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
33.0 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.77, Jaccard 0.53
Reason: no major geometry red flags detected
2 protein-contact clashes
41% of hydrophobic surface appears solvent-exposed (14/34 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
EcoTox / ADMET
In-silico prediction only
Fish LC₅₀
Cat. 2 — Toxic (1–10 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 High
Ames Clear
DILI Risk
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.454 kcal/mol/HA)
✓ Good fit quality (FQ -4.71)
✓ Deep burial (68% SASA buried)
✓ Lipophilic contacts well-matched (96%)
✗ Very high strain energy (33.0 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (20)
Score
-17.717
kcal/mol
LE
-0.454
kcal/mol/HA
Fit Quality
-4.71
FQ (Leeson)
HAC
39
heavy atoms
MW
531
Da
LogP
4.11
cLogP
Final rank
3.1170
rank score
Inter norm
-0.613
normalised
Contacts
16
H-bonds 1
Interaction summary
HBA 1
HY 10
PI 0
CLASH 2
Interaction summary
HBA 1
HY 10
PI 0
CLASH 2
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 1.
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: permissive.
| 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 | 10 | Native recall | 0.77 |
| Jaccard | 0.53 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 242 | 3.1170149600599717 | -0.613147 | -17.7167 | 1 | 16 | 10 | 0.77 | - | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-17.717kcal/mol
Ligand efficiency (LE)
-0.4543kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-4.714
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
39HA
Physicochemical properties
Molecular weight
530.8Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.11
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
33.02kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
138.17kcal/mol
Minimised FF energy
105.15kcal/mol
SASA & burial
✓ computed
SASA (unbound)
875.8Ų
Total solvent-accessible surface area of free ligand
BSA total
594.9Ų
Buried surface area upon binding
BSA apolar
574.0Ų
Hydrophobic contacts buried
BSA polar
20.9Ų
Polar contacts buried
Fraction buried
67.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
96.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3304.8Ų
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
1537.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)