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 high
Native strong
SASA done
Strain ΔE
23.2 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.77, Jaccard 0.45
Reason: no major geometry red flags detected
2 protein-contact clashes
50% of hydrophobic surface appears solvent-exposed (10/20 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. 3 — Harmful (10–100 mg/L)
Algae IC₅₀
Cat. 3 — Harmful (10–100 mg/L)
Bioaccum.
Not B (BCF≤2000)
Persistent
No
ADMET alerts (in-silico)
hERG High
Ames Clear
DILI Low
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.779 kcal/mol/HA)
✓ Good fit quality (FQ -7.66)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (77% SASA buried)
✓ Lipophilic contacts well-matched (74%)
✗ High strain energy (23.2 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (11)
Score
-24.919
kcal/mol
LE
-0.779
kcal/mol/HA
Fit Quality
-7.66
FQ (Leeson)
HAC
32
heavy atoms
MW
498
Da
LogP
3.56
cLogP
Final rank
2.7855
rank score
Inter norm
-0.810
normalised
Contacts
19
H-bonds 6
Interaction summary
HBD 1
HBA 5
HY 8
PI 1
CLASH 2
Interaction summary
HBD 1
HBA 5
HY 8
PI 1
CLASH 2
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 5.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
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 | 10 | Native recall | 0.77 |
| Jaccard | 0.45 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 599 | 2.7855282658837366 | -0.809655 | -24.9187 | 6 | 19 | 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
-24.919kcal/mol
Ligand efficiency (LE)
-0.7787kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.658
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
32HA
Physicochemical properties
Molecular weight
498.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.56
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
23.21kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-48.15kcal/mol
Minimised FF energy
-71.36kcal/mol
SASA & burial
✓ computed
SASA (unbound)
736.0Ų
Total solvent-accessible surface area of free ligand
BSA total
566.6Ų
Buried surface area upon binding
BSA apolar
419.6Ų
Hydrophobic contacts buried
BSA polar
147.1Ų
Polar contacts buried
Fraction buried
77.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
74.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2971.3Ų
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
1576.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)