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
Reject
SASA cached
Likely artefact or unreliable pose
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
40.6 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.68, Jaccard 0.59, H-bond role recall 0.57
Reason: no major geometry red flags detected
4 protein-contact clashes
4 intramolecular clashes
72% of hydrophobic surface is solvent-exposed (13/18 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
EcoTox / ADMET
In-silico prediction only
Fish LC₅₀
Not classified (>100 mg/L)
Daphnia EC₅₀
Not classified (>100 mg/L)
Algae IC₅₀
Not classified (>100 mg/L)
Bioaccum.
Not B (BCF≤2000)
Persistent
No
ADMET alerts (in-silico)
hERG Low
Ames Clear
DILI Low
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.635 kcal/mol/HA)
✓ Good fit quality (FQ -5.92)
✓ Strong H-bond network (10 bonds)
✓ Deep burial (75% SASA buried)
✓ Lipophilic contacts well-matched (75%)
✗ Extreme strain energy (40.6 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (5)
Score
-17.136
kcal/mol
LE
-0.635
kcal/mol/HA
Fit Quality
-5.92
FQ (Leeson)
HAC
27
heavy atoms
MW
407
Da
LogP
-0.86
cLogP
Final rank
2.8159
rank score
Inter norm
-1.094
normalised
Contacts
16
H-bonds 13
Interaction summary
HBD 3
HBA 7
PC 1
HY 1
PI 0
CLASH 4
Interaction summary
HBD 3
HBA 7
PC 1
HY 1
PI 0
CLASH 4
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 7.
PC · Polar contacts (possible, no H geometry)
HBD?/HBA? — heavy-atom distance only, H geometry unavailable. May be real H-bonds.
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 | 1F3T | Contacts | 19 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA111
ALA67
ARG154
ARG277
ASP332
ASP88
CYS70
GLU274
GLY236
GLY237
GLY276
HIS197
LYS69
PHE238
PRO275
SER200
TYR278
TYR331
TYR389
| ||
| Current overlap | 13 | Native recall | 0.68 |
| Jaccard | 0.59 | RMSD | - |
| HB strict | 5 | Strict recall | 0.56 |
| HB same residue+role | 4 | HB role recall | 0.57 |
| HB same residue | 5 | HB residue recall | 0.71 |
Protein summary
411 residues
| Protein target | T13 | Atoms | 6340 |
|---|---|---|---|
| Residues | 411 | Chains | 1 |
| Residue summary | VAL:624; LEU:551; LYS:506; ARG:480; PHE:460; ILE:418; ASP:348; GLU:332; THR:322; TYR:315; PRO:308; ALA:290; SER:264; GLY:224; ASN:210; GLN:170 | ||
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 621 | 2.815892833315614 | -1.09351 | -17.1355 | 13 | 16 | 13 | 0.68 | 0.57 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-17.136kcal/mol
Ligand efficiency (LE)
-0.6346kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.921
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
27HA
Physicochemical properties
Molecular weight
406.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
-0.86
Lipinski: ≤ 5
Rotatable bonds
11
Conformational strain (MMFF94s)
Strain energy (ΔE)
40.55kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
156.31kcal/mol
Minimised FF energy
115.76kcal/mol
SASA & burial
✓ computed
SASA (unbound)
650.0Ų
Total solvent-accessible surface area of free ligand
BSA total
490.0Ų
Buried surface area upon binding
BSA apolar
367.8Ų
Hydrophobic contacts buried
BSA polar
122.2Ų
Polar contacts buried
Fraction buried
75.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
75.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2605.4Ų
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
3461.2Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1375.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)