0Ų
Total solvent-accessible surface area of free ligand
BSA total
452.7Ų
Buried surface area upon binding
BSA apolar
325.2Ų
Hydrophobic contacts buried
BSA polar
127.6Ų
Polar contacts buried
Fraction buried
69.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
71.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2932.8Ų
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
4005.2Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1560.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)