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
Weak or marginal quality
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
15.6 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.62, Jaccard 0.44
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
44% of hydrophobic surface appears solvent-exposed (11/25 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
EcoTox / ADMET
In-silico prediction only
Fish LC₅₀
Cat. 1 — Very toxic (≤1 mg/L)
Daphnia EC₅₀
Cat. 1 — Very toxic (≤1 mg/L)
Algae IC₅₀
Cat. 1 — Very toxic (≤1 mg/L)
Bioaccum.
Not B (BCF≤2000)
Persistent
No
ADMET alerts (in-silico)
hERG Medium
Ames Clear
DILI Risk
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.645 kcal/mol/HA)
✓ Good fit quality (FQ -6.29)
✓ Good H-bonds (4 bonds)
✓ Deep burial (67% SASA buried)
✓ Lipophilic contacts well-matched (82%)
✗ Moderate strain (15.6 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (15)
Score
-20.002
kcal/mol
LE
-0.645
kcal/mol/HA
Fit Quality
-6.29
FQ (Leeson)
HAC
31
heavy atoms
MW
406
Da
LogP
4.85
cLogP
Final rank
2.9396
rank score
Inter norm
-0.774
normalised
Contacts
13
H-bonds 6
Interaction summary
HBD 3
HBA 1
HY 5
PI 0
CLASH 3
Interaction summary
HBD 3
HBA 1
HY 5
PI 0
CLASH 3
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 2.
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 | 8 | Native recall | 0.62 |
| Jaccard | 0.44 | 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
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 429 | 0.3763685020700806 | -1.11733 | -30.2356 | 4 | 13 | 0 | 0.00 | - | - | no | Open |
| 456 | 0.8291394658452832 | -1.13404 | -36.6273 | 9 | 15 | 0 | 0.00 | - | - | no | Open |
| 460 | 1.4845961023568308 | -0.936064 | -28.1676 | 4 | 18 | 0 | 0.00 | - | - | no | Open |
| 479 | 2.2465523555658673 | -1.07372 | -31.8463 | 6 | 14 | 0 | 0.00 | - | - | no | Open |
| 478 | 2.6811516906246866 | -0.848983 | -23.9664 | 4 | 16 | 0 | 0.00 | - | - | no | Open |
| 431 | 2.7950112958399265 | -0.797896 | -16.0129 | 3 | 18 | 0 | 0.00 | - | - | no | Open |
| 531 | 2.9396166091762534 | -0.774253 | -20.0016 | 6 | 13 | 8 | 0.62 | - | - | no | Current |
| 440 | 5.900848019733364 | -0.907256 | -20.21 | 8 | 14 | 0 | 0.00 | - | - | no | Open |
| 457 | 7.7386159492059985 | -1.02476 | -29.1943 | 16 | 22 | 0 | 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
-20.002kcal/mol
Ligand efficiency (LE)
-0.6452kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.286
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
31HA
Physicochemical properties
Molecular weight
406.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.85
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
15.63kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
117.69kcal/mol
Minimised FF energy
102.05kcal/mol
SASA & burial
✓ computed
SASA (unbound)
672.7Ų
Total solvent-accessible surface area of free ligand
BSA total
448.1Ų
Buried surface area upon binding
BSA apolar
365.6Ų
Hydrophobic contacts buried
BSA polar
82.4Ų
Polar contacts buried
Fraction buried
66.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
81.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2985.6Ų
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
1593.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)